RIKEN Plant Science Center
Towards the Further Development of Plant Science

R I K E N P S C 13 - Y e a r
Commemorative Publication

RIKEN Yokohama Institute独立行政法人

理化学研究所 横浜研究所

RIKEN Plant Science Center
Towards the Further Development of Plant Science

R I K E N P S C 13 - Y e a r
Commemorative Publication

RIKEN Yokohama InstituteContents

Foreword

Foreword
Director, RIKEN Yokohama Institute
Director, RIKEN Plant Science Center

0 0 3

Akihiro Fujita
Kazuo Shinozaki

Overview of the Plant Science Center

For the Further Development of Plant Science
Akihiro Fujita[Director, RIKEN Yokohama Institute]
0 0 4

Organization / Network of the Plant Science Center

The 13 Years of the Plant Science Center［2000 ̶2012］

0 0 6

Plant Science Center 13th Anniversary Talk―a

Looking Back at the Plant Science Center s 13 Years

0 1 0

Tatsuo Sugiyama / Kazuo Shinozaki / Shigeo Yoshida
Plant Science Center 13th Anniversary Talk―b

Fusion between Genomics and Metabolomics

0 1 6

Kazuki Saito / Minami Matsui / Kazuo Shinozaki
Plant Science Center 13th Anniversary Talk―c

Plant Hormone Research at the Plant Science Center0 2 0Yuji Kamiya / Hitoshi Sakakibara
Plant Science Center 13th Anniversary Talk―dInternationalization of the Plant Science Center

0 2 4

Yunike Shimizu / Ken Shirasu
Report on Research Activities―a ［Metabolomics Research Division］

Metabolomics and Metabolic Genomics Research

The RIKEN Yokohama Institute was established in 2000 as a major Japanese research center in thelife sciences.
Although its history spans a mere 13 years, the research that it conducts is at the world's highest
levels. Moreover, it not only has strong ties with other institutes inside the RIKEN organization; its
relations with outside research institutions, universities and corporations are continuing to deepenand expand.
The Plant Science Center, like the Yokohama Institute, was founded in 2000. In recent years, society's expectations regarding the contributions that can be made, through scientifically elucidating
the functions of plants, to solving environmental problems and modern social problems have grownconsiderably.
As part of RIKEN's 3rd Medium-Term Plan, set to begin in 2013, the Plant Science Center will makea new start when it merges with chemical biology and catalytic chemistry projects of Advance Science Institutes at Wako to start a new Center for Sustainable Resource Science.
This pamphlet looks back at the Plant Science Center's history over these past 13 years from various
perspectives, and also seeks to look ahead at the future development of plant science research.
I would like to sincerely thank you for your past support of our activities, and ask that you please
continue to provide us with your valued understanding and cooperation in the future.

0 2 8

Report on Research Activities―b ［Functional Genomics and Bioinformatics］

Developing Mutant Resources and Information Platforms

0 3 0

Report on Research Activities―c ［Growth Regulation and Productivity Systems ――1］

Kazuo Shinozaki▲

Growth Regulation Research Group / Dormancy and Adaptation Research Unit

Elucidating Plant Hormone Biosynthesis and Signal Transduction

The 13 years of the Plant Science Center

0 3 2[Director, RIKEN Plant Science Center]

0 3 4

The Plant Science Center was established in 2000 as part of the Millennium Project of Japan.
In its first period, in parallel with genome sequencing of rice, the Center elucidated key functionsof model plants like Arabidopsis under the guidance of previous Center Director Tatsuo Sugiyama.
Based on the motto, "Learn from plants, utilize plants," considerable progress was achieved inbasic plant research cooperated with the Rice Genome Research Program under the Ministry ofAgriculture, Forestry and Fisheries.
In its second period, the Center began a new project to analyze the functions of plant genes related to "improving the quantitative and qualitative productivity of plants," and initiated metabolome research, leading to the establishment of world-leading research platform.
It published numerous highly-cited papers and developed into a world-class research institution.
Society's expectations for the Center to contribute, as a social outcomes of plant science research,
to solving not only food problems but also environmental and energy problems have also become
sizable in recent years. The activities which the Center is now being asked to conduct cover a broad
range, from research on plant genome functions to applying the results of research to agriculture
and industry by cooperating with other fields.
In 2013, we will make a new start as the Center for Sustainable Resource Science, an organization
combining plant science, chemical biology and catalytic chemistry.
We will aim to create, and to use and apply, renewable resources for sustainable production.
Based on the Plant Science Center's 13 years of experience and achievements, we look forward toundertaking new challenges. I would like to ask your continuous guidance and encouragement.

Report on Research Activities―d ［Growth Regulation and Productivity Systems ――2］▲

Plant Productivity Systems Research Group / Cell Function Research Team

Identification and Utilization of Genes Useful for
Improving Crop Productivity

Report on Research Activities―e ［Environmental Response and Adaptation ――1／ R&D Programs for PSC］▲

Gene Discovery Research Group, Signaling Pathway Research Unit, Regulatory Network Research Unit, R&D Programs for PSC
0 3 6

Development of Crops with High Abiotic Stress Tolerance
Report on Research Activities―f ［Environmental Response and Adaptation ――2 ］▲

Plant Immunity Research Group / Plant Proteomics Research Unit

Research on Plant Immunity Systems for Sustainable Production

0 3 8

13 Years of the Plant Science Center

Representative Research Publications

0 4 0

Principal Investigators from the Plant Science Center

0 5 2

Awards0 5 3Factual Data of the Plant Science Center

0 5 6

Publications / Patent applications in Japan and overseas / Budget / Employees

0 0 2Contents

Greeting

0 0 3

Overview of the Plant Science Center❖ The Plant Science Center (PSC) was es-

tablished in 2000 as a part of the national
government’s Millennium Project.
In the five years of its first period, PSC
cooperated with Japanese and foreign
research institutions and was able to produce various noteworthy results, including the synthesis of plant hormones andthe distribution of related information;an
integration of chemistry, biochemistry
and molecular genetics; and genome information and resources for Arabidopsis.
❖ In the second period, which began in
2005, PSC undertook efforts – based onfunctional genomics (transcriptomics, proteomics, metabolomics, etc.) that usedmodel plants –to understand plant growth
regulation, morphogenesis, photosynthesis, metabolism, environmental responses and other phenomena as an
overall system. We also searched forgenes related to increasing food production and improving health, and promoted
basic research on the functions by whichplants produce their various substances.
❖ These and other research results from
PSC in past 13 years have been highly
regarded by plant research institutions
throughout the world. In the future they
will continue to be used to safeguardfood, health and the environment, andwill contribute to building a sustainable
society for the coming generation.

̶ 1st Period (April 2000 - March 2005) — 6-Group, 12-Team System

Advisory Council

Genomic Function Research Group

Review Committee

Laboratory for Interdisciplinary Analysis ofPlant Development
Laboratory for Genetic Regulatory Systems

Morphogenesis Research Group

Director̶ Network of the Plant Science Center

Laboratory for Gene Regulation
Laboratory for Structural Construction

Executive Advisor

Functional Control Research Group

Laboratory for Growth Regulation
Laboratory for Biochemical Resources

Environmental Plant Research Group

Laboratory for Remediation ResearchLaboratory for Adaptation and Resistance

Growth Physiology Research Group

Laboratory for Cellular Growth and Development
Laboratory for Reproductive Growth Regulation

Metabolic Function Research Group■̶From 2001

Laboratory for Metabolic Compartmentation
Laboratory for Communication Mechanisms

7-Group, 20-Team/Unit System. First̶ 2nd Period, Initial Phase (April 2005 – March 2010) — female leaders and foreign leaders.

Advisory Council

Metabolomics Research Group

Director
Gene Discovery Research Group
Senior Advisor
Coordinator

Growth Regulation Research Group—Female leaders◎ —Foreign leaders◉

Metabolome Analysis Research Team
Metabolic Systems Research Unit
Advanced NMR Metabomics Research Unit
Integrated Genomics Research Team
Integrated Genome Informatics Research Unit
Metabolome Informatics Research Unit
Gene Discovery Research Team
Cell Function Research Team▶Unit
Gene Expression Research Team
Genetic Regulatory Systems Research Team
Regulatory
個体統合解析研究チーム
Network Research Unit
Signaling Pathway Research Unit
R&D Programs for PSC
Growth Regulation Research Team
Dormancy and Adaptation Research Team▶Unit
Cellular Growth and Development Research Team

Metabolic Function Research Group

Metabolic Function Research Team
Metabolic Diversity Research Team
Plant Nutrition and Basal Metabolism Research Team

Plant Productivity Systems Research Group

Biodynamics Research Team
Morphoregulation Research Team

Plant Immunity Research Group

Plant Immunity Research Team

Plant Functional Genomics Research Group

Plant Functional Genomics Research Team
Plant Genomic Network Research Team

7 Groups, Over 20 Teams/Units.
̶ 2nd Period, Latter Phase (April 2010 – March 2013) — Towards a flat system.

Advisory Council

Director

Deputy Director
Senior Advisor
Coordinator

0 0 4

Overview of the Plant Science Center

Metabolomics Research Division
Metabolomic Function Research Group
Metabolic Systems Research Team
Advanced NMR Metabomics Research Team
Metabolome Informatics Research Unit▶Team

Plant Functional Genomics Research Group
Plant Genomic Network Research Team
Integrated Genome Informatics Research Unit
Integrated Genomics Research TeamR&D Programs for PSC

Functional Genomics and Bioinformatics

Growth Regulation Research Group
Dormancy and Adaptation Research Unit
Cellular Growth and Development Research Team
Plant Productivity Systems Research Group
Cell Function Research Unit▶Team

Growth Regulation and Productivity Systems

Gene Discovery Research Group
Signaling Pathway Research Unit
Regulatory Network Research Unit
Nutrient Response Research Team
Plant Immunity Research Group
Plant Proteomics Research Unit

Environmental Response and Adaptation［Leading-edge Research Infrastructure
Program Japan

Advanced Plant Science Research
Network］▶Tohoku University▶University of Tsukuba▶The University of Tokyo▶RIKEN Plant Science Center▶Nagoya University

F
GA D
C❻ ❹

❷


E
❸
B


▶National Institute for Basic Biology▶Nara Institute of Science and Technology❽▶Kyoto University




❺

H


❾

❶

▶Okayama University［ Domestic Collaboration］▶Building a Metabolomics Research
Platform● Kazusa DNA Research Institute● Institute for Advanced Biosciences,
Keio University▶Research on Wheat● Kihara Institute for BiologicalResearch, Yokohama City University▶Research on Rice● National Institute of Agrobiological Sciences● Japan International Research Center for
Agricultural Sciences● Okayama Prefectural Technology
Center for Agriculture, Forestry,
and Fisheries, Research Institute for
Biological Sciences▶Disposal of Waste Containing Heavy
Metal with Moss
● DOWA Holdings Co., Ltd.
▶Plant Genome Science andBiotechnology for Increase in Biomass● Forestry and Forest Products ResearchInstitute［ Partner Schools］▶Yokohama City University
Kihara Institute for Biological Research▶Yokohama City University
Graduate School of Nanobioscience▶University of Tsukuba
Graduate School of Life andEnvironmental Science▶Tokyo Metropolitan University
Graduate School of Science and Engineering▶Nagoya University
Graduate School of Bioagricultural Sciences▶The University of Tokyo
Graduate School of Sciences▶Tohoku University
Graduate School of Agricultural Science▶Chiba University
Graduate School of Advanced Integration
Science❼［International Collaboration ̶

Collaborative Research］［International Collaboration ̶

Memorandum of Understanding for
Research Collaboration］

Collaborative Research Agreement
for Each Research Laboratory

Research Exchange and Research Collaboration
as a Research Center❶ International Center for Tropical Agriculture

A Max Planck Institute of Molecular Plant(CIAT), Colombia (2006-)❷ University of Erlangen-Nuremberg (FAU),
Germany (2007-)❸ Korea Advanced Institute of Science andTechnology (KAIST), Korea (2007-)❹ Max Planck Institute for Chemical Ecology,
Germany (2007-)❺ Michigan State University, USA (2008-)❻ University of Karlsruhe, Germany (2008-)❼ Commonwealth Scientific andIndustrial Research Organisation (CSIRO),
Australia (2008-)❽ Rajiv Gandhi Centre for Biotechnology (RGCB),
India (2009-)❾ International Rice Research Institute (IRRI),
Philippines (2008-)
 Mahidol University, Thailand (2009-)
 Trent University, Canada (2009-)
 International Maize and Wheat Improvement
Center (CIMMYT), Mexico (2008-)
 Phenomenome Discoveries Inc., Canada (2005-)
 China Agricultural University, China (2007-)
 French National Institute for Agricultural
Research (INRA), France (2011-)
 Institute of Agricultural Genetics, Vietnam (2011-)
 The Brazilian Agricultural Research Corporation,
Brazil (2012-)

Physiology, Germany (2005-)
B College of Forest and Environment, Nanjing

Forestry University, China (2007-)C Flanders Institute for Biotechnology (VIB),

Belgium (2007-)
D Leibniz Institute of Plant Biochemistry, Germany(2007-)E College of Biological Sciences, China Agricultural

University, China (2007-)F Umea Plant Science Centre, Sweden (2010-)
G John Innes Centre and the Sainsbury Laboratory,

UK (2007-)
H Division of Biological Sciences, The University ofCalifornia, San Diego, USA (2010-)

Changes of Organization / Network of the Plant Science Center

0 0 5

The 13 Years of the Plant Science Center*Mention of the location has been omitted for events held at the RIKEN Yokohama Institute.

2000

2001

2002

2003

2004

2005

2006

1st PSC Symposium

RIKEN Open House 2001
April 21

1st Advisory Council Meeting

2nd Advisory Council Meeting

Start of PSC s 2nd period (5 groups)
April

Opening ceremony for Yokohama
Institute
November 6

2nd PSC International Symposium
Plant Morphogenesis

Each laboratory of PSC moves fromRIKEN Wako Campus and Kyoto
University to RIKNE Yokohama Institute.
April

RIKEN Yokohama Institute Open House
2003
June 14Public Lecture
Plant Power Supporting Better Lifeand Living – Research Results from theMillennium ProjectMay 8, at Yayoi Auditorium, The Universityof Tokyo Faculty of Agriculture

6th International Workshop on Plant
Sulfur Metabolism
May 17-21, at Kazusa Akademia Center

Joint seminar with Max Planck Instituteof Molecular Plant Physiology (Golm,
Germany)
March 16-17

RIKEN Yokohama Institute Open House
2004
June 26

November 1, at RIKEN Wako Campus

22nd RIKEN Science Symposium
November 6, at Pacifico Yokohama
Conference Center

Symposium of National Projects for
Plant Science● Plant Gene Project of the Japan Society
for the Promotion of Science● RIKEN Plant Science Center● Ministry of Agriculture, Forestry and
Fisheries Rice Genome ProjectDecember 6, at Cross Tower Hall (Tokyo)

November 26-27, at the University of Tokyo,
Yayoi Auditorium

Symposium of National Projects for
Plant Science● Plant Genetics Research Promotion
Committee, JSPS Research for the Future
Program● RIKEN Plant Science Center● Ministry of Agriculture, Forestry and
Fisheries Rice Genome ProjectDecember 3-4, at Yasuda Life Hall

Joint symposium of PSC and Grantin-Aid for Scientific Research on
Priority Areas Signal perception andtransduction in Higher Plants
April 26, at RIKEN Wako Campus
Joint Meeting between Max-PlanckInstitute of Molecular Plant Physiology
and PSC"Nutrients, Metabolism andDevelopment"
May 27-28, at Max-Planck Golm Institute(Golm, Germany)
RIKEN Yokohama Institute Open House
2002
July 20
To commemorate the consolidationof the Yokohama Institute, a gingko
tree (whose sperm is first discovered)is planted by PSC Director and Mayor
Nakata of Yokohama.
PSC Retreat
October 8-9, at Kazusa Akademia Park

Plant
Science
Center［PSC］

France-Japan Binational Symposium on
Plant Biology 2002
"Communication of regulatory signals
among cellular compartmentation inplant metabolisms"
October 29-31, at Nara Prefectural New
Public Hall

March 12-14

Industry-Government-Academia
Symposium on Plant Science
Bioscience that learns from plants andutilizes themAugust 25, at Nagoya University Graduate
School of Bioagricultural Sciences

March

13th Dolichol and Isoprenoid Workshop
Regular research meeting
September 4International Workshop on Tobacco
BY-2 Cells
September 14-16

The research entitled Rapid
Identification of Useful Traits Using
Rice Full-Length cDNAs started, being
supported by Special Coordination
Funds for Promoting Science andTechnology
May

PSC International Symposium 2003
Plant Science and the Environment
November 10-11

Joint Meeting of Millennium Plant
Science Research Projects
December 2, at Kokuyo Hall (Shinagawa)Signed letter of intent for metabolome
research with Keio University
June 1

Arabidopsis Workshop 2003
November 12

RIKEN Yokohama Institute Open House
2005
June 25

PSC Science Retreat
November 27

France-Japan Workshop on Plant
Sciences 2005
"Cellular signaling and development"
September 25-29, at Sofitel Toulouse Centre,
Toulouse, France

Joint Meeting of Millennium Plant
Science Research Projects● Plant Genetics Research Promotion
Committee, JSPS research for the Future
Program● RIKEN Plant Science Center● Ministry of Agriculture, Forestry and
Fisheries Rice Genome ProjectDecember 4-5, at Yasuda Life Hall

Start of Pant Immunity Research Group
October 1
Protein Phosphorylation in Plant
Signaling
October 20-21, at Tsukuba International
Congress Center (Epochal Tsukuba)
Functional Network of Transcription
Factors in Plants
November 16-17, at Tsukuba International
Congress Center (Epochal Tsukuba)

3rd PSC International Symposium"Biosyntheses of plant hormones andbeyond"November 18-19, at RIKEN Wako Campus

PI List［1st Period］［Genomic Function Research Group］

Kiyotaka OKADA［Laboratory for Interdisciplinary Analysis ofPlant Development］
Takuji WADA
［Laboratory for Genetic Regulatory Systems］

Tatsuya SAKAI［Morphogenesis Research Group］

Hiroo FUKUDA［Laboratory for Gene Regulation］

Taku DEMURA［Laboratory for Structural Construction］

Ken MATSUOKA［Functional Control Research Group］

Shigeo YOSHIDA［Environmental Plant Research Group］

Isamu YAMAGUCHI

Deciding on PSC s logo
May

Plant Functional Genomics ResearchGroup moves from Genomic Sciences
Research Center to PSC.
April 1

3rd Advisory Council Meeting
April 19-21

Metabolomics Research Group achieves
top ranking in plant biotechnology field
for number of papers cited.
April
PSC Retreat
May 12
RIKEN Yokohama Institute Open House
June 24
Special Seminar on Plant Metabolism
and Metabolome
August 1
Plant Science Symposium
Towards a General Understandingof Plants and Improving Plant
Productivity● Network of University Plant Scientists● National Institute of Agrobiological
Sciences● RIKEN Plant Science Center
December 1, at Kokuyo Hall
Outreach lecture on Rapid
Identification of Useful Traits Using Rice
Full-Length cDNAs
December 23, at Sanyo Newspaper s Santa
Hall

Plant Science Research Project
Symposium
Green Techno-Planning: Aiming
to Comprehensively Improve Plant
Productivity● National Institute of Agrobiological
Sciences● RIKEN Plant Science Center● Network of University Plant Scientists
December 2, at Kokuyo Hall

Joint Meeting of Millennium Plant
Science Research Projects
December 2, at Yasuda Life Hall

［Laboratory for Adaptation and Resistance］

Hiroshi HAMAMOTO［Growth Physiology Research Group］

Yuji KAMIYA［Laboratory for Reproductive Growth
Regulation］
Eiji NAMBARA［Metabolic Function Research Group］

Tomoyuki YAMAYA［Laboratory for Metabolic Compartmentation］

Hideki TAKAHASHI［Laboratory for Communication Mechanisms］

Hitoshi SAKAKIBARA［Laboratory for Biochemical Resources］

Toshiya MURANAKA

AprMain Events
Outside the Center［RIKEN history and important
domestic /foreign news］

0 0 6

Opening of RIKEN Yokohama
Institute
RIKEN Plant Science Center(4 groups) and RIKEN SNP ResearchCenter established as part ofMillennium Project.
RIKEN Center for Developmental
Biology established.
Name of Tsukuba Life Science Centerchanged to RIKEN Tsukuba Institute

Aug Sydney Olympics
Dec

Dr. Hideki Shirakawa receives Nobel
Prize.

The 13 Years of the Plant Science Center

Jan

RIKEN BioResource Centerestablished(in Tsukuba Institute).

Apr

Apr Start of Koizumi administrationJun

17th World Cup Tournament, jointly
hosted by Japan and South Korea.

Dec

Drs. Masatoshi Koshiba andKoichi Tanaka receive Nobel Prizes.

Jul

RIKEN Research Center for Allergy
and Immunology established(inYokohama Institute).

Sep 9/11 terrorist attacks
Oct

Dr. Ryoji Noyori wins Nobel Prize in
Chemistry.

RIKEN Discovery Research Instituteestablished
RIKEN Kobe Institute established

Sep RIKEN s status as a public
corporation, terminated in
preparation for becoming an
Independent Administrative
Institution
Oct RIKEN reorganaized as an
Independent Administrative
Institution
First President: Ryoji NOYORI

Sep RIKEN announces discovery of 113th
chemical element.

Mar Millennium Genome Project ends.

Aug Athens Olympics

Apr RIKEN Center for Intellectual Property
Strategies established

Dec Sumatra earthquakeJul

RIKEN Center of Research Network
for Infectious Diseases established

Sep RIKEN Molecular Imaging Research
Program launched
Oct RIKEN Spring-8 Center establishedJan

RIKEN Next -Generation
Supercomputer R&D CenterestablishedSingapore Representative Officeopened.

Mar XFEL Project office opened
Apr RIKEN Nishina Center for
Accelerator-Based Scienceestablished
Sep Start of Abe administration
Oct Emperor and Empress visit RIKEN.

The 13 Years of the Plant Science Center

0 0 7

The 13 Years of the Plant Science Center

2007

2008

2009

2010

2011

2012

PSC International Symposium
̶Trends in Plant Hormones̶
March 1-2

UK-Japan Workshop: Frontiers in Plant
Post-Genomics
January 18

RIKEN Science Lecture
February 28, at Marunouchi Building HallInternational Plant RNA Workshop 2011
June 20-21

Signed memorandum of understanding
for research cooperation with Nanjing
Forestry University, China
March 1490th Sustainable Humanosphere
Symposium Tree Biotechnology thatWill Open up the Future
February 18

Symposium for Green Innovation
Utilizing Plants
May 29, at Science Council of Japan LectureHall

2nd Meeting for Young Scientists
Synthetic Biology, Aiming to Create
New Materials
January 27

Memorial symposium of Kihara Institutefor Biological Research
Edible Medicine co-hosted with
Yokohama City University s Kihara
Institute for Biological Research
June 1

Arabidopsis mutant in space! HMG1
mutant launched aboard the space
shuttle Endeavor
March 11

RIKEN Yokohama Institute Open House
June 23

13th Seminar by RIKEN Friends in
Industry The relationship between
plant science and industry/theenvironment
November 1, at the Industry Club of Japan
Building
Outreach lecture on Rapid Identificationof Useful Traits Using Rice Full-Length
cDNAs Searching for Unknown Gene
Functions in Plants
November 3, at Tsukuba International
Congress Center (Epochal Tsukuba)

Plant
Science
Center［PSC］

JSPS/JST Joint International Symposium
Towards the Advanced Use of African
Resources in Plant Science
November 20
Plant Science Symposium
The Development of Plant Science● National Insitute of Agrobiological
Sciences● RIKEN Plant Science Center● Network of University Plant Scientists● Forestry and Forest Products ResearchInstitute
December 3, at Kokuyo Hall
Arabidopsis Workshop 2007
December 10
Super Science High School Program for
Plant Science as an outreach activity of
Rapid Identification of Useful Traits
Using Rice Full-Length cDNAs
December 18, at Tamasima High Schoolin Okayama Pref.

Japan-Korea Symposium
June 9-10
Introductory Workshop on RIKEN
Genetic Transformation Network
June 16
RIKEN Yokohama Institute Open House
July 55th International Conference on Plant
Metabolomics
July 15-18, at Pacifico Yokohama (Annex
Hall)

PSC s catchphrase decided:
Cultivating Tomorrow
July

Signed MOU for research cooperation
with College of Biological Sciences,
China Agricultural University.
May 19RIKEN Yokohama Institute Open House
July 3
PSC Retreat
September 16

4th Metabolome Symposium

21st International Conference on
Arabidopsis Research
June 6-10, at Pacifico Yokohama

Agenda of VIB-PSC meeting
June 10
ICAR2010 Satellite Workshop
June 11-12

November 18-19, at Yokohama Science
Frontier High School

RIKEN Yokohama Institute Open House
July 3

Japanese Society for Plant Cell andMolecular Biology, Public Symposium
The Familiar Power of Plant
Biotechnology
November 21, at Otemachi Sankei Plaza

1st International Symposium on the
Nitrogen Nutrition of Plants
July 26-30, at Inuyama International
Sightseeing Center (Freude Hall)

Plant Science Symposium
Eliciting the Potential of Plant Science:
Aiming to Achieve Made-in-Japan GM
Plants
December 1, at Kokuyo HallRIKEN Yokohama Science Café
How Plants Live Tenaciously
August 28, at Yokohama City Central Library
PSC Retreat
October 2
International Symposium on Plant
Productivity
October 24-26, at Trent University,
Peterborough, Ontario, Canada

Joint Retreat (RIKEN PSC, Kazusa DNA
Research Institute, Kihara Institute for
Biological Research)
October 2-3, at Kazusa Akademia Park2010 Plant Electron Microscopy
Workshop forJunior Scientists
November 18-19

Plant Hormone Technology Workshop
October 28

Plant Science Symposium A New Plant
Science Geared to Green Innovation
December 1, at Kokuyo Hall

3rd Metabolome Symposium

October 30 – November 1, at Keio University
Institute for Advanced Biosciences

PI List

4th Advisory Council Meeting
Japanese Society for Plant Cell andMolecular Biology, Public Symposium
Food, Environment, Health andEnergy: the Power and Hope of Plant
Biotechnology
November 29, at Otemachi Sankei Plaza［Metabolomics Research Group］

Kazuki SAITO［Metabolic Systems Research Unit］

Masami Yokota HIRAI［Advanced NMR Metabomics Research Unit］

Plant Science Symposium
Utilizing Plant Power for the Future of
Humanity
December 1, at Kokuyo Hall

Jun KIKUCHI［Integrated Genomics Research Team］

Yukihisa SHIMADA［Integrated Genome Informatics Research Unit ］［Metabolome Informatics Research Unit］

Apr RIKEN Molecular Imaging Research
Program launched at Kobe Institute.

Mar Genomic Sciences Research Center
closed.

Sep Change of government: start of
Hatoyama administration

Sep Start of Fukuda administration

Apr Launching of second midterm plan
Established Advanced Science Institute,
Omics Science Center, Systems
and Structural Biology Center, andBioinformatics and Systems Engineering
Division. Name of SNP Research Centerchanged to Center for Genomic Medicine.

Nov RIKEN s activities become the subjectof a review by the government
budget-screening process.

［RIKEN history and important
domestic /foreign news］

Sep Lehman shock. Start of Aso
administration2011 Joint Retreat(RIKEN PSC, BMEP, Kihara Institute for
Biological Research)
September 29-30, at RIKEN Yokohama
Institute and Kihara Institute for BiologicalResearch, Yokohama City University
RIKEN Yokohama Institute Open House
October 4

2011RIKEN Chemical Biology
Symposium
Next-Generation Tools for Molecular
Target Discovery
October 20-21, at RIKEN Wako Campus

Fascination of Plants Day(International Plant Day)
(April 21 – June 22), at RIKEN Wako
Institute, etc.
International Symposium of Plant
Science"Plant Science for the Future"
November 20
Plant Science Symposium
Expectations for Leading-Edge Plant
Science Research
December 3, at Kokuyo Hall2011 Plant Electron Microscopy
Workshop for Junior Scientists
November 21-22
Plant Science Symposium
Plant Science – Contributing to Solving
Food, Energy and Environmental
Problems
December 2, at Kokuyo Hall
Joint Workshop of the Japan Advanced
Plant Science Research Network andthe Network of the Center of Carbon
Dioxide Resource Studies in Plants
December 12, at the University of Tokyo,
Faculty of Science Building No. 2 Auditorium
RIKEN Science Seminar V
Secrets of 400 Million Years – Beautyof Japan, Power of Mosses
December 16, at Roppongi Academy Hills［Cell Function Research Team ］

Ken MATSUOKA［Gene Expression Research Team］

Takuji WADA

［Genetic Regulatory Systems Research Team］

Tatsuya SAKAI［Growth Regulation Research Group］

Yuji KAMIYA［Dormancy and Adaptation Research Team］

Eiji NAMBARA

Masanori ARITA［Cellular Growth and Development ResearchTeam］
Shinjiro YAMAGUCHI［Metabolic Diversity Research Team ］

Kazuo SHINOZAKI

Toshiya MURANAKA［Gene Discovery Research Group］

Aug Beijing Olympics

July 19-21［2nd Period,
Initial Phase］

November 25-27

Tetsuya SAKURAI

Main Events
Outside the Center

5th Advisory Council Meeting

Apr RIKEN Research Cluster for
Innovation establishedStart of RIKEN Biomass Engineering
Program (BMEP)
Japanese name for RIKEN Centerof Research Network for Infectious
Diseases changed.
JunStart of Kan administration

Jul

RIKEN Advanced Institute for
Computational Science established［Plant Nutrition and Basal Metabolism Research
Team］
Hideki TAKAHASHI［Plant Productivity Systems Research Group］

Hitoshi SAKAKIBARA［Morphoregulation Research Team］

Taku DEMURA［Plant Immunity Research Group］

Ken SHIRASU［Plant Functional Genomics Research Group］

Minami MATSUI［Plant Genomic Network Research Team］

Motoaki SEKIMar Great East Japan EarthquakeJul

Apr RIKEN Quantitative Biology Centerestablished
RIKEN HPCI Program for
Computational Life Sciences
establishedDec Dr. Shinya Yamanaka receives Nobel
Prize.

London Olympics

Dec Drs. Akira Suzuki and Eiichi Negishi
receive Nobel Prize.

Oct RIKEN Center for Molecular Imaging
Science establishedDec Drs. Makoto Kobayashi, Toshihide
Maskawa, Yoichiro Nambu and Osamu
Shimomura receive Nobel Prize.

0 0 8

The 13 Years of the Plant Science Center

The 13 Years of the Plant Science Center0 0 9

植物科学研究センター
Plant
Science Center
13年記念座談会─b
13th Anniversary Talk─a

Looking Back at the Plant Science Center’s 13 Years

The Plant Science Center —Progressing Together with
the Development of Plant Science
Shinozaki: The RIKEN Plant Science

Center (PSC) has progressed extensively
in the 13 years since it was established in
2000. During that time, plant science has
also progressed, and I feel that PSC has
contributed to leading the way. The
Center was founded at a time when new
developments in plant science were burgeoning. For example, gene recombination technology was advancing, as wasfunctional genomics that used model
plants. But before getting to that, I would
like to ask Dr. Yoshida to talk about thebackground to the founding of PSC.
Yoshida: Up to 1999, the year before
the founding, the International Frontier
Research System, a unique research system centered around limited-term contract researchers – Japan’s first such system – was in operation at RIKEN. In theplant research that, based on the themeof biological homeostasis, was carriedout under that system, attention was focused on two areas in particular: phytochrome and plant hormone function. In
connection with that, the national government wanted to introduce an innovative research system for science andtechnology at the turn of the new century. We then suggested to the government that Japanese plant science should
concentrate on elucidating plant functions as its primary undertaking.
Shinozaki: This was related to the Millennium Project, which became the catalyst for the birth of PSC. PSC took chargeof the part of the Project related to functional genomics of model plants like Arabidopsis. I remember that we started off
by teaming up with the Ministry of Agriculture, Forestry and Fisheries to research
the rice genome. At the time of thefounding, PSC’s first director, Dr. Sugiyama, had some major headaches, if I remember correctly. How was the situationback then?
Sugiyama: For the Millennium Project,
we were asked to elucidate the genome
functions of model plants other than rice,and to contribute to the development ofhigh-function crops and low-pesticide
crops. We gathered superior personnel
by a top-down method in which thecenter director chose the group directors,
the group directors chose the team leaders, and the group directors and team0 1 0

In the first period, we promoted projects under the motto, “Learn from plants, utilize plants.”
In the second period, we focused on improving plant productivity andbuilt foundations for metabolome analysis.
Then we entered a new phase related to green innovation.
Three researchers who nurtured and led the Plant Science Center discuss its 13 yearsof history and future prospects.

leaders chose their respective staffs.
However, these units were located in different places, and I was faced with thedifficult task of creating, in a short spanof five years, a situation where we could
all tackle a single objective with a senseof unity. At any rate, two groups werehoused at the Brain Science Institute's
Building, and three groups were in the
Bioscience Building and the Central Research Building on the Wako campus. We
also had a group that was located in partof the Botanical Garden of the Kyoto
University, Faculty of Science.
Under those conditions, the individual
teams and groups held working lunches
to which I was invited; they increased thejoint seminars; and they otherwise consciously tried to maintain a sense of unity.
For that reason alone we ardently wanted
to consolidate PSC. And finally, in 2002,
we succeeded in bringing everyone together at this Yokohama Institute. The
first thing I did after we moved to Yokohama was to establish a shared facility forgrowing plants that would become ourlifeline.

ProfileTatsuo SUGIYAMA［left］
Special Advisor・Former Director,
Plant Science Centera1963: Graduated from Nagoya University, Graduate School of Agricultural Sciences. Successively
served as researcher, International Rice ResearchInstitute; assistant, Nagoya University, Institute for
Biochemical Regulation; researcher, John Hopkins
University, School of Medicine; associate professor,
Shizuoka University, Faculty of Agriculture; associate professor and professor, Nagoya University,
School of Agricultural Sciences. 2001: Retired as
professor from Nagoya University, Graduate Schoolof Bioagricultural Sciences. 2000-05: Director, RIKEN Plant Science Center. Currently: Special Advisor
to Center. Doctor of Agricultural Science. Specialization: molecular physiology of photosynthesis.

Kazuo SHINOZAKI［center］
Director, Plant Science Centera1974: Graduated from Nagoya University, Graduate School of Science. 1977: Obtained doctorate ofscience, Nagoya University, Graduate School of Science. Successively served as researcher, National
Institute of Genetics; associate professor, Nagoya
University, Department of Biology; associate professor, Nagoya University, Center for Gene Research. 1989: Took office as Chief Scientist, RIKEN
Plant Molecular Biology Laboratory, and as Project
Director, RIKEN Genome Sciences Center. 2005:
Took office as Director, RIKEN Plant Science Center,and 2010: as Director, Biomass Engineering Program.

The First All-Japan System

Shigeo YOSHIDA［right］

Shinozaki: In the first period Dr. Sugiya-ma and group directors carried out projects under the motto, “Learn from plants,
utilize plants. ”PSC was Japan’s premierinstitution in the plant sciences, so it waspossible to plan joint conferences with
the Ministry of Agriculture, Forestry and
Fisheries and with universities and others.
But promoting projects with the all-Japansystem had its difficulties, I think.
Sugiyama: We confronted the researchhead-on. What made that possible wasour excellent staff. We were also blessedwith public funding. As you know, it’sclose to impossible to provide a succinct
definition of what a living organism is.
But what I thought we should aim to research, based on genome science, wasthe distinctive attributes of living organisms, particularly plants.
Those three attributes are photosynthesis, which functions as the primary producer of the organic compounds onwhich all earthly life relies; morphogenesis, by which plants grow towards lightand thereby defy gravity; and immobility.
We put our focus on unraveling the underlying molecular mechanisms of those

Plant Science Center 13th Anniversary Talk─ a

Coordinator, Plant Science Center

three attributes. However, those days
were a time of confusion. It was when
RIKEN became an independent administrative institution, and when the Scienceand Technology Agency merged with the
Ministry of Education. We therefore took
a two-pronged approach. We encouraged young people to focus on fundamental and basic research linked to the
future, while senior researchers concentrated on utilizing plants by using theirelucidated molecular mechanisms.
As a result, we were fortunately able tocreate a sense of unity, a kind of centripetal force, in the first period. However, nomajor national policy was issued for Japanese plant researchers, so I think they
were lacking in a spirit that would havebrought them together into a kind of allJapan team. To overcome that situation,
we decided to go beyond what the government agencies were providing andcreate opportunities for the researchers

to become united – to create a setting
where they could report their research
results and exchange information.
Shinozaki: You mean the Plant Science
Symposium held in December, right? Thisannual event for reporting research still
exists. I feel it is one of the most representative activities of the plant research in
the all-Japan system.
Sugiyama: At that time, I attended
meetings of expert committees of the
Cabinet Office and so on. But the committee members had serious questions
about the vertical structure of government agencies and the concomitant lackof coordination between them. Creating
an all-Japan system for plants underthose circumstances was a major achievement, I think.
Shinozaki: In research, RIKEN is especially strong in the plant sciences related
to chemistry; its plant hormone research
and metabolism research have madegreat strides. On the other hand, researchers who specialize in molecular
genetic research on Arabidopsis or inmorphogenesis were concentrated atuniversities. Trying to harmonize thosedifferent types of research must havebeen difficult.
Yoshida: Actually, I entered RIKEN
around the same time as Dr. Shinozaki.
From a nearly stage I was aware thatplant science research might take two
directions. Dr. Shinozaki conducted plantresearch based on a genomic viewpoint,
while I analyzed the physiological responses of plants based on their physicochemical aspects. So the idea of integrating those two through the all-Japansystem was born. To a certain extent, myresearch depended on an appropriate
combination of chemistry and plant
physiology. At that time, though, this was
generally not well understood. But Dr.
Shinozaki’s group was already conduct-a1971: Withdrew from doctoral program, the University of Tokyo, Graduate School of Agricultural
Sciences; became research associate in the University of Tokyo, Faculty of Agriculture. 1974: Obtained Doctor of Agriculture degree. 1979: Research fellow, Australian National University,
Faculty of Science, Department of Chemistry. 1987:
Senior Scientist, RIKEN Chemical Regulation of Biomechanisms Laboratory. 1990: Chief Scientist,
RIKEN Plant Functions Laboratory. 2000: assumed
additional post of Group Director, RIKEN Plant Science Center. 2005: Coordinator, Plant Science Center, and Specially Appointed Professor, Osaka University, Graduate School of Engineering. 2011:
Took office as Director, Yokohama City University,
Kihara Institute for Biological Research. Specializations: plant molecular physiology and plant biochemistry.

Looking Back at the Plant Science Center s 13 Years

0 1 1

Looking Back at the Plant Science Center’s 13 Years

植物科学研究センター
Plant
Science Center
13年記念座談会─b
13th Anniversary Talk─aing research as part of the Genomic Sciences Research Center (GSC), so I hopedthat we could link up with him there inorder to create a new type of research
center for plant science at RIKEN.
Shinozaki: Ultimately, we were fortunately able to join together and exchange
information in Yokohama. We had astrong foundation in terms of personnel,
and I think that’s what led to today’s
progress.
Sugiyama: I wanted us to make maximaluse of RIKEN’s advantage of excelling inchemistry. The infrastructure common to
the plant function research groups of Dr.
Yoshida and Dr. Yuji Kamiya, and to themicroorganism control research group of
Dr. Isamu Yamaguchi, is a primary asset
of RIKEN’s plant science research. From
universities, there were Dr. Kiyotaka
Okada’s group, researching genetic functions, and Dr. Hiroo Fukuda; they dealt
with morphogenesis. Then there was themetabolic function research group of Dr.

Kazuo
SHINOZAKI

Director, Plant Science Center

Tomoyuki Yamaya, which conducted
function analysis, which forms the basisof today’s research linked to productivity.
With such a talented array of people, I
believed we could create a globally preeminent research institute under any circumstances. RIKEN’s president also gave
me a mandate, which I agreed withwholeheartedly, and I continued to carryit out.

0 1 2

The Plant Science Center’s Strengths,
Born from Joint Research
Yoshida: Unlike a university, we had tostrongly “pitch” our research results toobtain a budget, which was also somewhat perplexing to the researchers. If you
don’t envision a clear scenario and makea pitch that’s easy to understand, public
institutions will change when unforeseeable factors come along.
Sugiyama: As the center director it tookme, too, quite of bit of time to achieve
the necessary revolution of consciousness. In order to increase joint research at
PSC, I always tried to stir up curiosity byasking people to ask themselves, “Whatis the person next to you doing?” Since
there was an all-Japan system, I also tried
my best to promote joint researchthrough a give and take with other institutions. Internationally, too, we held
two-country symposia with plant science
researchers from France and from Germany. I did many things to which I was
unaccustomed (laughs).
Yoshida: Joint research is important,
isn’t it? Actually, nearly 10% of my dissertation was a joint paper with Dr. Shinozaki. There are many cases where ourmethods are completely different although we’re dealing with the same
phenomenon, but from different angles.
Shinozaki: There is indeed the impression that university researchers and RIKEN
researchers have worked well together. In
particular, in Yokohama, Genomic Sciences Center of RIKEN was conducting
major activities, for which it had a sizablebudget, and I think it was able to makeprogress in part because of that budget.
Also, young researchers were entering
the organization, which helped in achieving various research results.
Sugiyama: One result was research thatcombined chemistry and physiology – research on plant hormones, which became
the foundation for today’s metabolome
research. In this field are Dr. Yoshida’s
brassinosteroid, and the abscisic acid andgibberellin of Dr. Yuji Kamiya’s group,
right? And the cytokinin of Dr. Hitoshi
Sakakibara’s group. Based on these three,
PSC is leading the world in plant hormone
research, I think.
Also, epoch-making results were produced by the research of Dr. Hiroo Fukuda’s group on morphogenesis, and by the
research of Dr. Kiyotaka Okada’s group

Plant Science Center 13th Anniversary Talk─ a

TatsuoSUGIYAMA

Special Advisor, Former Director,
Plan Science Centeron the molecular mechanisms of morphogenesis. Also noteworthy is the research on vessel formation by Dr. Fukuda’sgroup. Then there was the progress madeby Dr. Isamu Yamaguchi’s group in thetechnical development that used plantand microbe functions related to environmental hormones and which is close tosocial outcomes.
Regarding such research, the Millennium
Project’s outside evaluating committee
said, “You have obtained results that, although unspectacular, have beensound.” On the other hand, from anoverseas advisory council composed ofexperts, we received a far more glowing
evaluation: “You have skillfully combined
biochemistry, chemistry and molecular
genetics, and grown to be one of theworld’s preeminent plant research institutions.”
So as not to end those efforts in the first
period but rather to link them to the succeeding period, we established a “NextPeriod Planning Committee” in the Center; and it decided that what would be
most appropriate would be to integrate
the results from biochemistry, physiology,
and molecular genetics and link them towhat today is called metabolome research.
Shinozaki: In the next phase, underwhat was called the “Green Techno
Plan,” we sought to provide the government with various proposals through the
all-Japan system. Heading into the sec-

ond period was a time when new difficulties arose, wasn’t it?
Sugiyama: I talked about wanting
young people to develop research plans
where they would play the central role
and which they would be responsible forin the future. Sometimes, despite myage, I even raised my voice, didn’t I? As aresult of those discussions, we ended up
settling on metabolomics. Metabolomics
is connected to the diversity of plants.
Plants have far more species than animals. Two hundred thousand doesn’t
even come close to the number. Diversity
could be called one of the attributes ofplants. Also, historically speaking, plants
have been traditionally used, especially in
the Orient, as so-called “medicinal
herbs,” for maintaining health and curing illness. From the standpoint of contributing to society, too, we ended up
wanting to put our main effort into metabolomics.
Shinozaki: In that regard, in the second

ShigeoYOSHIDA

Coordinator,
Plant Science Center

period, based on the Green Techno Plan,
we created a plan to explore, with plantmodels, various genes and metabolic
products that could both quantitatively
and qualitatively improve plant productivity, and to then actually apply the findings
to crops. One major need for achieving
this was to acquire a mass spectrographand NMR and create a new infrastructure
for metabolome analysis. Another was tointegrate genome, transcriptome andproteome. Dr. Yoshida contributed tocreate a gene expression database named
AtGenExpress by international collaboration. Research to integrate that withplant hormone functions and the functions of metabolic products has progressed considerably, I think.
Towards Establishing
the RIKEN Brand
Shinozaki: In the second phase of PSC, I

asked Dr. Yoshida to create a system forcooperating with industry and reliably
obtaining patents.
Yoshida: This project was positioned as
basic research for supporting Japan’s industries through intellectual properties,
so we had to make its flow of operations
clearly understandable. But basic researchers dealing with the model plant
Arabidopsis prefer curiosity driven studies
rather than research intended for practical applications.
So I asked them to explain the content of
their research to a patent attorney, and I
advised him to write a scenario with adetailed flow of operations for how torequest a substantive examination of an
intellectual property. This flow of operations enabled the number of requests tobe greatly increased. We discovered that
it is extremely important to give young
people a clear map to follow. In addition,
we established a new model for the
projects that are sponsored by companies, in which the corporations bear thecost of the research activities, including
the salaries of the researchers.
Shinozaki: With regard to requests for a
substantive examination, there wereabout seven IP requests a year during thefirst period, but that number increased totwenty in the second period. I felt likethere was a revolution in consciousness.
Regarding our cooperation with industry,
there is a corporate group called the“RIKEN Friends in Industry,” and we also
occasionally have Dr. Yoshida hold a networking event called “Green Innovation
Plaza” (GrIP), and these led to several licensings. Two other things to which we
paid attention were internationalizationand hiring female leaders. At present wehave three female leaders and two foreigners, so I feel that the policies which
we have consciously pursued have borne
fruit.
Sugiyama: In the first period we had

zero female leaders.

Shinozaki: Yes, that’s right. We struggledquite a bit, but in the end we were able
to hire some good young leaders. Then,in the second period, many PSC teamleaders were appointed as university professors. Our young leaders developed,
and I feel that the individuals will form
the core of plant sciences in Japan.
Also, and this is something that surprisedme, but, according to Thomson Reuters,
papers published by RIKEN are cited at anextremely high rate. RIKEN ranks secondin the world, for the number of citations
per paper, among universities and research institutions related to the plantsciences that have published at least 500
papers in the past 10 years. Number one
is the world famous John Innes Center, ofGreat Britain. Number three is the Max
Planck Institute, of Germany. We thus
called this to the attention of the Independent Administrative Institution Evaluation Committee and the Advisory
Council for the international evaluation.
From that ranking I strongly felt that we
had gained in ability and become truly
international.
Sugiyama: Even domestically, many of
our researchers have received the Young
Investigator Award, which is given by theJapanese Society of Plant Physiologists
and which might be called a gateway tosuccess. There’s that and the newly created Japan Society for the Promotion of
Science Prize. Then there’s the Kihara
Memorial Foundation Special Award, of
Yokohama – this, too, we’ve received foroutstanding achievements.
Shinozaki: Yes, Dr. Hitoshi Sakakibara
and Dr. Ken Shirasu both received it.
Yoshida: In the plant science field, Dr.
Shinozaki has continued to have thehighest number of paper citations for five
years, and numerous other RIKEN- and
PSC-related people also rank high on thatlist.
Shinozaki: The number of citations per
manuscript of plant science ranks in thesecond place among all fields at RIKEN. In
that sense I think plant science becomesa distinctive RIKEN brand in the world.
An Output System Geared
to Industry
Shinozaki: I feel that what RIKEN has

done at the Plant Science Center in thepast 10 years has great importance in the

Looking Back at the Plant Science Center s 13 Years

0 1 3

Looking Back at the Plant Science Center’s 13 Years

植物科学研究センター
Plant
Science Center
13年記念座談会─b
13th Anniversary Talk─asense that, through fulfilling the role of aso-called “Research Infrastructure,” RIKEN has enabled plant sciences to gain
greater visibility, not only internationally
but also among academic fields in general. As part of that, how RIKEN’S research differs from that of universities isnow being sharply questioned.
Yoshida: Recently, at universities, the oldsystem of class courses has been waning,and organized research has become extremely difficult to do. On the other
hand, the research at RIKEN’s centers
functions through the organization, so, if
you can effectively use that, you can
produce unique strengths, I feel.
Shinozaki: I also think it was a plus that,in the second period, we were able tohold international conferences, such as
the International Conference on Plant
Metabolomics and the International
Conference on Arabidopsis Research. Inthat way, we were able to show, I think,that RIKEN has become a center of plant
metabolome research and Arabidopsis
functional genomics.
In 2009, however, together with thechange of government administration,
there was a critical review of our work in
PSC. And the government of the Democratic Party began asking questions.
What relationship does plant science
have to society? What is the difference
between RIKEN PSC and the National Institute of Agrobiological Sciences (NIAS)
of Ministry of Agriculture, Forestry and
Fisheries? We even heard some extreme
opinions to the effect that the functionsof the two institutions should be rearranged and merged. At the time, however, there were a lot of public comments,
made on our behalf by the plant science
community and people related to it, tothe effect that plant science research isimportant and that PSC should be protected as a base of operations in plantscience of Japan. And in the end we fortunately escaped with what, I think, wasa minimum of damage. Actually, opinions
were also voiced to the effect that thecontribution of the plant sciences wasnecessary for the Green Innovation which
the Democratic Party was then promoting. And based on the keywords “plantscience research and green innovation,”
we received several budget allocations.
One was for the Cutting-Edge Infrastructure Development Project, which wascentered at RIKEN. For this project, a total
budget of 2.7 billion yen was provided

0 1 4

for upgrading and maintaining equipment. Subsequently we participated in
CREST (JST Strategic Basic Research Programs), a project related to research on
plant photosynthesis and biomass andaimed at contributing to the creation of alow-carbon society. There was also theGreen Network of Excellence (GRENE), a
project, centered around university researchers, to increase and use plant biomass. Thus, plant science researchers
joined together and showed a will tocontribute to green innovation, and that,
I think, made a big difference.
Sugiyama: Plants are something society
hardly notices. Also, because of the vertical structure of Japanese government
agencies, they don’t cooperate with eachother. For example, with regard to theenormous and pressing problem of thefood supply, why can’t knowledge developed from perspectives other than thatof the Ministry of Agriculture, Forestry
and Fisheries also be used? That kind ofthing puts a big twist, I think, in the relationship between government and science.
Yoshida: In the future I think it will be
important for the Center to have a multiperspective survey system, so that, basedon technological progress, output can beskillfully and effectively allocated according to the direction of industry.
Shinozaki: Recently, using the term “biomass” or “biorefinery,” projects about how
to employ the biomass created by plants inindustry have been getting off the ground.
Yoshida: At present, the distinction between agriculture and industry is steadily
disappearing. For example, there exists
technology such as plant factories andtissue culturing. That being the case, I
strongly feel that we will come to see industrial raw materials, such as rubber andoil, which have heretofore not been included under the rubric of plant science,as important subjects of ours.
Shinozaki: The metabolism research isalso, I think, close to social outcomes, asis the research on oil production, the research on rubber, and the research on fiber. Much attention is also being paid tosecondary metabolites related to health.
Health and longevity will probably also
become important areas of research anddevelopment for us. So will sustainable
food production geared to climatechange. Contributing to that will be an
important mission of ours. RIKEN has
certain problems – we don’t have farm

Plant Science Center 13th Anniversary Talk─ afields or greenhouses – so I think it’s goodthat we’re conducting research in cooperation with domestic and foreign researchers who have access to such facilities.
Sugiyama: Indeed, this is not an age, I
think, when you can solve problems related plants with plant researchers alone
or if you just research plants. But I also
think that the actual power that individual living organisms have in the natural
world is now finally beginning to be understood.
Our Mission for the Future

Shinozaki: I’d like to shift the focus of theconversation to how PSC should develop
in the future. At present, two centers related to green innovation are planned at
RIKEN. One is the Emergent Materials Science Center, which is centered around
Professor Yoshinori Tokura, who came to
RIKEN from the University of Tokyo; theother is the Center for Sustainable Resource Science, which is centered around
PSC and will conduct basic research anddevelopment by integrating chemical biology and chemistry as well as research
activities in several fields related to thecreation of resources for Green Innovation. This is truly a fusion of interdisciplinary fields. An output that will contributeto society is also being demanded of us. I
think it will be quite a difficult challenge,
but I look forward to working hard as weapproach this new phase.
Yoshida: The sensibilities of pharmacology and materials science are very close
to each other, so if we can quickly findobjectives that can be pursued jointly
from both angles, I think we can achieve
results in a very short time.
Shinozaki: As for which direction totake, one would be research on the recycling and reuse of carbon. We could improve the functions of the plant metabolic
products
producedbyphotosynthesis; we could also include
chemical biology and synthetic chemistry
in that effort. Also, how about if we
worked on what many plant researchers
have suggested, low-input crop production? In that we could also include thenitrogen problem, the absorption ofphosphorous, increasing the efficiency ofwater use, disease resistance, and otherissues. A third direction would be the re-cycling and reuse of metal elements.
Here, I think, plants could make a big
contribution: they could be used to recover rare metals and maintain water
quality.
Yoshida: People from the microbial sciences will also be participating. The interaction between plants and microbes is a
research field that goes back a long way.
I think it’s an area in which joint research
will proceed smoothly.
Shinozaki: In 2010, RIKEN started a newprogram, the Research Cluster for Innovation. This program arose from President
Ryoji Noyori’s strong desire that RIKEN’s
research not be merely for its own sake,but rather that it promote the development of “social wisdom.” In the plantsciences we have also been able to makea significant contribution to this endeavor.
The Biomass Engineering Program,
whose purpose is to serve as a bridge tocompanies who will create new biomass
from chemical engineering, especiallyfrom plant materials, has been progressing through the cooperative efforts of
Yokohama and Wako. This program will
move in tandem with the new Center, so
I expect that various plans aimed at prac-

tical application of the plant sciences willbe created.
Yoshida: In a certain sense, I think theviability of the term “plant science” hasended. Initially, when we decided on thename “Plant Science Center,” I was
asked, “Is such a simple name good?”(laughs). However, in these thirteen years,
plant science has become a science in thetrue sense, and since it will progressively
disappear into a larger science, I thinkthat our name has finished serving its
purpose.
Sugiyama: I agree.
Shinozaki: What’s most difficult is collaboration with industry. In the future
we’ll probably be doing applied researchon such subjects as, How do you use
plants not just as food but also as industrial material? Or: How do you find things
that will contribute to health? In any
case, collaboration, including international collaboration, will become vital for
us in the future, I believe. d

Looking Back at the Plant Science Center s 13 Years

0 1 5

植物科学研究センター
Plant
Science Center
13年記念座談会─b
13th Anniversary Talk─b

Fusion between Genomics and Metabolomics

Reasons for the Focus
on Arabidopsis
Shinozaki: In the last 20 years, “ge-conduct some truly unique research.
Shinozaki: Speaking of new equipment,
the development of metabolomics research came in tandem with the development of mass spectrometry, I believe.
Saito: True. We were fortunate to have afull lineup of mass spectrometers, including time-of-flight mass spectrometry(TOF-MS), Fourier-transform mass spectrometry (FT-MS), and even triple quadrupole mass spectrometry. Also notable isthat we have an NMR center in the Yokohama Institute. Ours is probably the only
center in the world with a full lineup ofmass spectrometers and NMR all on asame platform.
Interdisciplinary
Metabolomics Research

ProfileKazuki SAITO［left］

Deputy Director, Plant Science Centera1977: Graduated from the University of Tokyo(Faculty of Pharmaceutical Sciences).1982: Obtained Ph.D. in pharmaceutical sciences. After staying at Keio University, School of Medicine andGhent University in Belgium, he was appointed as aprofessor at Chiba University, Graduate School of
Pharmaceutical Sciences in 1995. 2005: Group Director at RIKEN Plant Science Center. 2010: Deputy
Director of RIKEN Plant Science Center. He wasawarded the Commendation for Science and Technology (research division) by the Japanese Ministerof Education, Culture, Sports, Science and Technology in 2010 and the JSPCMB Award for Distinguished Research in 2011. He specializes in metabolomics-based functional genomics, biosynthesis ofplant metabolites, and biotechnology.

Minami MATSUI［center］

Shinozaki: While collaboration is one of

the strengths of our Center, I feel thatmetabolomics scientists are particularly
good at forming collaborative networks. You collaborated with Professor
Masaru Tomita of Keio University at Tsuruoka Campus in introducing capillaryelectrophoresis mass spectrometry, andyou shared a database called Mass Bank
internationally, just to give a few examples. Does this mean that cooperation
was necessary to promote research as awhole?
Saito: One of the reasons is that we arenaturally not as aggressive as scientists inGroup Director,
Plant Functional Genomics Research Groupa1981: Graduated from Saitama University (Department of Biochemistry and Molecular Biology,
Faculty of Science). 1986: Obtained a degree ofDoctor of Science from Kyoto University, Graduate
School. 1992: Studied at Yale University. After returning to Japan, he was appointed as Deputy
Head of RIKEN Frontier Research Program’s Laboratory for Photoperception and Signal Transductionin 1995. 1999: Appointed as Team Leader of RIKEN
Genomics Sciences Center, Plant Functional Genomic Research Group. 2006: Appointed to thecurrent post. He is involved in the development of
the Arabidopsis activation-tagged line and gene
exploration methods using full-length cDNAs of
Arabidopsis and rice.

Kazuo SHINOZAKI［right］
Diretor, Plant Sciense Center
aP.011 Reference.

 ̶ Mass spectrometers at PSC

Shinozaki: In 2005, PSC launched new

UPLC-TriQ-MS

CE-TOF-MS

700MHz NMR▲

LC-FT-ICR-MS

UPLC-Q-TOF-MS▲

GC(xGC)-TOF-MS▲

metabolomics-based genome researchwith Dr. Saito joining forces. Were there
any reasons that the uptake of metabolomics started mainly from the plant sciences?
Saito: We use plants as foods and raw
materials for drugs and industrial energy,
all of which are dependent on their inherent metabolic functions. Therefore, we
realized that it was important to study
metabolism that contributed to plantutility. Another reason, I think, is the remarkable chemical diversity of the plant
metabolome. If humans have 3,000 to
5,000 metabolites, plants have over
200,000 metabolites, mostly called as‘secondary metabolites’. Some recent estimates say 1 million. When we started▲Plant Science Center 13th Anniversary Talk─ b

The Dawn ofMetabolomics Researchand Development of PSC

▲

0 1 6

genes, and the other is the activationtagged mutant line, which activates
genes. We used these resources to analyze gene functions based on reverse genetic approaches.

the research, full-length cDNAs, mutants,
and other resources were becoming
available, so there was a sense that thetime was ripe. In other words, it coincidedwith the beginning of integrated omics
research that tried to have one-to-one
matches between genome functions andmetabolites. Because this kind of omics
research could not be conducted by university laboratories, we were acutely
aware when we started that we had arole in providing a kind of a platform thatwould “contribute to the entire plantscience community.”Our metabolome
research was a project for building a research platform by fully utilizing some of
the unique features of RIKEN.
Shinozaki: I have a real sense that PSC is
gradually becoming well-known globally
today. I suppose that having outstanding,leading scientists come to work at theCenter was a major factor.
Saito: One characteristic of RIKEN and of
PSC, for that matter, is that each scientist
is high-minded about his or her researchand is committed to leading the wider
science community. I think that is an integral part of the respect that RIKEN hascome to earn around the world.
Matsui: It would be hard to find a centerwith such a convergence of experts fromdifferent fields. Regular meetings and research presentations allow us to knowwhat each of us is doing. We conduct
joint research freely, which generates
new ideas. We use new equipment to▲nome” has been the keyword in the development of plant science. RIKEN, andparticularly the Yokohama Institute, promoted genome research with the Plant
Science Center (PSC) playing a role froma new perspective of metabolomics. In
this process, the sequencing and analysesof Arabidopsis thaliana and rice genomes
were key developments. Whereas countries had their own resources of cultivatedrice species, Arabidopsis, for which there
were no practical commercial uses, wasfreely used for research from the outset.
This, I think, led to promoting international collaboration.
Saito: I agree. Another important development I would point out would be theestablishment, immediately preceding
the sequencing of the genomes, of inplanta transformation technology (introduction of genes) for Arabidopsis andtransformation technology for rice using
Agrobacteria.
Shinozaki: Such technology development

was followed by sequencing of the entire
Arabidopsis genome in 2000, a release of adraft sequence of rice genome in 2001,
and sequencing of the entire rice genome
in 2004. But even before that, we sawsome characteristic advances in individual
genome research projects, didn’t we? For
example, RIKEN Genomic Sciences Center(GSC) initiated human genome analysis,collection of full-length complementary
DNAs of mouse, and structural analysis ofproteins in its core projects, which precipitated “saturation mutagenesis” that tries
to analyze biological functions by gathering a large number of mutants. This, inturn, led to the birth of PSC. As for preparing resources such as mutants and fulllength cDNAs, it began in the GSC days inthe form of Japan contributing to an international network, didn’t it?
Matsui: To analyze individual gene functions, it is simply essential that you haveaccess to mutants as research resources. RIKEN promoted collection of fulllength cDNAs and mutants, which included
plans
for
international
collaborations. There are two types ofmutants. One group is the transposontagged mutant line, which destroys

The Plant Science Center (PSC) inherited the direction of research set by the Plant Functional Geniomics Researchat Genomic Sciences Center (GSC) and strong biochemistry and hormone research in the fist period of PSC,
and in 2005 embarked on a new metabolomics-based genome research.
Three scientists who have successfully promoted interdisciplinary research under the watchwordof “collaboration” speak about the strengths of PSC in functional genomics and the future steps
towards building connections between plants and the industry.

Fusion between Genomics and Metabolomics

0 1 7

Fusion between Genomics and Metabolomics

植物科学研究センター
Plant
Science Center
13年記念座談会─b
13th Anniversary Talk─b

Kazuo
SHINOZAKI

Director, Plant Science Center

other basic biology or genome research(laughs). In some respects, we cannot
carry on our research without cooperation. Another thing is that the size of thecommunity is just about right for forging
collaborations among scientists. For example, a new project that came out ofthat is a joint effort between the National
Science Foundation (NSF) and Japan Science and Technology Agency (JST) for
research on “Metabolomics for a LowCarbon Society.” This is a good example
where forging and maintaining an arrayof collaborative relationships has led to aframework for a joint public research
project between Japan and the UnitedStates.
Shinozaki: It seems to me that there is,relatively speaking, quite a lot of cooperation within the plant science community.
Even when competitive relations develop,
they seem to manage quite well by sharing. This approach is actually like plants’ inthat you occupy segregated habitats but
combine your respective outputs (laughs).
Saito: On the other hand, we might
produce toxins if we are overstressed(laughs).
Results of Metabolomics Research

Saito: We have had several results fromour metabolomics research, one of whichis research on assigning genome func-

0 1 8

tions of rice that was undertaken with Dr.
Matsui’s group. More recently, we published a paper on metabolomic QTL ofrice. Another is research using Arabidopsis. In this research, we were able to determine new gene functions using the
AtMetExpress database and by combining metabolomic approaches, to identify
important genes associated with suchsecondary metabolites of plants as glucosinolates and flavonoids. In terms of applied research, we were able to propose amethod for evaluating the substantial
equivalence of genetically modified
plants. We also had results with medicinal
plants. For example, I think our research
to determine genes involved in the production of glycyrrhizin in licorice roots
and biotechnologically produce glycyrrhizin is a new type of research that derived from metabolomics.
Shinozaki: My group also had results
coming out of joint research with Dr.
Saito on environmental stress.The methodology of focusing not only on gene
expressions but also exhaustively comparing them with metabolites was extremely effective. We were able to discover new metabolites that protected
cells affected by stress. By conducting
gene expression analysis simultaneously,
we were also able to identify importanttranscription factors that regulated
genes. We believe that we can makemany new discoveries using this analytical system.

NET became operational, we received
quite a large number of requests, and weare currently moving ahead with theanalysis.
Shinozaki: With regard to transformation, in 2003 Dr. Matsui and his colleagues launched the venture company
Inplanta Innovations Inc. to offer RIKEN’s
technology and infrastructure.
Matsui: It is the first plant-based venturecompany to come out of the Yokohama
Institute and is founded on three key
components: a system for comprehensively adding specific functions to plants,
gene mapping, and transformation. The
company is conducting joint research on
the development of transformations in arange of useful plants.
Future Developmentsin the Employment of Useful Plants
Shinozaki: I would now like to turn tothe subject of future developments. How
do you see the future in terms of metabolomics platform?
Saito: One thing that is clear is that genome research, which has been limited
to a number of what are known as model
plants, will expand to all of the 200,000
plant species. From the perspective of
how we integrate transcriptome andproteome, I also think that omics research
focusing on the usefulness of plants willbe essential. For example, there could be

Launch ofPlant Transformation Network( TRANSNET)
Shinozaki: In seeking ways to apply ba-

sic research in actual crops, we launched
the Plant Transformation Network(TRANSNET) with Dr. Matsui’s group in
2008. This, I think, set a direction of theCenter in some respects.
Matsui: In the TRANSNET that the Center is supporting, we ask transformation
experts to incorporate useful genes takenfrom Arabidopsis or other plants into
practical plants, so we can verify theirtransformations. The crops that we actually use are tomatoes, soybeans, andrapeseeds, and we asked the assistanceof Professor Hiroshi Ezura of University ofTsukuba, Dr. Masao Ishimoto of NARO
Hokkaido Agricultural Research Center,
and Professor Jun Imamura of Tamagawa
University, respectively. Once the TRANS-

Plant Science Center 13th Anniversary Talk─ b

Kazuki
SAITO

Deputy Director, Plant Science Center

we obtain from decoding genome sequences of a variety of living beings tointroduce new pathways within plants
and thereby efficiently produce usefulmetabolites or introduce new metabolic
pathways or synthetic pathways for producing such materials as biomass or bioplastic.

Agriculture, Biodiversity and Poverty), an
acronym summarized by Kofi Annan, theseventh U.N. Secretary General, to describe the most pressing issues facing
humanity. The new center named Center
for Sustainable Resource Science, nodoubt, will be promoting basic researchin pursuit of providing some of the solutions to these important issues.d

Future Roles of Plant Science

Minami
MATSUIGroup Director, Plant Functional
Genomics Research Groupextensive research on the mechanisms of
how substances, such as lipids and carbohydrates, which are sources of energy,
are produced in plants that produce energy. In medicinal plants, there could beresearch on how specific metabolites areproduced. Ultimately, we need to go beyond basic research and expand into
fields that are more closely related to ourdaily lives, such as industry, bioenergy
materials, drugs, healthful food components, and increasing food production,
which also tie in with the Japanese government’s Green Innovation and Life Innovation policy goals.
Shinozaki: I agree. In contrast to genome research, which so far has been likewriting an encyclopedia, I have the impression that we are now at a point
where we can write textbooks, so to
speak, on individual biological systems. Therefore, I expect there will be research done to link the ways individual
genes relate to each other and guidethem to specific functions. The other isthe application of synthetic biology. I feel
we are probably entering a new era
where humans will work on living beingsto generate new added value. In this respect, we note that PSC launched RIKEN
Biomass Engineering Program (BMEP) in2010.
Matsui: I think synthetic biology will become important in the span of the next
five years. Some of the central issues may
be how we use the genetic information

Future Roles of Plant Science
Shinozaki: RIKEN is now promoting organizational integration and restructuring, and will establish a new center thatwill be related to the environment, energy
and resources. In this context, we arehaving discussions about the role of PSC
in conducting research that would contribute to the government’s Green Innovation policy objectives in conjunction
with chemical biology, synthetic chemistry, and catalytic chemistry. This is a challenge that aims to improve food production as well as to create sustainable,
environmentally friendly production systems based on organisms like plants andmicrobes. I think you will both agree thatplant science will play a very importantrole in this.
Saito: In terms of fusion with chemical
biology and catalytic chemistry, I think aphotosynthesis platform, where carbon
dioxide assimilation occurs and whereultimately plants are provided high value
added also through the help of microorganisms, would be an important keyword
to further expand on the achievements of
PSC. This system will not be limited tometabolomics research in the narrow
sense, but will also relate to everythingfrom stress biology to developmental biology and hormone and metabolic regulation. In terms of output, synthetic biology will also be included.
Matsui: In my mind, the linkage between
chemistry and plants and microorganisms
is inevitable. In a county like Japan with aheavy emphasis on manufacturing, research that joins photosynthesis of plants
with materials production should be interesting. I think that the RIKEN Biomass
Engineering Program (BMEP), when it isintegrated into the new center, can also
play a role in providing connections between plants and the industry.
Shinozaki: One of the expressions thatRIKEN President Ryoji Noyori likes to use
is “WEHAB + P”(Water, Energy, Health,Fusion between Genomics and Metabolomics

0 1 9

植物科学研究センター
Plant
Science Center
13年記念座談会─b
13th Anniversary Talk─c

Plant Hormone Research at the Plant Science Center

The trend of plant hormone research in Japan was passed on to the Plant Science Center, becoming one of
the cores of the Center. In the face of the pressure of rigorous external assessments,
the Center steadily turned out research contributing to improvement of crop productivity.
Two scientists exploring plant hormones from the perspectives of chemical genetics, biochemistry,
and molecular biology talked about the results of plant hormone researchand their enthusiasm for future research.

 ̶ Results of Plant Hormone Research at RIKEN Plant Science Center

Research on biosynthesis and metabolism of gibberellin, brassinosteroid, cytokinin, auxin, and abscisic acid
Identification of abscisic acid and polyamine transporters
Discovery of the new plant hormone strigolactone
Integrated research on plant hormones involved in seed germination and dormancy
Simultaneous analysis of plant hormones and related gene expressions
Analysis of plant hormones and environmental responses related to desiccation, salt stress, and nutrition
Simultaneous high-sensitivity, high-resolution analysis of endogenous levels of plant hormones using LC-MS/MS

ty. Subsequently, I could measure the accurate endogenous levels of hormones in
my papers. At any rate, when people andequipment are invested in research andprovided that the research is founded ona strong concept, the quality of research
papers will inevitably improve.
RIKEN Spirit Conducive
to Joint Research

A Prehistory of
Plant Hormone Researchand Use of Mass Spectrometry
Kamiya: A history of plant hormone re-search provided a background for theestablishment of the Plant Science Center(PSC). Soon after the war, Dr. Yusuke
Sumiki, the former vice president of RIKEN, elucidated the chemical structure of
the toxin produced by Gibberella fujikuroi.
This research was an important work ofthis early period. Partly because Dr.
Sumiki was enthusiastic about gibberellin, a progress was made in gibberellin
research in Japan.
It was Dr. Akira Kawarada, who was thechief scientist of RIKEN’s plant pharmacology laboratory, first discovered in Japan that gibberellin was an endogenous
hormone of plants. He took water sprouts
from Citrus unshiu (Japanese mikan) tree
to look for growth promoting substances
causing the elongation in rice bioassays,
and discovered that it was gibberellin
A1. This time consuming research deserves greater recognition, but Jake
MacMillan’s paper on the research on
gibberellins in immature seeds of Phaseo-

0 2 0

lus vulgaris is more often cited.
With the appointment of Dr. Nobutaka
Takahashi as a chief scientist and executive director for research at RIKEN, plant
hormone research went ahead in RIKEN
at around 1975. It was by his recommendation that I began research on gibberellins. At that time, we did not have any
concept like genomes, but there was asense that we could approach genes
through identification of hormonal enzymes.‍
Sakakibara: I was initially involved in research on nitrogen nutrition in my PhD
study. I knew that a plant hormone calledcytokinin may be involved as a second
messenger in the regulation of plant development by nitrogen nutrition. But because I was in a plant nutrition lab, I had
never used the mass spectrometer before
joining RIKEN (laughs). The entire genome sequence of Arabidopsis thaliana
was published in the same year that PSC
was established. I feel that the successful
fusion between genetics, using Arabidopsis, and chemistry, using mass spectrometry, owes much to the research environment provided by RIKEN.
In the end, I think the history of my re-Plant Science Center 13th Anniversary Talk─ csearch at RIKEN overlaps with the historyof the development of mass spectrometry. When I first came to RIKEN, we wereusing the rotary evaporator, ones thatstudents typically use, to measure eachsample by rotating the evaporator. And
then it became possible to measure 12
samples at once, and the number has
since increased to 192 samples. In addition, we can now measure a sample sizethat is a hundredth or a thousandth ofwhat was possible in the early days. The
introduction in 2003 of the high-performance liquid chromatography- tandem
quadrupole mass spectrometry (LC-qMS/MS) was definitely a turning point.
Kamiya: In raising the high sensitiveplant hormone analysis, there is inevitably
a need to introduce MS spectrometerwith high resolution. We introduced theliquid chromatography / time-of-flight /mass spectrometry (LC-TOFMS) in 2005.
This MS spectrometer had high resolution, but its sensitivity was not enoughfor our quantification of hormones. Therefore we intorduced quadrupole LC-MS/
MS. By using these two different MS
spectormeters, it was possible to analyze
hormones at a high level of reliabili-

Kamiya: Because we were strong on
biochemistry, there was a feeling that wewere competing in slightly different fields
when compared with overseas plant laboratories. For instance, we were dealing
with cytochrome P450 (a generic term
for a family of enzymes that catalyze oxidation) that are involved with major plant
hormones. You, for one, were trying to
identify the genes involved with hydroxylation of the side chain of cytokinins,weren’t you, Dr. Sakakibara?
Sakakibara: Yes, that paper was published in 2004. We used a screening
method based on mass spectrometry. We
were really fortunate to be working in
RIKEN that had the necessary analyticaltechnology.
Kamiya: After the launch of the PSC, we
headhunted Dr. Eiji Nambara because wewere interested in abscisic acid and hecould promote research both on abscisicacid and gibberellin. He had two research
themes. One was cloning of cytochrome
P450, which is a catabolic enzyme of abscisic acid. In agriculture, this is very important. The other was the abscisic acidreceptors. For nearly ten years, a Canadian group had been a leader in the func-

tional analysis of ABA degradation cytochrome P450 using enzyme purification,
but Dr. Tetsuo Kushiro took practicallyless than a year to catch up using a reverse genetic approach. The first device
that Dr. Kushiro wanted us to purchase
was the old style French press that is used
to extract enzymes from microorganisms(laughs). He was probably the first person
to succeed in producing enzyme activity
with a device that looks like cast iron.
Sakakibara: Even if we know the genome information, we normally do nothave a method to verify it. But at RIKEN,
collaboration is possible with multiple research teams, and unlike in a university
where there are boundaries between research groups, there is a sense within
RIKEN that we can freely strike up joint
research.
Kamiya: We are a “family.”
Sakakibara: It’s a “We are in the sameboat” mentality, right? (laughs).‍
Kamiya: It’s a blood relation linked byresearch. As long as we are a family, we
can’t lock ourselves up in our small, little
rooms.
Sakakibara: The meetings for reporting
research progress within the Center provided opportunities for constructive criticism before a paper was submitted andeverybody knew what the paper was
about by the time it was actually published. This, I think, also promoted joint
research. Dr. Kamiya and I also have threeor four papers that we co-authored.
Kamiya: For an institute like RIKEN thatneeds to have advanced technology development and international competitiveness, it is very important that we build
networks around the world and bring

ProfileYuji KAMIYA［left］

Group Director,
Growth Regulation Research Groupa1975: Graduated from the University of Tokyo,
Graduate School of Agriculture after completingthe doctoral program. In the same year, he joined
the Pesticide Synthesis Laboratory 3 of RIKEN as a
researcher. 1980: A research fellow at University ofGottingen for two years. 1991: Served as the Team
Leader of the RIKEN Frontier Research Program,Laboratory for Plant Hormone Function for eight
years. 2000: Served as Group Director of the Plant
Science Center, Growth Physiology Research Groupfor five years. 2005: Appointed as Group Directorof the Growth Regulation Research Group.

Hitoshi SAKAKIBARA［center］

Group Director,
Plant Productivity Systems Research Groupa1988: Graduated from Nagoya University (Schoolof Agricultural Sciences). 1992: Withdrew from thedoctoral program at Nagoya University, Graduate
School of Bioagricultural Sciences. In the same year,
he was appointed as a Research Associate at Nagoya University. 1995: Obtained Ph.D. in agriculture. 2000: Joined the RIKEN Plant Science Centeras Team Leader of the Communication Mechanisms Research Team. 2005: Team Leader of the
Biodynamics Research Team. 2006: Appointed asGroup Director of Plant Productivity Systems Research Group.

Plant Hormone Research at the Plant Science Center

0 2 1

Plant Hormone Research at the Plant Science Center

植物科学研究センター
Plant
Science Center
13年記念座談会─b
13th Anniversary Talk─c

Yuji
KAMIYAGroup Director,
Growth Regulation Research Groupdown barriers among scientists and help
each other out. And this is also one of themerits of RIKEN’s basic research.
Sakakibara: Because PSC started out asa time-limited project, we were subject torigorous inspection every two or three
years and there was a lot of pressure. In
those circumstances, I was able to identify
three key genes involved in the biosynthesis of cytokinin from 2001 to early
2007, and I think it was good that I wasable to gain global recognition for cytokinin biosynthesis.
Building a Brand for
the RIKEN Plant Science Center
Kamiya: I think it was around 2006 that
Dr. Shinjiro Yamaguchi began his researchon strigolactone. It was a happy amalgamation of Dr. Yamaguchi’s excellence inbiochemistry and Dr. Mikihisa Umehara’s
plant cultivation technique that led to thebig discovery in a short period oftime. Our hunch was that strigolactone‍s
did not exist for the parasitic plant Striga,
but were actually plant hormones.
Sakakibara: The results were publishedin Nature in the same issue that a Frenchgroup published their results, wasn’t it?
Kamiya: Yes, a friend of mine fromoverseas advised me that a similar paper
would be published soon, so we were
getting all geared up to publish ours
(laughs). But Dr. Yamaguchi was really0 2 2

cautious and said he wanted the paper tobe perfect so that he could be sure it
would be accepted. That made me really
nervous, but we waited until the lastminute before submitting the paper. We
learned that by that time, their paper was
already being examined. It was really aclose call. It reminded me how important
it was to have an international network.
Sakakibara: It’s also about building abrand for RIKEN Plant Science Center sothat the Center is recognized everywhere,
isn’t it?
Kamiya: During the time I was an international advisor for the Annual Review ofPlant Biology for ten years starting in
2000, I had a small wish of having many
principal investigators (PIs) at PSC contribute articles for the journal, becausethat would increase the number of citations from PSC. There are several research
institutes in the world that call themselves
plant science centers. Among them, RIKEN’s has its strength in hormone-related
biochemistry. After Dr. Kazuki Saito
joined our Center, we have added a newstrength in the field of metabolomics.
I am actually hesitant about enteringother fields where somebody else is already working on. For example, in gibberellin research, my area of specialization is mainly biosynthesis. Professor
Taiping ‍Sun is in the field of signaling,
and the University of Tokyo and Professor
Makoto Matsuoka are in the field of receptors. The remaining field of transporters is important but nobody is doing thisresearch. That’s why when Dr. Mitsunori
Seo put his hand up to do the research, I
thought it was suitable as the next generation of research, and I would verymuch encourage him to pursue thispath. In sum, whereas we extract hormones from the entire plant and analyze
them, research on transporters elucidates
how hormones are transported from individual cells and how they are consumed. This is research for the future.
Sakakibara: From my experience of
dealing with nitrogen and cytokinin, I
knew from literature that there were antagonistic interactions with abscisic acid.‍Kamiya: It is well-known that at low
concentrations, abscisic acid promotes
root growth. In Japan, abscisic acid ismixed in fertilizers. It is an interaction
between practical agricultural applications and transporters.
Sakakibara: It was Dr. Takashi Kuromori,in Dr. Shinozaki’s research group, who

Plant Science Center 13th Anniversary Talk─ cidentified the ABC transporter. I was saying to myself, “So this is the abscisic acidtransporter,” when Dr. Seo used anothercompletely different screening method
and found another transporter gene that
had previously been identified as a transporter for nitrate ion, and this surprised
us all. From this new vantage point, werealize that there was actually substantial
literature where both nitrogen nutrition
and abscisic acid were involved.
Kamiya: It was the discovery of the abscisic acid receptor that led to Dr. Seo’s
ideas. Receptors do not recognize hormones on their own but form complexes
to do so, and Dr. Seo skillfully integrated
this into his yeast-based screening system. An advantage of this screening
method is that it can be used for otherplant hormones. Now that his researchhas been published, I would think otherscientists will start using this system.

Hitoshi
SAKAKIBARA

Group Director, Plant Productivity
Systems Research GroupOn Scientist with a Trademark

On Scientist with a Trademark
Kamiya: When we were getting ready toorganize new teams in 2005, Dr. Hiroyuki
Kasahara, Dr. Mitsunori Seo, Dr. Shinjiro
Yamaguchi and I stayed overnight to discuss the future of our research. One of
the things I talked about was the importance of each scientist, and particularly

young scientists, to have their own trademarks. Scientists should not be swayedby the trend. It is important we carry ourown banners. As for me, I decided on atheme and have always pursued it. People
said hormones are out of date and that I
should move on, but I believe if you stick
to what you believe in, something good
has to come out of it. I think you should
all stand firm and continue with what
you really want to do. In the end, it’swhen you are doing what you really want
to do that your research has the greatest
strength.
Sakakibara: One of the reasons wewere able to continue research on plant
hormones at RIKEN was that we clearly
demonstrated that plant hormones wereclosely related to productivity and plantdevelopment. When we entered the second period of PSC, there was a numericaltarget for raising plant productivity by
30%. In that process, we were able todemonstrate, even in our papers, thatgibberellins and cytokinins are plant hormones actually involved with productivity
and therefore, research on plant hormones is important for improving productivity. That was probably also one of
the reasons that plant hormone researchbecame one of the cores of research at
PSC.
Kamiya: I was originally in a pesticide
laboratory, so I actually did research withpeople from private companies. The sizeof the gibberellin market is very small if
you look at the entire agricultural chemicals market. But even then, fine tuningwith hormones is very important. It will
be indispensable for aseptic culture in
future plant factories.
Sakakibara: With further improvement
in mass spectrometry technology, somescientists at other RIKEN centers are attempting to conduct mass spectrometry
on a sample that consists of only a single
cell. If we can go down that path, I think
we will ultimately be able to clarify the
dynamics of plant hormones in single
cells. Another thing is that I think there
are still many undiscovered plant hormones. In those respects, I feel there is
still much room where RIKEN can contribute. The overall direction of research at
the Center will probably change next
year. Still, scientific excitement is a hallmark of RIKEN’s research we need topreserve, and I hope to take on exciting
new challenges. I also feel, without any
exaggeration, that development of PSC
owes much to you Dr. Kamiya, who, as aleader in plant hormone research in Japan, maintained friendly communication
with all sorts of people.
Kamiya: PSC was open to the world eversince its birth. I think that’s very important. When I was a student, I felt utterly
humiliated when scientists overseas
called Japanese scientists who had done
exceptional work not by his or her name,but simply as the “Japanese scientist.”
For me, I will respect a scientist for the
research that he or she has done. Affiliation is irrelevant. For PSC to gain instrength, how it will change is very important. I think I was able to survive because I was always willing tochange. Young people need to change
after being appointed to their new positions. It’s important that they set their aim
on new directions that few people haveeven thought about.
Sakakibara: I agree. I think there are still
many more undiscovered treasure-trovesin the world of plant hormones (laughs).
The only other requirement is devotionand enthusiasm. d

Plant Hormone Research at the Plant Science Center0 2 3

植物科学研究センター
Plant
Science Center
13年記念座談会─b
13th Anniversary Talk─❹Internationalization of the Plant Science Center

The Plant Science Center provides a strong research environment and support system for receiving foreign researchers.
Following the trend in internationalization, the Center also actively promotes joint research with overseas laboratories,
which enhances the profile and brand of the Plant Science Center.
A staff member of the RIKEN Global Relations Office and a scientist who has hosted a number of foreign researchers
at his lab discuss the internationalization of the research environment at the Plant Science Center.

to their countries with good impressionsof the PSC that will lead to the next recruitment of overseas researchers. Their
first impression will be based on whether
or not systems and procedures are inplace in the research laboratories. In
some cases, we have had researcherswith us for only a three-month period but
who later applied for the FPR or JSPS
program. Therefore, we perhaps need totreat short-term researchers with particular care as potential PR messengers forresearch at PSC.
Shimizu: I also think the arrangementsfor our foreign researchers are very important. If they speak enthusiastically
about the kind of research they wereable to engage in and the kind of research environment they experienced
here when they go back to their homecountries, people will have a positive image of RIKEN. Therefore, I think it is important to turn foreign researchers thatcome to Japan into avid fans of RIKEN.
Giving Priority to English
at the Plant Science Center

Special Postdoctoral
Researchers Program Supporting
the RIKEN brandShirasu: I took up my current position at
the Plant Science Center (PSC) in April
2006, about five years after the Center
was established. At that time there werevery few non-Japanese researchers at either RIKEN or PSC. There were a numberof reasons for this, I believe. First of all,there was very little support for foreign
researchers at the time, and the seminars
as a general rule were conducted in Japanese, so it was not an environment where
foreigners could easily participate unlessthey were proficient in Japanese. I had
just returned from overseas and, as a scientist, I personally found the working
environment very odd and felt that making the organization more international
would definitely be to our advantage.
Shimizu: I joined RIKEN in 2007 as the
person in charge of the newly established
Foreign Postdoctoral Researcher (FPR)
program, the equivalent of the Special
Postdoctoral Researcher Program but foroverseas researchers. At that time theinitial recruitment was already underway

0 2 4

in preparation for the first intake of foreign researchers in 2008. The labs selecttheir applicants in advance, so I believe
there is a high level of competition in theplacement of these overseas researchers.
Shirasu: PSC has hosted six Foreign
Postdoctoral Researchers to date. Two of
the six came to my lab. Both were very
competent female researchers from Australia. This year we will see an increase in
the number of FPRs, and I believe in theend we will host about eight at a time.
About 30 foreign researchers also cometo PSC under the Postdoctoral Fellowships for Foreign Researchers program
sponsored by the Japan Society for the
Promotion of Science (JSPS). Their stay isfor a maximum of two years, however.
Unlike for FPRs, there are no positions
under this program that allow for a threeyear stay. Therefore, I feel those whocome on the FPR program have a greater
opportunity to engage in research as coreresearchers here at PSC.
Shimizu: This must be a very meaningfulprogram in terms of activities at yourlaboratory.
Shirasu: It certainly is. The compensation
package provided for the researchers is

Plant Science Center 13th Anniversary Talk─ dalso very generous. It is definitely a special
scholarship program even by international standards, and it has turned out
some very outstanding people. I feel FPR
is achieving success as a prestigious program that will contribute significantly to
making RIKEN an international brand.
When it comes to internationalization,
the importance of critical mass is always
foremost in my mind and the ratio ofoverseas researchers I always bear inmind as a target is 30%. In other words,
I consider having three out of 10 researchers from overseas as a reasonableratio. At our lab, however, this ratio has
at times reached as high as 50%.
If we have a number of overseas researchers in the program, they can share theirknowledge about living in Japan witheach other. But unless we develop a welcoming research environment, researchers will not come here, and unless theycome, we cannot continue this program.
What we have to do is to create an attractive environment that will entice talented researchers to join our program, so
we can continue to host researchers fromvarious countries. It is always my hopethat our overseas researchers will return

Shirasu: One thing that overseas researchers find quite offputting when theyfirst enter the research lab is the amountof notices and signs written in Japanese.
Even though they can imagine that thesenotices contain important information,
they have no idea what they say. If wethink about it, that kind of environment is
actually very exclusionist. To remedy this,we decided to give English priority over
all other languages in my lab and not toallow any sign or notice unless it was alsoin English. I also asked other sections
with whom we share the work environment to cooperate in this initiative. Of
course, there are some who complainthat this arrangement is rather troublesome, so it is still a bit of an uphill battle.
Shimizu: It must be quite a challenge. As
we know, Japanese are generally quite
proficient at reading English but quite
hesitant when it comes to writing.
Shirasu: The same goes for email. Firstof all, I have told everyone at the lab that
I want all email in English. When they arecomposing email, I ask everyone to writein English first and then in Japanese. The
reason for doing this is because I find thatwhen researchers who cannot read Japanese see a message written in Japanese
first, they tend to dismiss the entire mes-

sage. The decision to make English theofficial language at seminars within PSC
took about a year to make but today I am
glad that I pushed for this.
Shimizu: I think that is great, because it
is important for Japanese to acquire a
foreign language. At the same time, I feel
it is important for children to be able tostudy science in Japanese during theirprimary education. Whether it is physics
or biology, I have heard that there are notmany countries where people can study
such subjects in their mother tongue
alone.
Shirasu: I believe there are various viewson the subject but being able to think in
one’s mother tongue is an extremely
strong argument.
Shimizu: If Japanese were proficient attheir own language as well as a foreign
language, I believe they would be in themost advantageous position in scientificresearch too. Just the other day I was
reading a book by science journalist
Shimpei Miyata, with a title that in English means:“A Paradise of Freedom for
Scientists – The Glory of RIKEN”. It seems
that researchers in the Meiji Period were
not inclined to differentiate between thearts and sciences. When I read the partdescribing how Dr. Kikunae Ikeda, who
was instrumental in the founding of RIKEN, had a strong influence on the writer
Soseki Natsume, I felt that it would begreat if scientists today were knowledgeable in the arts as well as sciences.
Shirasu: To be both a person of letters aswell as a scientist, I feel, is quite appropriate. In today’s world, however, we deal
with a massive amount of information,and people in science without competency in English will be at a decided disadvantage in their fields. However, I think
it would be good to have scientists who
not only can speak English well but also
have a sound understanding of Japanese
literature and can express it in English. At
any rate, I think we agree that it is very
important to create an environment
where people are proficient in both English and Japanese.

ProfileYunike SHIMIZU［left］

Program Coordinator for Junior Scientists,
Global Relations Office, RIKEN
aResearch Personnel Support Section, Global Relations Office, RIKEN
2007: Joined RIKEN. In charge of Foreign Postdoctoral Researcher Program at Research General Affairs Section, DRI/FRS Promotion Division. Since
2010: In charge of programs for junior scientists at
Research Personnel Support Section, Global Relations Office.

Ken SHIRASU［right］

Group Director,
Plant Immunity Research Groupa1988: Graduated from the University of Tokyo, Faculty of Agriculture, Department of Agricultural Chemistry. 1993: Awarded Ph.D. in genetics at University ofCalifornia, Davis. After studying at the Salk Institutefor Biological Studies (United States) and the Sainsbury
Laboratory (Great Britain), became an independent PI
at the Sainsbury Laboratory. 2005: became Group Director at RIKEN Plant Science Center. Since 2008: visiting professor at the University of Tokyo Graduate
School.

Creating a Support System
and Community
for Overseas Researchers
Shimizu: Although English is understoodat our institute, foreigners who can’t
speak Japanese generally have great difficulty in conducting their everyday affairs

Internationalization of the Plant Science Center

0 2 5

Internationalization of the Plant Science Center

植物科学研究センター
Plant
Science Center
13年記念座談会─b
13th Anniversary Talk─❹Ken
SHIRASUGroup Director,
Plant Immunity Research Groupin Japan and often comment that they
don’t know where to begin.
Shirasu: Yes, it seems the first one or
two weeks after arrival in Japan can bequite difficult. Initially, the individual labs
offered support to some extent, but PSC
now has a dedicated person who was
employed to look after our researchers
from overseas. Procedures and systems
have also been put in place to help withthe kinds of difficulties that all newcomers encounter. We also provide all kindsof information to overseas researchers
prior to their arrival in Japan. And themoment they arrive, we are there to givethem reassurance and any support theymight need. We want them to get off toa smooth start so that they will have theimpression that Japan is a wonderfulplace to live. Once they get over the initial
one to two weeks without any major issues, the people at their respective laboratories will be able to help in whatever
way they can.
Shimizu: The Global Relations Office has
a translation team, and many of the rules
and regulations have already been translated into English. This has been very
useful to non-Japanese staff. The HelpDesk at the Brain Science Institute (BSI)on the Wako Campus also serves as amodel for other universities, and we havevisitors from those universities coming tosee how it operates.
Shirasu: Perhaps no other research institutes or universities in Japan provide as

0 2 6much support to foreign researchers as
we do. RIKEN can serve as a template foruniversities that want to increase thenumber of their foreign researchers. I
think it would be ideal for RIKEN to takethe lead in internationalization in this respect. As the number of overseas researchers increases, a community of foreigners naturally forms without theassistance of Japanese staff. In Yokohama, there is a network of overseas staff,
more like an international village, whichis quite active outside PSC. But it takes a
lot of time for this to occur. It is importantfor us to create opportunities for people
to get together in activities outside thescience environment. It can be anything– like football or other social events.
Shimizu: Once a month the Global Relations Office holds an event called “Discovery Evening” on Wako Campus. Thisis for researchers of the Special Postdoctoral Research and Foreign Postdoctoral
Research programs as well as postgraduate students. In the future, we hope tohold similar events at the Yokohama
Campus too. We would also like to plan
events where both non-Japanese andJapanese alike can participate.
Disseminating Information about
the PSC Brand andResearch Environment
Shimizu: I have heard that in Germany
scientists cannot establish a successfulcareer path in their own country unlessthey do some postdoctoral study abroad.
Shirasu: That is correct. And that is why
many German researchers go to theUnited States or the United Kingdom tostudy. I think it would also be good if they
made Japan one of their options. In fact,
we did have one German postdoctoral
researcher with us who later became aprincipal investigator (PI) upon his returnto Germany. We need to strengthen the
RIKEN brand and create an environment
where researchers keep turning out excellent papers. In that way, those researchers who produce quality papers
during their time at RIKEN will have an
image as researchers who are not only
quite competent in English but also capable of engaging in research with anopen mind.
The Plant Science Center currently is at
the forefront of biochemistry worldwide.
Japanese are known for their special
techniques for measuring minutePlant Science Center 13th Anniversary Talk─ damounts of compounds like metabolomes or hormones and, because of its
long history in agricultural chemistry andchemistry in general, RIKEN is particularly
strong in these areas. Many researchers
from around the world come to Japan tolearn these techniques. In that respect, I
believe PSC offers some unique facilities
and research areas that no other institution in the world can offer.
Shimizu: We need to promote theseunique features more at an international
level, so that people will feel they mustcome to RIKEN and PSC for their research.
Shirasu: You’re right. It will take sometime but sending out information is vital.
It is only recently that we’ve been able toestablish this kind of platform and begin
to turn out a significant number of papers. PSC has risen in status internationally, so it has been well worth the effort.
There are many advantages in having
talented postdoctoral researchers comefrom overseas to PSC. To begin with, it
provides opportunities to work with laboratories overseas and to expand our network in a more dynamic manner than if
our research activities were confined toworking with Japanese researchers herein Japan.
Like our joint research with the Max

 Foreign postdoctoral researchers at PSC

 ̶ The FPR Program and RIKEN's Internationalization

Fiscalyear

YunikeSHIMIZU

Research Personnel Support Section
Global Relations Office, RIKEN

Planck Institute and other institutions, we
can cooperate with world hubs in joint
initiatives. In the area of plant research,
there are a number of very prestigious
centers in the world and, as a hub, PSC
should cooperate with these centers, notjust in name but in meaningful relationships. As researchers of these centers
move about and continue their joint research with each other, it is important for
us to hire them. A culture will also develop
where it is taken for granted that science
is conducted in English among Japanese
researchers, who see English as a vehicle
for conducting their work in science.
People who are used to conducting lab
meetings in English will also be able todeliver smooth presentations in English.
Shimizu: In this regard, I think that you
could actively take advantage of the“Discovery Evening.”
Shirasu: I would like to create opportunities for our researchers to become more
proficient in English through day-to-day
communication. The greater their proficiency, the easier it will be for them toprepare papers in English. We have someresearchers who are extremely capable in
conducting experiments but miss out ona lot of opportunities because they cannot write papers in English. Another important skill is the ability to collect information. When researchers attend academic
conferences overseas, it is important toknow how to source information. Whenno new information is forthcoming fromNo. ofRatio of foreignTotal
foreign
researchers to No. of
number of
researchers total number of FPRs
staff
at RIKEN research staff

Foreigners –FPRs

Year-onRatio to total
Ratio ofyear change number of
FPRs to allin number research staff
foreigners atof foreigners (excluding
RIKEN(excluding FPRs)
FPRs)
9.11%

-

H18

2853

260

9.11%

0

260

H19

2671

256

9.58%

0

256

-4

9.58%

-

H20

2538

241

9.50%

17

224

-32

8.83%

7.05%

H21

2552

288

11.29%

36

252

28

9.87%

12.50%

H22

2656

332

12.50%

47

285

33

10.73%

14.16%

H23

2686

352

13.10%

50

302

17

11.24%

14.20%

presentations at an academic conference,
they have to take the initiative to go visit
some labs, make friends with other scientists and on occasion socialize by goingout for a few drinks together. If they
don’t develop skills in forming relationships and gathering information, I thinkthey will have a hard time.
A Place where Researchers can

A Place
where
PursueTheir Researchers
Aspirations can Pursue
Their Aspirations
Shimizu: Under the present FPR program, the 30% allocation of foreign researchers based on the approximate 150
places originally established for Special
Postdoctoral Researchers is spread acrossthe labs on a mandatory basis. Of course,
the ideal situation would be to recruit acertain percentage of foreign researchers
without fail and have all candidates
compete on the same playing field. To
some extent, for the time being however,I feel that perhaps we need to direct ourefforts to boosting our numbers on acompulsory basis, as you suggested.
Shirasu: It may not be fair unless the
30% of the people on the selecting side
are also foreigners (laugh). Increasing thenumber of PIs is another important area
where we need to make efforts.
Shimizu: The fact that RIKEN employs
foreign PIs as Initiative Research Unit
Leader also sends out an important message, I believe.
Shirasu: So, essentially, the challenges
for us are to create an attractive environment and to change people’s mindset
through efforts on a daily basis. If we canattract foreign PIs who can be outstanding examples, others will want to follow
in their footsteps. It would also be won-

derful if we could have something like anexchange program for postgraduate students.
Shimizu: Actually, right now we areplanning a series of “RIKEN Day” events
overseas where we will hold joint symposiums with professors and students. As
part of the program, we hope to encourage research at RIKEN as a career option
for students and postdocs. If we can use
this event in tandem with PSC’s initiatives
at internationalization to date, it could
lead to the internationalization of RIKEN
as a whole.
Shirasu: To a certain extent, RIKEN has
already established an environment thatno other university or research instituteoffers. I would like researchers who cometo RIKEN to understand that if they makethe most of their time with us, they will
be able to take their research to the nextlevel. We are very eager to gather many
serious researchers at PSC. We would beinterested in talking to aspiring young
scientists who may not be able to gooverseas at the moment but who havefuture ambitions to do so after hearing
about our institution. dInternationalization of the Plant Science Center

0 2 7

Report on Research Activities─a［Metabolomics Research Division］

Research in plant metabolomics is of particular importance today
because of the contribution of diverse metabolites to the usefulness of plants.
At the Plant Science Center research in metabolomics and metabolic genomics is aimed
at understanding and applying matter production systems in plants
through integrated omics including bioinformatics.

Metabolomics and Metabolic Genomics Research

Importance ofMetabolomics Research

2006
Genomics

Metabolite annotation
Metabolite accumulation(AtMetExpress)

Coexpression networks(AtGenExpress, ATTED-II)
Deep transcriptome

Evolutional consideration
Natural variants
Next-generation seq.

▲

0 2 8

Report on Research Activities─ a▲▲Metabolomics consists of three main areas: 1) instrumental analysis of metabolites, 2) bioinformatics, and 3) integration and expansion to genome
biology. The Metabolomics Research Division constructed a research platform to organically linkthese three areas and succeeded in launching aworld-first analysis platform in metabolite profiling. This platform consists of two pillars: mass
spectrometry (MS) with high sensitivity and specificity, and nuclear magnetic resonance (NMR),
which has the advantages of quantitative and noninvasive performance.
In MS analyses, we have established the world’s
most comprehensive MS platform by linking andcombining non-target mass analyses to a numberof high-performance separation systems (gas andhigh-speed liquid chromatography, capillary electrophoresis). By further combining wide target
analysis through robotics, we achieved further
high-throughput and quantitative performance. In
NMR analysis, we have also developed software
for the automatic assignment of metabolome signals and multidimensional NMR metabolomics.
Since the inception of the Plant Science Center, wehave devoted significant efforts to the development of bioinformatics research because our mission was to build a metabolomics platform not
only for RIKEN and Japan but a platform thatwould lead the world in metabolomics. Therefore,
we developed databases and analysis softwarethat would also contribute to the world researchcommunity. The results of this initiative are thePlatform for RIKEN Metabolomics (PRIMe) website,
an integrated metabolomics portal, and a wide2007

Data processing, databasing, integration

Systems biology(hypothesis generation)

range of databases and analysis softwarethat are
stored there.
Since 2010, with support in the form of equipmentfrom the Leading Edge Research Infrastructure
Programme, this metabolomics platform that integrates metabolite analysis and bioinformatics has
been contributing significantly to the promotion ofresearch in Japan and overseas as a leading centerof metabolomics research led by plant science researchers in Japan.
Contribution toFunctional Genomics Science

It is believed that plants have anywhere from
200,000 to one million kinds of metabolites, andthe source of their chemical diversity is hidden in
their genes. Therefore, one of the main objectivesof metabolomics research is the study of functional
genomics, which identifies the gene functions involved in plant functions. The Plant Science Centerhas a wide range of genome research resources
based on Arabidopsis thaliana, which researchers
have been able to use effectively.
We elucidated the linkages between genes andmetabolites based on co-occurrence from mutant
and stress-treated plant metabolomes, integrated
transcriptome analyses, and publicly-available
transcriptome data. We then proceeded to comprehensively identify gene functions and elucidate
gene-to-metabolite networks through biochemical
research using reverse genetics analyses and recombinant proteins based on mutants of thegenes we identified. With this method we madeDiscovery of a transcription factor that regulates sulfur metabolism in plants［Advanced NMR Metabomics Research Unit］
Jun KIKUCHI［Metabolome Informatics Research Team］                                 Masanori ARITA

Discovery of an enzyme that determines the structure of plant flavonoids● Discovery of a new gene that causes cruciferous vegetables to produce
cancer-inhibiting components● Commencement of full-scale metabolomic profiling using
the world s largest NMR facility● Elucidation of plant metabolic networks using metabolomic profiling
Elucidation of plant s self-resistance mechanism to anti-cancer substanceproduced by plants● Discovery of a new biosynthetic route of plant anti-oxidative flavonoids● Identification of an enzyme gene that synthesizes a component of a natural
low-calorie sweetener● Preparation of a spectral library of tandem mass spectrometry for plantsecondary metabolites● Development of bird s-eye view analysis technology for metabolic pathwaysof all living organisms including plants and animals

2008

Discovery of a new sterol biosynthetic pathway for plant sterol, the existenceof which had been denied for 30 years● Discovery of a new gene key to sulpho-lipid synthesis through lipid
metabolome analysis● Development of a real time analytical method for whole metabolite in theprocess of microorganism fermentation● Elucidation of the close relationship between the plant circadian clock andmitochondrial functions● Development of a new method of standardization for analytical data

2010

significant strides using Arabidopsis thaliana and,following on from these positive results, weachieved further success by expanding our research
to various agricultural crops including rice andmedicinal plants.
Application to
Crop Plant Biotechnology

In addition to identifying gene functions, metabolomics research opens pathways for the broad application of research results in areas such as crop
breeding, biotechnology, and synthetic biology ofuseful substances. Some specific examples of applications are metabolome QTL analysis of major
crop products including rice, regressive predictionof agricultural traits through metabolomic analysis,
biotechnological production of useful secondary
metabolites (glucosinolate, polyphenol, etc.), andmetabolic function research for woody biomass,
bioenergy crops and algae.
Furthermore, the application of metabolomics isalready being demonstrated in broad, diverse areas
such as substantial equivalence assessment of genetically-modified tomatoes, the analysis of single
cells and vacuoles, plant triterpene production using enzymes, bioplastic material production using
photosynthetic bacteria, and the application of
NMR metabolomics in medicine.

●

Tracing of bacterial interactions using RIKEN s unique analysis of metabolic
dynamics
Elucidation of metabolic balance adjustment function of rice cytosolic
glutamine synthase● Objective assessment of genetically-modified crop using metabolomics● Confirmation for the first time of the localization and dynamics ofalgae-produced metabolites within a single cell
● Discovery of glycosyltransferase genes involved in the accumulation ofplant pigment anthocyanin● Discovery of an enzyme gene for synthesizing pharmaceutical component ina rare herbal plant licorice
●
●

2011

●

2009

Discovery of new facts about site-specific secondary metabolite biosynthesis
in plants
Development of a new NMR assessment technique for metabolized
bio-resources mixtures for effective use of unutilized metabolites● Study of taste and fragrance-producing components of dadachamame beanusing metabolome analysis●●

Reverse genetics/biochemistry/chemistry,mathematical modeling

Functional genomics (hypothesis validation)and biotech application (crop breeding, synthetic biology)

●

●

▲

Transcriptomics▲

Metabolomics

Establishment of a Platform
for Metabolomics Research                                             Kazuki SAITO    Masami Yokota HIRAI ̶ Main Research in Metabolomics and Metabolic Functions Over the Past 8 Years ̶ Diagram: From Metabolomics to Systems Biology▲

One of the so-called omics sciences, metabolomics
is the systematic identification and quantificationof metabolites. Diverse metabolites contribute to
the usefulness of plants in food, medicine, healthfunction components, and raw materials in industry and energy. Therefore, metabolomics researchin plants is particularly important.
The integration of metabolomics with techniquessuch as transcriptomics enables the scope of research to extend to functional genomics science,
which identifies new gene functions leading toapplication to biotechnology and synthetic biology.
In the same way, the integration of metabolomics
with mathematical science allows for expansion of
the scope of research to systems biology. Therefore, metabolomics has the potential to make asignificant contribution to sustainable biologicalresources, and human survival and health. It wasagainst this background that metabolomics research at the Plant Science Center commenced in
2005.

PI［Principal Investigator］［Metabolomic Function Research Group］［Metabolic Systems Research Team］

2012

●
●

Comprehensive study to shed light on genetics of brown rice metabolism
Elucidation of causal genes of bitter beanssome areas which need to be addressed such as:(1) improvement in metabolite annotation, (2) dynamic profiling in areas such as metabolic flux,
channelling, and imaging, etc., and (3) integration
with mathematical science in areas such as metabolic simulation.
In the future, metabolomics research is expected
to display its formidable power not only in basic
research in areas such as the identification of newgene functions and systems biology but also in areas of research that affect our everyday lives suchas the production of useful materials in green innovation and life innovation (industrial and biofuel
materials, medicine and health-promoting compounds, etc.), and in improving food yields andcrop breeding. d

New Developments
and Challenges

Although metabolomics research has achieved
significant results in plant science, there are still

Metabolomics and Metabolic Genomics Research

0 2 9

Report on Research Activities─b［Functional Genomics and Bioinformatics］

In functional genomics and bioinformatics research, we have collected mutant andgene resources that form an important platform for profiling genes in the research of
the model plant Arabidopsis thaliana. We have elucidated genomic networks involved inlight environment and stress responses. To expand the scope of our research touseful plant crops, we have developed similar databases for various plant species.

Developing Mutant Resources andInformation Platforms
tant lines and a database for these. We also developed a proprietary FOX line, which is a
gain-of-function mutant Arabidopsis line (Arabidopsis FOX line) where the gain of function isforcefully conferred through over-expression of
Arabidopsis full-length cDNA.
In joint research with the National Institute ofAgrobiological Sciences (NIAS) and the ResearchInstitute for Biological Science (Okayama Prefecture) which commenced in 2005, we have also
developed a functional analysis platform for various plant species through the production of arice-FOX Arabidopsis line (rice-FOX line) for conducting functional analysis using rice full-length
cDNAs.
Using rice-FOX lines, we identified high-accumulation lines for drought tolerance, high-temperature
tolerance, disease resistance, hormonal mutations
and secondary metabolites, and performed rapid
identification of the causal genes. We also jointly
established a database with the Integrated Genome Informatics Research Unit and provided it to
the public. In a joint research project with the National Institute of Advanced Industrial Science andTechnology commencing in 2007, we promoted
the development of new gain-of-function lines bycollecting about 2,000 transcription factor genes
from Arabidopsis and produced function-inducible
transcription factors lines. In joint research with
the Gene Discovery Research Group, we also engaged in the production of high-expression lines of
peptide proteins.
As a laboratory theme, we have been researching
how plants interpret the light environment to
conduct morphogenesis, and in this research wehave been utilizing various resources. From our

Progress in Research Overthe Past Seven Years

The Plant Functional Genomics Research Group,
Plant Genomic Network Research Team, and theIntegrated Genome Informatics Research Unit,
which make up functional genomics and bioinformatics, have made a start from the Plant Functional Genomics Research Group in the RIKEN Genomic Sciences Center (GSC) in 1999, andcommenced the production of mutants of themodel plant Arabidopsis thaliana, the collection of
full-length cDNA gene information and the development of a database for this, and the provision of
resources and data to researchers in Japan andoverseas.
In 2006, the Plant Functional Genomics ResearchGroup of the RIKEN Plant Science Center (PSC)
was established. Since then, this group has been
responsible for the production of gain-of-function
resources for the genetic analysis of Arabidopsis,and has produced and analyzed a total of 100,000
activation tag lines and various FOX lines (fulllength cDNA over expressors), which will be discussed later. In cooperation with the RIKEN BioResource Center (BRC), the PSC provides theseresources to researchers in Japan and overseas.
Using these resources, the group has also conducted research on the response of plants to thelight environment.
Overview of the Plant Functional
Genomics Research Group

The Plant Functional Genomics Research Grouphas been promoting the production of Arabidopsis
gain-of-function lines. At the GSC, our group developed approximately 60,000 activation tag mu-

Transcription Control+DEX

CullinInfrared
Light

Transcriptional
activation
Blue

Red

F-box
Ub
Ub
Ub

Far-RedPhotoreceptor

・
・
・
・
・
・
Photomorphogenesis
Search for transcriptional factor involved influorescence signal using TF-GR line

TF-GR line

Far redYeast two-hybrid

DNA microarray

GAL4 DNA binding
domain fusion plasmid

FOX line, KO line

-DEX +DEX-DEX +DEX

Report on Research Activities─ b

F-box

Ub
Ub

Ub Ub

Ub Ub

BiFC

Multi-yeast MATa

Selection based on
nutritional requirements

Joining of yeast

LR reaction

Gateway
entry vector
N.tabacam

TF4

Joining of
yeast

F-box
cDNA

ASK
cDNA

TF3

0 3 0

Preparation of genome resource

TF2

TF1

F-box

Control of matrix protein

F-box panel
Blue

Rbx1

Analysis using F-box protein collection

Transcription control, protein control

Screening under monochronal light condition

ASK

GAL4 activation domain
fusion plasmid
Subcellular localization

Multi-yeast MATa

01

Investigation of genes using gain-of-function mutants involved in photoperception
and cell cycles

09

Identification of new peptides involved in drought, cold, high-salinity, and hightemperature stress responses

02

Production of a total of 100,000 gain-of-function mutants in activation tagging
lines, Arabidopsis FOX lines, and rice-FOX lines

10

Collection of full-length cDNAs in various crops, and transcriptome analysis

03

Collection of Arabidopsis transcription factors, production of function induction
transformation lines, and profiling of transcription factors responsible forphotoperception

11

Development of functional genomic analysis platform in cassava, and advancementof molecular breeding

04

Collection of F-BOX proteins responsible for protein decomposition, andcomprehensive analyses of interactions

12

Epigenome and Transcriptome analysis using next generation sequencer(a projectof the Japan Advanced Plant Science Research Network)

05

Development of multi-gene expression systems in plants

13

Promotion of research resource development for trees and crops, and genomics
research

06

Management of transformation network for the promotion of crop research

14

Integration of soybean and wheat genetic mapping

07

Analysis of RNA and epigenetic regulatory mechanism involved in drought, lowtemperature, high-salinity, high-temperature stress and ABA responses

15

Construction of database for Arabidopsis mutant organism expression traits

08

Analysis of transcriptional and post-transcriptional regulation mechanisms throughchromatin remodelling and RNAs

16

Support in the development of metabolomic tools

research on light reception and the plant cell cycle,
we found that CYCA2;1 and CYCA2;3 play key
functions in the endoreduplication of plants.
We also undertook research to isolate an Arabidopsis FOX line which displays a distinctive bluelight morphology, and new genes from an integrated transcription factor line. In addition, we
engaged in the comprehensive collection andfunctional genomics analysis of F-BOX proteins involved in specific protein decomposition importantin various types of physiology［Diagram］.
At the RIKEN Biomass Engineering Program established in 2010, we are responsible for research as
the Synthetic Genomics Research Team. This teamwill take part in an international collaboration with
Malaysia and other countries to develop basic
technologies for the production of biomaterials
utilizing the light reception of plants and using
genomic analysis techniques and gene induction
techniques as well as integrated gene co-expression systems in plants (IRES).

Protein Control
Ultraviolet［Integrated Genome Informatics Research Unit］                     Tetsuya SAKURAI ̶ Main Research Over the Past 7 Years

̶ Genomic Resource Platform for Comprehensive Analyses［Diagram］

Inductive line for transcription factor (TF-GR line)

PI［Principal Investigator］［Plant Functional Genomics Research Group］                                Minami MATSUI［Plant Genomic Network Research Team］                                              Motoaki SEKI

Overview of the Plant Genomic
Network Research TeamWe have explored the mechanism of RNA andepigenetic regulation, and new peptides involvedin environmental stress responses. We found that
antisense strand RNA is produced by RDR (RNAdependent RNA polymerase) under environmental
stress conditions. We also found that mutants ofArabidopsis Histone Deacetylase HDA6 showeddrought stress tolerance through activation of acetate biosynthesis pathway. We demonstrated thatdrought stress tolerance can be enhanced by addition of acetate before drought stress treatment. In
addition, we found that overexpressors of several
stress-inducible small ORFs showed stress toler-ance phenotype.
We have developed cutting-edge genome technologies and advanced gene identification andfunctional analysis of genes in joint research withdomestic and oversea collaborators. We established a cassava functional genomics platform ofinternational standard and advanced cassava molecular breeding in collaboration with Colombian,Thai and Vietnamese researchers.
Integrated
Genome Informatics Research Unit

Utilizing sequence information including expressedsequence tags (EST), we have been focusing ourresearch on understanding various gene functions
in plants and the overview of genomes. To promote the development of research resources fortrees and crops and the advancement of genomics
research, we collected full-length cDNAs of poplar,soybean, cassava, and etc. and analyzed their sequences. Moreover, we provided the sequence information and results of our analyses to the public
as databases on the Internet.
We have also contributed to the promotion of research related to the above areas through analyses
and the development of databases for soybean
genome decoding, genetic map integration forwheat (TriMEDB), full-length protein code sequencing (TriFLDB), phenotypes of various Arabidopsis mutants (RAPID, Chloroplast Function Database, RiceFOX), and transcripti on factors(LegumeTFDB, GramineaeTFDB, TreeTFDB). We
developed and assisted metabolomics-related
tools (PRIMe). d

Developing Mutant Resources and Information Platforms

0 3 1

Report on Research Activities─c

Elucidating Plant Hormone Biosynthesis
and Signal Transduction
Progress of the Growth Regulation
Research Group (Growth Physiology)
Over the past 13 years.

Established in 2000, the Growth Regulation Research Group originally had a two-team structure
consisting of the Laboratory for Cellular Growthand Development (Yuji Kamiya, PI) and the Laboratory for Reproductive Growth Regulation (Eiji
Nambara, PI). The Laboratory for Cellular Growthand Development promoted biosynthesis andmetabolic research of gibberellins (GAs) using
Arabiodopsis seeds, which require GAs for germination, and identified the regulatory mechanismsof the main GA biosynthesis enzymes. Focusing on
dormancy, the Laboratory for Reproductive Growth
Regulation promoted research on the metabolism
of abscisic acid (ABA) and the profiling of gene
expression, and elucidated ABA inactivation enzyme genes and their functions.
Following an organizational restructure, the groupassumed a three-team structure for promoting
projects since 2005: the Growth Regulation Research Group (Yuji Kamiya, PI), the Dormancy and
Adaptation Research Team (Eiji Nambara, PI), andthe Cellular Growth and Development Research
Team (Shinjiro Yamaguchi, PI). In addition to his
work on GA research, in 2008 Dr. Yamaguchi
identified strigolactones as a new plant hormonethat regulates shoot branching. This discovery of
the function of strigolactones as a plant hormone
was an exciting result.
In 2011 Dr. Yamaguchi moved to Tohoku University to take up a position as professor there. Dr.
Hiroyuki Kasahara, Senior Research Scientist of the
Growth Regulation Research Group, through his
research in functional analysis of the yucca gene,succeeded in identifying the biosynthesis pathwayof auxins, which had remained a mystery for overhalf a century. Dr. Kasahara had been appointed asa Sakigake research scientist just prior to 2011.
After team leader Dr. Nambara took up a positionat the University of Toronto in 2008, the groupwelcomed Dr. Mitsunori Seo from France and reorganized the Dormancy and Adaptation Research
Team as the new Dormancy and Adaptation Re-

̶ Auxin Biosynthesis Pathways［Diagram 1］

CO2H

Trp

N
H
IAA

01

Research on the regulation of gibberellin biosynthesis, its
reception and signal transduction

02

Research on abscisic acid (ABA) biosynthesis and metabolism

03Studies on the regulation of ABA (regulation of biosynthesis,
biosynthesis sites and transport)

04

Identification of factors involved in lateral bud dormancy andseed dormancy

05

Transcriptome analysis of seeds

06

Research on biosynthesis and regulation of jasmonic acids,
brassinosteroids and auxins

07

Development of a simultaneous hormone analysis system,high-sensitivity analysis of hormones (which had beendifficult to measure with the use of conventional methods),
and measurement of intermediates

08

Chemical genetics approach for identification of inhibitors of
isoprenoid biosynthesis and secondary metabolites in plastids

09

Role of the non-mevalonate pathway in diterpene
biosynthesis, and production of useful materials

10

Functional analysis of P450 genes involved in hormone
biosynthesis

11

Development of growth regulation technologies based on theregulation of plant hormone biosynthesis

12

Development of growth regulation technologies based onplant hormone-related genes and chemicals

13

Identification of new signaling molecules that regulate plant
growth and development including strigolactones

search Unit. As head of this unit, Dr. Seo developed
a unique hormone transporter isolation method
using a plant hormone receptor complex and discovered a new ABA transporter involved in nitrogen metabolism. Our group has contributed to theworld through plant hormone research over the
past 13 years.
Overview of the Growth Regulation
Research Group and Research Results

Plant hormone research has generally been promoted through targeted research projects but theRegulating of Shoot Branching                                                     by Strigolactone［Diagram 2］
̶

O

TAA1

Strigolactone O

H

O

IAOx
IPA

IAAId
YUCCA
AMl1

O

CYP79B

TAM
IAM

0 3 2

 ̶ Main Research of the Growth Regulation(Growth Physiology) Research Group

IAA

IAN
IAM
‑

Arabidopsis thaliana

Report on Research Activities─ c

Wild-type‑+d10 mutant

Strigolactone (2µM)

O

PI［Principal Investigator］

The Growth Regulation Research Group engages in efforts to shed light on
the biosynthesis of plant hormones such as auxins, gibberellins, abscisic acid,and strigolactones which regulate plant growth and differentiation.
Through this research, we are also contributing to improvement in plant productivity.

Plant Science Center has adopted an omics approach in expression analysis of all hormone-related genes from its establishment. Since the metabolomics research group began participating in
the PSC in 2005, we have been promoting hormonome research. In hormonome research, we
conduct high-sensitive simultaneous analyses ofhormones and their intermediates using LC-MS/
MS. We integrate a high-sensitive analysis systemwith biosynthetic studies of GAs, ABAs, brassinosteroids and jasmonic acid, which we have beenworking on for many years, and isolate enzymes
involved in the biosynthesis of plant hormones
and their genes before conducting functional
analyses of these.
Dr. Kasahara took up the challenge of biosynthesis
research on auxins in 2007, and not only achieved
success in the expression of yucca enzyme functions but also identified the main auxin biosynthesis pathways［Diagram 1］.
The joint research of enzyme inhibitors in auxin
biosynthesis has significant potential in the development of plant growth regulators. GA biosynthesis enzyme inhibitors are widely used all over
the world as environmentally friendly plant growth
regulators.
Overview of the Cellular Growth andDevelopment Research Teamand Research Results

Dr. Shinjiro Yamaguchi has been promoting research in the light regulation of seed germination
and also GA inactivation enzymes such as EUI and
GA methyl transferase as well as research in newplant hormones. Although there were reports ofthe existence of a plant growth substance which
regulated shoot branching in a number of plants
through the biosynthesis of carotenoids, thechemical structure of this substance was notknown. Using tillering dwarf rice mutants isolated
by Dr. Junko Kyozuka of the University of Tokyo
and Arabidopsis mutants, Dr. Yamaguchi and Dr.
Umehara (Reseach Scientist) identified strigolactones for the first time as a new plant hormonethat regulates shoot branching in plants  ［Diagram 2］. Strigolactone is also known as a hormone thatinduces hyphae branching in mycorrhizal fungi.
Through this research, they found that there weredifferences in the structural activity of strigolactone in two bioactivities. In 2011 Dr. Yamaguchi
moved as a professor at Tohoku University where
he is continuing his research on strigolactone.
Laboratory for Reproductive
Growth Regulation, and then Dormancy
and Adaptation Research Unit

Viviparous germination in wheat that occurs during the rainy season in Japan is a serious problem
in agriculture. If ABA could be made to accumulate
in the wheat seeds, seed dormancy would become［Growth Regulation Research Group］
                                                 Yuji KAMIYA［Dormancy and Adaptation Research Unit］                                         Mitsunori SEO

̶ Encoding of CYP707A Gene / New ABA Transporter［Diagram 3］-CYP9707A encodes ABA 8'-hydroxylase［Diagram 3-A］

HO
OH

OH
CHO

O

O

OH
COOH
(+)-ABA

Wild type

COOH

O

cyp707o2 mutant-Identification of an ABA transporter［Diagram 3-B］
］

28C˚

25C˚

0.6

Stomatal aperture(width/length)［Growth Regulation and Productivity Systems —1 a Growth Regulation Research Group/Dormancy and Adaptation Research Unit］

0.4

ait1-1WT

0.2
0deeper and viviparous germination could be regulated. While it was known that the ABA degradation enzyme was a P450 enzyme, its gene was
unknown. From out of the nearly 270 Arabidopsis
P450 genes, Dr. Nambara along with Dr. Kushiro(Reseach Scientist) hypothesized that gene CYP707
was involved in the metabolism of ABA based onreverse genetics approach, and they proved that
CYP707 is the P450 enzyme gene that catalyzes
the hydration of 8’-postion of ABA. The CYP707
deficient mutants exhibit deep dormancy, and viviparous［Diagram 3-A］ does not occur. This was amajor breakthrough from an agricultural perspective. Furthermore, the group also elucidated a new
ABA-related factor from analysis of the ABA expression profile in seeds. Dr. Mitsunori Seo, thesuccessor of Dr. Nambara, developed a methodthat involved the skillful use of ABA receptor
complexes and also discovered a new ABA transporter［Diagram 3-B］. This method has significant application potential in the research of other plant
hormones and transporters of physiologically active substances. d

Elucidating Plant Hormone Biosynthesis and Signal Transduction

0 3 3

Report on Research Activities─d［Growth Regulation and Productivity Systems — 2 a Plant Productivity Systems Research Group/Cell Function Research Team］

Identification and Utilization of  Genes Useful for Improving Crop Productivity
Progress of the Research GroupOver the Past 13 Years

In October 2000 the Laboratory for Communication Mechanisms headed by Dr. Hitoshi Sakakibara
was established to clarify mechanisms regulating
plant growth in response to nitrogen nutrition using Arabidopsis. The scope of this research then
expanded to include the elucidation of biosynthesis pathways of cytokinin effectively involved in theregulation of plant production functions and thestudy of the regulation mechanisms.
In April 2005, the team’s name changed to the
Biodynamics Research Team and the scope of research expanded to include rice and developmentof a comprehensive analysis platform for plant
hormones. Focusing on the diversity of the growthenvironment of bryophytes, the team also engaged
in research on heavy metal accumulation in moss
and its application to industry.
In April 2010, the team became the Plant Productivity Systems Research Group and again expanded
the scope of its research. The group currently engages in the elucidation of biomass production
utilizing plant hormone action and mechanisms
for optimizing plant growth in response to environmental changes.
In July 2007 the Cell Function Research Unit
headed by Dr. Keiko Sugimoto was established topromote the identification of gene clusters involved in the regulation of plant organ and cellsize. Continuing to pursue research as the Cell
Function Research Team since 2012, the team aims
to establish new methods for improving plant
productivity by utilizing the results obtained from ̶ Main Research of the Research Group overthe Past 13 Years

01

Identification and functional analysis of the key genes
involved in cytokinin biosynthesis

02

Elucidation of cytokinin biosynthesis and its translocation
mechanism in response to nitrogen nutrition

03

Structural biology based analysis of cytokinin biosynthesis
and its signalling system

04

Elucidation of cytokinin biosynthesis pathway inphytopathogenic bacteria05

Development of recovery technology for lead and gold using
protonemal cells of bryophytes

06

Research on the circadian rhythm mechanism and plant
growth regulation

07

Development and utilization of an highly-sensitive highthroughput plant hormone analysis platform

08

Elucidation of molecular mechanisms underlying plant cellproliferation and growth09

Elucidation of molecular mechanisms underlying regulating
pluripotency in plants

10

Elucidation and application of molecular mechanisms that
determine organ size in plants

0 3 4

Report on Research Activities─ d̶ Auxin Biosynthesis Pathways［Diagram 1］

basic research.
Overview of Researchby the Plant Productivity Systems
Research Group

The Plant Productivity Systems Research Group
expanded its research to include improving the
productivity of crops in areas such as altering thesink (growth and storage)-source (synthesis) balance and the effective transport and storage ofassimilated products by focusing on the elucidation of cytokinin metabolism and its action. This
research resulted in the identification of three enzyme genes responsible for biosynthesis: IPT, CYP735A and LOG. IPT is responsible for the primary
reaction of the cytokinin biosynthesis pathway,
CYP735A is responsible for playing a major role inthe synthesis of highly-active cytokinin trans-zeatin,and LOG catalyzes the final step of cytokinin biosynthesis and also plays an important role inmaintaining shoot meristem activity. The identification of LOG resulted in the discovery of a novel
pathway of cytokinin activation. The group also
identified a key IPT gene for regulating the biosynthesis of cytokinin in response to nitrogen nutrientsand elucidated its regulation mechanism［Diagram 1］. The results obtained from this research are important in the regulation of cytokinin biosynthesis
and are expected to contribute to improving the
productivity of various crops in the future.
In addition to plants, some phytopathogenic bacteria are known to synthesize cytokinin. Thesebacteria infect plants and cause tumors formation

With plant hormone research at the core, the Plant Productivity Systems Research Group
engages in research to elucidate systems involved in production regulation,
sink functions, and the effective transport of substances and undertakes research anddevelopment in techniques for use in production regulation.
The Cell Function Research Team aims to elucidate networks that regulate plant organ
and cell size using Arabidopsis as a model plant.

as a result of uncontrolled synthesis of cytokinin.
We demonstrated that Agrobacterium-derived IPT
altered the cytokinin biosynthesis pathway to produce more trans-zeatin in the host plant, effectively causing the formation of tumors. The elucidation of this strategy for altering metabolic
function in plant cells was a groundbreaking finding.
For deeper understanding of plant hormone actions, a comprehensive knowledge of distribution
and concentrations of multiple hormones is essential. Therefore, we developed a highly sensitive
high-throughput analysis platform of major plant
hormones (six hormones, 45 molecular species),and discovered new genes through hormone QTL
analysis utilizing this technology.
The productivity of plants is determined not only
by genetic factors but also by environmental factors. Therefore, we engaged in research on environmental response mechanisms and the interaction of genes and the environment. As the main
result of our research, our group demonstrated
that PRR5, 7, 9 were transcription repressors incircadian rhythm regulation. We also determinedthat nitrate transporter 2.4 (NRT2.4) in Arabidopsis
has a role in nitrate uptake under low external
supply. Moreover, we found that protonemal cellsof Funaria hygrometrica could accumulate metals
such as lead and gold in large amounts and identified the modes of accumulation. Applying thesefindings to environmental purification and resource recovery for industrial purposes, we also
developed a purifying system jointly with DOWA
Holdings.
Research Overview of the Cell Function
Research TeamThe Cell Function Research Team engages in research to elucidate molecular systems that determine the size of higher plants by identifying geneclusters involved in the regulation of plant cell andorgan growth. The team aims to apply its researchoutcome to establish new methods for improving
crop productivity. We have recently discovered a
new gene HPY2 necessary for cell division anddemonstrated that cell proliferation in plants isregulated by the SUMO protein produced by thegenetic information of HPY2. The requirement of
SUMO in the meristem development has neverbeen shown before.
Until now, there has been little study on themechanisms that actively regulate and arrest thegrowth of plant cells. We isolated and analyzed amutant from the FOX (full-length cDNA over expressor) mutant collection of Arabidopsis in whichleaf trichome cells grew to a gigantic size. Basedon these results, we demonstrated that the plantspecific trihelix transcription factor GTL1 is involved
in regulating ploidy-dependent cell growth.

PI［Principal Investigator］［Plant Productivity Systems Research Group］         Hitoshi SAKAKIBARA［Cell Function Research Team］
                           Keiko SUGIMOTO̶ Overexpression of GTL1 Leads to Dwarf Plants［Diagram 2］

Wild Strain

GTL1 Over-expression Strain

There are still many unknown aspects in the molecular mechanisms underlying plant dedifferentiation and regeneration, which are both used as abasis for technologies in the nursery, flower, andhorticultural industries. The team identified atranscription factor WIND1 which displays elevatedexpression after wounding. Strong expression of
WIND1 results in the formation of callus and thesedata together revealed the role of WIND1 as amaster regulator of wound-induced dedifferentiation in plants. These results may help establishing a
new technology for plant propagation and production of useful materials based on the plant tissue culture.
What factors determine the size of plant organs is
an important question in both basic and appliedbiology. In our investigation of plant organ-size
control, our team identified a new enzyme involved in the inactivation of brassinosteroids as afactor that regulates plant organ size. d［Diagram 2］

Identification and Utilization of Genes Useful for Improving Crop Productivity

0 3 5

Report on Research Activities─e［Environmental Response and Adaptation— 1 / R&D Programs for PSC      a Gene Discovery Research Group, Signaling Pathway Research Unit, Regulatory Network Research Unit, R&D Programs for PSC ］

Development of Crops with High Abiotic Stress Tolerance
Progress of the Research Group Overthe Past Eight Years

In 2005, the Gene Discovery Research Group wasestablished along with the appointment of Dr.
Kazuo Shinozaki as Center Director. Utilizing themodel plant Arabidopsis and omics techniques, thegroup began its research by exploring important
genes and later expanded its research to include
the elucidation of gene co-adjustment networks.
The R&D Program, which supports the Plant Science Center as a whole, was established in 2007
to undertake three specific tasks: the developmentof common use microscopes and imaging technologies, development of technologies and support in genome sequencing and comparative genomic analysis, and the utilization of mutant
resources for elucidating gene functions. In 2008
the Regulatory Network Research Unit headed by
Dr. Ryoung Shin was established to promote research in signal transduction and metabolic regulation of plants in nutrient-deficient conditions. In
2009 the Signaling Pathway Research Unit headed
by Dr. Lam-Son Phan Tran was established to undertake elucidation of genes related to plant adaptation to stress and plant hormone networks. Bothunits are also planning to undertake research thatwill lead to the development of crop species. With
the inception of these two units, the Plant Science
Center made significant progress in internationalization.
In tandem with the establishment of the Biomass
Engineering Research Program in 2010, the Gene
Discovery Research Group expanded the scope of
its research to include the research and development of resource infrastructure relating to the improvement of soft cellulose biomass production.
Aiming for stable agricultural production amid climate change conditions, the group analyzes systems by which plants respond and adapt to abiotic
stress and nutrient-deficient environments andexplores useful genes and the elucidation of theirfunctions in efforts to demonstrate maximum
productivity irrespective of the cultivation environment.
Overview of the Gene Discovery
Research GroupThe Gene Discovery Research Group promotes exploration of new genes and functional analyses of
new genes involved in stress responses and resistance acquisition to elucidate plant response
mechanisms to abiotic stress such as drought andsalt damage. This group has developed stress-tolerant crops and trees and has achieved results inbreeding drought-resistant crops in collaboration.
Through analyses of responses and adaptation to
drought stress in plants at the genetic level, we
have demonstrated the existence of a pathway
mediated by plant hormone abscisic acid (ABA)
and a pathway not mediated by ABA. In particular,

0 3 6

Report on Research Activities─ e ̶ Elucidating a Stress Response Mechanism through Hormone Signaling

High Salinity

Drought

Heat

Environmental
Stresses

Cold

Reactive Oxygen
Species

Abscisic
Acid

PerceptionofStresses

Cytokinin

Pathogen Nutrient Conditions

Jasmonic
Acid

Plant Hormones / Signaling Factors
Auxin

Ethylene
SignalTransduction

Regulation of Gene Expression
Adaptation to Environment Stress Tolerance

we have demonstrated the involvement of protein
phosphorylation in the ABA-dependent pathway.
We have also devoted considerable efforts to elucidating relevant enzymes, and found that SnRK2
protein kinase plays a major role and is an important molecular switch that controls the downstream stress-responsive gene expression. The results achieved by the Gene Discovery ResearchGroup have been highly evaluated and Group Director Dr. Kazuo Shinozaki was selected by Thomson Reuters as the world’s 5th most cited researcher in 2011.
Overview of the Regulatory Network
Research Unit

Since 2008 the Regulatory Network Research Unit
has been elucidating components that regulate
nutrient sensing and metabolic processes in plants
to develop plants that will grow even in a nutrientdeprived soil environment. Dr. Shin has succeeded
in isolating many candidate plants that will give us
an insight into the signal transduction pathway for
detecting potassium deficiency. To identify ricewith nutrient deficiency tolerance, this unit undertook the screening of FOX (full-length cDNA overexpressor) rice plants in nitrogen-deprived conditions and identified many candidate plants. Although it took considerable time to screen the
mutant organisms, new, interesting mutants has
been isolated. Utilizing these mutants, Dr. Shin is

Crop production under stress conditions has become an important issue as elevated
PI［Principal Investigator］
temperatures, drought and other effects of global warming become increasingly evident［Gene Discovery Research Group］
                         Kazuo SHINOZAKI
because of accumulation of carbon dioxide. The Gene Discovery Research Group has begun ［Regulatory Network Research Unit］                                         Lam-Son Phan TRAN
to address this issue by exploring the acquisition of resistance in plants and［Signaling Pathway Research Unit］
                                                Ryoung SHIN
the regulation of their growth as means of coping with abiotic stress caused by drought,［R&D Programs for PSC］
elevated temperatures, salt damage, and nutrient-deficient soil. In research
infrastructure activity named R&D Programs, the group is also developing
a center-wide research platform and resources, and cooperating with external organizations.

 ̶ Research of the Gene Discovery Research Group Over the Past 8 Years

01

Exploration and analysis of regulatory factors andsignaling factor involved in environmental stress responses

10

Elucidation of signaling networks regulating abitoic stress response
and plant growth02

Functional analysis of genes involved in abiotic stress tolerance, and developmentof drought resistant crops using genetic transformation

11

Biotechnology based on the knowledge of Arabidosis

03

Exploration and application of genes involved in plant productivity using a reverse
genetic approach

12

Relationship between cytokinin metabolism and osmotic stress response04

Development of environmental stress-resistant wheat and rice

13

Role of cytokinin-responsive phosphorelay network in osmotic stress regulation

05

Exploration and use of genes involved in improving soft biomass production using
Brachypodium, a biofuel model herbaceous plant

14

Comprehensive analysis and comparative genome analysis of transcription factor
in soybean and bean model plants

06

Dissection of signaling cascades in plant nutrient sensing and deficiency signaling

15

Management of bio-imaging technology and microscopy technologies

07

Isolation of nutrient-deficiency-tolerant rice plants

16

Collection of Arabidopsis knockout mutants for phenome analysis in gene discovery

08

Dissection of 14-3-3 regulated light signaling and 14-3-3 s regulation

17

Comparative and evolutional genomics based on informatics

09

Role of cytokinin in environmental stress response, and the impact of osmotic
stress on cytokinin metabolism

18

Comparative genomics and its application to crop improvement

now conducting analyses of signal transduction
cascades in plant nutrient sensing and nutrient
deficient sensing.
Since 2012, this unit has also been engaging in the
research and development of phytoremediation toremove radioactive cesium contaminated in areas
surrounding damaged Fukushima nuclear power
plants.
Overview of the Signaling Pathway
Research Unit

In 2009 the Signaling Pathway Research Unit
launched a research project to demonstrate abiotic
stress responses, the functions of plant growth
regulators (brassinosteroids, cytokinins, ABAs,
polyamines, etc.), in plant growth and performance, signal transmission, and crosstalk among
hormones. At present Dr. Tran is conducting research mainly in functional analysis of a two-component regulatory system (TCS) related to cytokinin
in osmotic stress response. In this research, thisunit is focusing on the relationship of osmotic
stress responses and crosstalk of cytokinin and
ABA. To improve grain productivity, this unit is also
directing its effort to the exploration of genes
based on comparative genetic research using soybeans in adverse environments with the objectiveof developing stress tolerance in soybeans.

improve research efficiency and exchanges intechniques among research groups by centralizing
costly microscopes and making them available to
PSC as a whole. After several years of efforts, thisgroup succeeded in establishing a superior microscope platform that benefits all groups and individuals engaged in research at the Center. The establishment of this platform is also resulting in thedevelopment of high-quality techniques at themolecular level.
In the R&D Programs, we have also promoted thedevelopment of genome analysis, an information
platform for transcriptome analysis, and the collection of mutant resources for the functional analysis
of genes for the advancement of research at theCenter. We have also promoted phenotype analysis. The outstanding researchers and engineers
who gather here play role in research and development at PSC. d

Overview of the R&D Programs for PSC

While supporting the Plant Science Center as awhole through the use of various technologies andresources, the R&D Programs has achieved many
results in joint research projects. This group
launched a microscope platform facility for analysis
at the cellular level. This group also made effort to

Development of Crops with High Abiotic Stress Tolerance

0 3 7

Report on Research Activities─f［Environmental Response and Adaptation— 2 a Plant Immunity Research Group / Plant Proteomics Research Unit］

Pathogenic organisms in plants cause serious damage to agricultural production
around the world. To mitigate this threat, the development ofcrop protection technologies that simultaneously demonstrate high efficiency
and stability and a low environmental impact are essential.
In Environmental Response and Adaptation – 2, the Plant Immunity Research Group engages
in research on plant immunity systems that will contributeto sustainable agricultural production, and promote the analysis ofplant signaling networks through proteomics technologies.

Research on Plant Immunity Systems
for Sustainable Production
Progress of the Research Group Overthe Past Seven Years

In October 2005, the Plant Immunity ResearchGroup was established to contribute to sustainableagricultural production by improving the disease
resistance mechanisms in plants. Initially, theGroup Director, Ken Shirau, held a concurrent postat the Sainsbury Laboratory in the United Kingdom
but in April 2006 commenced full-time research at
RIKEN as his main occupation.
To elucidate the molecular structure of plant immune systems, the group focuses its research efforts on the discovery of useful genes, novel protein
complexes, and the development of useful lowmolecular weight compounds through the use of
new methods such as genomics, proteomics,
structure analysis, and chemical biology. This group
has made progress in the area of proteomics inparticular, and has developed an analysis method
for plant proteins that undergo post-translational
modifications such as phosphorylation. This method has been applied to rice and other grains. Basedon the research results, the Plant Proteomics Research Unit, lead by Hirofumi Nakagami as a Unit
Leader, was established in April 2010 and contributed to the promotion of proteomics at the Plant
Science Center as well as plant research in Japan.
Characterization of Resistance Signaling
Complexes

The elucidation of signaling pathways leading todisease resistance responses in plant-pathogen interactions will lead to revealing the full picture of
immune response mechanisms in plants. For example, is there a correlation between plant immunity and the natural immune systems of animals? To understand this fundamental question,
the research group explored the functional analysis
of protein complexes, which hold the key to thisquestion. The researchers in the group found thatthe protein known as SGT1, which is necessary for
immune responses in both plants and animals,
forms a complex with proteins known as RAR1
and HSP90, which play an important role in immunosensor functions for recognizing pathogenderived substances. (Boter et al Plant Cell 19:37913804, Zhan et al EMBO J 27:2789, Kadota et al
EMBO R 9:1209-1215, Shirasu Annu Rev Plant Biol
60: 139-164, Zhang et al Mol Cell 39:269-281)［Diagram］.
The next challenge for the group will be to reveal
how this protein complex, which is necessary forboth plant and animal immunity, regulates immunosensors.
Research on Plant Immunity Regulation
through Post-translational Modification

Many proteins are involved in gene expression ofplant immunity, and many of these are regulated
by post-translational modification. However, the0 3 8Report on Research Activities─ f

PI［Principal Investigator］［Plant Immunity Research Group］［Plant Proteomics Research Unit］

                                               Ken SHIRASU             Hirofumi       NAKAGAMI ̶ 3-Dimensional Structure of the Immune Signaling Complex
PAR1-SGT1-HSP90 Site Formation

SGT1

RAR1

HSP90

HSP90
SGT1

overall image is still not clear. To tackle this theme,
the researchers in the group adopted an approachfor detecting the overall post-translational modifications in proteins (modified proteomes) as well asa method for elucidating individual modified proteins. For example, phosphoproteomes in Arabidopsis and rice plants (Sugiyama et al Mol Sys Biol
4:193, Nakagami et al Plant Physiol 153: 11611174) as well as ubiquitin-related proteomes,(Maor et al Mol Cell Proteome 6:601-610) were
investigated. In addition, this group discoveredthat PUB protein cluster, which is a novel ubiquitinrelated ligase, regulates plant immunity (Trujillo et
al Curr Biol 18:1396-1401). Furthermore, the rolesof MEKK1, a phosphorylation protein (kinase) (JBC281: 36969-36976), and autophagy protein ATG,
which performs ubiquitin ligase-like modifications(Plant Cell 21: 2914-2927) in plant immunity were
elucidated. In the future the research group aims
to demonstrate an overall image of plant immunity
regulation through post-translational modifications.
Research of Pathogen Genomics

Pathogens suppress immune systems in plants andcause diseases. Thanks to revolutionary progress ingenome sequencing technologies, determining
these suppression mechanisms through the elucidation of pathogen genes is possible today. The
group is currently focusing our attention on theanthracnose disease caused by Colletotrichum apathogenic fungi, which is a very serious problem
in Japan, and Striga, a parasitic plant causing serious damage to agriculture in Africa. Genome andtranscriptome analyses of these pathogens were
initiated.

RAR1

Among the anthracnose diseases in Japan, Colletotrichum on strawberry in particular causes damages
in total about 3.5 billion yen annually, so finding
an early solution to this fungus is an urgent issue.
Our research group succeeded in analyzing theColletotrichum genome and in identifying thegenes that are likely to be involved in pathogenicity (Gan et al New Phytologist). By finding out
which gene is predetermining the strength ofpathogenicity, it is possible to develop a molecularmarker that will enable early detection of the virulent fungi. This knowledge may also be helpful inthe early discovery of pesticide-resistant fungi.
Striga, a parasitic plant, is causing serious damage
in Africa, and research of Striga at the molecularlevel using genome and transcriptome analyses isalready underway. The surprising discovery is thatit not only acquires nutrients and water from thehost plant but also genes (Yoshida et al Science
328: 1128). Detailed analyses are yet to be conducted but an understanding of the infection
mechanism of the pathogen is likely to pave theway to establishing a counter strategy.d Striga, a parasitic plant that attacks sorghum,a major grain in Sudan ̶ Main Research Over the Past 7 Years

01

Characterization of resistance signaling complexes

02

Isolation and characterization of novel proteins involvedin plant immunity by proteomics

03

Molecular elucidation of parasitism ofAfrican witchweed Striga

04

Method development for post-translational modification
analysis05

Dissection of plant immunity signaling using proteomics
methods

06

Analysis of pathogen genomes

07

Chemical biology of plant immunity

Research on Plant Immunity Systems for Sustainable Production

0 3 9

13 Years of the Plant Science Center

Representative Research Publications

01

Arabidopsis NPL1: A Phototropin Homolog Controlling

the Chloroplast High-Light Avoidance Response

Science vol.291 no.5511, pp.2138   -2141
［

］

03

Transcription switches for protoxylem andmetaxylem vessel formation

Genes & Development vol.19 no.16, pp.1855-1860［

16 Mar. 2001

］ 15 Aug. 2005

Takatoshi Kagawa, Tatsuya Sakai, Noriyuki Suetsugu, Kazusato Oikawa, Sumie Ishiguro, Tomohiko Kato,
Satoshi Tabata, Kiyotaka Okada, Masamitsu Wada

Minoru Kubo, Makiko Udagawa, Nobuyuki Nishikubo, Gorou Horiguchi, Masatoshi Yamaguchi, Jun Ito,
Tetsuro Mimura, Hiroo Fukuda, Taku Demura

From Science Cover Vol. 291, no. 5511, 16 March 2001.
Reprinted with permission from AAAS.

Reprinted by permission from Cold Spring Harbor
Laboratory Press. Genes & Development Vol.19, No.16,
15 August 2005, copyright 2005.

aIndividual plants require a particular optimum intensity oflight for efficient photosynthesis, which becomes apparent in
where they prefer to grow. Plants which favor strong lightgrow best in direct sunlight, while plants which favor weak
light prefer shaded areas, such as under foliage. Light intensity in these preferred environments will also vary dependingon the weather or time of day. In response to the intensity ofincident light, chloroplasts can actually migrate within a cell;
this migration is a system that plants use to maintain the optimal photosynthetic efficiency.
aThe research group isolated many mutants of Arabidopsis
Thaliana which were defective in their chloroplast movement;
the genome of Arabidopsis Thaliana has been completely sequenced and serves as a model plant. We selected four lines
which don’t show any movement of chloroplast even under02

strong light and searched for the gene that was causing thisloss of function. This search led to the responsible gene, NPL1,
whose base sequence had already been reported but its function was unknown. We demonstrated that the encoded protein of this gene is clearly involved in the recognition of strong
light.
aThe chloroplasts in plants with this mutated gene do not
move away to avoid strong blue light. Instead, they gather tomove closer, which may also explain why chloroplasts gather
under weak light. Two kinds of cryptomes have already beenreported as blue light receptors. The results here clarify thatthe various phenomena exhibited by plants in response toblue light are co-regulated by at least four kinds of blue light
receptors.

Cytokinin Oxidase Regulates Rice Grain Production

Science［vol.309 no.5735, pp.741-745］

Motoyuki Ashikari, Hitoshi Sakakibara, Shaoyang Lin, Toshio Yamamoto, Tomonori Takashi, Asuka Nishimura,
Enrique R. Angeles, Qian Qian, Hidemi Kitano, Makoto Matsuoka

0 4 0

Representative Research Publications

04

This is the first achievement that identified QTL directly involved in crop yield.
aFurthermore, we successfully created a Koshihikari strain thatis about 18% shorter and has a 20% increase in yield.
Shorter rice leads to reduced lodging injury (stalks broken bywind and weather). QTL analysis enables future identificationof responsible genes for agriculturally useful traits and transferring such genes to existing cultivars. Such “tailor-mademolecular breeding” is expected to be the fundamental technology driving the “Second Green Revolution” to combat thepossible food crisis which may strike as the world population
increases.

ate cells which wouldn’t naturally differentiate into xylem suchas epidermal cells. Additionally, repression of the function ofthese genes disables the normal formation/development ofxylem, which reveals that these are the master genes for xylem
formation.
aThis marks the world’s first results to identify the genes which
are able to directly induce xylem formation. By analyzing indetail the entire gene expression network that VBD6 and VND
control, it will be possible to artificially regulate the productivity and quality of biomass. This result is also expected to establish molecular breeding technology to realize super trees withenhanced productivity and quality.

Direct control of shoot meristem activity
by a cytokinin-activating enzyme

Nature vol.445 no.7128, pp.652-655［

29 July 2005

aIn the long history of plant breeding, humankind has selected
and accumulated agriculturally useful traits resulting fromvarious mutations. The desirable traits of individual rice cultivars are produced by the sum total of such mutated genetic
loci. This set of mutated genes that produce a trait is called its
quantitative trait locus (QTL).
aIn this research, we conducted QTL analysis to identify thegenes which give rise to the difference in the rice grain productivity, and found QTL (Gn1) on the upper arm of chromosome 1 to greatly impact the grain yield. In the end, together
with identifying gene for cytokinin oxidase /dehydrogenase(OsCKX2) as a responsible gene, we revealed the mechanism
how the gene involves in determination of the grain yield.

aMost of the biomass on earth is derived from xylem vessel
cells included in wood. In this research, we found many genes(about 200 genes) which are expressed in xylem formation bycomprehensive expression analysis of approximately 23,000
Arabidopsis genes with a newly established xylem formation
system of Arabidopsis cultured cells by our research group inorder to identify the genes which regulate the xylem formation.
aWe focused on NAC-domain proteins which have been suggested to be involved in regulation of gene expression andanalyzed the function of these genes in detail using Arabidopsis and poplar. We showed that two analogous NAC-domain
proteins named VND5 and VND7 have the ability to differenti-］

8 Feb. 2007

Takashi Kurakawa, Nanae Ueda, Masahiko Maekawa, Kaoru Kobayashi,
Mikiko Kojima, Yasuo Nagato, Hitoshi Sakakibara, Junko Kyozuka

aCytokinin is a plant hormone with crucial roles in plant
growth and crop yield by repressing leaf senescence, activating photosynthesis, regulating apical dominance, and determining the number of rice grains. Generally, hormones arepresent at very low concentration. For this reason, plants usually synthesize the hormone’s inactive precursors, which areactivated as the need arises. The genes involved in the biosynthesis of cytokinin precursors were known prior to our work,
but the gene functioning in the most important activation
step of the precursors had yet to be discovered.
aThe research group discovered that the LOG gene, the responsible gene for log mutant of rice which causes abnormal❖ Phenotype of log mutant

formation of ears and flowers, encodes enzymes for cytokinin
activation. That is, we revealed that the LOG protein madefrom this gene removes sugar phosphate from the cytokinin
nucleotide to generate the active form of cytokinin in a truly
novel fashion. The LOG gene works only in a limited group ofcells in meristem tissue, which shows how finely the amountof active cytokinin is tuned in a plant.
aBy using LOG genes, it becomes possible to directly control
the cytokinin activity inside the plant body. We expect thatmanipulating the functioning of LOG genes in various crops
will greatly enhance agricultural productivity.

13 Years of the Plant Science Center

0 4 1

13 Years of the Plant Science Center

Representative Research Publications

05

08

Inhibition of shoot branchingby new terpenoid plant hormones

Nature vol.455 no.7210, pp.195-200［］ 11 Sept. 2008

The Arabidopsis cytochrome P450 CYP707A encodes ABA 80-hydroxylases:
key enzymes in ABA catabolism

The EMBO Journal vol.23 no.7, pp.1647-1656［

Mikihisa Umehara, Atsushi Hanada, Satoko Yoshida, Kohki Akiyama, Tomotsugu Arite,
Noriko Takeda-Kamiya, Hiroshi Magome, Yuji Kamiya, Ken Shirasu, Koichi Yoneyama, Junko Kyozuka,
Shinjiro Yamaguchi］

7 Apr. 2004

Tetsuo Kushiro, Masanori Okamoto, Kazumi Nakabayashi, Kazutoshi Yamagishi, Sayaka Kitamura, Tadao Asami,
Nobuhiro Hirai, Tomokazu Koshiba, Yuji Kamiya, Eiji NambaraaWe discovered which genes encode ABA 8’-hydroxylases, which are the key enzymes to activate the plant hormone abscisic acid
(ABA) and also demonstrated that plants which have lost this gene lie deeply dormant.

Reprinted by permission from Macmillan Publishers Ltd.
Nature Vol.455, 11 September 2008, copyright 2008.

shoot branching.

aThe pattern and extent of shoot branching of plants determine the above-ground plant shape, and ultimately influence
the quantity and quality of flowers and seeds, and are thus
agriculturally and horticulturally important traits. Adequate
regulation of shoot branching is a key to maintain the survival
strategy of plants in nature, as well as the quality of crops andyield in cultivated production.
aThe research team has analyzed mutants with enhanced
shoot branching and shorter height, and found that a series ofcompounds called strigolactones act as a hormone to control

06

aThe research team proved that the these mutants that lackthe gene for strigolactone biosynthesis are also more difficult
to be infected by Striga. Striga parasitizes on the root of crops
and deprives them of nutrients and water, which interfereswith their growth.
aWe expect that this discovery will trigger further research on
strigolactone and lead to development of a method for controlling shoot branching and also a method for inhibiting plantparasites, both of which affect crop yield.

phot1 and phot2 mediate blue light-induced transient increases
in cytosolic Ca2+ differently in Arabidopsis leaves

Proc Natl Acad Sci USA vol.100 no.14, pp.8583-8588［］

8 July 2003

Akiko Harada, Tatsuya Sakai, Kiyotaka Okada

09
012

Agrobacterium tumefaciens increases cytokinin production in plastids
by modifying the biosynthetic pathway in the host plant

Proc Natl Acad Sci USA vol.102 no.28, pp.9972-9977［］

12 July 2005

Hitoshi Sakakibara, Hiroyuki Kasahara, Nanae Ueda, Mikiko Kojima, Kentaro Takei, Shojiro Hishiyama,Tadao Asami, Kazunori Okada, Yuji Kamiya, Tomoyuki Yamaya, Shinjiro Yamaguchi
aWe discovered that after Agrobacterium (a crown gall bacterium) infected a plant, it modifies the me-❖ A crown galls formed

by infection of a tomato
by Agrobacterium.

tabolism of the host by sending its proteins into plastids (e.g. chloroplasts); this invasion induces tumor
formation.

10013

ELONGATED UPPERMOST INTERNODE Encodes a Cytochrome P450 Monooxygenase
That Epoxidizes Gibberellins in a Novel Deactivation Reaction in RiceThe Plant Cell vol.18 no.2, pp.442-456［］

Feb. 2006

Yongyou Zhu, Takahito Nomura, Yonghan Xu, Yingying Zhang, Yu Peng, Bizeng Mao, Atsushi Hanada,
Haicheng Zhou, Renxiao Wang, Peijin Li, Xudong Zhu, Lewis N. Mander, Yuji Kamiya, Shinjiro Yamaguchi, Zuhua He

aWe were the first in the world to reveal that calcium ions are a common signal for two blue light receptors, phototropin1(photo1) and phototropin2 (photo2). We demonstrated that each receptor regulates calcium ion concentration differently.

aWe discovered a novel deactivation mechanism of gibberellins, a growth promoting hormone of plants. This is an epoch-making
discovery that proves the existence of a novel mechanism for regulation of growth hormone in a specific organ of plants. Thus,
we opened new avenues for technology that regulates growth of plants by using growth hormones.

野生株

07

Functional analysis of each blue light receptor, cry1, cry2, phot1,
and phot2, by using combinatorial multiple mutants in Arabidopsis

Proc Natl Acad Sci USA vol.101 no.8, pp.2223-2228［］

24 Feb. 2004

Maki Ohgishi, Kensuke Saji, Kiyotaka Okada, Tatsuya SakaiaWe revealed the function of each of the four blue light sensors that are involved in plant growth. Cryptochrome1 and Cryptochrome2 are only involved in photomorphogenesis or regulation of gene expression, each of which takes a long time to respondto stimulation by light. In contrast, phototropin1 and phototropin 2 mainly regulate the movement response, which responds
immediately to the light.

0 4 2

Representative Research Publications

11（ilpl-ID）
変異株

INCREASED LEVEL OF POLYPLOIDY1, a Conserved Repressor of
CYCLINA2 Transcription, Controls Endoreduplication in Arabidopsis

The Plant Cell vol.18 no.10, pp.2452-2468［］❖ Morphology of wild-type seedlings

Oct. 2006

Takeshi Yoshizumi, Yuko Tsumoto, Tomoko Takiguchi, Noriko Nagata, Yoshiharu Y. Yamamoto,Mika Kawashima, Takanari Ichikawa, Miki Nakazawa, Naoki Yamamoto, Minami Matsui(left) and mutant seedlings (right).
Mutants have bigger leaves comparedto those of wild-type plants by about
30%.

aWe discovered a gene which regulates the amount of nucleic DNA in a cell and makes it possible to change the size of cells. The
size of an organism is determined by the number and size of cells which constitute the organism; hence, the more DNA in the
nucleus, the bigger plant cells become.

13 Years of the Plant Science Center

0 4 3

13 Years of the Plant Science Center

Representative Research Publications

親株（野生株）12

slim1 変異株

16

Arabidopsis SLIM1 Is a Central Transcriptional Regulator of

Plant Sulfur Response and Metabolism

The Plant Cell vol.18 no.11, pp.3235-3251［］❖ Isolation of slim1 mutants by

Nov. 2006

Akiko Maruyama-Nakashita, Yumiko Nakamura, Takayuki Tohge, Kazuki Saito, Hideki Takahashi

fluorescent imaging. Mutants havebigger leaves compared to those ofwild-type plants by about 30%.

Structural insight into the reaction mechanism andevolution of cytokinin biosynthesis

Proc Natl Acad Sci USA vol.105 no.7, pp.2734-2739［］

19 Feb. 2008

Hajime Sugawara, Nanae Ueda, Mikiko Kojima, Nobue Makita, Tomoyuki Yamaya, Hitoshi Sakakibara❖ 3D structure of IPT protein

aWe analyzed Arabiopsis mutants with abnormal sulfur metabolism and discovered SLIM1, a transcription factor regulating thecontent of an organosulfur compound named Glucoraphanin; this compound exhibits anti-cancer effects. This discovery will be
useful for applied research to enhance the productivity and utility of cruciferous plants.

aWe succeeded in performing 3D structural analysis of the synthase of cytokinin which is involved in disease and regulation ofyield in plants. And we revealed the reaction mechanisms of cytokinin biosynthesis. By artificially changing the function of IPT,
productivity of various crops is expected to improve.

13

17012

The Mitogen-Activated Protein Kinase Cascade MKK3–MPK6 Is an Important
Part of the Jasmonate Signal Transduction Pathway in Arabidopsis

The Plant Cell vol.19 no.3, pp.805-818［］

Comprehensive Flavonol Profiling and Transcriptome Coexpression Analysis
Leading to Decoding Gene–Metabolite Correlations in Arabidopsis

The Plant Cell vol.20 no.8, pp.2160-2176［

Mar. 2007］

Aug. 2008

Fuminori Takahashi, Riichiro Yoshida, Kazuya Ichimura, Tsuyoshi Mizoguchi, Shigemi Seo, Masahiro Yonezawa,
Kyonoshin Maruyama, Kazuko Yamaguchi-Shinozaki, Kazuo Shinozaki

Keiko Yonekura-Sakakibara, Takayuki Tohge, Fumio Matsuda, Ryo Nakabayashi,
Hiromitsu Takayama, Rie Niida, Akiko Watanabe-Takahashi, Eri Inoue, Kazuki Saito

aWe discovered the MKK3-MPK6s cascade regulating the signaling of jasmonic acid, a key plant hormone for plants to respondto damage caused by insects and pathogens, and succeeded for the first time in the world to regulate the expression of genes
involved in defense responses to insects and pathogens.

aWe discovered a new pathway to transfer arabinose to flavonol in the biosynthesis of flavonoids, which are a major antioxidant
for plants. We revealed the metabolomics network in detail. Further understanding will allow modified plants to produce essential ingredients for materials in medicine, food, and industry.

14

18013

Omics-based identification of Arabidopsis Myb transcription factors
regulating aliphatic glucosinolate biosynthesis

Proc Natl Acad Sci USA vol.104 no.15, pp.6478-6483［］

Negative Regulation of PAMP-Triggered Immunity byan E3 Ubiquitin Ligase Triplet in Arabidopsis

Current Biology vol.18 no.18, pp.1396–1401［

10 Apr. 2007

Masami Yokota Hirai, Kenjiro Sugiyama, Yuji Sawada, Takayuki Tohge, Takeshi Obayashi, Akane Suzuki, Ryoichi Araki,
Nozomu Sakurai, Hideyuki Suzuki, Koh Aoki, Hideki Goda, Osamu Ishizaki Nishizawa, Daisuke Shibata, Kazuki Saito］ 23 Sept. 2008

Marco Trujillo, Kazuya Ichimura, Catarina Casais, Ken Shirasu

aWe discovered a key gene which regulates the biosynthesis of glucosinolates (mustard oil glycosides), anti-cancer compounds
contained in vegetables such as broccoli. This is expected to lead to the creation of “functional vegetables” with high anti-cancer
effects, or alternatively, to making glucosinolates in culture tanks of plant cells.

aWe succeeded to identify three genes which negatively regulate the defense response of plants against pathogens such asbacteria or fungus. And we revealed that plants have a system to fine-tune the defense response by using this negative regulation. We expect that regulating this function will contribute to the development of disease tolerant crops.

1519Functional Analysis of the Epidermal-Specific MYB GenesCAPRICE and WEREWOLF in Arabidopsis

The Plant Cell vol.19 no.7, pp.2264-2277［］

Proc Natl Acad Sci USA vol.105 no.37, pp.14204-14209［

July 2007

Rumi Tominaga, Mineko Iwata, Kiyotaka Okada, Takuji Wada
❖ Evolution from WER to CPC

aWe revealed that CPC genes which have the function to make root hair of Arabidopsis evolved from the WER gene which has
the function of eliminating root hair. This will be useful to understand the complicated mechanism of the differentiation of epidermal cells into root hair, trichomes, stomata, etc.

0 4 4Representative Research Publications

Licorice β-amyrin 11-oxidase, a cytochrome P450 with a key role inthe biosynthesis of the triterpene sweetener glycyrrhizin］ 16 Sept. 2008

Hikaru Seki, Kiyoshi Ohyama, Satoru Sawai, Masaharu Mizutani, Toshiyuki Ohnishi, Hiroshi Sudo,
Tomoyoshi Akashi, Toshio Aoki, Kazuki Saito, Toshiya Muranaka❖ The licorice root and theminced one that are used asa herbal medicine.

aWe revealed the key enzyme gene for the biosynthesis of glycyrrhizin, a natural sweetener. Glycyrrhizin is extracted from theunderground parts (turnip roots and rhizomes) of licorice, a legume, and is in demand, worldwide, as a natural sweetener andmedicine.

13 Years of the Plant Science Center

0 4 5

13 Years of the Plant Science Center

Representative Research Publications

20

A Heterocomplex of Iron Superoxide Dismutases Defends Chloroplast Nucleoids against Oxidative
Stress and Is Essential for Chloroplast Development in Arabidopsis

The Plant Cell vol.20 no.11, pp. 3148-3162
［

］

24

A Chloroplastic UDP-Glucose Pyrophosphorylase from
Arabidopsis Is the Committed Enzyme for the First Step of Sulfolipid Biosynthesis

The Plant Cell vol.21 no.3, pp.892-909［

Nov. 2008

Fumiyoshi Myouga, Chieko Hosoda, Taishi Umezawa, Haruko Iizumi, Takashi Kuromori,
Reiko Motohashi, Yuriko Shono, Noriko Nagata, Masahiko Ikeuchi, Kazuo Shinozaki❖ A phylogenic tree of SOD gene family］

Mar. 2009

Yozo Okazaki, Mie Shimojima, Yuji Sawada, Kiminori Toyooka, Tomoko Narisawa, Keiichi Mochida, Hironori Tanaka,
Fumio Matsuda, Akiko Hirai, Masami Yokota Hirai, Hiroyuki Ohta, Kazuki Saito

aWe revealed that two specific proteins which are involved in removing reactive oxygen species (ROS) form a heteromeric complex. This complex protects the chloroplast nucleoids from ROS, which are harmful for Arabidopsis. This is a necessary mechanism
for the early development of chloroplasts, which are essential for plants.

aWe discovered a novel gene involved in the biosynthesis of sulfolipid, which exists in a wide variety of plant species. We succeeded

21

012
25

Dual biosynthetic pathways to phytosterol via cycloartenol
and lanosterol in Arabidopsis

Proc Natl Acad Sci USA vol.106 no.3, pp.725-730［］

to identify the function of sulfolipid and can now regulate sulfolipid biosynthesis by using the discovered gene. Regulating sulfolipid biosynthesis enables the development of plants tolerant to phosphate deficiency, which is a challenge we might face in future.

Impact of clock-associated Arabidopsis pseudo - response regulators
in metabolic coordination

Proc Natl Acad Sci USA vol.106 no.17, pp.7251-7256［

20 Jan. 2009

Kiyoshi Ohyama, Masashi Suzuki, Jun Kikuchi, Kazuki Saito, Toshiya Muranaka］

28 Apr. 2009

Atsushi Fukushima, Miyako Kusano, Norihito Nakamichi, Makoto Kobayashi, Naomi Hayashi,
Hitoshi Sakakibara, Takeshi Mizuno, Kazuki Saito❖ Revealed output function of discovered

PRR9, 7, and 5

aSterols are a vital compounds for life and exist universally among organisms. Their biosyntheses are believed to be different between animals and plants; however we discovered that one of the sterol biosynthesis pathways that plants have occurs via lanosterol which is known to as the sterol biosynthesis pathway in animals.

aBy comprehensive analysis of plant metabolites, we discovered that the circadian clock in cells have close relationship with the

22

013
26

Genome-wide suppression of aberrant mRNA-likenoncoding RNAs by NMD in Arabidopsis

Proc Natl Acad Sci USA vol.106 no.7, pp.2453-2458［］

function of mitochondria, which are organelles that generate necessary cellular energy. This relationship has been suggested inanimals and fungi, but this is the first discovery in plants.

A Mobile Secretory Vesicle Cluster Involved in
Mass Transport from the Golgi to the Plant Cell Exterior

The Plant Cell vol.21 no.4, pp.1212-1229［

17 Feb. 2009

Yukio Kurihara, Akihiro Matsui, Kousuke Hanada, Makiko Kawashima, Junko Ishida, Taeko Morosawa, Maho Tanaka,
Eli Kaminuma, Yoshiki Mochizuki, Akihiro Matsushima, Tetsuro Toyoda, Kazuo Shinozaki, Motoaki Seki］

Golgi Body

Apr. 2009

SVC

Kiminori Toyooka, Yumi Goto, Satoru Asatsuma, Masato Koizumi, Toshiaki Mitsui, Ken Matsuoka❖ SVC & Golgi BodyaAs a plant grows, the massive amount of cell wall material that is synthesized by Golgi machinery is se-aWe revealed that NMD, a pathway to degrade aberrant mRNA, suppresses many mRNA-like nonprotein-coding RNAs (mln-cRNAs) by detecting the RNA expression level of Arabidopsis genes with tiling array.

creted out into the extracellular space. We discovered that the cellular transport machinery is a clusteredstructure of secretory vesicles, which are characteristically found in plant cells. We termed the machinery“Secretory Vesicle Cluster”.

23

27

Biochemical analyses of indole-3-acetaldoxime-dependent auxin
biosynthesis in Arabidopsis

Proc Natl Acad Sci USA vol.106 no.13, pp.5430-5435［］

31 Mar. 2009

Satoko Sugawara, Shojiro Hishiyama, Yusuke Jikumaru, Atsushi Hanada, Takeshi Nishimura,
Tomokazu Koshiba, Yunde Zhao, Yuji Kamiya, Hiroyuki Kasahara❖Transgenic Arabidopsis plants thatoverexpress auxin biosynthesis genes(TAAI and YUCCA)

aBy using a cutting-edge mass spectrometer, we detected an intermediate in the synthesis of auxin, a plant hormone. This al-

lowed us to understand the auxin biosynthetic pathway in plants, which had otherwise evaded elucidation.

0 4 6

Representative Research Publications

SUMO E3 Ligase HIGH PLOIDY2 Regulates Endocycle Onset andMeristem Maintenance in Arabidopsis

The Plant Cell vol.21 no.8, pp.2284-2297［］

Aug. 2009

野生株

Takashi Ishida, Sumire Fujiwara, Kenji Miura, Nicola Stacey, Mika Yoshimura, Katja Schneider,
Sumiko Adachi, Kazunori Minamisawa, Masaaki Umeda, Keiko Sugimoto

hpy2 変異株

野生株

hpy2 変異株❖ HPY2 regulates cell divisionaWe discovered a new gene HPY2 (HIGH PLOIDY2) that is necessary for cell division in multicellular organisms. We revealed that

this gene also has an important role in regulating the activity of cell division. In the future, this will enable breeding of higher-yieldcrops.

13 Years of the Plant Science Center

0 4 7

13 Years of the Plant Science Center

Representative Research Publications

28

The Trihelix Transcription Factor GTL1 Regulates Ploidy-Dependent
Cell Growth in the Arabidopsis Trichome

The Plant Cell vol.21 no.8, pp.2307-2322
［

］

野生株

gtl1 変異株

32

PSEUDO-RESPONSE REGULATORS 9, 7, and 5 Are
Transcriptional Repressors in the Arabidopsis Circadian Clock

The Plant Cell vol.22 no.3, pp.594-605［

Aug. 2009

Christian Breuer, Ayako Kawamura, Takanari Ichikawa, Rumi Tominaga-Wada, Takuji Wada,
Youichi Kondou, Shu Muto, Minami Matsui, Keiko Sugimoto❖ GTL1 has the function to suppress plant

growth.

］Mar. 2010

Norihito Nakamichi, Takatoshi Kiba, Rossana Henriques, Takeshi Mizuno, Nam-Hai Chua, Hitoshi Sakakibara

aWe discovered a new transcription factor GTL1 (GT2-LIKE 1) which suppresses plant cell growth. Using this discovery, we succeeded to make plant cells grow more than twice their normal size by reducing the level of GTL1. GTL1 is the first regulation
factor that has been found to actively suppress plant cell growth.

aWe found that three proteins PRR9, PRR7, and PRR5 involved in the internal clock in plants (circadian clock) have the functionof repressing transcriptional activity. Through activity that is elevated particularly around dawn, they repress the transcriptional
activity of CCA1 and LHY genes, which are known to be related to the internal clock.

29

33

Type 2C protein phosphatases directly regulate abscisic
acid-activated protein kinases in Arabidopsis

Proc Natl Acad Sci USA vol.106 no.41, pp.17588 -17593［］

Horizontal Gene Transfer by
the Parasitic Plant Striga hermonthica

Science vol.328 no.5982, p.1128［

13 Oct. 2009

Taishi Umezawa, Naoyuki Sugiyama, Masahide Mizoguchi, Shimpei Hayashi, Fumiyoshi Myouga,
Kazuko Yamaguchi-Shinozaki, Yasushi Ishihama, Takashi Hirayama, Kazuo Shinozaki❖ The mechanism of ABA signaling］

28 May 2010

Satoko Yoshida, Shinichiro Maruyama, Hisayoshi Nozaki, Ken Shirasu❖ Parasite plant Striga on

rice

aWe revealed the signaling pathway of abscisic acid (ABA), a plant hormone involved in the response to severe environmental
conditions. In the future, various applications are anticipated, such as development of crops that are tolerant to drought, salinity,and cold, as well as improvement of seed stability or repression of pre-harvest sprouting.

aBy large-scale genome analysis of parasite plants Striga, we uncovered the first instance in which genes are horizontally transferred from nuclei of host plants to parasitic plants.

30

34

Autophagy Negatively Regulates Cell Death by Controlling NPR1-Dependent Salicylic Acid
Signaling during Senescence and the Innate Immune Response in Arabidopsis

The Plant Cell vol.21 no.9, pp.2914-2927［］

A small-molecule screen identifies new functions forthe plant hormone strigolactone

Nature Chemical Biology vol.6 no.10, pp.741-749［

Sept. 2009］

5 Sept. 2010

Kohki Yoshimoto, Yusuke Jikumaru, Yuji Kamiya, Miyako Kusano, Chiara Consonni, Ralph Panstruga, Yoshinori Ohsumi,
Ken Shirasu

Yuichiro Tsuchiya, Danielle Vidaurre, Shigeo Toh, Atsushi Hanada, Eiji Nambara, Yuji Kamiya,
Shinjiro Yamaguchi, Peter McCourtaWe revealed that autophagy, a cellular degradation and recycling system, negatively regulates the signaling of salicylic acid, aplant hormone. Autophagy suppresses senescence and programmed cell death in response to infection by a pathogen.

aWe discovered that strigolactones which stimulates germination of Striga, also stimulates germination of Arabidopsis in the same
way that light does. Striga is parasitic plant which is causing great damage to crops.

3135❖ Analysis of expression and

ABC transporter AtABCG25 is involved in
abscisic acid transport and responses

localization in planta

Proc Natl Acad Sci USA vol.107 no.5, pp.2361-2366［］

根の拡大写真2 Feb. 2010

Takashi Kuromori, Takaaki Miyaji, Hikaru Yabuuchi, Hidetada Shimizu, Eriko Sugimoto, Asako Kamiya,
Yoshinori Moriyama, Kazuo Shinozaki
aWe discovered AtABCG255, one of the transporters of abscisic acid (ABA), which makes plants tolerant todrought. We demonstrated that we are able to produce drought tolerant plants by regulating ABA inplanta.

0 4 8

Representative Research Publications

植物体の染色写真

Calmodulin-Dependent Activation of MAP
Kinase for ROS Homeostasis in Arabidopsis

Molecular Cell vol.41, no.6, pp.649-660［］

18 Mar. 2011

Fuminori Takahashi, Tsuyoshi Mizoguchi, Riichiro Yoshida, Kazuya Ichimura, Kazuo Shinozaki
葉の断面写真aWe revealed that the protein kinase MAPK (Mitogen-activated protein kinase) is deeply involved in the signaling of productionof reactive oxygen species that occurs in plant response to severe environmental conditions such as disease caused by insects or
pathogen, drought, or salinity.

13 Years of the Plant Science Center

0 4 9

13 Years of the Plant Science Center

Representative Research Publications

野生株

36
012

WIND1 過剰発現株

The AP2/ERF Transcription Factor WIND1 Controls Cell
Dedifferentiation in Arabidopsis

Current Biology vol.21 no.6, pp.508–514［❖ A plant that over-expresses WIND1］

forms callus.

22 Mar. 201140

The main auxin biosynthesis pathway in Arabidopsis

Proc Natl Acad Sci USA vol. 108 no. 45, pp.18512-18517［］

8 Nov. 2011

Akira Iwase, Nobutaka Mitsuda, Tomotsugu Koyama, Keiichiro Hiratsu, Mikiko Kojima,
Takashi Arai, Yasunori Inoue, Motoaki Seki, Hitoshi Sakakibara, Keiko Sugimoto, Masaru Ohme-Takagi

Kiyoshi Mashiguchi, Keita Tanaka, Tatsuya Sakai, Satoko Sugawara, Hiroshi Kawaide, Masahiro Natsume, Atsushi Hanada,
Takashi Yaeno, Ken Shirasu, Hong Yao, Paula McSteen, Yunde Zhao, Ken-ichiro Hayashi, Yuji Kamiya, Hiroyuki Kasahara

aWe discovered WIND1, a switch protein functions for callus (de-differentiated cellular mass) formation in wounded plants. Thisis the first key to understanding the long-known phenomenon that plants promote de-differentiation at the molecular level in
response to wound stress.

aFrom the high-resolution mass analysis of intermediates of IAA biosynthesis, which is the key to elucidate the biosynthesis
pathway of auxin in Arabidopisis, we revealed that plants synthesize IAA by TAA1 and YUCCA catalyzers from the amino acidtryptophan.

37

41

Analysis of Cytokinin Mutants and Regulation of Cytokinin Metabolic Genes Reveals Important Regulatory
Roles of Cytokinins in Drought, Salt and Abscisic Acid Responses, and Abscisic Acid Biosynthesis

The Plant Cell vol.23 no.6, pp.2169-2183［］

The Arabidopsis Nitrate Transporter NRT2.4 Plays a Double Role in
Roots and Shoots of Nitrogen-Starved Plants

The Plant Cell vol.24 no.1, pp.245-258［

June 2011］

Jan. 2012

Rie Nishiyama, Yasuko Watanabe, Yasunari Fujita, Dung Tien Le, Mikiko Kojima, Tomás Werner, Radomira Vankova,
Kazuko Yamaguchi-Shinozaki, Kazuo Shinozaki, Tatsuo Kakimoto, Hitoshi Sakakibara, Thomas Schmülling, Lam-Son Phan Tran

Takatoshi Kiba, Ana-Belen Feria-Bourrellier, Florence Lafouge, Lina Lezhneva, Stéphanie Boutet-Mercey, Mathilde Orsel,
Virginie Bréhaut, Anthony Miller, Françoise Daniel-Vedele, Hitoshi Sakakibara, Anne KrappaWe discovered the mechanism by which interaction between cytokinins (CKs) and abscisic acid (ABA) regulates plant response

to drought and salt stress. Development of novel breeding methods are expected.

aWe discovered that NRT2.4, an Arabidopsis nitrogen transporter, has a role in nitrogen uptake under conditions of nitrogenstarvation. This may contribute to development of crops adapted to low input, i.e., sustainable agriculture with small environmental impact.

38

42Structural Basis for Assembly of Hsp90-Sgt1-CHORD Protein Complexes:
Implications for Chaperoning of NLR Innate Immunity Receptors

Molecular Cell vol.39, no.2, pp.269–281［］

30 July 2010

❖ RAR1 transgenic proteins which cannot

Minghao Zhang, Yasuhiro Kadota, Chrisostomos Prodromou, Ken Shirasu, Laurence H. Pearlbind to SGT1 cannot suppress the
spread of the pathogen (virus).

Natural variation in a polyamine transporter determines
paraquat tolerance in Arabidopsis

Proc Natl Acad Sci USA vol.109 no.16, pp.6343-6347［］

17 Apr. 2012

Miki Fujita, Yasunari Fujita, Satoshi Iuchi, Kohji Yamada, Yuriko Kobayashi, Kaoru Urano, Masatomo Kobayashi, Kazuko
Yamaguchi-Shinozaki, Kazuo Shinozaki

aWe determined the structure of a protein complex (constituted of three proteins, RAR1, SGT1 and HSP90) that is present in bothanimals and plants. This complex regulates immune sensing. From the structure, we revealed the mechanism by which RAR1
promotes formation of the complex, enhances the function, and thus prevents the invasion of the tobacco mosaic virus.

aWe discovered that RMV1 protein is the transporter of the bioactive substance polyamines, which are essential for the growthand survival of organisms. Artificial control of the concentration of cellular polyamines is expected to improve stress tolerance orcrop yield.

39

43

Phosphatidylinositol monophosphate-binding interface in the oomycete RXLR effector
AVR3a is required for its stability in host cells to modulate plant immunity

Proc Natl Acad Sci USA vol.108 no.35, pp.14682-14687［］ 30 Aug. 2011

Identification of an abscisic acid transporter byfunctional screening using the receptor complex as a sensor

Proc Natl Acad Sci USA vol.109 no.24, pp.9653-9658［］ 12 June 2012

❖ Identification of the importer using

yeast two-hybrid assay

Takashi Yaeno, Hua Li, Angela Chaparro-Garcia, Sebastian Schornack, Seizo Koshiba, Satoru Watanabe, Takanori Kigawa,
Sophien Kamoun, Ken Shirasu

Yuri Kanno, Atsushi Hanada, Yasutaka Chiba, Takanari Ichikawa, Miki Nakazawa,
Minami Matsui, Tomokazu Koshiba, Yuji Kamiya, Mitsunori Seo

aFor the first time we determined the 3D structure of AVR3a, a plant immune-repressing protein. Phytophthora infestans secretes
AVR3a, which causes disease in plants. The study revealed a well-conserved lipid binding region, which is required to repress theimmune system.

aThe receptor of abscisic acid (ABA), a necessary plant hormone to close stomata, makes a complex with a specific protein when
the receptor recognizes ABA. By focusing on this interaction, we discovered that nutrient (nitrate) transporter protein NRT1.2
also functions as an ABA importer.

0 5 0

Representative Research Publications

13 Years of the Plant Science Center

0 5 1

Principal Investigators from the Plant Science Center

Name

Affiliation

Position

Belay T.
AYELE

Department of Plant Science, University of
Manitoba, Canada

Assistant
Professor

Ivan GALISInstitute of Plant Science andResources, Okayama University

Professor

Doug ＶＡＮ
HOEWYK

Department of Biology, Coastal Carolina University,
USA

Assistant
Professor

Marco
TRUJILLO

Independent Junior Research Group / Ubiquitination Independent
in Immunity, Leibniz Institute of Plant Biochemistry, Junior Research
Germany
Group Leader

Rungaroon
WADITEESIRISATTHA

Department of Microbiology, Faculty of Science,
Chulalongkorn University, Thailand

Lecturer

Koh AOKI

Graduate School of Life and Environmental
Sciences, Osaka Prefecture University

Professor

Masashi
ASAHINA

Department of Biosciences, Teikyo University

Assistant
Professor

Takanari
ICHIKAWA

Technology Licensing, and DNA Sequencing
Sections, Okinawa Institute of Science andTechnology Graduate University

Senior Manager
and Section
Leader of Business
Development

KazuyaICHIMURA

Faculty of Agriculture, Kagawa University

Associate
professor

Hiroki INOUEThe University of Tokyo Forests, Graduate Schoolof Agricultural and Life Sciences, The University ofTokyo

Research
AssociateAwardsName

Affiliation

Position

Kazuo
SOENO

National Agricultural Reseach Center for Western
Region, National Agriculture and Food Research
Organization

SeniorResearcher

Nobutaka
SOMEYA

Hokkaido Agricultural Research Center, National
Agriculture and Food Research Organization

SeniorResearcher

Tomoyuki
TAKASE

Department of Life Science, Faculty of Science,
Gakushuin University

Assistant
Professor

Hideki
TAKAHASHI

Department of Biochemistry and Molecular Biology, AssistantMichigan State University
Professor

KiyoshiTATEMATSU

Laboratoy of Plant Organ Development, National
Institute for Basic Biology

Assistant
Professor

Taku
DEMURA

Graduate School of Biological Sciences,
Nara Institute of Science and Technology

Professor

MakotoTOKUDA

Department of Applied Biological Sciences, Facultyof Agriculture, Saga University

Associate
Professor

Hirofumi
NAKAGAMI

Plant Proteomics Research Unit, RIKEN Plant
Science Center

Unit Leader

NorikoNAGATA

Department of Chemical Biological Sciences, Faculty Associateof Science, Japan Women's University
Professor
AssistantInstitute for Advanced Research, Nagoya University
Professor

Norihito
NAKAMICHI
Eiji
NAMBARA

Department of Cell & Systems Biology,
University of Toronto, Canada

Assistant
Professor

Kanae
NIINUMA

Department of Life Science and Technology, Facultyof Engineering, Hokkai-Gakuen University

Associate
Professor

TakumiNISHIUCHI

Advanced Science Research Center, Kanazawa
University

Associate
Professor

Nobuyuki
NISHIKUBO

Forest Technology Laboratories, Research andDevelopment Division, Oji Paper Co., Ltd.

SeniorResearcher

Yoshiteru
NOUTOSHI

Research Core for Interdisciplinary Sciences,
Okayama University

PositionGroup / Laboratory

Team

Name of award

Presentation title, research subject andsubject of paper etc.

Research
Scientist

Functional Control
Research Group

Laboratory for
Growth Regulation

The JSCRP Award

Synthesis of Molecular Probes of Plant Hormones
Based on Fine and Precision Synthetic Chemistry Oct.
and Their ApplicationGroup
Director

Functional Control
Research GroupThe JSPCMB Award for Technical
Advance

Development of mutant induction by heavy ion
beam and its applicatio

Jul.

Nobutaka SOYEYA

Research
Scientist

Environmental Plant
Research GroupAward for Paper of excellence,
The Phytopathological Society ofJapan

Synergistic Antifungal Activity of Chitinolytic
Enzymes and Prodigiosin Produced by Biocontrol
Bacterium Serratia marcescens strain B2 against theGray Mold Pathogen, Botrytis cinerea

Mar.

Yuji KAMIYA

Group
Director

Growth Physiology
Research Group

Corresponding Member（conferred

Research activities to dateJul.

Functional Control
Research GroupThe JSCRP Award for the
Encouragement of Young
Scientists

Molecular Biological Study of Brassinosteroidrelated Genes

Oct.

Name

2001
Hideharu SETO

2002
Shigeo YOSHIDA

2003

Yukihisa SHIMADA

Research
Scientist

Tatsuo SUGIYAMA

Director

Laboratory for
Adaptation andResistanceby The American Society of Plant Biologists）

Laboratory for
Growth Regulation

Research and other activities to date.
L'Ordre des Palmes AcadémiquesContribution to education and research activities Nov.
Officier
between Japan and France

2004
Hitoshi SAKAKIBARA Team Leader

Metabolic Function
Research Group

Laboratory for
Communication
Mechanisms

Japanese Society of Plant
Physiologists Young InvestigatorAward

Research on nitrogen nutrient informationtransfer mechanisms in higher plants

Group
Director

Environmental Plant
Research Group

Japan Prize of Agricultural
Science, Yomiuri Agriculture Prize

Research on the pathological structure andmetabolism of environmentally harmonized plant 5 Apr.
disease inhibitors

Assistant
Professor
Associate
Professor

Tomoyuki YAMAYA
Keiki ISHIYAMA
Naoya HIROSE

Group
Director,
Research
Scientist

Metabolic Function
Research GroupThe JSPCMB Excellent Paper Award

Organization and Structure of Intracellular
Localization of the Enzyme Protein in Rice Plants

9 Aug.

Yuji KAMIYA

Associate
Professor

Growth Physiology
Research Group

Laboratory for
IPGSA Distinguished Research
Cellular Growth andAward
Development

Research on gibberellin biosynthesis and its
contribution to the internationalization ofresearch in that field

21 Sep.

Frontier Research Academy for Young Researchers,
Kyushu Institute of Technology

Group
Director

2005

Faculty of Bioscience and Applied Chemistry, Hosei
University

Professor

Hideki TAKAHASHITeam Leader

Laboratory
for Metabolic
Compartmentation

Japanese Society of Plant
Physiologists Young InvestigatorAward

Research on the physiological functions andcontrol of sulphate ion transport systems

25 Mar.

Department of Biology, Osaka Medical College

Junior Associate
Professor

Metabolic Function
Research Group

Department of Life Science, College of Science,
Rikkyo University

Associate
Professor

Shigeo YOSHIDA

Coordinator

Japan Prize of Agricultural
Science, Yomiuri Agriculture Prize

Research on the development of a technologicalplatform for plant growth adjustment

5 Apr.

Professor
Yukihisa SHIMADA

SeniorResearch
Scientist

Metabolomics Research Integrated Genomics Emerging Research Fronts inGroup
Research Team
Plant & Animal Science

Paper : Brassinolide induces IAA5, IAA19,
and DR5, a synthetic auxin response elementin arabidopsis, implying a cross talk point ofbrassinosteroid and auxin signaling

1 Jun.

Unit Leader

Metabolomics Research Metabolic Systems
Group
Research Unit

The JSPCMB Award for Young
Scientists

Postgenomics approaches for the elucidation of
the adaptive responses to sulfur deficiency

5 Aug.

Morphoregulation
Research Team

BSJ Award for Young Scientists

Analysis of molecular mechanism controlling
differentiation of xylem cells

22 Sep.

The JSCRP Award for the
Encouragement of Young
Scientists

Research on biosynthesis of brassinosteroids, and
1 Nov.
the isolation and functions of receptor genes

Department of Applied Biosciences, Undergraduate
School of Life Sciences, Toyo University

Akira
OIKAWA

Faculty of Agriculture, Yamagata University

Naoko
OHKAMA‐
OHTSU

Department of Science of Biological Production,
Graduate School of Agriculture, Tokyo University ofAgriculture and Technology

Assistant
Professor

KiyoshiOHYAMA

Department of Chemistry and Materials Science,
Graduate School of Science and Engineering, Tokyo
Institute of Technology

Assistant
Professor

MakotoKIMURA

Department of Biological Mechanisms & Functions,
Graduate School of Bioagricultural Sciences,
Nagoya University

Associate
Professor

Hiroaki
KUSANO

Department of Biological Science and Technology,
Tokyo University of Science

Assistant
Professor

Akiko
HARADA
Gorou
HORIGUCHI

Tetsuo
KUSHIRODepartment of Agricultural Chemistry, School of
Agriculture, Meiji University

Associate
Professor

Ken
MATSUOKA

Faculty of Agriculture, Kyushu University

Tetsuya
KURATA

Plant Global Education Project, Graduate School of
Associate
Biological Sciences, Nara Institute of Science andProfessor
Technology

Fumio
MATSUDA

Graduate School of Information Science andTechnology, Osaka University

Mareshige
KOJOMA

Faculty of Pharmaceutical Sciences, Health Sciences Associate
University of Hokkaido
Professor

Akiko
Bioscience & Biotechnology, Graduate School of
Associate
MARUYAMA‐ Bioresource and Bioenvironmental Sciences, Kyushu
Professor
NAKASHITA University

Masami Yokota
HIRAI

Soichi
KOJIMA

Department of Applied Plant Science, Graduate
School of Agricultural Science, Tohoku University

Assistant
Professor

Toshiya
MURANAKA

Department of Biotechnology, Graduate School ofEngineering, Osaka University

Taku DEMURATeam Leader

Plant Productivity
Systems ResearchGroup

YutakaKODAMA

Center for Bioscience Research and Education,
Utsunomiya University

Assistant
Professor

Masatoshi
YAMAGUCHI

Institute for Environmental Science and Technology, Associate
Saitama University
Professor

Takahito NOMURA

Koichi
KOBAYASHI

Department of Life Sciences, Graduate School ofArts and Sciences, The University of Tokyo

Assistant
Professor

Shinjiro
YAMAGUCHI

Growth Regulation
Research Group

Graduate School of Life Sciences, Tohoku University

Professor

Special
Postdoctoral
Researcher

Cellular Growthand Development
Research Team

Youichi
KONDOU

Department of Applied Material and Life Science,
Faculty of Engineering, Kanto Gakuin University

Assistantprofessor

Yoshiharu Y.
YAMAMOTO

Faculty of Applied Biological Sciences, Gifu
University

Associate
Professor

Eiji NAMBARATeam Leader

Tatsuya
SAKAI

Graduate School of Science and Technology, Niigata Associate
University
Professor

Kohki
YOSHIMOTO

The Jean-Pierre Institute at the INRA VersaillesGrignon Center, France

INRA
Researcher

Growth Regulation
Research Group

Dormancy andJapanese Society of Plant
Adaptation Research Physiologists Young Investigator
Team
Award

Yukihisa
SHIMADA

Kihara Institute for Biological Science, Yokohama
City University

Professor

Naoko
YOSHIMOTO

Graduate School of Pharmaceutical Sciences, Chiba
University

Assistant
Professor

Kazuo SHINOZAKI

Director

Mitsunori
SEO

Dormancy and Adaptation Research Unit, RIKEN
Plant Science Center

Unit Leader

Arata
YONEDA

Graduate School of Biological Sciences, Nara
Institute of Science and Technology

Assistant
Professor

HikaruSEKI

Department of Biotechnology, Graduate School ofEngineering, Osaka University

Associate
Professor

Madoka AYANO

Research
Associate

0 5 2

Principal Investigators from the Plant Science Center

Takahito
NOMURA
Kousuke
HANADA
Hiroshi
HAMAMOTO

28 Mar.

Isamu YAMAGUCHI

Mikihisa
UMEHARA

Associate
Professor
Associate
Professor

Date ofaward

Weed Science Center, Utsunomiya University

Associate
professor

Professor

2006
Genetic analysis of abscisic acid action in seeds

20 Mar.

The Commendation for Scienceand Technology by the Minister of Research on abiotic stress responses and plant
Education, Culture, Sports, Science genomic functions in acquired tolerance
and Technology (Research Category)

18 Apr.

Developmental morphology of the Asian oneleaf plant, Monophyllaea glabra (Gesneriaceae) withemphasis on inflorescence morphology

15 Sep.

Metabolomics Research Integrated Genomics Best Paper Award（Journal of Plant Research）
Group
Research TeamAwards

0 5 3

Awards

Name

PositionGroup / Laboratory

Team

Name of award

Presentation title, research subject andsubject of paper etc.

Date ofaward

2007
Metabolic Function
Research Scientist
Research Group

Plant Nutrition andBasal Metabolism
Research TeamThe JSPCMB Award for Young
Scientists

Elucidation of sulfur and related metabolic
control mechanisms in plants

Yasuhiro KADOTA

Special
Postdoctoral
Researcher

Plant Immunity
Research Team

BSJ Award for Junior Young
Scientists

The role and cell cycle dependence of Ca2+ signaltransduction system in induced defense reaction
8 Sep.
mechanisms of BY-2 cultured tobacco cells
against blight stress and reactive oxygen stress

Plant Immunity
Research Group

Coordinator

8 Aug.

Local Commendation forInvention (Kanto block)

Constructing chimeric plants with heavy ion
beams

9 Nov.

EMBO Journal Cover Contest
higher-ranking winner"Plant neuron"- A scanning electron microscopy
image showing trichomes on a leaf of Verbascum
thapsus（Great Mullein）.

14 Feb.

Sequencing analysis of 20,000 full-length cDNA
clones from cassava reveals lineage specificexpansions in gene families related to stressresponse

18 Apr.

2008
Kiminori TOYOOKA
Mayuko SATO

Research Scientist Gene Discovery
Technical Scientist Research GroupR&D Programs for
PSC

Tetsuya SAKURAI
Motoaki SEKI
Kazuo SHINOZAKI

Unit Leader
Team Leader
Director

Integrated Genome
Informatics Research
CIAT-Outstanding Research
Unit, Plant Genomic
Publication Award
Network ResearchTeam

Kiminori TOYOOKA

Gene Discovery
Research Scientist
Research GroupR&D Programs for
PSC

Excellent Paper Award of theSociety for Biotechnology,
Japan

Development of Series of Gateway Binary Vectors,
27 Aug.
pGWBs, for Realizing Efficient Construction of
Fusion Genes for Plant Transformation

Misao ITOUGA

Plant Productivity
Research Scientist Systems ResearchGroup

Biodynamics
Research TeamAwards for young bryologists

Research on technology for using moss to reduce
30 Aug.
impacts on the aquatic environment

Keiko YONEKURASAKAKIBARA

Metabolic Function
Research Scientist
Research Group

Metabolic Function
Research TeamThe JSPCMB Award for Young
Scientists

Profiling of flavonoid regulatory mechanisms inhigher plants

1 Sep.

Hiroyuki KASAHARA

Senior Research
Scientist

Growth Regulation
Research TeamThe JSCRP Award for the
Encouragement of Young
Scientists

Biosynthesis of hormones through themethylerythritol phosphate (MEP) pathway

29 Oct.

Growth Regulation
Research Group2009
Kiminori TOYOOKA
Mayuko SATO
Mayumi WAKAZAKI

Research Scientist
Technical Scientist Gene Discovery
Research Group
Contract Technical

EMBO Journal Cover Contest
higher-ranking winner

Mushroom-shaped oil glands on the surface of a
Basil sepal

Japanese Society of Plant
Physiologists Award

Elucidation of the genetic regulatory network
involved in abiotic stress mechanisms andacquired resistance

22 Mar.

Genetic Regulatory
Systems Research
Team

Japanese Society of Plant
Physiologists Young
Investigator Award

Molecular genetic analysis of growth patterncontrol mechanisms in plant responses to light

22 Mar.

Metabolic Function
Research Group

Metabolic Function
Research TeamJSPP Plant and Cell Physiology Engineering of the Rose Flavonoid Biosynthetic
Award for the Paper ofPathway Successfully Generated Blue-Hued
Excellence
Flowers Accumulating Delphinidin

22 Mar.

Shinjiro YAMAGUCHI Team Leader

Growth Regulation
Research Group

Cellular Growthand Development
Research TeamJapan Society for Bioscience,
Biotechnology, and Agrochemist- Research on the biosynthesis and physiologicalry Award for the Encouragefunctions of terpenoid plant hormones
ment of Young Scientists

Hitoshi SAKAKIBARA Group Director

Plant Productivity
Systems ResearchGroup

Kazuo SHINOZAKI

Tatsuya SAKAI

Keiko SAKAKIBARA

Kazuo SHINOZAKI
KazukoYAMAGUCHISHINOZAKI

Date ofaward

Metabolomics Research Integrated Genomics New Hot Paper in Plant &Group
Research Team
Animal Science

The AtGenExpress hormone- and chemicaltreatment data set: Experimental design, data
evaluation, model data analysis, and data access

4 Jan.

Hitoshi SAKAKIBARA Group Director

Plant Productivity
Systems Research Group

JSPS Prize

Elucidation of cytokinin synthesis mechanism and1 Mar.
discovery of a new function in particle control

Keiko SUGIMOTOSHIRASU

Unit Leader

Gene Discovery
Research Group

Japanese Society of Plant
Physiologists Young
Investigator Award

Analysis of the developmental genetics of plantendoreduplication and cell size control

Yuji KAMIYAGroup Director

Growth Regulation
Research Group

Kazuki SAITO

Deputy Director

PositionGroup / Laboratory

Team Leader

Team

Name of award

2010

Akiko MARUYAMANAKASHITA

Sigeo YOSHIDA

Presentation title, research subject andsubject of paper etc.

Name

Assistant

R&D Programs for
PSC

Director

Team Leader

Research Scientist

Gene Discovery
Research GroupThe Olchemim Award(Gene Discovery
Research Group)

Growth Regulation
Research Group

Research Scientist Gene Discovery
Research Group

Kiminori TOYOOKA
Mayumi WAKAZAKI

Contract Technical
Assistant

Ayako KAWAMURA

Technical Staff

0 5 4Awards27 Mar.

11 Jul.

Two transcription factors, DREB1 and DREB2, with
an EREBP/AP2 DNA binding domain separate two
Top five Plant Cell manuscripts cellular signal transduction pathways in drought- 21 Jul.
and low-temperature-responsive gene expression,respectively, in Arabidopsis

Director
Visiting Scientist

Shinjiro YAMAGUCHI Team Leader

Biochemistry and molecular biology ofphytohormone cytokinin

11 Feb.

Gene Discovery
Research Group

Cellular Growthand Development
Research TeamThe JSCRP Award

Bioorganic chemical research on terpenoid plant
hormones using mutants

29 Oct.

R&D Programs for
PSC

Olympus BioScapesInternational Digital Imaging
Competition, Honorable
MentionEpidermal layer cells of Lotus japonicus dry seed

6 Dec.

Cell Function
Research Unit

Jury's Special Award, Leica
mycrosystems photo contest

Trichome

9 Dec.

Yukihisa SHIMADA

Cell Function
Research Unit

19 Mar.

Japan Prize of Agricultural
Research on mechanisms of actions in gibberellin
5 Apr.
Science, Yomiuri Agriculture Prize biosynthesis and plant growth regulators
The Commendation for Scienceand Technology by the Minister of Research on functional genomics for plants based
13 Apr.
Education, Culture, Sports, Science on metabolomics
and Technology (Research Category)

Hitoshi SAKAKIBARA Group Director

Kihara Memorial Foundation
Special Award

Elucidation of cytokinin biosynthesis pathways
and their use in breeding

Mikihisa UMEHARAThe JSPCMB Award for Young
Scientists

Research on strigolactones, a hormone controlling
2 Sep.
branching in plants

The JSPCMB Award for Young
Scientists

Development of methods for analyzing gene
coexpression for inferring comprehensivefunctions of plant genes and construction of ananalysis database

2 Sep.

The JSCRP Award for the
Encouragement of Young
Scientists

Molecular biological research on enzymes
controlling the gibberellin activation

1 Nov.

The JSCRP Award

Research on molecular genetics involved in
1 Nov.
abscisic acid metabolism and information transfer

Kihara Memorial Foundation
Academic Award

Elucidation of molecular mechanism of theimmune system in plants

20 MayThe JSPCMB Award forDistinguished ResearchIntegrated omics study based on plant
metabolomics and its development

6 Sep.
18 Sep.

Yoshiyuki OGATA

Hiroshi MAGOME
Eiji NAMBARA

Plant Productivity
Systems Research Group
Cellular Growth andResearch Scientist Development Research
Team
Advanced NMR
Research Scientist Metabomics Research
Team

Cellular Growth andResearch Scientist Development Research
Team
Senior Visiting
Growth Regulation
Scientist
Research Group

14 May2011
Plant Immunity
Research GroupKen SHIRASUGroup Director

Kazuki SAITO

Deputy Director

Takashi ISHIDASpecial
Postdoctoral
Researcher

Cell Function Research
Unit

BSJ Award for Junior Young
Scientists

Research on molecular mechanisms responsible
for cell morphogenesis

Jun KIKUCHI
Yasuhiro DATETeam Leader
Postdoctoral
Researcher

Advanced NMR
Metabomics ResearchTeam

Excellent Paper Award of theSociety for Biotechnology,Japan

New monitoring approach for metabolic dynamics
26 Sep.
in microbial ecosystems using stable-isotopelabeling technologies

Shinjiro YAMAGUCHI Team Leader

Cellular Growth andDevelopment Research
Team

Research Front Award,
Thomson Reuters

New developments in strigloactone researchbased on the discovery of plant hormone
functions

21 Feb.

R&D Programs for PSC

EMBO Journal Cover Contest
higher-ranking winneｒ

Love Dust - Pheromone transfer particles called"love dust" produced in the hindwing of a malebutterfly (Tirumala formosa)

12 Mar.

Plant Productivity
Systems Research
Group

Japan Mining Industry
Association Award

Moss as a material for recovering heavy metals

30 Mar.

2012

Kei HASHIMOTO

Technical
Scientist

Group Director,
Hitoshi SAKAKIBARA
Senior Research
Misao ITOUGA
Scientist,
Seiji NAKATSUKA
Visiting Scientist
Kazuo SHINOZAKI

Director

Miyako KUSANO

Senior Research
Scientist

Metabolomic Function
Research Group

Satoko YOSHIDA

Senior Research
Scientist

Plant Immunity
Research Group

Kensuke KAWADE"With 11 of his papers selected as hot papers
Hottest Researchers, Thomson
Nominated as the world s 5th Hottest
Reuters
Researcher"
The JSPCMB Award for Young Elucidation of plant metabolic networks using
Scientists
metabolomics

12 Apr.
4 Aug.

Establishment of an analysis platform for the
BSJ Award for Young Scientists parasitic plant striga and identification of its
parasitic structure

16 Sep.

Special Postdoctoral Metabolic Systems
Researcher
Research Team

BSJ Award for Junior Young
Scientists

16 Sep.

Hiroo FUKUDA

Senior Visiting
Scientist

The Medal with Purple Ribbon Achievements in plant physiology research

13 Nov.

Hiroyuki KASAHARA

Senior Research
Scientist

Elucidation of the major pathways of auxin
biosynthesis in plants

17 Dec.

Growth Regulation
Research Group

JSPS Prize

Leaf size control that develops in multicellularorganisms

Awards0 5 5Factual Data of the Plant Science Center̶ Number of papers / Number of patent applications in Japan and Overseas

̶ Number of employees (as of March 31, 2012)

132

■—

Number of papers■—

Number of patent applications overseas■—

Number of patent applications in Japan

108
94

87
（Number）

63

30

47

52

（Number）

23

60

28

27

14

19

14

0

3

9

15

8

68

20
10

09
20

20

07

08

4

20

04
20

03

16

6

4

20

02
20

20

01

00

18

21

12

06

6

4

20

250

19

16

14

1

05

7

7

14

20
11

7

2

20

8
6

20

10

0

19

16

10

2

300

20

15

5

Junior Research Associate / International Program Associate］

20

15

7

■̶ Student［Research Fellow / Student Trainee / Intern /

40

23
20

17

13

Researcher

Special Postdoctoral Researcher / Foreign Postdoctoral Researcher /Research Associate / Visiting Researcher / Joint Researcher /RIKEN Fellow / Collaboration Research from Industry］

80

43■̶ Support staff［Senior Advisor / Coordinator / Executive Advisor / Assistant /Part-timer / Temporary staff ］■̶［Senior Research Scientist / Research Scientist / Postdoctoral Researcher /

100

84

66

25
20

120

113

■̶ Technical staff［Special Support Engineer / Technical Scientist / Technical Staff］■̶ Principal investigator［Director / Deputy Director / Division Director / Deputy Division Director /Group Director / Deputy Group Director / Team Leader / Unit Leader］（Number）

78

200

76

73

72

63
63
15

15

̶ Budget
72

Research funds for metabolomic
analysis for safety assessments ofgenetically-modiﬁed crops■— Plant science research promotion funds■— Plant science research funds■—

Reduction following the budget
reallocation from the Plant Science
Center to Biomass Engineering
Research

62

888

1006

841

1006

841

62

62

421
226

20

21

24
14

40

43

49

48
33

18

20

05

0

03

4

02

20
10

09
20

08
20

07
20

06
20

05
20

04
20

03
20

02
20

01
20

00

219

9

20

450

01

530

221

Factual Data of the Plant Science Center

62

35

20

525

00

621

198

First Period

45

14［revised budget］

20

55

18

20

750

846

20
12

776

20
11

833

198

9

13

14
846

19
9

72

38

50

36

864

0 5 6

1,133

966

500

0

74

1,126

996

1376

72

88

1,248
62

845

90
30

20

803

1000

43

20
12

64

47

33

1,478

20
11

1,519

67

20
10

64

09

1,413

90
87

20

1,462

51

100

08

1,599

1,595

1328

49
32

04

1,579

524

1500

47

06

1,721

43

72

70

20

1,900

15

07

2000

42

39

43

20

2,192

38

15

20

2500

150

20

Increase following the organizationaltransfer of the Plant Genome
Research Group from GSC to PSC

45

Second Period

Publications / Patent applications in Japan and overseas / Budget / Employees

0 5 7

PSC Publications 2000 – 2012001

Estevez J, Cantero A, Romero C, Kawaide H, Jimenez L, Kuzuyama T, Seto H, Kamiya Y, Leon P, "Analysis of the expression of CLA1, a gene that encodes the 1-deoxyxylulose 5-phosphate synthase of the 2-C-methyl-D-erythritol-4-phosphatepathway in Arabidopsis" Plant Physiology 124 95-103 (2000)

002

Fukazawa J, Sakai T, Ishida S, Yamaguchi I, Kamiya Y, Takahashi Y, "Repression of Shoot Growth, a bZIP transcriptional
activator, regulates cell elongation by controlling the level ofgibberellins" The Plant Cell 12 901-915 (2000)

003

Fukuda H, "Programmed cell death of tracheary elements as aparadigm in plants" Plant Molecular Biology 44 245-253 (2000)

004

Ghassemian M, Nambara E, Cutler S, Kawaide H, Kamiya Y,
McCourt P, "Regulation of abscisic acid signaling by the ethylene response pathway in Arabidopsis" The Plant Cell 12 11171126 (2000)

005
006

007

008

009

010

011

012

016

017

018

Jones R, Harberd N, Kamiya Y, "Gibberellins 2000" Trends in
Plant Science 5 320-321 (2000)
Min X, Okada K, Brockmann B, Koshiba T, Kamiya Y, "Molecular cloning and expression patterns of three putative functional aldehyde oxidase genes and isolation of two aldehydeoxidase pseudogenes in tomato" Biochimica et Biophysica
Acta 1493 337-341 (2000)
Nakashima J, Takabe K, Fujita M, Fukuda H, "Autolysis duringin vitro tracheary element differentiation: Formation and location of the perforation" Plant Cell Physiology 41 1267-1271(2000)
Nambara E, Hayama R, Tsuchiya Y, Nishimura M, Kawaide H,
Kamiya Y, Naitou S, "The role of ABI3 and FUS3 loci in Arabidopsis thaliana on phase transition from late embryo development to germination" Developmental Biology 220 412-423(2000)
Sang S, Lao A, Chen Z, Uzawa J, Fujimoto Y, "Three new triterpenoid saponins from the seeds of Vaccaria segetalis" Jounal
of Asian Natural Products Research 2 187-193 (2000)
Sang S, Lao A, Leng Y, Gu Z, Chen Z, Uzawa J, Fujimoto Y,"Segetoside F a new triterpenoid saponin with inhibition ofluteal cell from the seeds of Vaccaria segetalis" Tetrahedron
Letters 41 9205-9207 (2000)

019

020

021

022

Seo M, Peeters A, Koiwai H, Oritani T, Marion-Poll A, Zeevaart
J, Koornneef M, Kamiya Y, Koshiba T, "The Arabidopsis aldehyde oxidase 3 (AAO3) gene product catalyzes the final stepin abscisic acid biosynthesis in leaves" Proceedings of the National Academy of Sciences of the United States of America 97
12908-12913 (2000)
Sugiyama M, Ito J, Aoyagi S, Fukuda H, "Endonucleases" Plant
Molecular Biology 44 387-397 (2000)

014

Arai Y, Nakashita H, Doi Y, Yamaguchi I, "Plastid targeting ofpolyhydroxybutyrate biosynthetic pathway in tobacco" Plant
Biotechnology 18 289-293 (2001)
Asami T, Mizutani M, Fujioka S, Goda H, Min Y, Shimada Y,

Bhaya D, Takahashi A, Grossman A, "Light regulation of typeIV pilus-dependent motility by chemosensor-like elements in
Synechocystis PCC6803" Proceedings of the National Academy of Sciences of the United States of America 98 7540-7545(2001)
Bhaya D, Takahashi A, Shahi P, Grossman A, "Novel motility
mutants of Synechocystis strain PCC 6803 generated by invitro transposon mutagenesis" Journal of Bacteriology 183
6140-6143 (2001)
Brockmann B, Smith M, Zarainsky A, Harrison K, Okada K,
Kamiya Y, "Subcellular localization and targeting of glucocorticoid receptor protein fusions expressed in transgenic Arabidopsis thaliana" Plant Cell Physiology 42 942-951 (2001)
Eckardt N, Araki T, Benning C, Cubas P, Goodrich J, Jacobsen
S, Masson P, Nambara E, Simon R, Somerville S, Wasteneys
G, "Arabidopsis research 2001" The Plant Cell 13 1973-1982(2001)

Endo S, Demura T, Fukuda H, "Inhibition of proteasome activity by the TED4 protein in extracellular space: A novel mechanism for protection of living cells from injury caused by dying
cells" Plant Cell Physiology 42 9-19 (2001)
Grossman A, Takahashi H, "Macronutrient utilization by photosynthetic eukaryotes and the fabric of interactions" Annual
Review of Plant Physiology Plant Molecular Biology 52 163210 (2001)
Hamamoto H, Hasegawa K, Nakaune R, Lee Y, Akutsu K, Hibi
T, "PCR-based detection of sterol demethylation inhibitorresistant strains of Penicillium digitatum" Pest Management
Science 57 839-843 (2001)024

Hamamoto H, Nawata O, Hasegawa K, Nakaune R, Lee Y,
Makizumi Y, Akutsu K, Hibi T, "The role of the ABC transporter gene PMR1 in demethylation inhibitor resistance in Penicillium digitatum" Pesticide Biochemistry and Physiology 70 1926 (2001)

025

028

Maruyama-Nakashita A, Saito K, Ishizawa K, "β-Cyanoalaninesynthase and cysteine synthase from potato: Molecular cloning, biochemical characterization, and spatial and hormonal
regulation" Plant Molecular Biology 46 749-760 (2001)

041

Obara M, Kajiura M, Fukuta Y, Yano M, Hayashi M, Yamaya T,
Sato T, "Mapping of QTLs associated with cytosolic glutaminesynthetase and NADH‐glutamate synthase in rice (Oryza sativa L.)" Journal of Experimental Botany 52 1209-1217 (2001)

029

Matsuoka K, Schekman R, Orci L, Heuser J, "Surface structureof the COPII-coated vesicle" Proceedings of the National Academy of Sciences of the United States of America 98 1370513709 (2001)

042

030

Motose H, Sugiyama M, Fukuda H, "An arabinogalactan
protein(s) is a key component of a fraction that mediates local intercellular communication involved in tracheary element
differentiation of zinnia mesophyll cells" Plant Cell Physiology
42 129-137 (2001)

Oikawa H, Toyomasu T, Toshima H, Ohashi S, Kawaide H, Kamiya Y, Ohtsuka M, Shinoda S, Mitsuhashi W, Sassa T, "Cloning
and functional expression of cDNA encoding aphidicolan-16β-ol synthase: A key enzyme responsible for formation of an
unusual diterpene skeleton in biosynthesis of aphidicolin"
Journal of the American Chemical Society 123 5154-5155(2001)

043

Ozaki T, Ambe S, Minai Y, Enomoto S, Yatagai F, Abe T, Yoshida S, Makide Y, "Effects of ionic valency of interacting
metal elements in ion uptake by carrot (Daucas carota cv. U.S.
harumakigosun)" Biological Trace Element Research 84 197211 (2001)

044

Saijo Y, Kinoshita N, Ishiyama K, Hata S, Kyozuka J, Hayakawa
T, Nakamura T, Shimamoto K, Yamaya T, Izui K, "A Ca2+-dependent protein kinase that endows rice plants with cold- andsalt-stress tolerance functions in vascular bundles" Plant Cell
Physiology 42 1228-1233 (2001)

045

Saikawa Y, Okamoto H, Inui T, Makabe M, Okuno T, Suda
T, Hashimoto K, Nakata M, "Toxic principles of a poisonous
mushroom Podostroma cornu-damae" Tetrahedron 57 82778281 (2001)

046

Sakai T, Kagawa T, Kasahara M, Swartz T, Christie J, Briggs W,
Wada M, Okada K, "Arabidopsis nph1 and npl1: Blue light
receptors that mediate both phototropism and chloroplast
relocation" Proceedings of the National Academy of Sciencesof the United States of America 98 6969-6974 (2001)

047

Sakurai N, Katayama Y, Yamaya T, "Overlapping expression ofcytosolic glutamine synthetase and phenylalanine ammonialyase in immature leaf blades of rice" Physiologia Plantarum
113 400-408 (2001)

048

Shimada Y, Fujioka S, Miyauchi N, Kushiro M, Takatsuto S,
Nomura T, Yokota T, Kamiya Y, Bishop G, Yoshida S, "Brassinosteroid-6-oxidases from Arabidopsis and tomato catalyze
multiple C-6 oxidations in brassinosteroid biosynthesis" Plant
Physiology 126 770-779 (2001)049

Shimada Y, Ohbayashi M, Nakano-Shimada R, Okinaka Y, Kiyokawa S, Kikuchi Y, "Genetic engineering of the anthocyanin
biosynthetic pathway with flavonoid-3',5'-hydroxylase: specific switching of the pathway in petunia" Plant Cell Reports
20 450-462 (2001)

050

Silverstone A, Jung H, Dill A, Kawaide H, Kamiya Y, Sun T, "Repressing a repressor: Gibberellin-induced rapid reduction of
the RGA protein in Arabidopsis" The Plant Cell 13 1555-1565(2001)

051

Someya N, Nakajima M, Hirayae K, Hibi T, Akutsu K, "Synergistic antifungal activity of chitinolytic enzymes and prodigiosin
produced by biocontrol bacterium, Serratia marcescens strain
B2 against gray mold pathogen, Botrytis cinerea" Journal of
General Plant Pathology 67 312-317 (2001)

052

Suzuki H, Nakayama T, Sakakibara K, Fukui Y, Nakamura N,
Nakao M, Tanaka Y, Yamaguchi M, Kusumi T, Nishino T, "Malonyl-CoA:Anthocyanin 5-O-glucoside-6'''-O-malonyltransfer-

031

Motose H, Sugiyama M, Fukuda H, "Cell-cell interactions during vascular development" Journal of Plant Research 114 473481 (2001)

032

Nagata N, Asami T, Yoshida S, "Brassinazole, an inhibitor ofbrassinosteroid biosynthesis, inhibits development of secondary xylem in cress plants (Lepidium sativum)" Plant and Cell
Physiology 42 1006-1011 (2001)

033

Nagatsuka Y, Kasama T, Ohashi Y, Uzawa J, Ono Y, Shimizu K,
Hirabayashi Y, "A new phosphoglycerolipid, 'phosphatidylglucose', found in human cord red cells by multi-reactive monoclonal anti-i cold agglutinin, mAb GL-1/GL-2" FEBS Letters 497
141-147 (2001)

034

Nakajima N, Hiradate S, Fujii Y, "Plant growth inhibitory activity of L-canavanine and its mode of action" Journal of Chemical Ecology 27 19-31 (2001)

035

Nakashita H, Arai Y, Shikanai T, Doi Y, Yamaguchi I, "Introduction of bacterial metabolism into higher plants by polycistronic transgene expression" Bioscience Biotechnology andBiochemistry 65 1688-1691 (2001)

Eizuka T, Sato T, Chida T, Yamaguchi I, "Simple method formonitoring the sensitivity of Pyricularia oryzae to fthalide"
Journal of Pesticide Science 26 385-389 (2001)

023

Seo M, Koiwai H, Akaba S, Komano T, Oritani T, Kamiya Y,
Koshiba T, "Abscisic aldehyde oxidase in leaves of Arabidopsis
thaliana" The Plant Journal 23 481-488 (2000)

013

015

Nakano T, Takatsuto S, Matsuyama T, Nagata N, Sakata K,
Yoshida S, "Selective interaction of triazole derivatives with
DWF4, a cytochrome P450 monooxygenase of the brassinosteroid biosynthetic pathway, correlates with brassinosteroid
deficiency in Planta" The Journal of Biological Chemistry 276
25687-25691 (2001)

Kagawa T, Sakai T, Suetsugu N, Oikawa K, Ishiguro S, Kato T,
Tabata S, Okada K, Wada M, "Arabidopsis NPL1: A phototropin homolog controlling the chloroplast high-light avoidance
response" Science 291 2138-2141 (2001)026

Kim H, Yamaguchi I, Cho K, "The secondary effects of Pencycuron on the formation of giant protoplasts and the lipid
peroxidation of Rhizoctonia solani AG4" The Plant Pathology
Journal 17 36-39 (2001)

027

Kimura M, Anzai H, Yamaguchi I, "Microbial toxins in plantpathogen interactions: Biosynthesis, resistance mechanisms,
and significance" The Journal of General and Applied Microbiology 47 149-160 (2001)

036

037

038

039

040

Nakayama T, Sato T, Fukui Y, Sakakibara K, Hayashi H, Tanaka
Y, Kusumi T, Nishino T, "Specificity analysis and mechanism ofaurone synthesis catalyzed by aureusidin synthase, a polyphenol oxidase homolog responsible for flower coloration" FEBS
Letters 499 107-111 (2001)
Nishitani C, Demura T, Fukuda H, "Primary phloem-specificexpression of a Zinnia elegans homeobox gene" Plant Cell
Physiology 42 1210-1218 (2001)
Noji M, Takagi Y, Kimura N, Inoue K, Saito M, Horikoshi M,
Saito F, Takahashi H, Saito K, "Serine acetyltransferase involved in cysteine biosynthesis from spinach: Molecular cloning, characterization and expression analysis of cDNA encoding a plastidic isoform" Plant Cell Physiology 42 627-634 (2001)
Nomura T, Sato T, Bishop G, Kamiya Y, Takatsuto S, Yokota
T, "Accumulation of 6-deoxocathasterone and 6-deoxocastasterone in Arabidopsis, pea and tomato is suggestive ofcommon rate-limiting steps in brassinosteroid biosynthesis"
Phytochemistry 57 171-178 (2001)
Obara K, Kuriyama H, Fukuda H, "Direct evidence of active
and rapid nuclear degradation triggered by vacuole rupture
during programmed cell death in zinnia" Plant Physiology 125
615-626 (2001)

PSC Publications 2000 – 2012

Okamura Y, Sassa N, Suzuki S, Yazaki J, Kikuchi S, Fukuda H,"Visualization by comprehensive microarray analysis of gene
expression programs during transdifferentiation of mesophyll
cells into xylem cells" Proceedings of the National Academyof Sciences of the United States of America 99 15794-15799(2002)

ase from scarlet sage (Salvia splendens) flowers" The Journalof Biological Chemistry 276 49013-49019 (2001)

053

054

055

056

057

058

059

060

061

062

063

064

065

Takahashi H, Braby C, Grossman A, "Sulfur economy and cellwall biosynthesis during sulfur limitation of Chlamydomonas
reinhardtii" Plant Physiology 127 665-673 (2001)
Takei K, Sakakibara H, Sugiyama T, "Identification of genes
encoding adenylate isopentenyltransferase, a cytokinin biosynthesis enzyme, in Arabidopsis thaliana" The Journal of
Biological Chemistry 276 26405-26410 (2001)
Takei K, Sakakibara H, Tanigutchi M, Sugiyama T, "Nitrogendependent accumulation of cytokinins in root and the translocation to leaf: Implication of cytokinin species that induces
gene expression of maize response regulator" Plant and Cell
Physiology 42 85-93 (2001)

066

067

068

Tobin A, Yamaya T, "Cellular compartmentation of ammonium assimilation in rice and barley" Journal of Experimental
Botany 52 591-604 (2001)
Yamada H, Suzuki T, Terada K, Takei K, Ishikawa K, Miwa K,
Yamashino T, Mizuno T, "The Arabidopsis AHK4 histidine kinase is a cytokinin-binding receptor that transduces cytokinin
signals across the membrane" Plant and Cell Physiology 42
1017-1023 (2001)
Yamaguchi S, Kamiya Y, Sun T, "Distinct cell-specific expression
patterns of early and late gibberellin biosynthetic genes during Arabidopsis seed germination" The Plant Journal 28 443453 (2001)
Yamaguchi T, Fukada-Tanaka S, Inagaki Y, Saito N, Sakakibara
K, Tanaka Y, Kusumi T, Iida S, "Genes encoding the vacuolar
Na+/H+ exchanger and flower coloration" Plant Cell Physiology 42 451-461 (2001)
Yamamoto R, Fujioka S, Demura T, Takatsuto S, Yoshida S,
Fukuda H, "Brassinosteroid levels increase drastically prior tomorphogenesis of tracheary elements" Plant Physiology 125
556-563 (2001)

069

070

071

072

Ambe S, Sekido S, Ozaki T, Yamaguchi I, "Uptake of trace elements by rice plants inoculated with Pyricularia oryzae" Applied Radiation and Isotopes 56 473-476 (2002)
Asahina M, Iwai H, Kikuchi A, Yamaguchi S, Kamiya Y, Kamada H, Satoh S, "Gibberellin produced in the cotyledon isrequired for cell division during tissue reunion in the cortex of
cut cucumber and tomato hypocotyls" Plant Physiology 129
201-210 (2002)
Cheng W, Endo A, Zhou L, Penney J, Chen H, Arroyo A, Leon
P, Nambara E, Asami T, Seo M, Koshiba T, Sheen J, "A unique
short-chain dehydrogenase/reductase in Arabidopsis glucose
signaling and abscisic acid biosynthesis and functions" The
Plant Cell 14 2723-2743 (2002)
Deji A, Sakakibara H, Okumura S, Matsuda T, Ishida Y, Yamada
S, Komari T, Kubo T, Yamaya T, Sugiyama T, "Accumulationof maize response regulator proteins in mesophyll cells after
cytokinin treatment" Bioscience Biotechnology and Biochemistry 66 1853-1858 (2002)
Demura T, Tashiro G, Horiguchi G, Kishimoto N, Kubo M,
Matsuoka N, Minami A, Nagata-Hiwatashi M, Nakamura K,

073

Endo M, Matsubara H, Kokubun T, Masuko H, Takahata Y,
Tsuchiya T, Fukuda H, Demura T, Watanabe M, "The advantages of cDNA microarray as an effective tool for identification of reproductive organ-specific genes in a model legume,Lotus japonicus" FEBS Letters 514 229-237 (2002)
Goda H, Shimada Y, Asami T, Fujioka S, Yoshida S, "Microarray
analysis of brassinosteroid-regulated genes in Arabidopsis"
Plant Physiology 130 1319-1334 (2002)
Hashimoto K, Matsumoto T, Nakamura K, Ohwada S, Ohuchi T,
Horikawa M, Konno K, Shirahama H, "Molecular orbital calculation for the model compounds of kainoid amino acids, agonists of excitatory amino acid receptors. Does the kainoid C4substituent directly interact with the receptors?" Bioorganic &Medicinal Chemistry 10 1373-1379 (2002)
Hatakeyama T, Matsuo N, Aoyagi H, Sugawara H, Uchida T,
Kurisu G, Kusunoki M, "Crystallization and preliminary crystallographic study of an invertebrate C-type lectin, CEL-I, fromthe marine invertebrate Cucumaria echinata" Acta Crystallographica Section D 58 143-144 (2002)
Hatakeyama T, Matsuo N, Shiba K, Nishinohara S, Yamasaki
N, Sugawara H, Aoyagi H, "Amino acid sequence and carbohydrate-binding analysis of the N-acetyl-D-galactosamine-specific C-type lectin, CEL-I, from the holothuroidea, Cucumariaechinata" Bioscience Biotechnology and Biochemistry 66 157163 (2002)
Hayashi M, Nito K, Takei-Hoshi R, Yagi M, Kondo M, Suenaga A,
Yamaya T, Nishimura M, "Ped3p is a peroxisomal ATP-binding
cassette transporter that might supply substrates for fatty acid
β -oxidation" Plant Cell Physiology 43 1-11 (2002)
Higashibayashi S, Hashimoto K, Nakata M, "Synthetic studies
on the thiostrepton family of peptide antibiotics: synthesis of
the tetrasubstituted dehydropiperidine and piperidine cores"
Tetrahedron Letters 43 105-110 (2002)
Higashibayashi S, Mori T, Shinko K, Hashimoto K, Nakata M,"Synthetic studies on thiostrepton family of peptide antibiotics: Synthesis of the tetrasubstituted dihydroquinoline portionof siomycin D1" Heterocycles 57 111-122 (2002)

074

Ito J, Fukuda H, "ZEN1 is a key enzyme in the degradation of
nuclear DNA during programmed cell death of tracheary elements" The Plant Cell 14 3201-3211 (2002)

075

Kamabe M, Miyazaki T, Hashimoto K, Shirahama H, "Formal
synthesis of FPA, a kainoid amino acid, via ketyl radical cyclization" Heterocycles 56 105-111 (2002)

076

Kang H, Jun S, Kim J, Kawaide H, Kamiya Y, An G, "Cloning ofgibberellin 3 β -hydroxylase cDNA and analysis of endogenous
gibberellins in the developing seeds in watermelon" Plant Cell
Physiology 43 152-158 (2002)

077

Kasahara H, Hanada A, Kuzuyama T, Takagi M, Kamiya Y, Yamaguchi S, "Contribution of the mevalonate and methyleryth-jiwara T, "Regulation of sulfur-responsive gene expression byexogenously applied cytokinins in Arabidopsis thaliana" Plant
Cell Physiology 43 1493-1501 (2002)

ritol phosphate pathways to the biosynthesis of gibberellins in
Arabidopsis" The Journal of Biological Chemistry 277 4518845194 (2002)

078

Kim H, Min J, Choi G, Kim J, Kim B, Chung B, Kim B, Kim Y,
Yamaguchi I, Cho K, "Synthesis of a new 1,2,4-oxadiazol-5-one
derivative, KC10017, and its controlling activity against rice
blast disease caused by Magnaporthe grisea" Journal of Pesticide Science 27 229-234 (2002)

091

Okada K, Kawaide H, Kuzuyama T, Seto H, Curtis I, Kamiya Y,"Antisense and chemical suppression of the nonmevalonate
pathway affects ent-kaurene biosynthesis in Arabidopsis"
Planta 215 339-344 (2002)

079

Kimura M, Furuichi M, Yamamoto M, Kumasaka T, Mizuno H,
Miyano M, Yamaguchi I, "The flexible C-terminal region ofAspergillus terreus blasticidin S deaminase: Identification of
its functional roles with deletion enzymes" Biochemical andBiophysical Research Communications 290 421-426 (2002)

092

Okano Y, Mizohata E, Xie Y, Matsumura H, Sugawara H, Inoue
T, Yokota A, Kai Y, "X-ray structure of Galdieria Rubisco complexed with one sulfate ion per active site" FEBS Letters 527
33-36 (2002)

093

Oshima M, Fujimura M, Banno S, Hashimoto C, Motoyama T,
Ichiishi A, Yamaguchi I, "A point mutation in the two-component histidine kinase BcOS-1 gene confers dicarboximide
resistance in field isolates of Botrytis cinerea" Phytopathology
92 75-80 (2002)

094

Putalun W, Tanaka H, Muranaka T, Shoyama Y, "Determination of aculeatisides based on immunoassay using a polyclonal
antibody against aculeatiside A" Analyst 127 1328-1332 (2002)

095

Motoyama T, Nakasako M, Yamaguchi I, "Crystallization of
scytalone dehydratase F162A mutant in the unligated state
and a preliminary X-ray diffraction study at 37 K" Acta Crystallographica Section D 58 148-150 (2002)

Saito C, Nagata N, Sakai A, Mori K, Kuroiwa H, Kuroiwa T,"Angiosperm species that produce sperm cell pairs or generative cells with polarized distribution of DNA-containing organelles" Sexual Plant Reproduction 15 167-178 (2002)

096

Nagata N, Suzuki M, Yoshida S, Muranaka T, "Mevalonic acidpartially restores chloroplast and etioplast development inArabidopsis lacking the non-mevalonate pathway" Planta 216
345-350 (2002)

Sakakibara H, Takei K, "Identification of cytokinin biosynthesis
genes in Arabidopsis: A breakthrough for understanding themetabolic pathway and the regulation in higher plants" Journal of Plant Growth Regulation 21 17-23 (2002)

097

Nakanomyo I, Kost B, Chua N, Fukuda H, "Preferential andasymmetrical accumulation of a Rac small GTPase mRNA in
differentiating xylem cells of Zinnia elegans" Plant Cell Physiology 43 1484-1492 (2002)

Sang S, Lao A, Leng Y, Cao L, Chen Z, Uzawa J, Yoshida S, Fujimoto Y, "Segetoside F a new triterpenoid saponin with inhibition of luteal cell from the seeds of Vaccaria segetalis" Jounal
of Asian Natural Products Research 4 297-301 (2002)

098

Sawa S, Ohgishi M, Goda H, Higuchi K, Shimada Y, Yoshida S,
Koshiba T, "The HAT2 gene, a member of the HD-Zip genefamily, isolated as an auxin inducible gene by DNA microarray
screening, affects auxin response in Arabidopsis" The Plant
Journal 32 1011-1022 (2002)

099

Schellmann S, Schnittger A, Kirik V, Wada T, Okada K, Beermann A, Thumfahrt J, Jurgens G, Hulskamp M, "TRIPTYCHON
and CAPRICE mediate lateral inhibition during trichome androot hair patterning in Arabidopsis" The EMBO Journal 215036-5046 (2002)100

Srivastava H, Shankar N, Yamaya T, "Role and regulation of
glutamate synthases in higher plants" Physiology and Molecular Biology of Plants 8 39-60 (2002)

080

Kuriyama H, Fukuda H, "Developmental programmed cell
death in plants" Current Opinion in Plant Biology 5 568-573(2002)

081

Makizumi Y, Takeda S, Matsuzaki Y, Nakaune R, Hamamoto H,
Akutsu K, Hibi T, "Cloning and selective toxicant-induced expression of BMR1 and BMR3, novel ABC transporter genes in
Botrytis cinerea" Journal of General Plant Pathology 68 338341 (2002)

082

083

084

085

Nakaune R, Hamamoto H, Imada J, Akutsu K, Hibi T, "A novel
ABC transporter gene, PMR5, is involved in multidrug resistance in the phytopathogenic fungus Penicillium digitatum"
Molecular Genetics and Genomics 267 179-185 (2002)

086

Nambara E, Suzuki M, Abrams S, McCarty D, Kamiya Y, McCourt P, "A screen for genes that function in abscisic acid signaling in Arabidopsis thaliana" Genetics 161 1247-1255 (2002)

087

Nishitani C, Demura T, Fukuda H, "Analysis of early processes
in wound-induced vascular regeneration using Ted3 and
ZeHB3 as molecular markers" Plant Cell Physiology 43 79-90(2002)

088

Ochiai N, Fujimura M, Oshima M, Motoyama T, Ichiishi A,
Yamada-Okabe H, Yamaguchi I, "Effects of iprodione andfludioxonil on glycerol synthesis and hyphal development in
Candida albicans" Bioscience Biotechnology and Biochemistry
66 2209-2215 (2002)

101

Sugiharto B, Ermawati N, Mori H, Aoki K, Sakakibara K, Yamaya T, Sugiyama T, Sakakibara H, "Identification and characterization of a gene encoding drought-inducible protein
localizing in the bundle sheath cell of sugarcane" Plant Cell
Physiology 43 350-354 (2002)

089

Ohashi-Ito K, Demura T, Fukuda H, "Promotion of transcript
accumulation of novel Zinnia immature xylem-specific HD-Zip
III homeobox genes by brassinosteroids" Plant Cell Physiology
43 1146-1153 (2002)

102

090

Ohkama N, Takei K, Sakakibara H, Hayashi H, Yoneyama T, Fu-

Suzuki H, Nakayama T, Sakakibara K, Fukui Y, Nakamura N,
Yamaguchi M, Tanaka Y, Kusumi T, Nishino T, "cDNA cloning,heterologous expressions, and functional characterizationof malonyl-coenzyme A:Anthocyanidin 3-O-Glucoside-6"-O-malonyltransferase from dahlia flowers" Plant Physiology
130 2142-2151 (2002)

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109

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115

Suzuki M, Kato A, Nagata N, Komeda Y, "A xylanase, AtXyn1,
is predominantly expressed in vascular bundles, and four putative xylanase genes were identified in the Arabidopsis thaliana genome" Plant Cell Physiology 43 759-767 (2002)

116

Suzuki Y, Kurano M, Arai Y, Nakashita H, Doi Y, Usami R, Horikoshi K, Yamaguchi I, "Enzyme inhibitors to increase poly3-hydroxybutyrate production by transgenic tobacco" Bioscience Biotechnology and Biochemistry 66 2537-2542 (2002)

117

Takahashi-Ando N, Kimura M, Kakeya H, Osada H, Yamaguchi
I, "A novel lactonohydrolase responsible for the detoxificationof zearalenone: enzyme purification and gene cloning" Biochemical Journal 365 1-6 (2002)
Takei K, Takahashi T, Sugiyama T, Yamaya T, Sakakibara H,"Multiple routes communicating nitrogen availability fromroots to shoots: a signal transduction pathway mediated bycytokinin" Journal of Experimental Botany 53 971-977 (2002)
Tamura K, Imamura M, Yoneyama K, Kohno Y, Takikawa Y, Yamaguchi I, Takahashi H, "Role of phaseolotoxin production by
Pseudomonas syringae pv. actinidiae in the formation of halo
lesions of kiwifruit canker disease" Physiological and Molecular Plant Pathology 60 207-214 (2002)
Wada T, Kurata T, Tominaga R, Kimura Y, Tachibana T, Goto K,
Marks M, Shimura Y, Okada K, "Role of a positive regulator ofroot hair development, CAPRICE, in Arabidopsis root epidermal cell differentiation" Development 129 5409-5419 (2002)
Yamaguchi S, Kamiya Y, "Gibberellins and light-stimulated
seed germination" Journal of Plant Growth Regulation 20
369-376 (2002)

118

Yuasa K, Maeshima M, "Equilibrium dialysis measurements of
the Ca2+-binding properties of recombinant radish vacuolar
Ca2+-binding protein expressed in Escherichia coli" Bioscience
Biotechnology and Biochemistry 66 2382-2387 (2002)
Asakura Y, Hagino T, Ohta Y, Aoki K, Sakakibara K, Deji A,
Yamaya T, Sugiyama T, Sakakibara H, "Molecular characterization of His-Asp phosphorelay signaling factors in maize leaves:
Implications of the signal divergence by cytokinin-inducible
response regulators in the cytosol and the nuclei" Plant Molecular Biology 52 331-341 (2003)
Banno S, Kimura M, Tokai T, Kasahara S, Higa-Nishiyama A,
Takahashi-Ando N, Hamamoto H, Fujimura M, Staskawicz B,
Yamaguchi I, "Cloning and characterization of genes specifically expressed during infection stages in the rice blast fungus" FEMS Microbiology Letters 222 221-227 (2003)
Delhaize E, Kataoka T, Hebb D, White R, Ryan P, "Genes encoding proteins of the cation diffusion facilitator family that
confer manganese tolerance" The Plant Cell 15 1131-1142(2003)

Fujimura M, Ochiai N, Oshima M, Motoyama T, Ichiishi A, Usami R, Horikoshi K, Yamaguchi I, "Putative homologs of SSK22
MAPKK kinase and PBS2 MAPK kinase of Saccharomyces cerevisiae encoded by os-4 and os-5 genes for osmotic sensitivity
and fungicide resistance in Neurospora crassa" Bioscience Biotechnology and Biochemistry 67 186-191 (2003)
Gawronska H, Deji A, Sakakibara H, Sugiyama T, "Hormonemediated nitrogen signaling in plants: implication of participation of abscissic acid in negative regulation of cytokinininducible expression of maize response regulator" Plant
Physiology and Biochemistry 41 605-610 (2003)

119

Hamada S, Ishiyama K, Choi S, Wang C, Singh S, Kawai N,
Franceschi V, Okita T, "The transport of prolamine RNAs toprolamine protein bodies in living rice endosperm cells" The
Plant Cell 15 2253-2264 (2003)

120

Hamada S, Ishiyama K, Sakulsingharoj C, Choi S, Wu Y, Wang
C, Singh S, Kawai N, Messing J, Okita T, "Dual regulated RNAtransport pathways to the cortical region in developing riceendosperm" The Plant Cell 15 2265-2272 (2003)

121

122

Yamaya T, Obara M, Nakajima H, Sasaki S, Hayakawa T, Sato T,"Genetic manipulation and quantitative-trait loci mapping fornitrogen recycling in rice" Journal of Experimental Botany 53
917-925 (2002)
Yoshimoto N, Takahashi H, Smith F, Yamaya T, Saito K, "Twodistinct high-affinity sulfate transporters with different inducibilities mediate uptake of sulfate in Arabidopsis roots" The
Plant Journal 29 465-473 (2002)

Fleet C, Yamaguchi S, Hanada A, Kawaide H, David C, Kamiya
Y, Sun T, "Overexpression of AtCPS and AtKS in Arabidopsis
confers increased ent-kaurene production but no increase inbioactive gibberellins" Plant Physiology 132 830-839 (2003)

123

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127

Harada A, Sakai T, Okada K, "Phot1 and phot2 mediate blue
light-induced transient increases in cytosolic Ca2+ differently inArabidopsis leaves" Proceedings of the National Academy of
Sciences of the United States of America 100 8583-8588 (2003)
Hayakawa T, Sakai T, Ishiyama K, Hirose N, Nakajima H,
Takezawa M, Naito K, Hino-Nakayama M, Akagawa T, Goto S,
Yamaya T, "Organization and structure of ferredoxin-dependent glutamate synthase gene and intracellular localization of
the enzyme protein in rice plants" Plant Biotechnology 20 4355 (2003)
Higa A, Kimura M, Mimori K, Ochiai-Fukuda T, Tokai T, Takahashi-Ando N, Nishiuchi T, Igawa T, Fujimura M, Hamamoto
H, Usami R, Yamaguchi I, "Expression in cereal plants of genesthat inactivate Fusarium Mycotoxins" Bioscience Biotechnology and Biochemistry 67 914-918 (2003)
Ishiyama K, Kojima S, Takahashi H, Hayakawa T, Yamaya T,"Cell type distinct accumulations of mRNA and protein for
NADH-dependent glutamate synthase in rice roots in responseto the supply of NH4+" Plant Physiology and Biochemistry 41
643-647 (2003)
Kimura M, Tokai T, Matsumoto G, Fujimura M, Hamamoto
H, Yoneyama K, Shibata T, Yamaguchi I, "Trichothecene nonproducer Gibberella species have both functional and nonfunctional 3-O-acetyltransferase genes" Genetics 163 677-684(2003)
Kimura M, Tokai T, O'Donnell K, Ward T, Fujimura M, Hamamoto H, Shibata T, Yamaguchi I, "The trichothecene biosynthesis gene cluster of Fusarium graminearum F15 contains
a limited number of essential pathway genes and expressed
non-essential genes" FEBS Letters 539 105-110 (2003)
Kurata T, Awai C, Sakuradani E, Shimizu S, Okada K, Wada T,"The YORE-YORE gene regulates multiple aspects of epidermal cell differentiation in Arabidopsis" The Plant Journal 36

55-66 (2003)

128

Kushiro T, Nambara E, McCourt P, "Hormone evolution: The
key to signalling" Nature 422 12298 (2003)

129

Lee J, Takei K, Sakakibara H, Cho H, Kim D, Kim Y, Min S, Kim
W, Sohn D, Lim Y, Pai H, "CHRK1, a chitinase-related receptorlike kinase, plays a role in plant development and cytokinin
homeostasis in tobacco" Plant Molecular Biology 53 877-890(2003)

130

131

Maruyama-Nakashita A, Inoue E, Takahashi A, Yamaya T,
Takahashi H, "Transcriptome profiling of sulfur-responsive
genes in Arabidopsis reveals global effects of sulfur nutrition
on multiple metabolic pathways" Plant Physiology 132 597605 (2003)
Mitsuhashi W, Toyomasu T, Masui H, Katoh T, Nakaminami
K, Kashiwagi Y, Akutsu M, Kenmoku H, Sassa T, Yamaguchi S,
Kamiya Y, Kamada H, "Gibberellin is essentially required forcarrot (Daucus carota L.) somatic embryogenesis: Dynamic
regulation of gibberellin 3-oxidase gene expressions" Bioscience Biotechnology and Biochemistry 67 2438-2447 (2003)

132

Nakaminami K, Sawada Y, Suzuki M, Kenmoku H, Kawaide H,
Mitsuhashi W, Sassa T, Inoue Y, Kamiya Y, Toyomasu T, "Deactivation of gibberellin by 2-oxidation during germinationof photoblastic lettuce seeds" Bioscience Biotechnology andBiochemistry 67 1551-1558 (2003)

133

Nakamura A, Higuchi K, Goda H, Fujiwara M, Sawa S, Koshiba
T, Shimada Y, Yoshida S, "Brassinolide induces IAA5, IAA19,
and DR5, a synthetic auxin response element in Arabidopsis,
implying a cross talk point of brassinosteroid and auxin signaling" Plant Physiology 133 1843-1853 (2003)

134

Nakamura A, Shimada Y, Goda H, Fujiwara M, Asami T, Yoshida S, "AXR1 is involved in BR-mediated elongation and
SAUR-ACI gene expression Arabidopsis" FEBS Letters 553 2832 (2003)

135

Nakamura T, Motoyama T, Hirokawa T, Hirono S, Yamaguchi
I, "Computer-aided modeling of pentachlorophenol 4-monooxygenase and site-directed mutagenesis of its active site"
Chemical and Pharmaceutical Bulletin 51 1293-1298 (2003)

136

Nambara E, Marion-Poll A, "ABA action and interactions inseeds" Trends in Plant Science 8 213-217 (2003)

137

Nishimura T, Yokota E, Wada T, Shimmen T, Okada K, "An Arabidopsis ACT2 dominant-negative mutation, which disturbs
F-actin polymerization, reveals its distinctive function in root
development" Plant Cell Physiology 44 1131-1140 (2003)

138

Nishioka M, Nakashita H, Suzuki H, Akiyama S, Yoshida S, Yamaguchi I, "Induction of resistance against rice blast disease
by a novel class of plant activator, pyrazolecarboxylic acid derivatives" Journal of Pesticide Science 28 416-421 (2003)

139

Nomura T, Bishop G, Kaneta T, Reid J, Chory J, Yokota T, "TheLKA gene is a BRASSINOSTEROID INSENSITIVE 1 homolog ofpea" The Plant Journal 36 291-300 (2003)

140

Ogawa M, Hanada A, Yamauchi Y, Kuwahara A, Kamiya Y,
Yamaguchi S, "Gibberellin biosynthesis and response during
Arabidopsis seed germination" The Plant Cell 15 1591-1604(2003)

141

Okinaka Y, Shimada Y, Nakano-Shimada R, Ohbayashi M, Kiyokawa S, Kikuchi Y, "Selective accumulation of delphinidin
derivatives in tobacco using a putative flavonoid 3',5'-hydroxylase cDNA from Campanula medium" Bioscience Biotechnology and Biochemistry 67 161-165 (2003)

142

Sakakibara H, "Differential response of genes for ferredoxin
and ferredoxin:NADP+ oxidoreductase to nitrate and light inmaize leaves" Journal of Plant Physiology 160 65-70 (2003)

143

Sakakibara H, "Nitrate-specific and cytokinin-mediated nitrogen signaling pathways in plants" Journal of Plant Research
116 253-257 (2003)

144

Sang S, Xia Z, Lao A, Cao L, Chen Z, Uzawa J, Fujimoto Y,"Studies on the constituents of the seeds of Vaccaria segetalis" Heterocycles 59 811-821 (2003)

145

Shimada Y, Goda H, Nakamura A, Suguru T, Fujioka S, Yoshida
S, "Organ-specific expression of brassinosteroid-biosynthetic
genes and distribution of endogenous brassinosteroids in Arabidopsis" Plant Physiology 131 287-297 (2003)

146

Someya N, Nakajima M, Watanabe K, Hibi T, Akutsu K, "Influence of bacteria isolated from rice plants and rhizospheres on
antibiotic production by the antagonistic bacterium Serratia
marcescens strain B2" Journal of General Plant Pathology 69
342-347 (2003)

147

Someya N, Numata S, Nakajima M, Hasebe A, Hibi T, Akutsu
K, "Biological control of rice blast by the epiphytic bacterium
Erwinia ananas transformed with a chitinolytic enzyme genefrom an antagonistic bacterium, Serratia marcescens strain
B2" Journal of General Plant Pathology 69 276-282 (2003)

148

Sonoda Y, Ikeda A, Saiki S, Von W, Yamaya T, Yamaguchi J,"Distinct expression and function of three ammonium transporter genes (OsAMT1;1-1;3) in rice" Plant Cell Physiology 44
726-734 (2003)

149

Sonoda Y, Ikeda A, Satomi S, Yamaya T, Yamaguchi J, "Feedback regulation of the ammonium Transporter gene family
AMT1 by glutamine in rice" Plant Cell Physiology 44 13961402 (2003)

150

Suenaga A, Moriya K, Sonoda Y, Ikeda A, Wiren N, Hayakawa
T, Yamaguchi J, Yamaya T, "Constitutive expression of a noveltype ammonium transporter OsAMT2 in rice plants" Plant Cell
Physiology 44 206-211 (2003)

151

Takei K, Dekishima Y, Eguchi T, Yamaya T, Sakakibara H, "A
new method for enzymatic preparation of isopentenyladenine-type and trans-zeatin-type cytokinins with radioisotopelabeling" Journal of Plant Research 116 259-263 (2003)

152

Takei K, Yamaya T, Sakakibara H, "A method for separationand determination of cytokinin nucleotides from plant tissues" Journal of Plant Research 116 265-269 (2003)

153

Woo S, Kimura M, Nishiyama A, Dohmae N, Hamamoto H,
Seung-Keun J, Yamaguchi I, "Proteome analysis of wheat
lemma" Bioscience Biotechnology and Biochemistry 67 24862491 (2003)

154

Yamaguchi M, Kato H, Yoshida S, Yamamura S, Uchimiya H,
Umeda M, "Control of in vitro organogenesis by cyclin-dependent kinase activities in plants" Proceedings of the National

PSC Publications 2000 – 2012

Academy of Sciences of the United States of America 100
8019-8023 (2003)

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160

Yoshimoto N, Inoue E, Saito K, Yamaya T, Takahashi H, "Phloem-localizing sulfate transporter, Sultr1;3, mediates re-distribution of sulfur from source to sink organs in Arabidopsis"
Plant Physiology 131 1511-1517 (2003)
Arai Y, Shikanai T, Doi Y, Yoshida S, Yamaguchi I, Nakashita H,"Production of polyhydroxybutyrate by polycistronic expression of bacterial genes in tobacco plastid" Plant Cell Physiology 45 1176-1184 (2004)
Buchner P, Takahashi H, Hawkesford M, "Plant sulphatetransporters: co-ordination of uptake, intracellular and longdistance transport" Journal of Experimental Botany 55 17651773 (2004)
Endo M, Tsuchiya T, Saito H, Matsubara H, Hakozaki H, Masuko H, Kamada M, Higashitani A, Takahashi H, Fukuda H,
Demura T, Watanabe M, "Identification and molecular characterization of novel anther-specific genes in Oryza sativa L. byusing cDNA microarray" Genes and Genetic Systems 79 213226 (2004)
Fujiwara M, Nakamura A, Ito R, Shimada Y, Yoshida S, Moller
S, "Chloroplast division site placement requires dimerizationof the ARC11/AtMinD1 protein in Arabidopsis" Journal of Cell
Science 117 2399-2410 (2004)
Galis I, Kakiuchi Y, Simek P, Wabiko H, "Agrobacterium tumefaciens AK-6b gene modulates phenolic compound metabolism in tobacco" Phytochemistry 65 169-179 (2004)

161

Galis I, Smith J, Jameson P, "Salicylic acid-, but not cytokinininduced, resistance to WClMV is associated with increased
expression of SA-dependent resistance genes in Phaseolus vulgaris" Journal of Plant Physiology 161 459-466 (2004)

162

Gazzarrini S, Tsuchiya Y, Lumba S, Okamoto M, McCourt P,"The Transcription Factor FUSCA3 Controls Developmental
Timing in Arabidopsis through the Hormones Gibberellin and
Abscisic Acid" Developmental Cell 7 373-385 (2004)

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bidopsis cytochrome P450 CYP707A encodes ABA 8'-hydroxylases: key enzymes in ABA catabolism" The EMBO Journal 23
1647-1656 (2004)

Otomo K, Kanno Y, Motegi A, Kenmoku H, Yamane H, Mitsuhashi W, Oikawa H, Toshima H, Itoh H, Matsuoka M, Sassa T,
Toyomasu T, "Diterpene cyclases responsible for the biosynthesis of phytoalexins, momilactones A, B, and Oryzalexins A-F
in rice" Bioscience Biotechnology and Biochemistry 68 20012006 (2004)

193

Otomo K, Kenmoku H, Oikawa H, Koenig W, Toshima H, Mitsuhashi W, Yamane H, Sassa T, Toyomasu T, "Biological functions of ent- and syn-copalyl diphosphate synthases in rice:
key enzymes for the branch point of gibberellin and phytoalexin biosynthesis" The Plant Journal 39 886-893 (2004)

194

Otsuka M, Kenmoku H, Ogawa M, Okada K, Mitsuhashi W,
Sassa T, Kamiya Y, Toyomasu T, Yamaguchi S, "Emission of ent-Kaurene, a diterpenoid hydrocarbon precursor for gibberellins, into the headspace from plants" Plant and Cell Physiology
45 1129-1138 (2004)

195

Nakamura A, Goda H, Shimada Y, Yoshida S, "Brassinosteroid
selectively regulates PIN gene expression in Arabidopsis" Bioscience Biotechnology and Biochemistry 68 952-954 (2004)

Pyo H, Demura T, Fukuda H, "Spatial and temporal tracing ofvessel differentiation in young Arabidopsis seedlings by theexpression of an immature tracheary element-specific promoter" Plant and Cell Physiology 45 1529-1536 (2004)

196

Nakamura T, Motoyama T, Hirono S, Yamaguchi I, "Identification, characterization, and site-directed mutagenesis of recombinant pentachlorophenol 4-monooxygenase" Biochimica
et Biophysica Acta 1700 151-159 (2004)

Sakakibara K, Kojima M, Yamaya T, Sakakibara H, "Molecularcharacterization of cytokinin-responsive histidine kinases inmaize. Differential ligand preferences and response to ciszeatin" Plant Physiology 134 1654-1661 (2004)

197

Nakamura T, Motoyama T, Suzuki Y, Yamaguchi I, "Biotransformation of pentachlorophenol by Chinese chive and arecombinant derivative of its rhizosphere-competent microorganism, Pseudomonas gladioli M-2196" Soil Biology & Biochemistry 36 787-795 (2004)

Seo M, Aoki H, Koiwai H, Kamiya Y, Nambara E, Koshiba T,"Comparative studies on the Arabidopsis aldehyde oxidase(AAO) gene family revealed a major role of AAO3 in ABA
biosynthesis in seeds" Plant and Cell Physiology 45 1694-1703(2004)

198

Someya N, Nakajima M, Hamamoto H, Yamaguchi I, Akutsu
K, "Effects of light conditions on prodigiosin stability in the
biocontrol bacterium Serratia marcescens strain B2" Journalof General Plant Pathology 70 367-370 (2004)

199

Narita N, Moore S, Horiguchi G, Kubo M, Demura T, Fukuda H,
Goodrich J, Tsukaya H, "Overexpression of a novel small peptide ROTUNDIFOLIA4 decreases cell proliferation and alters
leaf shape in Arabidopsis thaliana" The Plant Journal 38 699713 (2004)

Someya N, Niinuma K, Kimura M, Yamaguchi I, Hamamoto H,"Pattern of N gene-mediated systemic hypersensitive response
and turnover of viral replicase proten in tobacco" Archives ofVirology 149 2105-2113 (2004)

200

Nomura T, Jager C, Kitasaka Y, Takeuchi K, Fukami M, Yoneyama K, Matsushita Y, Nyunoya H, Takatsuto S, Fujioka S, Smith J,
Kerckhoffs L, Reid J, Yokota T, "Brassinosteroid deficiency due
to truncated steroid 5α -reductase causes dwarfism in the lk
mutant of pea" Plant Physiology 135 2220-2229 (2004)

Someya N, Numata S, Nakajima M, Hasebe A, Akutsu K, "Influence of rice-isolated bacteria on chitinase production by
the biocontrol bacterium Serratia marcescens strain B2 andthe genetically modified rice epiphytic bacterium" Journal of
General Plant Pathology 70 371-375 (2004)

201

Obara M, Sato T, Sasaki S, Kashiba K, Nagano A, Nakamura I,
Ebitani T, Yano M, Yamaya T, "Identification and characterization of a QTL on chromosome 2 for cytosolic glutamine synthetase content and panicle number in rice" Theoretical andApplied Genetics 110 1-11 (2004)

Sugawara H, Kusunoki M, Kurisu G, Fujimoto T, Aoyagi H,
Hatakeyama T, "Characteristic recognition of N-acetylgalactosamine by an invertebrate C-type lectin, CEL-I, revealed by xray crystallographic analysis" The Journal of Biological Chemistry 279 45219-45225 (2004)

202

Sugiyama K, Hayakawa T, Kudo T, Ito T, Yamaya T, "Interactionof N-acetylglutamate kinase with a PII-like protein in rice"
Plant Cell Physiology 45 1768-1778 (2004)

203

Suzuki M, Kamide Y, Nagata N, Seki H, Ohyama K, Kato H,
Masuda K, Sato S, Kato T, Tabata S, Yoshida S, Muranaka T,"Loss of function of 3-hydroxy-3-methylglutaryl coenzyme A

Magome H, Yamaguchi S, Hanada A, Kamiya Y, Oda K, "dwarf
and delayed-flowering 1, a novel Arabidopsis mutant deficient in gibberellin biosynthesis because of overexpression ofa putative AP2 transcription factor" The Plant Journal 37 720729 (2004)

Inada-Tominaga S, Ohgishi M, Mayama T, Okada K, Sakai T,"RPT2 is a signal transducer involved in phototropic response
and stomatal opening by association with phototropin 1 inArabidopsis thaliana" The Plant Cell 16 887-896 (2004)

169

Ishiyama K, Inoue E, Tabuchi M, Yamaya T, Takahashi H, "Biochemical background and compartmentalized functions ofcytosolic glutamine synthetase for active ammonium assimilation in rice roots" Plant Cell Physiology 45 1640-1647 (2004)

181

Maruyama-Nakashita A, Nakamura Y, Yamaya T, Takahashi H,"A novel regulatory pathway of sulfate uptake in Arabidopsis
roots: implication of CRE1/WOL/AHK4-mediated cytokinindependent regulation" The Plant Journal 38 779-789 (2004)

170

Ishiyama K, Inoue E, Takahashi A, Obara M, Yamaya T, Takahashi H, "Kinetic properties and ammonium-dependent
regulation of cytosolic isoenzymes of glutamine synthetase in
Arabidopsis" The Journal of Biological Chemistry 279 1659816605 (2004)

182

Maruyama-Nakashita A, Nakamura Y, Yamaya T, Takahashi H,"Regulation of high-affinity sulphate transporters in plants:
towards systematic analysis of sulphur signalling and regulation" Journal of Experimental Botany 55 1843-1849 (2004)

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Goda H, Shimada Y, Fujioka S, Yoshida S, "Classification ofbrassinosteroid-regulated genes based on expression profiles
in bri1 and in response to a protein kinase inhibitor, staurosporin" Bioscience Biotechnology and Biochemistry 68 16051607 (2004)

176

Gonai T, Kawahara S, Tougou M, Satoh S, Hashiba T, Hirai N,
Kawaide H, Kamiya Y, Yoshioka T, "Abscisic acid in the thermoinhibition of lettuce seed germination and enhancementof its catabolism by gibberellin" Journal of Experimental
Botany 55 111-118 (2004)

177

Kasahara H, Takei K, Ueda N, Hishiyama S, Yamaya T, Kamiya Y,
Yamaguchi S, Sakakibara H, "Distinct isoprenoid origins of cis- and trans-Zeatin biosyntheses in Arabidopsis" The Journal of
Biological Chemistry 279 14049-14054 (2004)
Kataoka T, Hayashi N, Yamaya T, Takahashi H, "Root-to-shoottransport of sulfate in Arabidopsis. Evidence for the role of
SULTR3;5 as a component of low-affinity sulfate transport system in the root vasculature" Plant Physiology 136 4198-4204(2004)
Kataoka T, Takahashi A, Hayashi N, Ohnishi M, Mimura T,
Buchner P, Hawkesford M, Yamaya T, Takahashi H, "Vacuolar
sulfate transporters are essential determinants controlling internal distribution of sulfate in Arabidopsis" The Plant Cell 162693-2704 (2004)
Kawabe M, Mizutani K, Yoshida T, Teraoka T, Yoneyama K,
Yamaguchi I, Arie T, "Cloning of the pathogenicity-related
gene FPD1 in Fusarium oxysporum f. sp. lycopersici" Journalof General Plant Pathology 70 16-20 (2004)
Kenmoku H, Tanaka K, Tanaka K, Kato N, Sassa T, "Erinacol(Cyatha-3,12-dien-14 β -ol) and 11-O-acetylcyathin A3, new cyathane metabolites from an erinacine Q-producing Hericium
erinaceum" Bioscience Biotechnology and Biochemistry 68
1786-1789 (2004)
Kenmoku H, Tanaka M, Ogiyama K, Kato N, Sassa T, "Identification of (+)-phyllocladene, (-)-sandaracopimaradiene,and (+)-kaurene as new fungal metabolites from fusicoccinproducing Phomopsis amygdali F6" Bioscience Biotechnology
and Biochemistry 68 1574-1577 (2004)
Kiba T, Aoki K, Sakakibara H, Mizuno T, "Arabidopsis response
regulator, ARR22, ectopic expression of which results in phenotypes similar to the wol cytokinin-receptor mutant" Plant
Cell Physiology 45 1063-1077 (2004)

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Koiwai H, Nakaminami K, Seo M, Mitsuhashi W, Toyomasu T,
Koshiba T, "Tissue-specific localization of an abscisic acid biosynthetic enzyme, AAO3, in Arabidopsis" Plant Physiology 134
1697-1707 (2004)

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Kushiro T, Okamoto M, Nakabayashi K, Yamagishi K, Kitamura
S, Asami T, Hirai N, Koshiba T, Kamiya Y, Nambara E, "The Ara-

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Goda H, Sawa S, Asami T, Fujioka S, Shimada Y, Yoshida S,"Comprehensive comparison of Auxin-regulated and Brassinosteroid-regulated genes in Arabidopsis" Plant Physiology
134 1555-1573 (2004)

Hatakeyama T, Shiba K, Matsuo N, Fujimoto T, Oda T, Sugawara H, Aoyagi H, "Characterization of recombinant CEL-I,
a GalNAc-specific C-type Lectin, expressed in Escherichia coli
using an artificial synthetic gene" Journal of Biochemistry 135
101-107 (2004)

Igawa T, Ochiai-Fukuda T, Takahashi-Ando N, Ohsato S, Shibata T, Yamaguchi I, Kimura M, "New TAXI-type xylanase
inhibitor genes are inducible by pathogens and wounding inhexaploid wheat" Plant Cell Physiology 45 1347-1360 (2004)

Matsuoka K, Demura T, Galis I, Horiguchi T, Sasaki M, Tashiro G,
Fukuda H, "A comprehensive gene expression analysis toward
the understanding of growth and differentiation of tobacco
BY-2 cells" Plant Cell Physiology 45 1280-1289 (2004)

Nakashita A, Nakamura Y, Takahashi A, Yamaya T, Takahashi
H, "Induction of SULTR1;1 sulfate transporter in Arabidopsis
roots involves protein phosphorylation/dephosphorylation
circuit for transcriptional regulation" Plant Cell Physiology 45
340-345 (2004)

Ohgishi M, Saji K, Okada K, Sakai T, "Functional analysis ofeach blue light receptor, cry1, cry2, phot1, and phot2, by using
combinatorial multiple mutants in Arabidopsis" Proceedings

PSC Publications 2000 – 2012

Palme K, Okada K, "The HALTED ROOT gene encoding the
26S proteasome subunit RPT2a is essential for the maintenance of Arabidopsis meristems" Development 131 2101-2111(2004)

reductase 1 (HMG1) in Arabidopsis leads to dwarfing, earlysenescence and male sterility, and reduced sterol levels" The
Plant Journal 37 750-761 (2004)

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Takahashi-Ando N, Ohsato S, Shibata T, Hamamoto H, Yamaguchi I, Kimura M, "Metabolism of zearalenone by geneticallymodified organisms expressing the detoxification gene from
Clonostachys rosea" Applied and Environmental Microbiology
70 3239-3245 (2004)

205

Takatsuka C, Inoue Y, Matsuoka K, Moriyasu Y, "3-Methyladenine inhibits autophagy in tobacco culture cells under sucrose
starvation conditions" Plant Cell Physiology 45 265-274 (2004)

206

Takehisa H, Shimodate T, Fukuta Y, Ueda T, Yano M, Yamaya T,
Kameya T, Sato T, "Identification of quantitative trait loci forplant growth of rice in paddy field flooded with salt water"
Field Crops Research 89 85-95 (2004)

207

Takei K, Ueda N, Aoki K, Kuromori T, Hirayama T, Shinozaki K,
Yamaya T, Sakakibara H, "AtIPT3 is a key determinant of nitrate-dependent cytokinin biosynthesis in Arabidopsis" Plant
Cell Physiology 45 1053-1062 (2004)

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Takei K, Yamaya T, Sakakibara H, "Arabidopsis CYP735A1 andCYP735A2 encode cytokinin hydroxylases that catalyze thebiosynthesis of trans-Zeatin" The Journal of Biological Chemistry 279 41866-41872 (2004)
Tarutani Y, Morimoto T, Sasaki A, Yasuda M, Nakashita H, Yoshida S, Yamaguchi I, Suzuki Y, "Molecular characterization of
two highly homologous receptor-like kinase genes, RLK902
and RKL1, in Arabidopsis thaliana" Bioscience Biotechnology
and Biochemistry 68 1935-1941 (2004)
Tarutani Y, Sasaki A, Yasuda M, Nakashita H, Yoshida S, Yamaguchi I, Suzuki Y, "Identification of three clones which commonly interact with the kinase domains of highly homologous
two receptor-like kinase, RLK902 and RKL1" Bioscience Biotechnology and Biochemistry 68 2581-2587 (2004)
Tatematsu K, Kumagai S, Muto H, Sato A, Watahiki M, Harper
R, Liscum E, Yamamoto K, "MASSUGU2 encodes Aux/IAA19,
an auxin-regulated protein that functions together with thetranscriptional activator NPH4/ARF7 to regulate differential
growth responses of hypocotyl and formation of lateral roots
in Arabidopsis thaliana" The Plant Cell 16 379-393 (2004)
Tian C, Muto H, Higuchi K, Matamura T, Tatematsu K, Koshiba T, Yamamoto K, "Disruption and overexpression of
auxin response factor 8 gene of Arabidopsis affect hypocotyl
elongation and root growth habit, indicating its possible involvement in auxin homeostasis in light condition" The Plant
Journal 40 333-343 (2004)
Tsuchiya Y, Nambara E, Naito S, McCourt P, "The FUS3 transcription factor functions through the epidermal regulator
TTG1 during embryogenesis in Arabidopsis" The Plant Journal
37 73-81 (2004)
Uchida T, Yamasaki T, Eto S, Sugawara H, Kurisu G, Nakagawa
A, Kusunoki M, Hatakeyama T, "Crystal structure of the hemolytic lectin CEL-III isolated from the marine invertebrate
Cucumaria echinata" The Journal of Biological Chemistry 279
37133-37141 (2004)
Ueda M, Matsui K, Ishiguro S, Sano R, Wada T, Paponov I,

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Li W, Liu X, Khan M, Yamaguchi S, "The effect of plant growth
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242

Maeda K, Kimura S, Demura T, Takeda J, Ozeki Y, "DcMYB1
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ammonia-lyase gene (DcPAL1) in response to elicitor treatment, UV-B irradiation and the dilution effect" Plant Molecular Biology 59 739-752 (2005)

Kawashima C, Berkowitz O, Hell R, Noji M, Saito K, "Characterization and expression analysis of a serine acetyltransferase
gene family involved in a key step of the sulfur assimilation
pathway in Arabidopsis" Plant Physiology 137 220-230 (2005)

243

Maruyama-Nakashita A, Nakamura Y, Takahashi A, Inoue E,
Yamaya T, Takahashi H, "Identification of a novel cis-acting
element conferring sulfur deficiency response in Arabidopsis
roots" The Plant Journal 42 305-314 (2005)

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Aoki K, Suzui N, Fujimaki s, Dohmae N, Sakakibara K, Fujiwara
T, Hayashi H, Yamaya T, Sakakibara H, "Destination-selective
long-distance movement of phloem proteins" The Plant Cell
17 1801-1814 (2005)

Kiba T, Naitou T, Koizumi N, Yamashino T, Sakakibara H,
Mizuno T, "Combinatorial microarray analysis revealing Arabidopsis genes implicated in cytokinin responses through theHis → Asp phosphorelay circuitry" Plant Cell Physiology 46
339-355 (2005)

Mase K, Sato K, Nakano Y, Nishikubo N, Tsuboi Y, Zhou J, Kitano H, Katayama Y, "The ectopic expression of phenylalanine
ammonia lyase with ectopic accumulation of polysaccharidelinked hydroxycinnamoyl esters in internode parenchyma ofrice mutant Fukei 71" Plant Cell Reports 24 487-493 (2005)

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Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T,
Nishimura A, Angeles E, Qian Q, Kitano H, Matsuoka M, "Cytokinin oxidase regulates rice grain production" Science 309
741-745 (2005)

Kimura Y, Wada T, Tachibana T, Tsugeki R, Ishiguro S, Okada
K, "Regulation of CAPRICE transcription by MYB proteins forroot epidermis differentiation in Arabidopsis" Plant and Cell
Physiology 46 817-826 (2005)

Matsui A, Yokoyama R, Seki M, Ito T, Shinozaki K, Takahashi T,
Komeda Y, Nishitani K, "AtXTH27 plays an essential role in cellwall modification during the development of tracheary elements" The Plant Journal 42 525-534 (2005)

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Awazuhara M, Fujiwara T, Hayashi H, Takahashi A, Takahashi H,
Saito K, "The function of SULTR2;1 sulfate transporter during
seed development in Arabidopsis thaliana" Physiologia Plantarum 125 95-105 (2005)

Kitajima M, Fujii N, Yoshino F, Sudo H, Saito K, Aimi N, Takiyama H, "Camptothecins and two new monoterpene glucosides
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Bulletin 53 1355-1358 (2005)

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Curtis I, Hanada A, Yamaguchi S, Kamiya Y, "Modification ofplant architecture through the expression of GA 2-oxidase
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Kohara A, Nakajima C, Hashimoto K, Ikenaga T, Tanaka H,
Shoyama Y, Yoshida S, Muranaka T, "A novel glucosyltransferase involved in steroid saponin biosynthesis in Solanum aculeatissimum" Plant Molecular Biology 57 225-239 (2005)

Mochizuki S, Harada A, Tominaga S, Sugimoto-Shirasu K,
Stacey N, Wada T, Ishiguro S, Okada K, Sakai T, "The arabidopsis WAVY GROWTH 2 protein modulates root bending in
response to environmental stimuli" The Plant Cell 17 537-547(2005)

235

Mok M, Martin R, Dobrev P, Vankova R, Ho S, Sakakibara K,
Sakakibara H, Mok D, "Topolins and hydroxylated thidiazuron
derivatives are substrates of cytokinin O-Glucosyltransferasewith position specificity related to receptor recognition" Plant
Physiology 137 1057-1066 (2005)

248

Montoya T, Nomura T, Yokota T, Farrar K, Harrison K, Jones J,
Kaneta T, Kamiya Y, Szekeres M, Bishop G, "Patterns of Dwarf
expression and brassinosteroid accumulation in tomato reveal
the importance of brassinosteroid synthesis during fruit development" The Plant Journal 42 262-269 (2005)

249

Nakabayashi K, Okamoto M, Koshiba T, Kamiya Y, Nambara E,"Genome-wide profiling of stored mRNA in Arabidopsis thaliana seed germination: epigenetic and genetic regulation oftranscription in seed" The Plant Journal 41 697-709 (2005)

250

Nakagawa H, Jiang C, Sakakibara H, Kojima M, Honda I, Ajisaka H, Nishijima T, Koshioka M, Tamaki H, Mander L, Takatsuji H,"Overexpression of a petunia zinc-finger gene alters cytokinin
metabolism and plant forms" The Plant Journal 41 512-523(2005)

251

Nambara E, Marion-Poll A, "Abscisic acid biosynthesis and catabolism" Annual Review of Plant Biology 56 165-185 (2005)

252

Narusaka Y, Narusaka M, Seki M, Ishida J, Shinozaki K, Nan Y,
Park P, Shiraishi T, Kobayashi M, "Cytological and molecularanalyses of non-host resistance of Arabidopsis thaliana to
Alternaria alternata" Molecular Plant Pathology 6 615-627(2005)

Uzawa J, Yoshida S, "A new selective population transfer
experiment using a double pulsed field gradient spin-echo"
Magnetic Resonance in Chemistry 42 1046-1048 (2004)

217

Yamauchi Y, Ogawa M, Kuwahara A, Hanada A, Kamiya Y,
Yamaguchi S, "Activation of gibberellin biosynthesis and response pathways by low temperature during imbibition of
Arabidopsis thaliana seeds" The Plant Cell 16 367-378 (2004)

218

Zheng M, Takahashi H, Miyazaki A, Hamamoto H, Shah J, Yamaguchi I, Kusano T, "Up-regulation of Arabidopsis thaliana
NHL10 in the hypersensitive response to Cucumber mosaic
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740-750 (2004)

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Galis I, Bilyeu K, Godinho M, Jameson P, "Expression of three
Arabidopsis cytokinin oxidase/dehydrogenase promoter::GUS
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224

Galis I, Bilyeu K, Wood G, Jameson P, "Rhodococcus fascians: shoot proliferation without elevated cytokinins?" Plant
Growth Regulation 46 109-115 (2005)

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206 (2005)

Henmi K, Demura T, Tsuboi S, Fukuda H, Iwasaki M, Ogawa K,"Change in the redox state of glutathione regulates differentiation of tracheary elements in Zinnia cells and Arabidopsis
roots" Plant Cell Physiology 46 1757-1765 (2005)
Hirai MY, Klein M, Fujikawa Y, Yano M, Goodenowe D,
Yamazaki Y, Kanaya S, Nakamura Y, Kitayama M, Suzuki H,
Sakurai N, Shibata D, Tokuhisa J, Reichelt M, Gershenzon J,
Papenbrock J, Saito K, "Elucidation of Gene-to-Gene andMetabolite-to-Gene Networks in Arabidopsis by Integrationof Metabolomics and Transcriptomics" The Journal of Biological Chemistry 280 25590-25595 (2005)
Hirose N, Makita N, Yamaya T, Sakakibara H, "Functional characterization and expression analysis of a gene, OsENT2, encoding an equilibrative nucleoside transporter in rice suggest
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228

Hoewyk D, Garifullina G, Ackley A, Abedel-Ghany S, Marcus M,
Fakra S, Ishiyama K, Inoue E, Pilon M, Takahashi H, Pilon-Smits
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229

Katagiri T, Ishiyama K, Katoh T, Tabata S, Kobayashi M, Shinozaki K, "An important role of phosphatidic acid in ABA signaling during germination in Arabidopsis thaliana" The Plant
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Kozuka T, Horiguchi G, Kim G, Ohgishi M, Sakai T, Tsukaya H,"The different growth responses of the Arabidopsis thaliana
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213-223 (2005)
Kubo M, Udagawa M, Nishikubo N, Horiguchi G, Yamaguchi M,
Ito J, Mimura T, Fukuda H, Demura T, "Transcription switches
for protoxylem and metaxylem vessel formation" Genes & Development 19 1855-1860 (2005)
Kurata T, Ishida T, Awai C, Noguchi M, Hattori S, Sano R, Nagasaka R, Tominaga R, Kimura Y, Kato T, Sato S, Tabata S, Okada
K, Wada T, "Cell-to-cell movement of the CAPRICE protein in
Arabidopsis root epidermal cell differentiation" Development
132 5387-5398 (2005)
Kurata T, Okada K, Wada T, "Intercellular movement of transcription factors" Current Opinion in Plant Biology 8 600-605(2005)
Li W, Khan M, Yamaguchi S, Kamiya Y, "Effects of heavy metals on seed germination and early seedling growth of Arabidopsis thaliana" Plant Growth Regulation 46 45-50 (2005)
Li W, Liu X, Khan M, Kamiya Y, Yamaguchi S, "Hormonal andenvironmental regulation of seed germination in flixweed (Descurainia sophia)" Plant Growth Regulation 45 199-207

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Nishimura T, Wada T, Yamamoto K, Okada K, "The Arabidopsis STV1 protein, responsible for translation reinitiation, is required for auxin-mediated gynoecium patterning" The Plant
Cell 17 2940-2953 (2005)
Nishioka M, Nakashita H, Yasuda M, Yoshida S, Yamaguchi I,"Induction of resistance against rice bacterial leaf blight by
3-chloro-1-methyl-1H-pyrazole-5-carboxylic acid" Journal of
Pesticide Science 30 47-49 (2005)
Nomura T, Kushiro T, Yokota T, Kamiya Y, Bishop G, Yamaguchi S, "The last reaction producing brassinolide is catalyzed
by cytochrome P-450s, CYP85A3 in tomato and CYP85A2 in
Arabidopsis" The Journal of Biological Chemistry 280 1787317879 (2005)
Ohashi-Ito K, Kubo M, Demura T, Fukuda H, "Class III Homeodomain Leucine-Zipper Proteins Regulate Xylem Cell Differentiation" Plant Cell Physiology 46 1646-1656 (2005)
Okada T, Hirai MY, Suzuki H, Yamazaki M, Saito K, "Molecularcharacterization of a novel quinolizidine alkaloid O-tigloyltransferase: cDNA cloning, catalytic activity of recombinant
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Physiology 46 233-244 (2005)

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Oksman-Caldentey K, Saito K, "Integrating genomics and metabolomics for engineering plant metabolic pathways" Current Opinion in Biotechnology 16 174-179 (2005)
Sakakibara H, Kasahara H, Ueda N, Kojima M, Takei K, Hishiyama S, Asami T, Okada K, Kamiya Y, Yamaya T, Yamaguchi S,"Agrobacterium tumefaciens increases cytokinin productionin plastids by modifying the biosynthetic pathway in the hostplant" Proceedings of the National Academy of Sciences of
the United States of America 102 9972-9977 (2005)
Sasaki-Sekimoto Y, Taki N, Obayashi T, Aono M, Matsumoto F,
Sakurai N, Suzuki H, Hirai MY, Noji M, Saito K, Masuda T, Takamiya K, Shibata D, Ohta H, "Coordinated activation of metabolic pathways for antioxidants and defence compounds byjasmonates and their roles in stress tolerance in Arabidopsis"
The Plant Journal 44 653-668 (2005)
Sawa S, Demura T, Horiguchi G, Kubo M, Fukuda H, "The ATE
genes are responsible for repression of transdifferentiation
into xylem cells in Arabidopsis" Plant Physiology 137 141-148(2005)
Seki H, Nishizawa T, Tanaka N, Niwa Y, Yoshida S, Muranaka T,"Hairy root-activation tagging: a high-throughput system foractivation tagging in transformed hairy roots" Plant Molecular Biology 59 793-807 (2005)
Shimizu M, Igasaki T, Yamada M, Yuasa K, Hasegawa J, Kato
T, Tsukagoshi H, Nakamura K, Fukuda H, Matsuoka K, "Experimental determination of proline hydroxylation and hydroxyproline arabinogalactosylation motifs in secretory proteins"
The Plant Journal 42 877-889 (2005)
Solfanelli C, Ceron F, Paolicchi F, Giorgetti L, Geri C, Ceccarelli
N, Kamiya Y, Picciarelli P, "Expression of two genes encoding
Gibberellin 2- and 3-oxidases in developing seeds of Phaseolus
coccineus" Plant Cell Physiology 46 1116-1124 (2005)
Someya N, Nakajima M, Watanabe K, Hibi T, Akutsu K, "Potential of Serratia marcescens strain B2 for biological control

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Sugawara H, Kawano Y, Hatakeyama T, Yamaya T, Kamiya N,
Sakakibara H, "Crystal structure of the histidine-containing
phosphotransfer protein ZmHP2 from maize" Protein Science
14 202-208 (2005)
Sugawara H, Yamaya T, Sakakibara H, "Crystallization andpreliminary X-ray diffraction study of the histidine-containing
phosphotransfer protein ZmHP1 from maize" Acta Crystallographica Section F 61 366-368 (2005)
Sun J, Hirose N, Wang X, Wen P, Xue L, Sakakibara H, Zuo J,"Arabidopsis SOI33/AtENT8 gene encodes a putative equilibrative nucleoside transporter that is involved in cytokinintransport in planta " Journal of Integrative Plant Biology (Acta
Botanica Sinica) 47 588-603 (2005)
Suzuki T, Nakajima S, Inagaki S, Hirano-Nakakita M, Matsuoka
K, Demura T, Fukuda H, Morikami A, Nakamura K, "TONSOKU
is expressed in S phase of the cell cycle and its defect delays
cell cycle progression in Arabidopsis" Plant Cell Physiology 46
736-742 (2005)
Tabuchi M, Sugiyama K, Ishiyama K, Inoue E, Sato T, Takahashi
H, Yamaya T, "Severe reduction in growth rate and grain filling of rice mutants lacking OsGS1;1, a cytosolic glutaminesynthetase1;1" The Plant Journal 42 641-651 (2005)
Takahashi H, Yoshimoto N, Saito K, "Anionic nutrient transport in plants: The molecular basis of the sulfate transporter
gene family" Genetic Engineering 27 67-80 (2005)
Tatematsu K, Ward S, Leyser O, Kamiya Y, Nambara E, "Identification of cis-Elements That Regulate Gene Expression during
Initiation of Axillary Bud Outgrowth in Arabidopsis" Plant
Physiology 138 757-766 (2005)
Terakado J, Fujihara S, Goto S, Kuratani R, Suzuki Y, Yoshida
S, Yoneyama T, "Systemic Effect of a Brassinosteroid on Root
Nodule Formation in Soybean as Revealed by the Applicationof Brassinolide and Brassinazole" Soil Science and Plant Nutrition 51 389-395 (2005)
Tohge T, Matsui K, Takagi M, Yamazaki M, Saito K, "Enhanced
radical scavenging activity of genetically modified Arabidopsis
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Tohge T, Nishiyama Y, Hirai MY, Yano M, Nakajima J, Awazuhara M, Inoue E, Takahashi H, Goodenwe D, Kitayama M, Noji
M, Yamazaki M, Saito K, "Functional genomics by integrated
analysis of metabolome and transcriptome of Arabidopsis
plants over-expressing an MYB transcription factor" The Plant
Journal 42 218-235 (2005)
Tokai T, Fujimura M, Inoue H, Aoki T, Ohta K, Shibata T, Yamaguchi I, Kimura M, "Concordant evolution of trichothecene 3O-acetyltransferase and an rDNA species phylogeny of trichothecene-producing and non-producing fusaria and other ascomycetous fungi" Microbiology 151 509-519 (2005)
Tokimatsu T, Sakurai N, Suzuki H, Ohta H, Nishitani K, Koyama
T, Umezawa T, Misawa N, Shibata D, Saito K, "Kappa-View: A
web-based analysis tool for integration of transcription andmetabolite data on plant metabolic pathway maps" Plant
Physiology 138 1289-1300 (2005)

278

Toyooka K, Takai s, Kirikae T, "Rhodococcus equi can survive aphagolysosomal environment in macrophages by suppressing
acidification of the phagolysosome" Journal of Medical Microbiology 54 1007-1015 (2005)

292

Galis I, Simek P, Narisawa T, Sasaki M, Horiguchi T, Fukuda H,
Matsuoka K, "Tobacco microarray reveals novel MYB transcription factor that selectively activates genes in phenylpropanoid metabolism" The Plant Journal 43 573-592 (2006)

293

Geisler-Lee J, Geisler M, Coutinho P, Segerman B, Nishikubo N,
Takahashi J, Aspeborg H, Djerbi S, Master E, Andersson-Gunneras S, Sundberg B, Karpinski S, Teeri T, Kleczkowski L, Henrissat B, Mellerowicz E, "Poplar carbohydrate-active enzymes.
Gene identification and expression analyses" Plant Physiology
140 946-962 (2006)

294

Yamauchi D, Sutoh K, Kanegae H, Matsuoka K, Horiguchi T,
Fukuda H, Wada M, "Analysis of expressed sequence tags inprothallia of Adiantum capillus-veneris" Journal of Plant Research 118 223-227 (2005)

Gonzalez-Lamothe R, Tsitsigiannis D, Ludwig A, Panicot M,
Shirasu K, Jones J, "The U-Box Protein CMPG1 Is Required for
Efficient Activation of Defense Mechanisms Triggered by Multiple Resistance Genes in Tobacco and Tomato" The Plant Cell
18 1067-1083 (2006)

295

Yoshida K, Endo M, Nakazono M, Fukuda H, Demura T, Tsuchiya T, Watanabe M, "cDNA microarray analysis of gene expression changes during pollination, pollen-tube elongation, fertilization, and early embryogenesis in rice pistils" Sexual Plant
Reproduction 17 269-275 (2005)

Gross J, Cho W, Lezhneva L, Falk J, Krupinska K, Shinozaki K,
Seki M, Herrmann R, Meurer J, "A plant locus essential forphylloquinone (Vitamin K 1) biosynthesis originated from afusion of four eubacterial genes" The Journal of Biological
Chemistry 281 17189-17196 (2006)

296

Hamada T, Igarashi H, Yao M, Hashimoto T, Shimmen T, Sonobe S, "Purification and characterization of plant dynaminfrom tobacco BY-2 cells" Plant Cell Physiology 47 1175-1181(2006)

297

Hatayama M, Ono E, Sakakibara K, Tanaka Y, Nishino T, Nakayama T, "Biochemical characterization and mutational studies of a chalcone synthase from yellow snapdragon (Antirrhinum majus) flowers" Plant Biotechnology 23 373-378 (2006)

298

Hayashi T, Harada A, Sakai T, Takagi S, "Ca2+ transient induced
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299

Higashi Y, Hirai MY, Fujiwara T, Naito S, Noji M, Saito K, "Proteomic and transcriptomic analysis of Arabidopsis seeds: Molecular evidence for successive processing of seed proteins andits implication in the stress response to sulfur nutrition" The
Plant Journal 48 557-571 (2006)

300

Hwang I, Sakakibara H, "Cytokinin biosynthesis and perception" Physiologia Plantarum 126 528-538 (2006)

279

Umeda M, Shimotohno A, Yamaguchi M, "Control of Cell Division and Transcription by Cyclin-dependent Kinase-activating
Kinases in Plants" Plant Cell Physiology 46 1437-1442 (2005)

280

Yamada M, Morishita H, Urano K, Shiozaki N, YamaguchiShinozaki K, Shinozaki K, Yoshiba Y, "Effects of free proline
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281

Yamaguchi-Shinozaki K, Shinozaki K, "Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive
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Yuasa K, Toyooka K, Fukuda H, Matsuoka K, "Membraneanchored prolyl hydroxylase with an export signal from theendoplasmic reticulum" The Plant Journal 41 81-94 (2005)

285

Akihiro T, Umezawa T, Ueki C, Mohamed B, Mizuno K, Ohta M,
Fujimura T, "Genome wide cDNA-AFLP analysis of genes rapidly induced by combined sucrose and ABA treatment in ricecultured cells" FEBS Letters 580 5947-5952 (2006)

286

Aniento F, Matsuoka K, Robinson D, "ER-to-Golgi transport:
the COPII-Pathwayc in the plant endoplasmic reticulum" Plant
Cell Monographs 4 99-124 (2006)

287

Arita M, Fujiwara Y, Nakanishi Y, "Map Editor for the Atomic
Reconstruction of Metabolism (ARM)" Biotechnology in Agriculture and Forestry 57: Plant Metabolomics 57 129-140 (2006)

288

Azevedo C, Betsuyaku S, Peart J, Takahashi A, Noel L, Sadanandom A, Casais C, Parker J, Shirasu K, "Role of SGT1 in resistance protein accumulation in plant immunity" The EMBO
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Bishop G, Nomura T, Yokota T, Montoya T, Castle J, Harrison
K, Kushiro T, Kamiya Y, Yamaguchi S, Bancos S, Szatmari A,
Szekeres M, "Dwarfism and cytochrome P450-mediated C-6oxidation of plant steroid hormones" Biochemical Society
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Ichikawa T, Nakazawa M, Kawashima M, Iizumi H, Kuroda H,
Kondou Y, Tsuhara Y, Suzuki K, Ishikawa A, Seki M, Fujita M,
Motohashi R, Nagata N, Takagi T, Shinozaki K, Matsui M, "TheFOX hunting system: an alternative gain-of-function gene
hunting technique" The Plant Journal 48 974-985 (2006)

290

Chono M, Honda I, Shinoda S, Kushiro T, Kamiya Y, Nambara
E, Kawakami N, Kaneko S, Watanabe Y, "Field studies on theregulation of abscisic acid content and germinability duringgrain development of barley: molecular and chemical analysis
of pre-harvest sprouting" Journal of Experimental Botany 57
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302

Ichimura K, Casais C, Peck S, Shinozaki K, Shirasu K, "MEKK1Is Required for MPK4 Activation and Regulates Tissue-specificand Temperature-dependent Cell Death in Arabidopsis" The
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303

Imai K, Ohashi Y, Tsuge T, Yoshizumi T, Matsui M, Oka A,
Aoyama T, "The A-Type Cyclin CYCA2;3 Is a Key Regulator of
Ploidy Levels in Arabidopsis Endoreduplication" The Plant Cell
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291

Fujita M, Fujita Y, Noutoshi Y, Takahashi F, Narusaka Y, Yamaguchi-Shinozaki K, Shinozaki K, "Crosstalk between abiotic
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304

Ishiyama K, Inoue E, Yamaya T, Takahashi H, "Gln49 andSer174 residues play critical roles in determining the catalytic
efficiencies of plant glutamine synthetase" Plant Cell Physiology 47 299-303 (2006)

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Kakiuchi Y, Galis I, Tamogami S, Wabiko H, "Reduction of polar auxin transport in tobacco by the tumorigenic Agrobacterium tumefaciens AK-6b gene" Planta 223 237-247 (2006)

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Kanno Y, Otomo K, Kenmoku H, Mitsuhashi W, Yamane H,
Oikawa H, Toshima H, Matsuoka M, Sassa T, Toyomasu T,"Characterization of a rice gene family encoding type-A diterpene cyclases" Bioscience Biotechnology and Biochemistry 70
1702-1710 (2006)
Kasukabe N, Watanabe-Sugimoto M, Matsuoka K, Okuma E,
Obi I, Nakamura Y, Shimoishi Y, Murata Y, Kakutani K, "Expression and Ca2+ dependency of plasma membrane K+ channels of Tobacco suspension cells adapted to salt stress" Plant
Cell Physiology 47 1674-1677 (2006)

F, Balliau T, Valot B, Davanture M, Terce-Laforgue T, Quillere I,
Coque M, Gallais A, Gonzalez-moro M, Bethencourt L, Habash
D, Lea P, Charcosset A, Perez P, Muringneux A, Sakakibara H,
Edwards K, Hirel B, "Two cytosolic glutamine synthetase isoforms of maize are specifically involved in the control of grain
production" The Plant Cell 18 3252-3274 (2006)

317

Maruyama A, Nakamura Y, Tohge T, Saito K, Takahashi H, "Arabidopsis SLIM1 is a central transcriptional regulator ofplant sulfur response and metabolism" The Plant Cell 18 32353251 (2006)

318

Mitchum M, Yamaguchi S, Hanada A, Kuwahara A, Yoshioka
Y, Kato T, Tabata S, Kamiya Y, Sun T, "Distinct and overlapping
roles of two gibberellin 3-oxidases in Arabidopsis development" The Plant Journal 45 804-818 (2006)

319

Muto H, Nagao I, Demura T, Fukuda H, Kinjo M, Yamamoto
K, "Fluorescence cross-correlation analyses of the molecularinteraction between an Aux/IAA protein, MSG2/IAA19, andprotein-protein interaction domains of auxin response factorsof Arabidopsis expressed in HeLa cells" Plant Cell Physiology
47 1095-1101 (2006)

Kikuchi J, Hirayama T, "Practical aspects of uniform stable isotope labeling of higher plants for heteronuclear NMR-based
metabolomics" Methods in Molecular Biology 358 273-286(2006)

320

Kita A, He Y, Sugiura R, Ma Y, Deng L, Takegawa K, Matsuoka K,
Shuntoh H, Takayoshi K, "Genetic and functional interaction
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pombe secretory pathway" Genes to Cells 11 207-221 (2006)

Myouga F, Motohashi R, Kuromori T, Nagata N, Shinozaki K,"An Arabidopsis chloroplast-targeted Hsp101 homologue,
APG6, has an essential role in chloroplast development as wellas heat-stress response" The Plant Journal 48 249-260 (2006)

321

Kojoma M, Seki H, Yoshida S, Muranaka T, "DNA polymorphisms in the tetrahydrocannabinolic acid (THCA) synthasegene in "drug-type" and "fiber-type" Cannabis sativa L."
Forensic Science International 159 132-140 (2006)

Nakajima J, Sato Y, Hoshino T, Yamazaki M, Saito K, "Mechanistic study on the oxidation of anthocyanidin synthase by
quantum mechanical calculation" The Journal of Biological
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322

Nakamura A, Nakajima N, Goda H, Shimada Y, Hayashi K,
Nozaki H, Asami T, Yoshida S, Fujioka S, "Arabidopsis Aux/
IAA genes are involved in brassinosteroid-mediated growth
responses in a manner dependent on organ type" The Plant
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Kuroha T, Ueguchi C, Sakakibara H, Satoh S, "Cytokinin receptors are required for normal development of auxin-transporting vascular tissues in the hypocotyl but not in adventitious
roots" Plant Cell Physiology 47 234-243 (2006)

323

Kuromori T, Wada T, Kamiya A, Yuguchi M, Yokouchi T, Imura Y,Takabe H, Sakurai T, Akiyama K, Hirayama T, Okada K, Shinozaki K, "A trial of phenome analysis using 4000 Ds-insertional
mutants in gene-coding regions of Arabidopsis" The Plant
Journal 47 640-651 (2006)
Lefebvre V, North H, Frey A, Sotta B, Seo M, Okamoto M,
Nambara E, Marion-Poll A, "Functional analysis of Arabidopsis
NCED6 and NCED9 genes indicates that ABA synthesized in
the endosperm is involved in the induction of seed dormancy"
The Plant Journal 45 309-319 (2006)
Loque D, Yuan L, Kojima S, Gojon A, Wirth J, Gazzarrini S,
Ishiyama K, Takahashi H, Wiren N, "Additive contributionof AMT1;1 and AMT1;3 to high-affinity ammonium uptake
across the plasma membrane of nitrogen-deficient Arabidopsis roots" The Plant Journal 48 522-534 (2006)
Machida M, Takechi K, Sato H, Chung S, Kuroiwa H, Takio S,
Seki M, Shinozaki K, Fujita T, Hasebe M, Takano H, "Genes forthe peptidoglycan synthesis pathway are essential for chloroplast division in moss" Proceedings of the National Academyof Sciences of the United States of America 103 6753-6758(2006)
Martin A, Lee J, Kichey T, Gerentes D, Zivy M, Tatout C, Dubois

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Nishiuchi T, Masuda D, Nakashita H, Ichimura K, Shinozaki
K, Yoshida S, Kimura M, Kimura M, Yamaguchi I, Yamaguchi
K, "Fusarium phytotoxin trichothecenes have an elicitor-like
activity in Arabidopsis thaliana, but the activity differed significantly among their molecular species" Molecular PlantMicrobe Interactions 19 512-520 (2006)
Noji M, Kawashima C, Obayashi T, Saito K, "In silico assessment of gene function involved in cysteine biosynthesis in
Arabidopsis: expression analysis of multiple isoforms of serine
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328

Ohnishi T, Nomura T, Watanabe B, Ohta D, Yokota T, Miyagawa H, Sakata K, Mizutani M, "Tomato cytochrome P450
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329

Okamoto M, Kuwahara A, Seo M, Kushiro T, Asami T, Hirai N,
Kamiya Y, Koshiba T, Nambara E, "CYP707A1 and CYP707A2,
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Ono E, Fukuchi-Mizutani M, Nakamura N, Fukui Y, Sakakibara
K, Yamaguchi M, Nakayama T, Tanaka T, Kusumi T, Tanaka
Y, "Yellow flowers generated by expression of the aurone
biosynthetic pathway" Proceedings of the National Academyof Sciences of the United States of America 103 11075-11080(2006)
Ono E, Hatayama M, Isono Y, Sato T, Watanabe R, Sakakibara K,
Fukuchi-Mizutani M, Tanaka Y, Kusumi T, Nishino T, Nakayama
T, "Localization of a flavonoid biosynthetic polyphenol oxidase in vacuoles" The Plant Journal 45 133-143 (2006)

332

Oono Y, Seki M, Satou M, Iida K, Akiyama K, Sakurai T, Fujita M,
Yamaguchi-Shinozaki K, Shinozaki K, "Monitoring expression
profiles of Arabidopsis genes during cold acclimation and deacclimation using DNA microarrays" Functional & Integrative
Genomics 6 212-234 (2006)

333

Pyo H, Demura T, Fukuda H, "Vascular cell expression patternsof Arabidopsis bZIP group I genes" Plant Biotechnology 23497-501 (2006)

334

Rahman L, Kitamaura Y, Yamaguchi J, Mukai M, Akiyama K,
Yamamoto H, Muranaka T, Ikenaga T, "Exogenous plant H6H
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335

Saito S, Okamoto M, Shinoda S, Kushiro T, Koshiba T, Kamiya
Y, Hirai N, Todoroki Y, Sakata K, Nambara E, Mizutani M, "A
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ABA catabolism in Arabidopsis" Bioscience Biotechnology andBiochemistry 70 1731-1739 (2006)

Sasabe M, Soyano T, Takahashi Y, Sonobe S, Igarashi H, Itoh
T, Hidaka M, Machida Y, "Phosphorylation of NtMAP65-1
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343

Sato Y, Demura T, Yamawaki K, Inoue Y, Seiichi S, Sugiyama M,
Fukuda H, "Isolation and characterization of a novel peroxidase gene ZPO-C whose expression and function are closely
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344

Schroeder J, Nambara E, "A quick release mechanism for abscisic acid" Cell 126 1023-1025 (2006)

345

Seo M, Hanada A, Kuwahara A, Endo A, Okamoto M, Yamauchi Y, North H, Marion-Poll A, Sun T, Koshiba T, Kamiya Y, Yamaguchi S, Nambara E, "Regulation of hormone metabolism
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346

Shinya T, Menard R, Kozone I, Matsuoka H, Shibuya N, Kauffmann S, Matsuoka K, Saito M, "Novel β -1,3-, 1,6-oligoglucan
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347

Soeno K, Fujioka S, Hiranuma S, Seto H, Yoshida S, "Metabolic
conversion of castasterone and brassinolide into their glucosides in higher plants" Journal of Plant Growth Regulation 25
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348

Stacey N, Kuromori T, Azumi Y, Roberts G, Breuer C, Wada
T, Maxwell A, Roberts K, Sugimoto-Shirasu K, "Arabidopsis
SPO11-2 functions with SPO11-1 in meiotic recombination"
The Plant Journal 48 206-216 (2006)

349

Suzuki M, Xiang T, Ohyama K, Seki H, Saito K, Muranaka T,
Hayashi H, Katsube Y, Kushiro T, Shibuya M, Ebizuka Y, "Lanosterol Synthase in Dicotyledonous Plants" Plant Cell Physiology 47 565-571 (2006)

Sakakibara H, "Cytokinins: activity, biosynthesis, and translocation" Annual Review of Plant Biology 57 431-449 (2006)

337

Sakakibara H, Takei K, Hirose N, "Interactions between nitrogen and cytokinin in the regulation of metabolism and development" Trends in Plant Science 11 440-448 (2006)

350

Tanaka M, Takei K, Kojima M, Sakakibara H, Mori H, "Auxin
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351

Tanaka Y, Sano T, Tamaoki M, Nakajima N, Kondo N, Hasezawa S, "Cytokinin and auxin inhibit abscisic acid-induced
stomatal closure by enhancing ethylene production in Arabidopsis" Journal of Experimental Botany 57 2259-2266 (2006)

352

Togami J, Tamura M, Ishiguro K, Hirose C, Okuhara H, Ueyama
Y, Nakamura N, Sakakibara K, Fukuchi-Mizutani M, Suzuki
K, Fukui Y, Kusumi T, Tanaka Y, "Molecular characterizationof the flavonoid biosynthesis of verbena hybrida and thefunctional analysis of verbena and clitoria ternatea F3´5´
H genes in transgenic verbena" Plant Biotechnology 23 5-11
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353

Torada A, Koike M, Mochida K, Ogihara Y, "SSR-based linkage
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Nomura T, Bishop G, "Cytochrome P450s in plant steroid hormone synthesis and metabolism" Phytochemistry Reviews 5
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338

Sakakibara K, Saito K, "Review: genetically modified plants
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326

Noutoshi Y, Kuromori T, Wada T, Hirayama T, Kamiya A, Imura
Y, Yasuda M, Nakashita H, Shirasu K, Shinozaki K, "Loss of
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339

Sakamoto T, Sakakibara H, Kojima M, Yamamoto Y, Nagasaki
H, Inukai Y, Sato Y, Matsuoka M, "Ectopic Expression of KNOTTED1-like homeobox protein induces expression of cytokinin
biosynthesis genes in rice" Plant Physiology 142 54-62 (2006)

Oh E, Yamaguchi S, Kamiya Y, Bae G, Chung W, Choi G, "Light
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Yamaguchi-Shinozaki K, "Dual function of an Arabidopsis
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Sakuma Y, Maruyama K, Osakabe Y, Qin F, Seki M, Shinozaki K,
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Toyooka K, Liu F, Ishii M, Saito S, Kirikae T, Asano Y, Shinomiya
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Toyooka K, Moriyasu Y, Goto Y, Takeuchi M, Fukuda H, Matsuoka K, "Protein aggregates are transported to vacuoles bymacroautophagic mechanism in nutrient-starved plant cells"
Autophagy 2 96-106 (2006)
Tsuji H, Aya K, Ueguchi M, Shimada Y, Nakazono M, Watanabe R, Nishizawa N, Gomi K, Shimada A, Kitano H, Ashikari
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Umezawa T, Fujita M, Fujita Y, Yamaguchi-Shinozaki K, Shinozaki K, "Engineering drought tolerance in plants: discoveringand tailoring genes to unlock the future" Current Opinion in
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Umezawa T, Okamoto M, Kushiro T, Nambara E, Oono Y,
Seki M, Kobayashi M, Koshiba T, Kamiya Y, Shinozaki K, "CYP707A3, a major ABA 8'-hydroxylase involved in dehydration
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Yoshida R, Umezawa T, Mizoguchi T, Takahashi S, Takahashi F,
Shinozaki K, "The regulatory domain of SRK2E/OST1/SnRK2.6
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The Journal of Biological Chemistry 281 5310-5318 (2006)

Dittmer T, Stacey N, Sugimoto K, Richards E, "LITTLE NUCLEI
genes affecting nuclear morphology in Arabidopsis thaliana"
The Plant Cell 19 2793-2803 (2007)380

Yoshizumi T, Tsumoto Y, Takiguchi T, Nagata N, Yamamoto Y,
Kawashima M, Ichikawa T, Nakazawa M, Yamamoto N, Matsui
M, "INCREASED LEVEL OF POLYPLOIDY1, a Conserved Repressor of CYCLINA2 Transcription, Controls Endoreduplication in
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Dubouzet J, Ishihara A, Matsuda F, Miyagawa H, Iwata H,
Wakasa K, "Integrated metabolomic and transcriptomic analyses of high-tryptophan rice expressing a mutant anthranilate
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381

Fujita M, Mizukado S, Fujita Y, Ichikawa T, Nakazawa M, Seki
M, Matsui M, Yamaguchi-Shinozaki K, Shinozaki K, "Identification of stress-tolerance-related transcription-factor genes
via mini-scale Full-length cDNA Over-eXpressor (FOX) gene
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382

Haga N, Kato K, Murase M, Araki S, Kubo M, Demura T, Suzuki K, Muller I, Vob U, Jurgens G, Ito M, "R1R2R3-Myb proteins
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383

Heise C, Le Duff C, Boter M, Casais C, Airey J, Leech A,
Amigues B, Guerois R, Moore G, Shirasu K, Kleanthous C, "Biochemical Characterization of RAR1 Cysteine- and HistidineRich Domains (CHORDs): A Novel Class of Zinc-Dependent
Protein − Protein Interaction Modules" Biochemistry 46 16121623 (2007)

384

Hirai MY, Sugiyama K, Sawada Y, Tohge T, Obayashi T, Suzuki
A, Araki R, Sakurai N, Suzuki H, Aoki K, Goda H, Nishizawa O,
Shibata D, Saito K, "Omics-based identification of Arabidopsis
Myb transcription factors regulating aliphatic glucosinolate
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369

Zhong R, Demura T, Ye Z, "SND1, a NAC domain transcription
factor, is a key regulator of secondary wall synthesis in fibersof Arabidopsis" The Plant Cell 18 3158-3170 (2006)

370

Zhu Y, Nomura T, Xu Y, Zhang Y, Peng Y, Mao B, Hanada A,
Zhou H, Wang R, Li P, Zhu X, Mander L, Kamiya Y, Yamaguchi S,
He Z, "ELONGATED UPPERMOST INTERNODE Encodes a Cytochrome P450 Monooxygenase That Epoxidizes Gibberellins ina Novel Deactivation Reaction in Rice" The Plant Cell 18 442456 (2006)

Tsuji H, Md. A, Arita M, Shinbo Y, Kurokawa K, Kanaya S,"Comparison of Protein Complexes Predicted from PPI Networks by DPClus and Newman Clustering Algorithms" IPSJ
Transactions on Bioinformatics 47 31-41 (2006)
Tsumoto Y, Yoshizumi T, Kuroda H, Kawashima M, Ichikawa
T, Nakazawa M, Yamamoto N, Matsui M, "Light-dependent
polyploidy control by a CUE protein variant in Arabidopsis"
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371

Arita M, Tokimatsu T, "Detection of monosaccharide types
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372

Arite T, Iwata H, Ohshima K, Maekawa M, Nakajima M, Kojima M, Sakakibara H, Kyozuka J, "DWARF10 ,an RMS1/MAX4/
DAD1 ortholog, controls lateral bud outgrowth in rice" The
Plant Journal 51 1019-1029 (2007)

373

Asahina M, Yamauchi Y, Hanada A, Kamiya Y, Kamada H,
Satoh S, Yamaguchi S, "Effects of the removal of cotyledonson endogenous gibberellin levels in hypocotyls of young cucumber and tomato seedlings" Plant Biotechnology 24 99-106(2007)

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Boter M, Amigues B, Peart J, Breuer C, Kadota Y, Casais C,
Moore G, Kleanthous C, Ochsenbein F, Shirasu K, Guerois R,"Structural and functional analysis of SGT1 reveals that its
interaction with HSP90 is required for the accumulation of Rx,
an R protein involved in plant immunity" The Plant Cell 19
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375

Breuer C, Stacey N, West C, Zhao Y, Chory J, Tsukaya H, Azumi
Y, Maxwell A, Roberts K, Sugimoto K, "BIN4, a novel component of the plant DNA topoisomerase VI complex, is required
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361

Unno H, Uchida T, Sugawara H, Kurisu G, Sugiyama T, Yamaya
T, Sakakibara H, Hase T, Kusunoki M, "Atomic structure ofplant glutamine synthetase" The Journal of Biological Chemistry 281 29287-29296 (2006)

362

Uzawa J, Fujimoto Y, Yoshida S, "Incorporation of selective
population transfer and homo-spin decoupling into selective
one-dimensional experiments" Magnetic Resonance in Chemistry 44 45-53 (2006)

363

Yamaguchi S, "Gibberellin biosynthesis in Arabidopsis" Phytochemistry Reviews 5 39-47 (2006)

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Yamaguchi-Shinozaki K, Shinozaki K, "Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses" Annual Review of Plant Biology 57 781803 (2006)

Bylesjo M, Eriksson D, Kusano M, Moritz T, Trygg J, "Data integration in plant biology: the O2PLS method for combinedmodeling of transcript and metabolite data" The Plant Journal 52 1181-1191 (2007)

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Chunjie T, Chikayama E, Tsuboi Y, Kuromori T, Shinozaki K,
Kikuchi J, Hirayama T, "Top-down phenomics of Arabidopsis
thaliana metabolic profiling by one- and two-dimensional
nuclear magnetic resonance spectroscopy and transcriptome
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Yamazaki M, Saito K, "Isolation and characterization of anthocyanin 5-O-glucosyltransferase in Perilla frutescens var.
crispa by differential display" Methods in Molecular Biology
317 255-266 (2006)
Yano M, Kanaya S, Amin M, Kurokawa K, Hirai MY, Saito K,"Integrated data mining of transcriptome and metabolome
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378

Demura T, Fukuda H, "Transcriptional regulation in wood formation" Trends in Plant Science 12 64-70 (2007)

385

Hirano K, Nakajima M, Asano K, Nishiyama T, Sakakibara H,
Kojima M, Katoh E, Xiang H, Tanahashi T, Hasebe M, Banks J,
Ashikari M, Kitano H, Ueguchi-Tanaka M, Matsuoka M, "TheGID1-mediated gibberellin perception mechanism is conserved in the Lycophyte Selaginella moellendorffii but not in
the bryophyte Physcomitrella patens" The Plant Cell 19 30583079 (2007)

386

Hirose N, Makita N, Kojima M, Nobusada T, Sakakibara H,"Overexpression of a type-A response regulator Alters ricemorphology and cytokinin metabolism" Plant Cell Physiology
48 523-539 (2007)

387

Ishida T, Hattori S, Sano R, Inoue K, Shirano Y, Hayashi H,
Shibata D, Sato S, Kato T, Tabata S, Okada K, Wada T, "Arabidopsis TRANSPARENT TESTA GLABRA2 is directly regulated by
R2R3 MYB transcription factors and is involved in regulationof GLABRA2 transcription in epidermal differentiation" The
Plant Cell 19 2531-2543 (2007)

388

Ishihara A, Matsuda F, Miyagawa H, Wakasa K, "Metabolomics
for metabolically manipulated plants: Effects of tryptophan
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389

Iwabuchi K, Sakai T, Takagi S, "Blue light-dependent nuclear
positioning in Arabidopsis thaliana leaf cells" Plant Cell Physiology 48 1291-1298 (2007)

390

Iwama A, Yamashino T, Tanaka Y, Sakakibara H, kakimoto
T, Sato S, Kato T, Tabata S, Nagatani A, Mizuno T, "AHK5

histidine kinase regulates root elongation through an ETR1dependent abscisic acid and ethylene signaling pathway inArabidopsis thaliana" Plant Cell Physiology 48 375-380 (2007)

391

Jager C, Symons G, Nomura T, Yamada Y, Smith J, Yamaguchi S,
Kamiya Y, Weller J, Yokota T, Reid J, "Characterization of two
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143 1894-1904 (2007)

392

Katsumoto Y, Fukuchi-Mizutani M, Fukui Y, Brugliera F, Holton
T, Karan M, Nakamura N, Sakakibara K, Togami J, Pigeaire A,
Tao G, Nehra N, Lu C, Dyson B, Tsuda S, Ashikari T, Kusumi T,
Mason J, Tanaka Y, "Engineering of the rose flavonoid biosynthetic pathway successfully generated blue-hued flowers
accumulating delphinidin" Plant Cell Physiology 48 1589-1600(2007)

393

Kiba T, Henriques R, Sakakibara H, Chua N, "Targeted degradation of PSEUDO-RESPONSE REGULATOR5 by an SCFZTL
complex regulates clock function and photomorphogenesis inarabidopsis thaliana" The Plant Cell 19 2516-2530 (2007)

394

Kobayashi K, Suzuki M, Tang J, Nagata N, Ohyama K, Seki H,
Kiuchi R, Kaneko Y, Nakazawa M, Matsui M, Matsumoto S,
Yoshida S, Muranaka T, "LOVASTATIN INSENSITIVE 1, a Novel
Pentatricopeptide Repeat Protein, is a Potential Regulatory
Factor of Isoprenoid Biosynthesis in Arabidopsis" Plant Cell
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395

Kohara A, Nakajima C, Yoshida S, Muranaka T, "Characterization and engineering of glycosyltransferases responsible forsteroid saponin biosynthesis in Solanaceous plants" Phytochemistry 68 478-486 (2007)

396

Kurakawa T, Ueda N, Maekawa M, Kobayashi k, Kojima M,
Nagato Y, Sakakibara H, Kyozuka J, "Direct control of shootmeristem activity by a cytokinin-activating enzyme" Nature
445 652-655 (2007)

397

Kusano M, Fukushima A, Arita M, Jonsson P, Moritz T, Kobayashi M, Hayashi N, Tohge T, Saito K, "Unbiased characterization of genotype-dependent metabolic regulations by
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Biology 1 53 (2007)

398

Kusano M, Fukushima A, Kobayashi M, Hayashi N, Jonsson
P, Moritz T, Ebana K, Saito K, "Application of a metabolomic
method combining one-dimensional and two-dimensional
gas chromatography-time-of-flight/mass spectrometry tometabolic phenotyping of natural variants in rice" Journal of
Chromatography B 855 71-79 (2007)

399

Li-Yang J, Nakajima J, Kimura N, Saito K, Seo S, "Oleananetype triterpene glycosides from Glychyrrhiza ularensis" Natural Product Communications 2 243-248 (2007)

400

Lopez-Juez E, Bowyer J, Sakai T, "Distinct leaf developmental
and gene expression responses to light quantity depend on
blue-photoreceptor or plastid-derived signals, and can occur
in the absence of phototropins" Planta 227 113-123 (2007)

401

Luo J, Nishiyama Y, Fuell C, Taguchi G, Elliott K, Hill L, Tanaka Y,
Kitayama M, Yamazaki M, Bailey P, Parr A, Michael A, Saito K,
Martin C, "Convergent evolution in the BAHD family of acyltransferases: identification and characterization of anthocyanin acyl transferases from Arabidopsis thaliana" The Plant
Journal 50 678-695 (2007)

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Maor R, Jones A, Nuhse T, Studholme D, Peck S, Shirasu K,"Multidimensional Protein Identification Technology (MudPIT)
Analysis of Ubiquitinated Proteins in Plants" Molecular andCellular Proteomics 6 601-610 (2007)

414

Maruyama A, Inoue E, Saito K, Takahashi H, "Sulfur-responsive
promoter of sulfate transporter gene is potentially useful todetect and quantify selenate and chromate" Plant Biotechnology 24 261-263 (2007)

415

Matsuda F, Wakasa K, Miyagawa H, "Metabolic flux analysis
in plants using dynamic labeling technique: Application totryptophan biosynthesis in cultured rice cells" Phytochemistry
68 2290-2301 (2007)
Mitsuda N, Iwase A, Yamamoto H, Yoshida M, Seki M, Shinozaki K, Takagi-Ohme M, "NAC transcription factors, NST1 and
NST3, are key regulators of the formation of secondary walls
in woody tissues of Arabidopsis" The Plant Cell 19 270-280(2007)
Miwa K, Takano J, Omori H, Seki M, Shinozaki K, Fujiwara
T, "Plants tolerant of high boron levels" Science 318 14173(2007)
Miya A, Albert P, Shinya T, Desaki Y, Ichimura K, Shirasu K,
Narusaka Y, Kawakami N, Kaku H, Shibuya N, "CERK1, a LysM
receptor kinase, is essential for chitin elicitor signaling in Arabidopsis" Proceedings of the National Academy of Sciences of
the United States of America 104 19613-19618 (2007)
Mizuno S, Osakabe Y, Maruyama K, Ito T, Sato T, Shinozaki K,
Yamaguchi-Shinozaki K, "Receptor-like protein kinase 2 (RPK2) is a novel factor controlling anther development in Arabidopsis thaliana" The Plant Journal 50 751-766 (2007)
Morioka R, Kanaya S, Hirai MY, Yano M, Ogasawara N, Saito K,"Predicting state transitions in the transcriptome and metabolome using a linear dynamical system model" BMC Bioinformatics 8 343 (2007)
Motohashi R, Yamazaki T, Myouga F, Ito T, Ito K, Satou M,
Kobayashi M, Nagata N, Yoshida S, Nagashima A, Tanaka K,
Takahashi S, Shinozaki K, "Chloroplast ribosome release factor 1 (AtcpRF1) is essential for chloroplast development" Plant
Molecular Biology 64 481-497 (2007)
Naito T, Yamashino T, Kiba T, Koizumi N, Kojima M, Sakakibara H, Mizuno T, "A link between Cytokinin and ASL9 (asymmetric leaves 2 like 9) that belongs to the AS2/LOB (lateralorgan boundaries) family genes in Arabidopsis thaliana" Bioscience Biotechnology and Biochemistry 71 1269-1278 (2007)
Nakagawa Y, Katagiri T, Shinozaki K, Qi Z, Tatsumi H, Furuichi
T, Kishigami A, Sokabe M, Kojima I, Sato S, Kato T, Tabata S,
Iida K, Nakano M, Ikeda M, Yamanaka T, Iida H, "Arabidopsis
plasma membrane protein crucial for Ca2+ influx and touchsensing in roots" Proceedings of the National Academy of Sciences of the United States of America 104 3639-3644 (2007)
Nakamura H, Hakata M, Amano K, Miyao A, Toki N, Kajikawa
M, Jinhuang P, Higashi N, Ando S, Toki S, Fujita M, Enju A, Seki
M, Nakazawa M, Ichikawa T, Shinozaki K, Matsui M, Nagamura Y, Hirochika H, Ichikawa H, "A genome-wide gain-offunction analysis of rice genes using the FOX-hunting system"
Plant Molecular Biology 65 357-371 (2007)

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423

Nakashima K, Todaka D, Ahmed S, Umezawa T, Seki M, Shinozaki K, Yamaguchi-Shinozaki K, "Molecular analysis of abiotic
stress: tolerant mechanisms in soybean and its application tobreeding" JIRCAS Working Report 13-19 (2007)
Nakashima K, Tran LS, Van Nguyen D, Fujita M, Maruyama K,
Todaka D, Ito Y, Hayashi N, Shinozaki K, Yamaguchi-Shinozaki
K, "Functional analysis of a NAC-type transcription factor
OsNAC6 involved in abiotic and biotic stress-responsive gene
expression in rice" The Plant Journal 51 617-630 (2007)
Nanjo T, Sakurai T, Totoki Y, Toyoda A, Nishiguchi M, Kado T,
Igasaki T, Futamura N, Seki M, Sakaki Y, Shinozaki K, Shinohara K, "Functional annotation of 19,841 Populus nigra fulllength enriched cDNA clones" BMC Genomics 8 1-10 (2007)
Nishikubo N, Awano T, Banasiak A, Bourquin V, Ibatullin F,
Funada R, Brumer H, Teeri T, Hayashi T, Sundberg B, Mellerowicz E, "Xyloglucan endo-transglycosylase (XET) functions ingelatinous layers of tension wood fibers in poplar-A glimpse
into the mechanism of the balancing act of trees" Plant andCell Physiology 48 843-855 (2007)

426

427

428

Saika H, Okamoto M, Miyoshi K, Kushiro T, Shinoda S, Jikumaru Y, Fujimoto M, Arikawa T, Takahashi H, Ando M, Arimura S,
Miyao A, Hirochika H, Kamiya Y, Tsutsumi N, Nambara E, Nakazono M, "Ethylene promotes submergence-induced expression of OsABA8ox1, a gene that encodes ABA 8'-hydroxylase
in Rice" Plant Cell Physiology 48 287-298 (2007)
Sakakibara K, Tohge T, Niida R, Saito K, "Identification of aflavonol 7-O-rhamnosyltransferase gene determining flavonoid pattern in Arabidopsis by transcriptome coexpression
analysis and reverse genetics" The Journal of Biological Chemistry 282 14932-14941 (2007)
Sakurai T, Plata G, Rodriguez-Zapata F, Seki M, Salcedo A,
Toyoda A, Ishiwata A, Tohme J, Sakaki Y, Shinozaki K, Ishitani
M, "Sequencing analysis of 20,000 full-length cDNA clones
from cassava reveals lineage specific expansions in gene families related to stress response" BMC Plant Biology 7 1-17 (2007)

429

Nyarko A, Mosbahi K, Rowe A, Leech A, Boter M, Shirasu K,
Kleanthous C, "TPR-Mediated Self-Association of Plant SGT1"
Biochemistry 46 11331-113471 (2007)

Sasaki K, Saito T, Lamsa M, Oksman-Caldentey K, Suzuki M,
Ohyama K, Muranaka T, Ohara K, Yazaki K, "Plants utilize isoprene emission as a thermotolerance mechanism" Plant Cell
Physiology 48 1254-1262 (2007)

430

Obayashi t, Kinoshita K, Nakai K, Shibaoka M, Hayashi s, Saeki
M, Shibata D, Saito K, Ohta H, "ATTED-II: a database of coexpressed genes and cis elements for identifying co-regulated
gene groups in Arabidopsis" Nucleic Acids Research 35 863869 (2007)

Sato M, Nishikawa T, Kajitani h, Kawano S, "Conserved relationship between FtsZ and peptidoglycan in the cyanelles of
Cyanophora paradoxa similar to that in bacterial cell division"
Planta 227 177-187 (2007)

431

Oh E, Yamaguchi S, Hu J, Jikumaru Y, Jung B, Paik I, Lee H,
Sun T, Kamiya Y, Choi G, "PIL5, a phytochrome-interacting
bHLH protein, regulates gibberellin responsiveness by binding
directly to the GAI and RGA promoters in Arabidopsis seeds"
The Plant Cell 19 1192-1208 (2007)
Ohyama K, Suzuki M, Masuda K, Yoshida S, Muranaka T,"Chemical phenotypes of the hmg1 and hmg2 mutants ofArabidopsis demonstrate the in-planta role of HMG-CoA reductase in triterpene biosynthesis" Chemical and Pharmaceutical Bulletin 55 1518-1521 (2007)
Okuda K, Myouga F, Motohashi R, Shinozaki K, Shikanai T,"Conserved domain structure of pentatricopeptide repeat
proteins involved in chloroplast RNA editing" Proceedingsof the National Academy of Sciences of the United States ofAmerica 104 8178-8183 (2007)
Pyo H, Demura T, Fukuda H, "TERE; a novel cis-element responsible for a coordinated expression of genes related toprogrammed cell death and secondary wall formation during
differentiation of tracheary elements" The Plant Journal 51
955-965 (2007)

424

Qin F, Kakimoto M, Sakuma Y, Maruyama K, Osakabe Y, Tran
LS, Shinozaki K, Yamaguchi-Shinozaki K, "Regulation andfunctional analysis of ZmDREB2A in response to drought andheat stresses in Zea mays L" The Plant Journal 50 54-69 (2007)

425

Rivero R, Kojima M, Gepstein A, Sakakibara H, Mittler R,
Gepstein S, Blumwald E, "Delayed leaf senescence induces
extreme drought tolerance in a flowering plant" Proceedingsof the National Academy of Sciences of the United States ofAmerica 104 19631-19636 (2007)

Seki M, Umezawa T, Urano K, Shinozaki K, "Regulatory metabolic networks in drought stress responses" Current Opinion
in Plant Biology 10 296-302 (2007)

432

Sekiyama Y, Kikuchi J, "Towards dynamic metabolic network
measurements by multi-dimensional NMR-based fluxomics"
Phytochemistry 68 2320-2329 (2007)

433

Shen Q, Saijo Y, Mauch S, Biskup C, Bieri S, Keller B, Seki H,
Ulker B, Somssich I, Schulze-Lefert P, "Nuclear Activity of MLA
Immune Receptors Links Isolate-Specific and Basal DiseaseResistance Responses" Science 315 1098-1103 (2007)

434

Shimamura M, Akashi T, Sakurai N, Suzuki H, Saito K, Shibata
D, Ayabe S, Aoki T, "2-Hydroxyisoflavanone dehydratase is a
critical determinant of isoflavone productivity in hairy root
cultures of Lotus japonicus" Plant Cell Physiology 48 16521657 (2007)

Cell 19 1723-1737 (2007)

439

Sirikantaramas S, Sudo H, Asano T, Yamazaki M, Saito K,"Transport of camptothecin in hairy roots of Ophiorrhiza
pumila" Phytochemistry 68 2881-2886 (2007)

440

Sirikantaramas S, Yamazaki M, Saito K, "Mechanisms of resistance to self-produced toxic secondary metabolites in plants"
Phytochemistry Reviews 7 467-477 (2007)

441

Sirkikantaramas S, Asano T, Sudo H, Yamazaki M, Saito K,"Camptothecin: Therapeutic potential and biotechnology"
Current Pharmaceutical Biotechnology 8 196-202 (2007)

442

Sonoda Y, Shan G, Sako K, Sato T, Kato W, Ohto M, Ichikawa T,
Matsui M, Yamaguchi j, Ikeda A, "SHA1, a novel RING finger
protein, functions in shoot apical meristem maintenance inArabidopsis" The Plant Journal 50 586-596 (2007)

443

Takahashi F, Yoshida R, Ichimura K, Mizoguchi T, Seo S, Yonezawa M, Maruyama K, Yamaguchi-Shinozaki K, Shinozaki K,"The mitogen-activated protein kinase cascade MKK3–MPK6
is an important part of the jasmonate signal transduction
pathway in Arabidopsis" The Plant Cell 19 805-818 (2007)

444

Tanaka Y, Kutsuna N, Kanazawa Y, Kondo N, Hasezawa S,
Sano T, "Intra-vacuolar reserves of membranes during stomatal closure: The possible role of guard cell vacuoles estimatedby 3-D reconstruction" Plant and Cell Physiology 48 1159-1169(2007)

445

Thao N, Chen L, Nakashima A, Hara S, Umemura K, Takahashi
A, Shirasu K, Kawasaki T, Shimamoto K, "RAR1 and HSP90
form a complex with Rac/Rop GTPase and function in innateimmune responses in rice" The Plant Cell 19 4035-4045 (2007)

446

The Rice Annotation Project, "Curated genome annotation of
Oryza sativa ssp. japonica and comparative genome analysis
with Arabidopsos thaliana" Genome Research 17 175-183(2007)

447

Tohge T, Sakakibara K, Niida R, Takahashi A, Saito K, "Phytochemical genomics in Arabidopsis thaliana: A case study for
functional identification of flavonoid biosynthesis genes"
Pure and Applied Chemistry 79 10047 (2007)

448

Tomatsu H, Takano J, Takahashi H, Takahashi A, Shibagaki N,
Fujiwara T, "An Arabidopsis thaliana high-affinity molybdate
transporter required for efficient uptake of molybdate fromsoil" Proceedings of the National Academy of Sciences of theUnited States of America 104 18807-18812 (2007)

435

Shinozaki K, "Acceleration of soybean genomics using large
collections of DNA markers for gene discovery" DNA Research
14 23533 (2007)

436

Shinozaki K, Yamaguchi-Shinozaki K, "Gene networks involved in drought stress response and tolerance" Journal of
Experimental Botany 58 221-227 (2007)

449

Tominaga R, Iwata M, Okada K, Wada T, "Functional analysisof the epidermal-specific MYB genes CAPRICE and WEREWOLF in Arabidopsis" The Plant Cell 19 2264-2277 (2007)

437

Shinya T, Hanai K, Suzuki K, Matsuoka K, Matsuoka H, Saito M,"Characterization of NtChitIV, a class IV chitinase induced byb -1,3-, 1,6-glucan elicitor from Alternaria alternata 102: Antagonistic effect of salicylic acid and methyl jasmonate on the
induction of NtChitIV" Biochemical and Biophysical ResearchCommunications 32527 (2007)

450

Tran LS, Nakashima K, Sakuma Y, Osakabe Y, Qin F, Simpson
SD, Maruyama K, Fujita Y, Shinozaki K, Yamaguchi-Shinozaki
K, "Co-expression of the stress-inducible zinc finger homeodomain ZFHD1 and NAC transcription factors enhances expression of the ERD1 gene in Arabidopsis" The Plant Journal 49
46-63 (2007)

438

Shitsukawa N, Tahira C, Kassai K, Hirabayashi C, Shimizu T, Takumi S, Mochida K, Kawaura K, Ogihara Y, Murai K, "Genetic
and epigenetic alteration among three homoeologous genesof a class E MADS box gene in hexaploid wheat" The Plant

451

Tran LS, Nakashima K, Shinozaki K, Yamaguchi-Shinozaki K,"Plant gene networks in osmotic stress response: from genes
to regulatory networks" Methods in Enzymology 428 109-128(2007)

PSC Publications 2000 – 2012

452

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455

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457
458

459

460

461

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463

464

Tran L-SP, Urao T, Qin F, Maruyama K, Kakimoto T, Shinozaki K,
Yamaguchi-Shinozaki K, "Functional analysis of AHK1/ATHK1
and cytokinin receptor histidine kinases in response to abscisic
acid, drought, and salt stress in Arabidopsis" Proceedingsof the National Academy of Sciences of the United States ofAmerica 104 20623-20628 (2007)
Ukitsu H, Kuromori T, Toyooka K, Goto Y, Matsuoka K, Sakuradani E, Shimizu S, Kamiya A, Imura Y, Yuguchi M, Wada T,
Hirayama T, Shinozaki K, "Cytological and biochemical analysis
of COF1, an Arabidopsis mutant of an ABC transporter gene"
Plant Cell Physiology 48 1524-1533 (2007)
Varbanova M, Yamaguchi S, Yang Y, McKelvey K, Hanada A,
Borochov R, Yu F, Jikumaru Y, Ross J, Cortes D, Ma C, Noel J,
Mander L, Shulaev V, Kamiya Y, Rodermel S, Weiss D, Pichersky
E, "Methylation of gibberellins by Arabidopsis GAMT1 andGAMT2" The Plant Cell 19 32-45 (2007)
Yamamoto Y, Ichida H, Matsui M, Obokata J, Sakurai T, Satou
M, Seki M, Shinozaki K, Abe T, "Identification of plant promoter constituents by analysis of local distribution of shortsequences" BMC Genomics 8 1-23 (2007)
Yamauchi Y, Takeda N, Hanada A, Ogawa M, Kuwahara A,
Seo M, Kamiya Y, Yamaguchi S, "Contribution of gibberellin
deactivation by AtGA2ox2 to the suppression of germinationof dark-imbibed Arabidopsis thaliana seeds" Plant Cell Physiology 48 555-561 (2007)

nozaki K, Hirai MY, Sakurai T, Kikuchi J, Saito K, "PRIMe: a
Web site that assembles tools for metabolomics and transcriptomics" In Silico Biology 8 339-345 (2008)

465

Arita M, "A pitfall of wiki solution for biological databases"
Briefings in Bioinformatics 1-2 (2008)

466

Arita M, Suwa K, "Search extension transforms Wiki into a
relational system: a case for flavonoid metabolite database"
BioData Mining 1 1-8 (2008)

467

468

469

470

Yamazaki M, "Medicinal Plant Biotechnology" Current Pharmaceutical Biotechnology 8 967 3e25-1 (2007)
Yokoyama A, Yamashino T, Amano Y, Tajima Y, Imamura A,
Sakakibara H, Mizono T, "Type-B ARR transcription factors,
ARR10 and ARR12, are implicated in cytokinin-mediated regulation of protoxylem differentiation in roots of arabidopsis
thaliana" Plant Cell Physiology 48 84-96 (2007)

471

Yoneda A, Higaki T, Kutsuna N, Kondou Y, Osada H, Hasezawa
S, Matsui M, "Chemical Genetic Screening Identifies a Novel
Inhibitor of Parallel Alignment of Cortical Microtubules andCellulose Microfibrils" Plant Cell Physiology 48 1393-1403(2007)

472

Yoshimoto N, Inoue E, Takahashi A, Saito K, Takahashi H,"Posttranscriptional regulation of high-affinity sulfate transporters in Arabidopsis by sulfur nutrition" Plant Physiology
145 378-388 (2007)
Yuan L, Loque D, Kojima S, Rauch S, Ishiyama K, Inoue E, Takahashi H, von Wiren N, "The organization of high-affinity ammonium uptake in Arabidopsis roots depends on the spatial
arrangement and biochemical properties of AMT1-type transporters" The Plant Cell 19 2636-2652 (2007)
Zentella R, Zhang Z, Park M, Thomas S, Endo A, Murase K,
Fleet C, Jikumaru Y, Nambara E, Kamiya Y, Sun T, "Global
Analysis of DELLA Direct Targets in Early Gibberellin Signalingin Arabidopsis" The Plant Cell 19 3037-3057 (2007)
Zhou G, Kubo M, Zhong R, Demura T, Ye Z, "Overexpressionof miR165 affects apical meristem formation, organ polarity establishment and vascular development in Arabidopsis"
Plant Cell Physiology 48 391-404 (2007)
Akiyama K, Chikayama E, Yuasa H, Shimada Y, Tohge T, Shi-Babiychuk E, Bouvier-Nave P, Compagnon V, Suzuki M, Muranaka T, Montagu M, Kushnir S, Schaller H, "Albinism andcell viability in cycloartenol synthase deficient Arabidopsis"
Plant Signaling & Behavior 3 978-980 (2008)
Babiychuk E, Bouvier-Nave P, Compagnon V, Suzuki M, Muranaka T, Montagu M, Kushnir S, Schaller H, "Allelic mutant
series reveal distinct functions for Arabidopsis cycloartenol
synthase 1 in cell viability and plastid biogenesis" Proceedingsof the National Academy of Sciences of the United States ofAmerica 105 3163-3168 (2008)
Cartagene J, Matsunaga S, Seki M, Kurihara D, Yokoyama M,
Shinozaki K, Fujimoto S, Azumi Y, Uchimiya S, Fukui K, "TheArabidopsis SDG4 contributes to the regulation of pollen tube
growth by methylation of histone H3 lysines 4 and 36 in mature pollen" Developmental Biology 315 355-368 (2008)
Chikayama E, Suto M, Nishihara T, Shinozaki K, Hirayama T,
Kikuchi J, "Systematic NMR Analysis of Stable Isotope Labeled
Metabolite Mixtures in Plant and Animal Systems: Coarse
Grained Views of Metabolic Pathways" PLoS One 3 e3805(2008)
Ehrlich M, Sanchez C, Shao C, Nishiyama R, Kehrl J, Kuick R,
Kubota T, Hanash S, "ICF, an immunodeficiency syndrome:
DNA methyltransferase 3B involvement, chromosome anomalies, and gene dysregulation" Autoimmunity 41 253-271(2008)
Endo A, Sawada Y, Takahashi H, Okamoto M, Seo M, Toyomasu T, Mitsuhashi W, Shinozaki K, Nakazono M, Koshiba T,
Nambara E, "Drought induction of Arabidopsis 9-cis-epoxycarotenoid dioxygenase occurs in vascular parenchyma cells"
Plant Physiology 147 1984-1993 (2008)

473

Endo S, Pesquet E, Tashiro G, Kuriyama H, Goffner D, Fukuda
H, Demura T, "Transient transformation and RNA silencing in
Zinnia tracheary element differentiating cell cultures" The
Plant Journal 53 864-875 (2008)

474

Fukushima A, Wada M, Kanaya S, Arita M, "SVD-based anatomy of gene expressions for correlation analysis in Arabidopsis
thaliana" DNA Research 15 367-374 (2008)

475

Futamura N, Totoki Y, Toyoda A, Igasaki T, Nanjo T, Seki M,
Sakaki Y, Mari A, Shinozaki K, Shinohara K, "Characterizationof expressed sequence tags from a full-length enriched cDNA
library of Cryptomeria japonica male strobili" BMC Genomics
9 383 (2008)

476

Garcia M, Myouga F, Takechi K, Sato H, Nabeshima K, Nagata
N, Takio S, Shinozaki K, Takano H, "An Arabidopsis homologof the bacterial peptidoglycan synthesis enzyme MurE has an
essential role in chloroplast development" The Plant Journal
53 924-934 (2008)

477

Goda H, Sasaki E, Akiyama K, Maruyama A, Nakabayashi K, Li
W, Ogawa M, Yamauchi Y, Preston J, Aoki K, Kiba T, Takatsuto
S, Fujioka S, Asami T, Nakano T, Kato H, Mizuno T, Sakakibara
H, Yamaguchi S, Nambara E, Kamiya Y, Takahashi H, Hirai MY,
Sakurai T, Shinozaki K, Saito K, Yoshida S, Shimada Y, "TheAtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis anddata access" The Plant Journal 55 526-542 (2008)

for identification of salt-responsive genes in common wheat"
Functional & Integrative Genomics 8 277-286 (2008)

490

Kim D, Yamaguchi S, Lim S, Oh E, Park J, Hanada A, Kamiya Y,
Choi G, "SOMNUS, a CCCH-type zinc finger protein in Arabidopsis, negatively regulates light-dependent seed germination downstream of PIL5" The Plant Cell 20 1260-1277 (2008)

491

Kim J, To T, Ishida J, Morosawa T, Kawashima M, Matsui A,
Toyoda T, Kimura H, Shinozaki K, Seki M, "Alterations of lysine
modifications on the histone H3 N-tail under drought stressconditions in Arabidopsis thaliana" Plant and Cell Physiology
49 1580-1588 (2008)

492

Kondou Y, Nakazawa M, Kawashima M, Ichikawa T, Yoshizumi
T, Suzuki K, Ishikawa A, Koshi T, Matsui R, Muto S, Matsui
M, "RETARDED GROWTH OF EMBRYO1, a new basic helixloop-helix protein, expresses in endosperm to control embryo
growth" Plant Physiology 147 1924-1935 (2008)

478

Hamaguchi A, Yamashino T, Koizumi N, Kiba T, Kojima M,
Sakakibara H, Mizuno T, "A small subfamily of Arabidopsis
RADIALIS-LIKE SANT/MYB genes: a link to HOOKLESS1-Mediated signal transduction during early morphogenesis" Bioscience Biotechnology and Biochemistry 72 2687-2696 (2008)

479

Hanada K, Zou C, Lehti-Shiu M, Shinozaki K, Shiu S, "Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli1"
Plant Physiology 148 993-1003 (2008)480

Hashimoto K, Igarashi H, Mano S, Takenaka C, Shiina T, Yamaguchi M, Demura T, Nishimura M, Shinmen T, Yokota E, "Anisoform of Arabidopsis myosin XI interacts with small GTPases
in its C-terminal tail region" Journal of Experimental Botany
59 3523-3531 (2008)

493

Kurihara Y, Matsui A, Kawashima M, Kaminuma E, Ishida J,
Morosawa T, Mochizuki Y, Kobayashi N, Toyoda T, Shinozaki
K, Seki M, "Identification of the candidate genes regulated by
RNA-directed DNA methylation in Arabidopsis" Biochemical
and Biophysical Research Communications 376 553-557 (2008)

481

Hayashi S, Ishii T, Matsunaga T, Tominaga R, Kuromori T, Wada
T, Shinozaki K, Hirayama T, "The glycerophosphoryl diester
phosphodiesterase-like proteins SHV3 and its homologs play
important roles in cell wall organization" Plant Cell Physiology
49 1522-1535 (2008)

494

Kuromori T, Azumi Y, Hayakawa S, Kamiya A, Imura Y, Wada T,
Shinozaki K, "Homologous chromosome pairing is completed
in crossover defective atzip4 mutant" Biochemical and Biophysical Research Communications 370 98-103 (2008)

482

495

Hirai MY, "A robust omics-based approach for the identification of glucosinolate biosynthetic genes" Phytochemistry Reviews 8 15-23 (2008)

Magome H, Yamaguchi S, Hanada A, Kamiya Y, Oda K, "TheDDF1 transcriptional activator upregulates expression of agibberellin-deactivating gene, GA2ox7, under high-salinity
stress in Arabidopsis" The Plant Journal 56 613-626 (2008)

483

Hirai MY, Saito K, "Analysis of systemic sulfur metabolism inplants using integrated '-omics' strategies" Molecular BioSystems 4 967-973 (2008)

496

484

Hirano K, Aya K, Hobo T, Sakakibara H, Kojima M, Shim R,
Hasegawa Y, Ueguchi-Tanaka M, Matsuoka M, "Comprehensive transcriptome analysis of phytohormone biosynthesis andsignaling genes in microspore/pollen and tapetum of rice"
Plant Cell Physiology 49 1429-1450 (2008)

Matsui A, Ishida J, Morosawa T, Mochizuki Y, Kaminuma E,
Endo T, Okamoto M, Nambara E, Nakjima M, Kawashima M,
Satou M, Kim J, Kobayashi N, Toyoda T, Shinozaki K, Seki M, "Arabidopsis transcriptome analysis under drought, cold, highsalinity and ABA treatment conditions using a tiling array"
Plant Cell Physiology 49 1135-1149 (2008)

497

Matsuya A, Hanada K, Itoh T, "Evola: Ortholog database of all
human genes in H-InvDB with manual curation of phylogenetic trees" Nucleic Acids Research 36 D787-D792 (2008)

498

Mayama T, Nakano M, Uehara Y, Sano M, Fujisawa N, Okada
K, Sakai T, "Mapping of the phosphorylation sites on the phototropic signal transducer, NPH3" Plant Science 174 626-633(2008)

499

Mochida K, Saisho D, Yoshida T, Sakurai T, Shinozaki K,"TriMEDB: A database to integrate transcribed markers andfacilitate genetic studies of the tribe Triticeae" BMC Plant Biology 8 1-8 (2008)

500

Motose H, Tominaga R, Wada T, Sugiyama M, Watanabe Y, "A
NIMA-related protein kinase suppresses ectopic outgrowth of
epidermal cells through its kinase activity and the association
with microtubules" The Plant Journal 54 829-844 (2008)

501

Myouga F, Hosoda C, Umezawa T, Iizumi H, Kuromori T, Motohashi R, Shono Y, Nagata N, Ikeuchi M, Shinozaki K, "A heterocomplex of iron superoxide dismutases defends chloroplast
nucleoids against oxidative stress and is essential for chloroplast development in Arabidopsis" The Plant Cell 20 3148-

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Nobusada T, Hayashi M, Fukazawa M, Sakakibara H, Nishimura M, "A putative peroxisomal polyamine oxidase, AtPAO4,
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Ogata Y, Suzuki H, Sakurai N, Aoki K, Saito K, Shibata D,"Cryopreservation and metabolic profiling analysis of Arabidopsis T87 suspension-cultured cells" CryoLetters 29 427-436(2008)
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Oikawa A, Matsuda F, Kusano M, Okazaki Y, Saito K, "RiceMetabolomics" Rice 1 63-71 (2008)
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Sakakibara K, Tohge T, Matsuda F, Nakabayashi R, Takayama H,
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Seki H, Ohyama K, Sawai S, Mizutani M, Ohnishi T, Sudo H,
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Sirikantaramas S, Yamazaki M, Saito K, "Mutations in topoisomerase I as a self-resistance mechanism coevolved with the
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Sudo E, Itouga M, Yoshida K, Ono Y, Sakakibara H, "Geneexpression and sensitivity in response to copper stress in rice
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Sugawara H, Ueda N, Kojima M, Makita N, Yamaya T, Sakakibara H, "Structural insight into the reaction mechanism andevolution of cytokinin biosynthesis" Proceedings of the National Academy of Sciences of the United States of America
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Wangwattana B, Koyama Y, Nishiyama Y, Kitayama M,
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Watanabe M, Kusano M, Oikawa A, Fukushima A, Noji M,
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Watanabe M, Mochida K, Kato T, Tabata S, Yoshimoto N, Noji
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Yamaguchi M, Kubo M, Fukuda H, Demura T, "VASCULARRELATED NAC-DOMAIN7 is involved in the differentiation of
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Yamazaki M, Shibata M, Nishiyama Y, Springob K, Kitayama
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Yokotani N, Ichikawa T, Kondou Y, Matsui M, Hirochika H,
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Zhang M, Boter M, Li K, Kadota Y, Panaretou B, Prodromou
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Albinsky D, Kusano M, Higuchi M, Hayashi N, Kobayashi M,
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Fukushima A, Kanaya S, Arita M, "Characterizing gene coexpression modules in Oryza sativa based on a graph-clustering
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Fukushima A, Kusano M, Nakamichi N, Kobayashi M, Hayashi
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Hasegawa Y, Arita M, "Properties of the maximum q-likelihood estimator for independent random variables" Physica A
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Higuchi M, Ozaki H, Matsui M, Sonoike K, "A T-DNA insertion
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Igawa T, Fujiwara M, Takahashi H, Sawasaki T, Endo Y, Seki M,
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Journal of Experimental Botany 60 3067-3073 (2009)
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Ishida T, Fujiwara S, Miura K, Stacey N, Yoshimura M, Schneider K, Adachi S, Minamisawa K, Umeda M, Sugimoto K,"SUMO E3 Ligase HIGH PLOIDY2 Regulates Endocycle Onsetand Meristem Maintenance in Arabidopsis" The Plant Cell 212284-2297 (2009)
Ito-Inaba Y, Sato M, Masuko H, Hida Y, Toyooka K, Watanabe
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Kawakatsu T, Taramino G, Itoh J, Allen J, Sato Y, Hong S, Yule
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Kuromori T, Takahashi S, Kondou Y, Shinozaki K, Matsui M,"Phenome analysis in plant species using loss-of-function andgain-of-function mutants" Plant and Cell Physiology 50 12151231 (2009)576

Lee B, Johnston R, Yang Y, Gallavotti A, Kojima M, Travencolo B, Costa L, Sakakibara H, David J, "Studies of aberrant
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Lehti-Shiu M, Cheng Z, Hanada K, Shiu S, "Evolutionary History and Stress Regulation of Plant Receptor-Like Kinase/Pelle
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Maruyama K, Takeda M, Kidokoro S, Yamada K, Sakuma Y,
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Mochida K, Yoshida T, Sakurai T, Yamaguchi-Shinozaki K, Shinozaki K, Tran L-SP, "In silico analysis of transcription factor
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Morioka R, Arita M, Sakamoto K, Kawaguchi S, Tei H, Horimoto K, "Period-phase map: two-dimensional selection of circadian rhythm-related genes" IET System Biology 3 487-495(2009)

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Mugford S, Yoshimoto N, Reichelt M, Wirtz M, Hill L, Mugford
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Nakabayashi R, Kusano M, Kobayashi M, Tohge T, Sakakibara
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Nakamichi N, Fukushima A, Kusano M, Sakakibara H, Takeshi
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592

Nakamichi N, Kusano M, Fukushima A, Kita M, Ito S, Yamashino T, Saito K, Sakakibara H, Mizuno T, "Transcript profiling ofan Arabidopsis PSEUDO RESPONSE REGULATOR arrhythmic
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Nakashima K, Fujita Y, Kanamori N, Katagiri T, Umezawa T,
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Nambara E, Yamagishi K, Tatematsu K, Nakabayashi K, Kamiya Y, "Nitrate responses of Arabidopsis cho1 mutants: Obvious
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Matsuda F, Hirai MY, Sasaki E, Akiyama K, Sakakibara K, Provart N, Sakurai T, Saito K, "AtMetExpress Development: A
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580

Matsuda F, Redestig H, Sawada Y, Shinbo Y, Hirai MY, Kanaya S,
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Matsuda F, Sakakibara K, Niida R, Kuromori T, Shinozaki K,
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Kondou Y, Higuchi M, Takahashi S, Sakurai T, Ichikawa T,
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Hasegawa Y, Kuriyama T, Matsui K, Kusano M, Albinsky D,
Takahashi H, Tsuchiya Y, Suzuki M, Sakakibara H, Kojima M,
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Matsuda F, Shinbo Y, Oikawa A, Hirai MY, Fiehn O, Kanaya S,
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Matsukura K, Matsumura M, Takeuchi H, Endo N, Tokuda
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Narusaka M, Shirasu K, Noutoshi Y, Kubo Y, Shiraishi T, Iwabuchi M, Narusaka Y, "RRS1 and RPS4 provide a dual Resistance-gene system against fungal and bacterial pathogens" The
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Kurasawa K, Matsui A, Yokoyama R, Kuriyama T, Yoshizumi T,
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Matsukura K, Matsumura M, Tokuda M, "Host manipulationby the orange leafhopper Cicadulina bipunctata: gall induction on distant leaves by dose-dependent stimulation" Naturwissenschaften 96 1059-1066 (2009)

Nemoto K, Hara M, Goto S, Kasai K, Seki H, Suzuki M, Oka
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Nemoto K, Hara M, Suzuki M, Seki H, Muranaka T, Mano Y,"The NtAMI1 gene functions in cell division of tobacco BY-2
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Nobusada T, Sakakibara H, "Molecular basis for cytokinin biosynthesis" Phytochemistry 70 444-449 (2009)599

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Y, Saito K, Takahashi H, Dalmay T, "Sulphur starvation induces
the expression of microRNA-395 and one of its target genes
but in different cell types" The Plant Journal 57 313-321 (2009)
Kidokoro S, Maruyama K, Nakashima K, Imura Y, Narusaka Y,
Shinwari Z, Osakabe Y, Fujita Y, Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K, "The phytochrome-interacting factor PIF7
negatively regulates DREB1 expression under circadian control
in Arabidopsis" Plant Physiology 151 2046-2057 (2009)

Kurihara Y, Kaminuma E, Matsui A, Kawashima M, Tanaka
M, Morosawa T, Ishida J, Mochizuki Y, Shinozaki K, Toyoda T,
Seki M, "Transcriptome analyses revealed diverse expression
changes in ago1 and hyl1 Arabidopsis mutants" Plant and Cell
Physiology 50 1715-1720 (2009)
Kurihara Y, Matsui A, Hanada K, Kawashima M, Ishida J, Mo-

585

Mochida K, Furuta T, Ebana K, Shinozaki K, Kikuchi J, "Correlation exploration of metabolic and genomic diversity in rice"
BMC Genomics 10 1-10 (2009)

586

Mochida K, Yoshida T, Sakurai T, Ogihara Y, Shinozaki K, "TriFLDB: A database of clustered full-length coding sequencesfrom triticeae with applications to comparative grass genomics" Plant Physiology 150 1135-1146 (2009)

PSC Publications 2000 – 2012library of Arabidopsis transcription factors using a wheat cellfree protein production system and its application for DNA
binding analysis" Bioscience Biotechnology and Biochemistry
73 1661-1664 (2009)

600

Ogata Y, Sakurai N, Aoki K, Suzuki H, Okazaki K, Saito K,
Shibata D, "KAGIANA: An Excel-based tool for retrieving summary information on Arabidopsis genes" Plant Cell Physiology
50 173-177 (2009)

601

Oh E, Kang H, Yamaguchi S, Park J, Lee D, Kamiya Y, Choi G,"Genome-wide analysis of genes targeted by PHYTOCHROME
INTERACTING FACTOR 3-LIKE5 during seed germination in
Arabidopsis" The Plant Cell 201 403-419 (2009)

602

Ohyama K, Suzuki M, Kikuchi J, Saito K, Muranaka T, "Dualbiosynthetic pathways to phytosterol via cycloartenol and lanosterol in Arabidopsis" PNAS 106 725-730 (2009)

603

604

Okamoto M, Hanada A, Kamiya Y, Yamaguchi S, Nambara E,"Measurement of Abscisic Acid and Gibberellins by Gas Chromatography/Mass Spectrometry" Methods in Molecular Biology 495 53-60 (2009)
Okamoto M, Tanaka Y, Abrams S, Kamiya Y, Seki M, Nambara E,"High humidity induces abscisic acid 8'-hydroxylase in stomata
and vasculature to regulate local and systemic abscisic acidresponses in Arabidopsis" Plant Physiology 149 825-834 (2009)

605

Okamoto M, Tsuboi Y, Chikayama E, Kikuchi J, Hirayama T,"Metabolic movement upon abscisic acid and salicylic acidcombined treatments" Plant Biotechnology 26 551-560 (2009)

606

Okazaki Y, Shimojima M, Sawada Y, Toyooka K, Narisawa T,
Mochida K, Tanaka H, Matsuda F, Hirai A, Hirai MY, Ohta H,
Saito K, "A Chloroplastic UDP-Glucose Pyrophosphorylasefrom Arabidopsis Is the Committed Enzyme for the First Stepof Sulfolipid Biosynthesis" The Plant Cell 21 892-909 (2009)

607

608

609

610

611

Okuda K, Chateigner-Boutin A, Nakamura T, Delannoy E, Sugita M, Myouga F, Motohashi R, Shinozaki K, Small I, Shikanai T,"Pentatricopeptide repeat proteins with the DYW motif havedistinct molecular functions in RNA editing and RNA cleavage
in Arabidopsis chloroplasts" The Plant Cell 21 146-156 (2009)
Orlova I, Nagegowda D, Kish C, Gutensohn M, Maeda H,
Varbanova M, Fridman E, Krichevsky A, Yamaguchi S, Hanada
A, Kamiya Y, Citovsky V, Pichersky E, Dudareva N, "The small
subunit of snapdragon geranyl diphosphate synthase modifies
the chain length specificity of tobacco geranylgeranyl diphosphate synthase in planta" The Plant Cell 21 4002-4017 (2009)
Preston J, Tatematsu K, Kanno Y, Hobo T, Kimura M, Jikumaru
Y, Yano R, Kamiya Y, Nambara E, "Temporal expression patterns of hormone metabolism genes during imbibition of Arabidopsis thaliana seeds: a comparative study on dormant andnon-dormant accessions" Plant and Cell Physiology 50 17861800 (2009)
Redestig H, Fukushima A, Stenlund H, Moritz T, Arita M, Saito
K, Kusano M, "Compensation for systematic cross-contribution
improves normalization of mass spectrometry based metabolomics data" Analytical Chemistry 81 7974-7980 (2009)
Rubin G, Tohge T, Matsuda F, Saito K, Scheible W, "Membersof the LBD Family of Transcription Factors Repress Anthocyanin Synthesis and Affect Additional Nitrogen Responses in

The coevolution of the camptothecin biosynthetic pathway
and self-resistance mechanism" Phytochemistry 70 1894-1898(2009)

Arabidopsis" The Plant Cell 21 3567-3584 (2009)

612

Sakakibara K, "Functional genomics of family 1 glycosyltransferases in Arabidopsis" Plant Biotechnology 26 267-274 (2009)

613

Sakakibara K, Saito K, "Functional genomics for plant natural
product biosynthesis" Natural Product Reports 26 1466-1487(2009)

614

Sato A, Sato Y, Fukao Y, Fujiwara M, Umezawa T, Shinozaki K,
Hibi T, Taniguchi M, Miyake H, Goto D, Uozumi N, "Threonine
at position 306 of the KAT1 potassium channel is essential forchannel activity and is a target site for ABA-activated SnRK2/
OST1/SnRK2.6 protein kinase" Biochemical Journal 424 439448 (2009)

615

Sato K, Shin-l T, Seki M, Shinozaki K, Yoshida H, Takeda K,
Yamazaki Y, Conte M, Kohara Y, "Development of 5006 fulllength cDNAs in barley: A tool for accessing cereal genomics
resources" DNA Research 16 81-89 (2009)

616

Sato M, Mogi Y, Nishikawa T, Miyamura S, Nagumo T, Kawano
S, "The dynamic surface of dividing cyanelles and ultrastructure of the region directly below the surface in Cyanophoraparadoxa" Planta 229 781-791 (2009)

617

618

619

620

Tsutsui T, Kato W, Asada Y, Sako K, Sato T, Sonoda Y, Kidokoro
S, Yamaguchi-Shinozaki K, Tamaoki M, Arakawa K, Ichikawa T,
Nakazawa M, Seki M, Shinozaki K, Matsui M, Ikeda A, Yamaguchi J, "DEAR1, a transcriptional repressor of DREB proteinthat mediates plant defense and freezing stress responses in
Arabidopsis" Journal of Plant Research 122 633-643 (2009)

629

Suzuki M, Nakagawa S, Kamide Y, Kobayashi K, Ohyama K,
Hashinokuchi H, Kiuchi R, Saito K, Muranaka T, Nagata N,"Complete blockage of the mevalonate pathway results inmale gametophyte lethality" Journal of Experimental Botany
60 2055-2064 (2009)

642

Takahashi H, kawazoe M, Wada M, Hirai A, Nakamura K, Md.
Altaf-Ul A, Sawada Y, Hirai MY, Kanaya S, "KNApSAcK geneclassification system for Arabidopsis thaliana: Comparative
genomic analysis of unicellular to seed plants" Plant Biotechnology 26 509-516 (2009)

Uchida H, Yamashita H, Kajiwara M, Ohyama K, Nakayachi O,
Sugiyama R, Yamato K, Muranaka T, Fukuzawa H, Takemura
M, Ohyama K, "Cloning and characterization of a squalene
synthase gene from a petroleum plant, Euphorbia tirucalli L."
Planta 229 1243-1252 (2009)643

Umezawa T, Sugiyama N, Mizoguchi M, Hayashi S, Myouga F,
Yamaguchi-Shinozaki K, Ishihama Y, Hirayama T, Shinozaki K,"Type 2C protein phosphatases directly regulate abscisic acidactivated protein kinases in Arabidopsis" Proceedings of the
National Academy of Sciences of the United States of America
106 17588-17593 (2009)644

Urano K, Maruyama K, Ogata Y, Morishita Y, Takeda M, Sakurai N, Suzuki H, Saito K, Shibata D, Kobayashi M, YamaguchiShinozaki K, Shinozaki K, "Characterization of the ABAregulated global responses to dehydration in Arabidopsis bymetabolomics" The Plant Journal 57 1065-1078 (2009)645

Yamamoto Y, Yoshitsugu T, Sakurai T, Seki M, Shinozaki K,
Obokata J, "Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis" The Plant Journal 60 350362 (2009)

646

Yano R, Kanno Y, Jikumaru Y, Nakabayashi K, Kamiya Y,
Nambara E, "CHOTTO1, a putative double APETALA2 repeat
transcription factor, is involved in abscisic acid-mediated repression of gibberellin biosynthesis during seed germinationin Arabidopsis" Plant Physiology 151 641-654 (2009)647

Yokotani N, Ichikawa T, Kondou Y, Matsui M, Hirochika H,
Iwabuchi M, Oda K, "Overexpression of a rice gene encoding a small C2 domain protein OsSMCP1 increases tolerance
to abiotic and biotic stresses in transgenic Arabidopsis" Plant
Molecular Biology 71 391-402 (2009)648

Yoshida S, Shirasu K, "Multiple layers of incompatibility to theparasitic witchweed, Striga hermonthica" New Phytologist
183 180-189 (2009)649

Yoshida Y, Sano R, Wada T, Takabayashi J, Okada K, "Jasmonicacid control of GLABRA3 links inducible defense and trichome
patterning in Arabidopsis" Development 136 1039-1048(2009)

631

Takahashi H, Nozawa A, Seki M, Shinozaki K, Endo Y, Sawasaki T, "A simple and high-sensitivity method for analysis ofubiquitination and polyubiquitination based on wheat cellfree protein synthesis" BMC Plant Biology 9 1-11 (2009)

632

Takemoto K, Arita M, "Heterogeneous distribution of metabolites across plant species" Physica A 388 2771-2780 (2009)

633

Takeuchi M, Kawahata H, Gupta L, Itouga M, Sakakibara H,
Ohta H, Komai T, Ono Y, "Chemistry of fly ash and cyclone ash
leachate from waste materials and effects of ash leachates onbacterial growth, nitrogen-transformation activity, and metal
accumulation" Jounal of Hazardous Materials 165 967-973(2009)

634

Titapiwatanakun B, Blakeslee J, Bandyopadhyay A, Yang H,
Mravec J, Sauer M, Cheng Y, Adamec J, Nagashima A, Geisler
M, Sakai T, Friml J, Peer W, Murphy A, "ABCB19/PGP19 stabilises PIN1 in membrane microdomains in Arabidopsis" The Plant
Journal 57 27-44 (2009)

Shinozaki K, Sakakibara H, "Omics and bioinformatics: an essential toolbox for systems analyses of plant functions beyond2010" Plant and Cell Physiology 50 1177-1180 (2009)635

Shirasu K, "The HSP90-SGT1 Chaperone Complex for NLR Immune Sensors" Annual Review of Plant Biology 60 139-164(2009)

Tojo T, Tsuda K, Yoshizumi T, Ikeda A, Yamaguchi J, Matsui M,
Yamazaki K, "Arabidopsis MBF1s control leaf cell cycle and its
expansion" Plant Cell Physiology 50 254-264 (2009)

636

Tominaga R, Iwata M, Sugiyama J, Kotake T, Ishida T, Yokoyama R, Nishitani K, Okada K, Wada T, "The GLABRA2 homeodomain protein directly regulates CESA5 and XTH17 gene
expression in Arabidopsis roots" The Plant Journal 60 564-574(2009)

Sirikantaramas S, Yamazaki M, Saito K, "A survival strategy:

641

Sugita M, Nakano K, Sato M, Toyooka K, Numata O, "Theroles of actin cytoskeleton and microtubules for membrane
recycling of a food vacuole in Tetrahymena thermophila" Cell
Motility and the Cytoskeleton 66 371-377 (2009)

622

625

Tsunekawa K, Shijuku T, Hayashimoto M, Kojima Y, Onai K,
Morishita M, Ishiura M, Kuroda T, Nakamura T, Kobayashi H,
Sato M, Toyooka K, Matsuoka K, Omata T, Uozumi N, "Identification and characterization of the NA+/H+ antiporter NHAS3
from the thylakoid membrane of Synechocystis sp. PCC 6803"
The Journal of Biological Chemistry 284 16513-16521 (2009)

628

Sawada Y, Kuwahara A, Nagano M, Narisawa T, Sakata A,
Saito K, Hirai MY, "Omics-based approaches to methionine
side chain elongation in Arabidopsis: characterization of thegenes encoding methylthioalkylmalate isomerase and methylthioalkylmalate dehydrogenase" Plant Cell Physiology 50
1181-1190 (2009)

Shoji T, Inai K, Yazaki Y, Sato Y, Takase H, Shitan N, Yazaki K,
Goto Y, Toyooka K, Matsuoka K, Hashimoto T, "Multidrug
and Toxic Compound Extrusion-Type Transporters Implicatedin Vacuolar Sequestration of Nicotine in Tobacco Roots" Plant
Physiology 149 708-718 (2009)

640

Sugawara S, Hishiyama S, Jikumaru Y, Hanada A, Nishimura T,
Koshiba T, Zhao Y, Kamiya Y, Kasahara H, "Biochemical analyses of indole-3-acetaldoxime-dependent auxin biosynthesis
in Arabidopsis" Proceedings of the National Academy of Sciences of the United States of America 106 5430-5435 (2009)

Seki M, Shinozaki K, "Functional genomics using RIKEN Arabidopsis thaliana full-length cDNAs" Journal of Plant Research
122 355-366 (2009)624

Tran LS, Quach TN, Guttikonda SK, Aldrich DL, Kumar R,
Neelakandan A, Valliyodan B, Nguyen HT, "Molecular characterization of stress-inducible GmNAC genes in soybean"
Molecular Genetics and Genomics 281 647-664 (2009)

627

621

623

639

Sudo H, Seki H, Sakurai N, Suzuki H, Shibata D, Toyoda A,
Totoki Y, Sakaki Y, Iida O, Shibata T, Kojima M, Muranaka T,
Saito K, "Expressed sequence tags from rhizomes of Glycyrrhiza uralensis" Plant Biotechnology 26 105-107 (2009)

630

Seki M, Kamiya A, Carninci P, Hayashizaki Y, Shinozaki K,"Generation of full-length cDNA libraries: focus on plants"
Methods in Molecular Biology 533 49-68 (2009)

Toyooka K, Matsuoka K, "Exo- and endocytotic trafficking of
SCAMP2" Plant Signaling & Behavior 4 1196-1198 (2009)

626

Sawada Y, Akiyama K, Sakata A, Kuwahara A, Otsuki H, Sakurai T, Saito K, Hirai MY, "Widely Targeted Metabolomics Basedon Large-Scale MS/MS Data for Elucidating Metabolite Accumulation Patterns in Plants" Plant and Cell Physiology 50 3747 (2009)

Sawada Y, Toyooka K, Kuwahara A, Sakata A, Nagano M,
Saito K, Hirai MY, "Arabidopsis Bile Acid:Sodium Symporter
Family Protein 5 Is Involved in Methionine-derived Glucosinolate Biosynthesis" Plant Cell Physiology 50 1579-1586 (2009)

638

637

Toyooka K, Goto Y, Asatsuma S, Koizumi M, Mitsui T, Matsuoka K, "A mobile secretory vesicle cluster involved in masstransport from the Golgi to the plant cell exterior" The Plant
Cell 21 1212-1229 (2009)

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651

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661

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Yoshimoto K, Jikumaru Y, Kamiya Y, Kusano M, Consonni. C,
Panstruga. R, Ohsumi. Y, Shirasu K, "Autophagy negatively
regulates cell death by controlling NPR1-dependent salicylic
acid signaling during senescence and the innate immune response in Arabidopsis" The Plant Cell 21 2914-2927 (2009)ster G, Inze D, "Increased leaf size: Different means to an end"
Plant Physiology 153 1261-1279 (2010)

663

Gutierrez-Gonzalez JJ, Guttikonda SK, Tran LS, Aldrich DL,
Zhong R, Yu O, Nguyen HT, Sleper DA, "Differential Expressionof Isoflavone Biosynthetic Genes in Soybean During Water
Deficits" Plant and Cell Physiology 51 936-948 (2010)

664

Hadiarto T, Tran LS, "Progress studies of drought-responsive
genes in rice" Plant Cell Reports 30 297-310 (2010)

Zourelidou M, Muller I, Willige B, Nill C, Jikumaru Y, Li H,
Schwechheimer C, "The polarly localized D6 PROTEIN KINASE
is required for efficient auxin transport in Arabidopsis thaliana" Development 136 627-636 (2009)

665

Hanada K, Akiyama K, Sakurai T, Toyoda T, Shinozaki K, Shiu S,"sORF finder: a program package to identify small open reading frames (sORFs) with high coding potential" Bioinformatics
26 399-400 (2010)

Albinsky D, Sawada Y, Kuwahara A, Nagano M, Hirai A, Saito
K, Hirai MY, "Widely targeted metabolomics and coexpression analysis as tools to identify genes involved in the sidechain elongation steps of aliphatic glucosinolate biosynthesis"
Amino Acids 39 1067-1075 (2010)

666

Yuan L, Graff L, Loque D, Kojima S, Tsuchiya Y, Takahashi H,
von Wiren N, "AtAMT1;4, a Pollen-Specific High-Affinity Ammonium Transporter of the Plasma Membrane in Arabidopsis"
Plant Cell Physiology 50 13-25 (2009)

Ayele B, Magnus V, Mihaljevic S, Prebeg T, Coz-Rakovac R,
Ozga J, Reinecke D, Mander L, Kamiya Y, Yamaguchi S, Salopek-Sondi B, "Endogenous gibberellin profile during Christmas rose (Helleborus niger L.) flower and fruit development"
Journal of Plant Growth Regulation 29 194-209 (2010)
Baek D, Pathange P, Chung JS, Jiang J, Gao L, Oikawa A, Hirai
MY, Saito K, Pare PW, Shi H, "A stress-inducible sulphotransferase sulphonates salicylic acid and confers pathogen resistance in Arabidopsis" Plant, Cell and Environment 33 13831392 (2010)
Bidadi H, Yamaguchi S, Asahina M, Satoh S, "Effects of shootapplied gibberellin/gibberellin-biosynthesis inhibitors on root
growth and expression of gibberellin biosynthesis genes in
Arabidopsis thaliana" Plant Root 4 4-11 (2010)
Chikayama E, Kurotani A, Tanaka T, Yabuki T, Miyazaki S, Yokoyama S, Kuroda Y, "Mathematical Model for Empirically Optimizing Large Scale Production of Soluble Protein Domains"
BMC Bioinformatics 11 1-9 (2010)

667

668

669

670

671

Chikayama E, Sekiyama Y, Okamoto M, Nakanishi Y, Tsuboi Y,
Akiyama K, Saito K, Shinozaki K, Kikuchi J, "Statistical indicesfor simultaneous large-scale metabolite detections for a single
NMR spectrum" Analytical Chemistry 82 1653-1658 (2010)
Choi J, Huh S, Kojima M, Sakakibara H, Paek K, Hwang I, "Thecytokinin-activated transcription factor ARR2 promotes plant
immunity via TGA3/NPR1-dependent salicylic acid signaling in
Arabidopsis" Developmental Cell 19 284-295 (2010)

672

Date Y, Nakanishi Y, Fukuda S, Kato T, Tsuneda S, Ohno H,
Kikuchi J, "New monitoring approach for metabolic dynamics
in microbial ecosystems using stable-isotope-labeling technologies" Journal of Bioscience and Bioengineering 110 87-93(2010)

673

Fukazawa J, Nakata M, Ito T, Yamaguchi S, Takahashi Y, "Thetranscription factor RSG regulates negative feedback of NtGA20ox1 encoding GA 20-oxidase" The Plant Journal 62 10351045 (2010)
Gonzalez N, De Bodt S, Sulpice R, Jikumaru Y, Chae E, Dhondt
S, Van Daele T, De Milde L, Weigel D, Kamiya Y, Stitt M, Beem-

674

675

Hasegawa Y, Arita M, "Bistable Stochastic Processes in the q-Exponential Family" Physica A 389 4450-4461 (2010)
Hirai MY, Sawada Y, Kanaya S, Kuromori T, Kobayashi M,
Klausnitzer R, Hanada K, Akiyama K, Sakurai T, Saito K, Shinozaki K, "Toward genome-wide metabolotyping and elucidation of metabolic system: metabolic profiling of large-scalebioresources" Journal of Plant Research 123 291-298 (2010)
Hirai T, Sato M, Toyooka K, Sun H, Yano m, Ezura H, "Miraculin, a taste-modifying protein is secreted into intercellularspaces in plant cells" Journal of Plant Physiology 167 209-215(2010)
Hirayama T, Shinozaki K, "Research on plant abiotic stressresponses in the post-genome era: past, present and future"
The Plant Journal 61 1041-1052 (2010)
Horai H, Arita M, Kanaya S, Nihei Y, Ikeda T, Suwa K, Ojima Y,
Tanaka K, Tanaka S, Aoshima K, Oda Y, Kakazu Y, Kusano M,
Tohge T, Matsuda F, Sawada Y, Hirai MY, Nakanishi H, Ikeda K,
Akimoto N, Maoka T, Takahashi H, Ara T, Sakurai N, Suzuki H,
Shibata D, Neumann S, Iida T, Tanaka K, Funatsu K, Matsuura
F, Soga T, Taguchi R, Saito K, Nishioka T, "MassBank: a public
repository for sharing mass spectral data for life sciences"
Journal of Mass Spectrometry 45 703-714 (2010)
Hu Z, Yan H, Yang J, Yamaguchi S, Maekawa M, Takamure I,
Tsutsumi N, Kyozuka J, Nakazono M, "Strigolactones negatively regulate mesocotyl elongation in rice during germination and growth in darkness" Plant Cell Physiology 51 11361142 (2010)
Ishida T, Adachi S, Yoshimura M, Shimizu K, Umeda M, Sugimoto K, "Auxin modulates the transition from the mitotic
cycle to the endocycle in Arabidopsis" Development 137 6371 (2010)
Ishii T, Soeno K, Asami T, Fujioka S, Shimada Y, "Arabidopsis
seedlings Over-Accumulated Indole-3-acetic acid in response
to Aminooxyacetic acid" Bioscience Biotechnology and Biochemistry 74 2345-2347 (2010)
Ito S, Kitahata N, Umehara M, Hanada A, Kato A, Ueno K,
Mashiguchi K, Kyozuka J, Yoneyama K, Yamaguchi S, Asami
T, "A new lead chemical for strigolactone biosynthesis inhibitors" Plant and Cell Physiology 51 1143-1150 (2010)
Ito T, Nakata M, Fukazawa J, Ishida S, Takahashi Y, "Alterationof Substrate Specificity: The Variable N-Terminal Domain of
Tobacco Ca2+-Dependent Protein Kinase Is Important for Sub-strate Recognition" The Plant Cell 22 1592-1604 (2010)

3280-3294 (2010)

676

Jiang C, Shimono M, Sugano S, Kojima M, Yazawa K, Yoshida
R, Inoue H, Hayashi N, Sakakibara H, Takatsuji H, "Abscisic acidinteracts antagonistically with salicylic acid signaling pathway
in rice-magnaporthe grisea interaction" Molecular PlantMicrobe Interactions 23 791-798 (2010)

689

Kusano M, Fukushima A, Redestig H, Kobayashi M, Otsuki H,
Onouchi H, Naito S, Hirai MY, Saito K, "Comparative metabolomics charts the impact of genotype-dependent methionine
accumulation in Arabidopsis thaliana" Amino Acids 39 10131021 (2010)

677

Kadota Y, Shirasu K, Guerois R, "NLR sensors meet at the
SGT1-HSP90 crossroad" Trends in Biochemical Sciences 35 199207 (2010)

690

678

Kanno Y, Jikumaru Y, Hanada A, Nambara E, Abrams S, Kamiya Y, Seo M, "Comprehensive hormone profiling in developing arabidopsis seeds: examination of the site of ABA biosynthesis, ABA transport and hormone interactions" Plant andCell Physiology 51 1988-2001 (2010)

Kwon S, Joo Cho H, Hee Jung J, Yoshimoto K, Shirasu K, Prk O,"The Rab GTPase RabG3b functions in autophagy and contributes to tracheary element differentiation in Arabidopsis" The
Plant Journal 64 151-164 (2010)

691

Le DT, Choi JD, Tran LS, "Amino acids conferring herbicide
resistance in tobacco acetohydroxyacid synthase" GM Crops 1
62-67 (2010)

692

Le DT, Netsu O, Uehara-Ichiki T, Shimizu T, Choi I, Omura T, Sasaya T, "Molecular detection of nine rice viruses by a reversetranscription loop-mediated isothermal amplification assay"
Journal of Virological Methods 170 90-93 (2010)

693

Lee G, Jeon E, Kim W, Le DT, Yoo J, Chong C, "Evaluation of a
rapid diagnostic test, NanoSign® Influenza A/B Antigen, fordetection of the 2009 pandemic influenza A/H1N1 viruses"
Virology Journal 7 244 (2010)

694

Lohmann D, Stacey N, Breuninger H, Jikumaru Y, Muller D,
Sicard A, Leyser O, Yamaguchi S, Lenhard M, "SLOW MOTION
is required for within-plant auxin homeostasis and normal
timing of lateral organ initiation at the shoot meristem in
Arabidopsis" The Plant Cell 22 335-348 (2010)

695

Mano Y, Nemoto K, Suzuki M, Seki H, Fujii I, Muranaka T, "TheAMI1 gene family: Indole-3-acetamide hydrolase functions in
auxin biosynthesis in plants" Journal of Experimental Botany
61 25-32 (2010)

696

Maruyama A, Hirai MY, Funada S, Fueki S, "Exogenous application of 5-aminolevulinic acid increases the transcript levelsof sulfur transport and assimilatory genes, sulfate uptake, andcysteine and glutathione contents in Arabidopsis thaliana"
Soil Science and Plant Nutrition 56 281-288 (2010)

697

Masumoto C, Miyazawa S, Ohkawa H, Fukuda T, Taniguchi
Y, Murayama S, Kusano M, Saito K, Fukayama H, Miyao M,"Phosphoenolpyruvate carboxylase intrinsically located in thechloroplast of rice plays a crucial role in ammonium assimilation" Proceedings of the National Academy of Sciences of theUnited States of America 107 5226-5231 (2010)

698

Matsui A, Ishida J, Morosawa T, Okamoto M, Kim J, Kurihara Y,
Kawashima M, Tanaka M, To T, Nakaminami K, Kaminuma E,
Endo T, Mochizuki Y, Kawaguchi S, Kobayashi N, Shinozaki K,
Toyoda T, Seki M, "Arabidopsis tiling array analysis to identify
the stress-responsive genes" Methods in Molecular Biology
639 141-155 (2010)

699

Matsukura S, Mizoi J, Yoshida T, Todaka D, Ito Y, Maruyama
K, Shinozaki K, Shinozaki K, "Comprehensive analysis of rice
DREB2-type genes that encode transcription factors involvedin the expression of abiotic stress-responsive genes" Molecular
Genetics and Genomics 283 185-196 (2010)

700

Minakuchi K, Kameoka H, Yasuno N, Umehara M, Le L, Kobayashi K, Hanada A, Ueno K, Asami T, Yamaguchi S, Kyozuka
J, "FINE CULM1 (FC1) works downstream of strigolactones to679

Kasajima I, Ide Y, Hirai MY, Fujiwara T, "WRKY6 is involved in
the response to boron deficiency in Arabidopsis thaliana"
Physiologia Plantarum 139 80-92 (2010)

680

Kim J, To T, Nishioka T, Seki M, "Chromatin regulation functions in plant abiotic stress responses" Plant, Cell and Environment 33 604-611 (2010)

681

Kitamura S, Matsuda F, Tohge T, Sakakibara K, Yamazaki M,
Saito K, Narumi I, "Metabolic profiling and cytological analysis
of proanthocyanidins in immature seeds of Arabidopsis thaliana flavonoid accumulation mutants" The Plant Journal 62
549-59 (2010)

682

683

Kondou Y, Higuchi M, Matsui M, "High-throughput characterization of plant gene functions by using gain-of-function
technology" Annual review of plant biology 61 373-393 (2010)
Kozuka T, Kobayashi J, Horiguchi G, Demura T, Sakakibara
H, Tsukaya H, Nagatani A, "Involvement of auxin and brassinosteroid in the regulation of petiole elongation under the
shade" Plant Physiology 153 1608-1618 (2010)

684

Kudo T, Kiba T, Sakakibara H, "Metabolism and long-distancetranslocation of cytokinins" Journal of Integrative Plant Biology (Acta Botanica Sinica) 52 53-60 (2010)

685

Kuromori T, Miyaji T, Yabuuchi H, Shimizu H, Sugimoto E, Kamiya A, Moriyama Y, Shinozaki K, "ABC transporter AtABCG25
is involved in abscisic acid transport and responses" Proceedings of the National Academy of Sciences of the United Statesof America 107 2361-2366 (2010)

686

Kuromori T, Shinozaki K, "ABA transport factors found in Arabidopsis ABC transporters" Plant Signaling & Behavior 5 11241126 (2010)

687

Kurotani A, Takagi T, Toyama M, Shirouzu M, Yokoyama S, Fukami y, Tokmakov A, "Comprehensive bioinformatics analysis
of cell-free protein synthesis: identification of multiple protein properties that correlate with successful expression" The
FASEB Journal 24 1095-1104 (2010)

688

Kusano H, She K, Koizumi K, Yamakawa H, Hakata M, Imamura T, Fukuda M, Naito N, Tsurumaki Y, Yaeshima M, Tsuge T,
Matsumoto K, kudoh M, Itoh E, Kikuchi S, Kishimoto N, Yazaki
J, Ando T, Yano M, Aoyama T, Sasaki T, Satoh H, Shimada H,"A Novel Factor FLOURY ENDOSPERM2 Is Involved in Regulation of Rice Grain Size and Starch Quality" The Plant Cell 22

PSC Publications 2000 – 2012

inhibit the outgrowth of axillary buds in rice" Plant and Cell
Physiology 51 1127-1135 (2010)

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Mitsuda N, Ikeda M, Takada S, Takiguchi Y, Kondou Y, Yoshizumi T, Fujita M, Shinozaki K, Matsui M, Takagi-Ohme M,"Efficient yeast one-/two-hybrid screening using a librarycomposed only of transcription factors in Arabidopsis thaliana" Plant and Cell Physiology 51 2145-2151 (2010)
Mizoguchi M, Umezawa T, Nakashima K, Kidokoro S, Takasaki
H, Fujita Y, Shinozaki K, Shinozaki K, "Two closely related subclass II SnRK2 protein kinases cooperatively regulate droughtinducible gene expression" Plant and Cell Physiology 51 842847 (2010)
Mochida K, Yoshida T, Sakurai T, Shinozaki K, Shinozaki K,
Tran LS, "LegumeTFDB: an integrative database of Glycinemax, Lotus japonicus and Medicago truncatula transcription
factors" Bioinformatics 26 290-291 (2010)
Mosher S, Moeder W, Nishimura N, Jikumaru Y, Joo S, Urquhart W, Klessig D, Kim S, Nambara E, Yoshioka K, "The lesionmimic mutant cpr22 shows alterations in abscisic acid signaling and abscisic acid insensitivity in a salicylic acid-dependent
manner" Plant Physiology 152 1901-1913 (2010)
Myouga F, Akiyama K, Motohashi R, Kuromori T, Ito T, Iizumi
H, Ryusui R, Sakurai T, Shinozaki K, "The Chloroplast Function
Database: a large-scale collection of Arabidopsis Ds/Spm- or
T-DNA-tagged homozygous lines for nuclear-encoded chloroplast proteins, and their systematic phenotype analysis" The
Plant Journal 61 529-542 (2010)
Nakabayashi R, Yamazaki M, Saito K, "A polyhedral approachfor understanding flavonoid biosynthesis in Arabidopsis" New
Biotechnology 27 829-836 (2010)
Nakagami H, Sugiyama N, Mochida K, Daudi A, Yoshida Y,
Toyoda T, Tomita M, Ishihama Y, Shirasu K, "Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants" Plant Physiology 153 1161-1174 (2010)
Nakanishi H, Shoji R, Itouga M, Sakakibara H, "Applicationand comparison of two biotic ligand models predicting copper
toxicity and accumulation in heavy metal tolerant moss" Journal of Water and Environment Technology 8 339-345 (2010)
Nambara E, Okamoto M, Tatematsu K, Yano R, Seo M, Kamiya
Y, "Abscisic acid and the control of seed dormancy and germination" Seed Science Research 20 55-67 (2010)
Neelakandan AK, Nguyen HT, Kumar R, Tran LS, Guttikonda
SK, Quach TN, Aldrich DL, Nes WD, Nguyen HT, "Molecularcharacterization and functional analysis of Glycine max sterol
methyl transferase 2 genes involved in plant membrane sterol
biosynthesis" Plant Molecular Biology 74 503-518 (2010)

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717

Ohkama-Ohtsu N, Sekimoto Y, Oikawa A, Jikumaru Y, Shinoda
S, Inoue E, Kamide Y, Yokoyama T, Hirai MY, Shirasu K, Kamiya
Y, Oliver D, Saito K, "12-Oxo-Phytodienoic Acid-Glutathione
Conjugate is Transported into the Vacuole in Arabidopsis"
Plant and Cell Physiology 52 205-209 (2010)
Okamoto M, Tatematsu K, Matsui A, Morosawa T, Ishida J,
Tanaka M, Endo T, Mochizuki Y, Toyoda T, Kamiya Y, Shinozaki
K, Nambara E, Seki M, "Genome-wide analysis of endogenous
abscisic acid-mediated transcription in dry and imbibed seedsof Arabidopsis using tiling arrays" The Plant Journal 62 39-51(2010)O'Neill D, Davidson S, Clarke V, Yamauchi Y, Yamaguchi S, Kamiya Y, Reid J, Ross J, "Regulation of the gibberellin pathway
by auxin and DELLA proteins" Planta 232 1141-1149 (2010)
Osakabe Y, Mizuno S, Tanaka H, Maruyama K, Osakabe K,
Todaka D, Fujita Y, Kobayashi M, Shinozaki K, Shinozaki K,"Overproduction of the membrane-bound receptor-like protein kinase 1, RPK1, enhances abiotic stress tolerance in Arabidopsis" The Journal of Biological Chemistry 285 9190-9201(2010)

718

Redestig H, Kusano M, Fukushima A, Matsuda F, Saito K, Arita
M, "Consolidating metabolite identifiers to enable contextual
and multi-platform metabolomics data analysis" BMC Bioinformatics 11 214 (2010)

719

Rong J, Janson S, Ono M, Umehara M, Vrieling K, "Historical and contemporary gene dispersal in wild carrot (Daucus
carota ssp. carota) populations" Annals of Botany 106 285296 (2010)

720

Saito K, Matsuda F, "Metabolomics for functional genomics,
systems biology, and biotechnology" Annual Review of Plant
Biology 61 463-489 (2010)

721

722

723

Nishiyama R, Ishii K, Kifune E, Kazama Y, Nishihara K, Matsunaga S, Shinozaki K, Kawano S, "Sex chromosome evolution
revealed by physical mapping of SlAP3X/Y in the dioecious
plant Silene latifolia" Cytologia 75 319-325 (2010)
Nishiyama Y, Yun C, Matsuda F, Saito K, Tozawa Y, "Expressionof bacterial tyrosine ammonia-lyase creates a novel p-coumaric acid pathway in the biosynthesis of phenylpropanoids
in Arabidopsis" Planta 232 209-218 (2010)

Ogata Y, Sakurai N, Suzuki H, Aoki K, Saito K, Shibata D, "Theprediction of local modular structures in a co-expression network based on gene expression datasets" Genome Informatics 23 117-127 (2010)

724

Sasaki T, Mori I, Furuichi T, Munemasa S, Toyooka K, Matsuoka
K, Murata Y, Yamamoto Y, "Closing plant stomata requires ahomolog of an aluminum-activated malate transporter" Plant
and Cell Physiology 51 354-365 (2010)
Sato A, Toyooka K, Okamoto T, "Asymmetric cell division ofrice zygotes located in embryo sac and produced by in vitro
fertilization" Sexual Plant Reproduction 23 211-217 (2010)
Schmutz J, Cannon S, Schlueter J, Ma J, Mitros T, Nelson W,
Hyten D, Song Q, Thelen J, Cheng J, Xu D, Hellsten U, May
G, Yu Y, Sakurai T, Umezawa T, Bhattacharyya M, Sandhu D,
Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein
D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L,
Gill N, Joshi T, Libault M, Sethuraman A, Zhang X, Shinozaki K,
Nguyen H, Wing R, Cregan P, Specht J, Grimwood J, Rokhsar D,
Stacey G, Shoemaker R, Jackson S, "Genome sequence of thepalaeopolyploid soybean" Nature 463 178-183 (2010)
Sekiyama Y, Chikayama E, Kikuchi J, "Profiling polar and semipolar plant metabolites throughout extraction processes using
a combined solution-state and High-Resolution Magic Angle
Spinning NMR approach" Analytical Chemistry 82 1643-1652(2010)

725

Shinozaki K, "The ICAR201 for development of Arabidopsis
research beyond 2010" Journal of Plant Research 123 265-266(2010)

726

Singh D, Filardo F, Storey R, Jermakow A, Yamaguchi S, Swain S,"Overexpression of a gibberellin inactivation gene alters seeddevelopment, KNOX gene expression, and plant development
in Arabidopsis" Physiologia Plantarum 138 74-90 (2010)

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731

732

Son O, Hur Y, Kim Y, Lee H, Kim S, Kim M, Nam K, Lee M, Kim
B, Park J, Park J, Lee S, Hanada A, Yamaguchi S, Lee I, Kim S,
Yun D, Soderman E, Cheon C, "ATHB12, an ABA-inducible
homeodomain-leucine zipper (HD-Zip) protein of Arabidopsis,
negatively regulates the growth of the inflorescence stem bydecreasing the expression of a Gibberellin 20-oxidase gene"
Plant Cell Physiology 51 1537-1547 (2010)
Suetsugu S, Toyooka K, Senju Y, "Subcellular membrane curvature mediated by the BAR domain superfamily proteins"
Seminars in Cell & Developmental Biology 21 340-349 (2010)
Suzuki M, Kusano M, Takahashi H, Tsuchiya Y, Hayashi N, Kobayashi M, Ichikawa T, Matsui M, Hirochika H, Saito K, "RiceArabidopsis FOX line screening with FT-NIR-based fingerprinting for GC-TOF/MS-based metabolite profiling" Metabolomics
6 137-145 (2010)
Taji T, Komatsu K, Katori T, Kawasaki Y, Sakata Y, Tanaka S, Kobayashi M, Toyoda A, Seki M, Shinozaki K, "Comparative genomic analysis of 1047 completely sequenced cDNAs from an
Arabidopsis-related model halophyte, Thellungiella halophila" BMC Plant Biology 10 261 (2010)
Takahashi N, Quimbaya M, Schubert V, Lammens T, Vandepoele K, Schubert I, Matsui M, Inze D, Berx G, De Veylder L,"The MCM-binding protein ETG1 aids sister chromatid cohesion required for postreplicative homologous recombination
repair" PLoS Genetics 6 e1000817 (2010)
Takasaki H, Maruyama K, Kidokoro S, Ito Y, Fujita Y, Shinozaki
K, Shinozaki K, Nakashima K, "The abiotic stress-responsive
NAC-type transcription factor OsNAC5 regulates stress-inducible genes and stress tolerance in rice" Molecular Genetics andGenomics 284 173-183 (2010)

733

Takemoto K, Arita M, "Nested structure acquired throughsimple evolutionary process" Journal of Theoretical Biology
264 782-786 (2010)

734

Tameling W, Nooijen C, Ludwig N, Boter M, Slootweg E, Goverse A, Shirasu K, Joosten M, "RanGAP2 Mediates Nucleocytoplasmic Partitioning of the NB-LRR Immune Receptor Rx in the
Solanaceae, Thereby Dictating Rx Function" The Plant Cell 224176-4194 (2010)

735

Tanaka R, Rothbart M, Oka S, Takabayashi A, Takahashi K, Shibata M, Myouga F, Motohashi R, Shinozaki K, Grimm B, Tanaka A, "LIL3, a light-harvesting-like protein, plays an essential
role in chlorophyll and tocopherol biosynthesis" Proceedingsof the National Academy of Sciences of the United States ofAmerica 107 16721-16725 (2010)

736

Tran LS, Mochida K, "A platform for functional prediction andcomparative analyses of transcription factors of legumes andbeyond" Plant Signaling & Behavior 5 550-552 (2010)

737

Tran LS, Mochida K, "Functional genomics of soybean for im-

provement of productivity in adverse conditions" Functional& Integrative Genomics 10 447-462 (2010)

738

Tran LS, Mochida K, "Identification and prediction of abiotic
stress responsive transcription factors involved in abiotic stresssignaling in soybean" Plant Signaling & Behavior 5 1-3 (2010)

739

Tran LS, Nishiyama R, Shinozaki-Yamaguchi K, Shinozaki K,"Potential utilization of NAC transcription factors to enhance
abiotic stress tolerance in plants by biotechnological approach" GM Crops 1 1-8 (2010)

740

Tran LS, Shinozaki K, Yamaguchi-Shinozaki K, "Role of cytokinin responsive two-component system in ABA and osmotic
stress signalings" Plant Signaling & Behavior 5 1-3 (2010)

741

Trujillo M, Shirasu K, "Ubiquitination in plant immunity" Current Opinion in Plant Biology 13 402-408 (2010)

742

Tsuchiya Y, Vidaurre D, Toh S, Hanada A, Nambara E, Kamiya Y,
Yamaguchi S, McCourt P, "A small-molecule screen identifies
new functions for the plant hormone strigolactone" Nature
Chemical Biology 6 741-749 (2010)

743

Uchida H, Ohyama K, Suzuki M, Yamashita H, Muranaka T,
Ohyama K, "Triterpenoid levels are reduced during Euphorbia
tirucalli L. callus formation" Plant Biotechnology 27 105-109(2010)

744

Ueno K, Hanada A, Yamaguchi S, Asami T, "Preparation ofmultideuterated 5-deoxystrigol for use as an internal standard
for quantitative LC/MS" Journal of Labelled Compounds andRadiopharmaceuticals 53 763-766 (2010)

745

Ukaji N, Kuwabara C, Takezawa D, Seo M, Kanno Y, Arakawa K,
Fujiwara S, "Endoplasmic reticulum-localized small heat shockprotein that accumulates in mulberry tree (Morus bombycis
Koidz.) during seasonal cold acclimation is responsive to abscisic acid" Tree Physiology 30 502-513 (2010)

746

Umehara M, Hanada A, Magome H, Takeda N, Yamaguchi S,"Contribution of strigolactones to the inhibition of tiller bud
outgrowth under phosphate deficiency in rice" Plant and Cell
Physiology 51 1118-1126 (2010)

747

Umezawa T, Nakashima K, Miyakawa T, Kuromori T, Tanokura
M, Shinozaki K, Shinozaki K, "Molecular basis of the coreregulatory network in ABA responses: sensing, signaling andtransport" Plant and Cell Physiology 51 1821-1839 (2010)

748

Urano K, Kurihara Y, Seki M, Shinozaki K, "'Omics' analyses ofregulatory networks in plant abiotic stress responses" Current
Opinion in Plant Biology 13 132-138 (2010)

749

Watanabe M, Hubberten H, Saito K, Hoefgen R, "Generalregulatory patterns of plant mineral nutrient depletion as
revealed by serat quadruple mutants disturbed in cysteinesynthesis" Molecular Plant 3 438-66 (2010)

750

Yamada K, Osakabe Y, Mizoi J, Nakashima K, Fujita Y, Shinozaki K, Shinozaki K, "Functional analysis of an Arabidopsis thaliana abiotic stress-inducible facilitated diffusion transporter
for monosaccharides" The Journal of Biological Chemistry 285
1138-1146 (2010)

751

Yamanaka T, Nakagawa Y, Mori K, Nakano M, Imamura T,
Kataoka H, Terashima A, Iida K, Kojima I, Katagiri T, Shinozaki

PSC Publications 2000 – 2012

K, Iida H, "MCA1 and MCA2 that mediate Ca2+ uptake havedistinct and overlapping roles in Arabidopsis" Plant Physiology 152 1284-1296 (2010)752

Yamazaki M, Asano T, Yamazaki Y, Sirikantaramas S, Sudo H,
Saito K, "Biosynthetic system of camptothecin: An anticancer
plant product" Pure and Applied Chemistry 82 213-218 (2010)753

Yoshida S, Ishida J, Kamal N, Ali A, Namba S, Shirasu K, "A
full-length enriched cDNA library and expressed sequence tag
analysis of the parasitic weed, Striga hermonthica" BMC Plant
Biology 10 1-10 (2010)754

Yoshida S, Maruyama S, Nozaki H, Shirasu K, "Horizontal Gene
Transfer by the Parasitic Plant Striga hermonthica" Science
328 1128 (2010)755

Yoshida T, Fujita Y, Sayama H, Kidokoro S, Maruyama K, Mizoi
J, Shinozaki K, Shinozaki K, "AREB1, AREB2, and ABF3 aremaster transcription factors that cooperatively regulate ABREdependent ABA signaling involved in drought stress tolerance
and require ABA for full activation" The Plant Journal 61 672685 (2010)756

Yoshimoto K, "Physiological roles of autophagy in plants:
Does plant autophagy have a pro-death function?" Plant Signaling & Behavior 5 1128 (2010)757

Yoshimoto K, "Plant autophagy puts the brakes on cell deathby controlling salicylic acid signaling" Autophagy 6 192-193(2010)

758

Yoshimoto K, Takano Y, Sakai Y, "Autophagy in plants andphytopathogens" FEBS Letters 584 1350-1358 (2010)

759

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761

762

763

764

765

Membrane Aquaporin AqpZ Protein Is Essential for Glucose
Metabolism during Photomixotrophic Growth of Synechocystis sp. PCC 6803" The Journal of Biological Chemistry 286
25224-25235 (2011)

777

Diaz C, Kusano M, Sulpice R, Araki M, Redestig H, Saito K, Stitt
M, Shin R, "Determining novel functions of Arabidopsis 14-3-3
proteins in central metabolic processes" BMC Systems Biology
5 1-12 (2011)

Ando S, Sato Y, Shigemori H, Shimizu T, Okada K, Yamane
H, Jikumaru Y, Kamiya Y, Yamada K, Akimoto-Tomiyama C,
Tanabe S, Nishizawa Y, Minami E, "Identification and characterization of 2'-deoxyuridine from the supernatant of conidial
suspensions of rice blast fungus as an infection-promoting
factor in rice plants" Molecular Plant-Microbe Interactions 24519-532 (2011)

778

Dubouzet J, Maeda S, Sugano S, Ohtake M, Hayashi N, Ichikawa T, Kondou Y, Kuroda H, Horii Y, Matsui M, Oda K, Hirochika H, Takatsuji H, Mori M, "Screening for resistance against
Pseudomonas syringae in rice-FOX Arabidopsis lines identified
a putative receptor-like cytoplasmic kinase gene that confers
resistance to major bacterial and fungal pathogens in Arabidopsis and rice" Plant Biotechnology Journal 9 466-485 (2011)

Asahina M, Azuma K, PITAKSARINGKARN W, Yamazaki T,
Mitsuda N, Ohme-Takagi M, Yamaguchi S, Kamiya Y, Nambara E, Okada K, Nishimura T, Koshiba T, Yokota T, Kamada
H, Satoh S, "Spatially selective hormonal control of RAP2.6L
and ANAC071 transcription factors involved in tissue reunionin Arabidopsis" Proceedings of the National Academy of Sciences of the United States of America 108 16128-16132 (2011)

779

Fernie A, Aharoni A, Willmitzer L, Stitt M, Tohge T, Kopka J,
Carroll A, Saito K, Fraser P, DeLuca V, "Recommendations forreporting metabolite data" The Plant Cell 23 2477-82 (2011)

780

Aya K, Hiwatashi Y, Kojima M, Sakakibara H, Ueguchi-Tanaka
M, Hasebe M, Matsuoka M, "The gibberellin perception
system evolved to regulate a pre-existing GAMYB-mediatedsystem during land plant evolution" Nature Communications
2 1-9 (2011)

781

769

Azuma M, Osanai T, Tanaka K, Saito K, Hirai MY, Ikeuchi M,"A response regulator Rre37 and an RNA polymerase sigma
factor SigE represent two parallel pathways to activate sugar
catabolism in a cyanobacterium Synechocystis sp. PCC 6803"
Plant Cell Physiology 52 404-412 (2011)

782

Fukui K, Ito S, Ueno K, Yamaguchi S, Kyozuka J, Asami T, "Newbranching inhibitors and their potential as strigolactone mimics in rice" Bioorganic & Medicinal Chemistry Letters 21 49054908 (2011)

770

783

Betsuyaku S, Takahashi F, Kinoshita A, Miwa H, Shinozaki K,
Fukuda H, Sawa S, "Mitogen-activated protein kinase regulated by the CLAVATA receptors contributes to shoot apicalmeristem homeostasis" Plant and Cell Physiology 52 14-29(2011)

Fukushima A, Kusano M, Redestig H, Arita M, Saito K, "Metabolomic correlation-network modules in Arabidopsis basedon a graph-clustering approach" BMC Systems Biology 5 1(2011)

784

Fukushima E, Seki H, Ohyama K, Ono E, Umemoto N, Mizutani
M, Saito K, Muranaka T, "CYP716A subfamily members are
multifunctional oxidases in triterpenoid biosynthesis" Plant
and Cell Physiology 52 2051-2061 (2011)

785

Furukawa J, Abe Y, Mizuno H, Matsuki K, Sagawa K, Kojima
M, Sakakibara H, Iwai H, Satoh S, "Seasonal fluctuation oforganic and inorganic components in xylem sap of populus
nigra" Plant Root 5 56-62 (2011)

786

Gallego-Giraldo L, Jikumaru Y, Kamiya Y, Tang Y, Dixon R,"Selective lignin downregulation leads to constitutive defense
response expression in alfalfa (Medicago sativa L.)" New Phytologist 190 627-639 (2011)

787

Hamasaki H, Yoshizumi T, Takahashi N, Higuchi M, Kuromori T,
Imura Y, Shimada H, Matsui M, "SD3, an Arabidopsis thaliana
Homolog of TIM21, Affects Intracellular ATP Levels and Seedling Development" Molecular Plant 5 461-471 (2011)

788

Hanada K, Hase T, Toyoda T, Shinozaki K, Okamoto M, "Origin
and evolution of genes related to ABA metabolism and its
signaling pathways" Journal of Plant Research 124 455-465(2011)

789

Hanada K, Sawada Y, Kuromori T, Saito K, Toyoda T, Shinozaki
K, "Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana" Molecular Biology and Evolution 28 377-382 (2011)

766

767

768

Yoshimoto K, van Doorn W, "Role of chloroplasts and otherplastids in ageing and death of plants and animals: a tale ofVishnu and Shiva" Aging Research Reviews 9 117-130 (2010)
Yuguchi M, Yokouchi T, Tominaga R, Kuromori T, Shinozaki K,
Okada K, Wada T, "Phenome analysis of root development inArabidopsis" Plant Biotechnology 27 345-347 (2010)
Zhang M, Kadota Y, Prodromou C, Shirasu K, Pearl L, "Structural Basis for Assembly of Hsp90-Sgt1-CHORD Protein Complexes: Implications for Chaperoning of NLR Innate Immunity
Receptors" Molecular Cell 39 269-281 (2010)
Ziaratnia S, Ohyama K, Hussein A, Muranaka T, Lall N, Kunert K,
Meyer J, "Isolation and identification of a novel chlorophenol
from a cell suspension culture of Helichrysum aureonitens"
Chemical and Pharmaceutical Bulletin 57 1282-1283 (2010)"Metabolomics reveals comprehensive reprogramming involving two independent metabolic responses of Arabidopsis
to UV-B light" The Plant Journal 67 354-369 (2011)
Adachi S, Minamisawa K, Okushima Y, Inagaki S, YOSHIYAMA
K, Kondou Y, Kaminuma E, Kawashima M, Toyoda T, Matsui M,
Kurihara D, Matsunaga S, Umeda M, "Programmed inductionof endoreduplication by DNA double-strand breaks in Arabidopsis" Proceedings of the National Academy of Sciences of
the United States of America 108 1-6 (2011)
Akai M, Onai K, Kusano M, Sato M, Redestig H, Toyooka K,
Morishita M, Miyake H, Hazama A, Checchetto V, Szabo I,
Matsuoka K, Saito K, Yasui M, Ishiura M, Uozumi N, "Plasma

771

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774

Bishopp A, Lehesranta S, Vaten A, Help H, El-showk S, Scheres
B, Helariutta K, Mahonen P, Sakakibara H, Helariutta Y, "Phloem-transported cytokinin regulates polar auxin transport andmaintains vascular pattern in the root meristem" Current Biology 21 927-932 (2011)
Blair M, Fernandez A, Ishitani M, Moreta D, Seki M, Ayling S,
Shinozaki K, "Construction and EST sequencing of full-length,
drought stress cDNA libraries for common beans (Phaseolus
vulgaris L.)" BMC Plant Biology 11 171 (2011)
Bunsupa S, Okada T, Saito K, Yamazaki M, "An acyltransferaselike gene obtained by differential gene expression profiles ofquinolizidine alkaloid-producing and nonproducing cultivarsof Lupinus angustifolius" Plant Biotechnology 28 89-94 (2011)
Choudhary S, Tran LS, "Phytosterols: Perspectives in Human
Nutrition and Clinical Therapy" Current Medicinal Chemistry
18 4557-4567 (2011)

775

Cramer G, Urano K, Delrot S, Pezzotti M, Shinozaki K, "Effects
of abiotic stress on plants: a systems biology perspective" BMC
Plant Biology 11 163 (2011)

776

Cui H, hao Y, Kovtun M, Stolc V, Deng XY, Sakakibara H, Kojima M, "Genome-wide direct target analysis reveals a role for
SHORT-ROOT in root vascular patterning through cytokinin
homeostasis" Plant Physiology 157 1221-1231 (2011)

790

Higuchi M, Ichikawa T, Kondou Y, Matsui K, Hasegawa Y,
Kawashima M, Sonoike K, Mori M, Hirochika H, Matsui M,"Functional analysis of two isoforms of leaf-type ferredoxinNADP+-oxidoreductase in rice using heterologous expression
system of Arabidopsis thaliana" Plant Physiology 157 96-108(2011)

791

Himuro Y, Tanaka H, Hashiguchi M, Ichikawa T, Nakazawa M,
Seki M, Fujita M, Shinozaki K, Matsui M, Akaishi R, Hoffmann
F, "FOX-superroots of Lotus corniculatus, overexpressing Arabidopsis full-length cDNA, show stable variations in morphological traits" Journal of Plant Physiology 168 181-187 (2011)

792

Fujita Y, Fujita M, Shinozaki K, Shinozaki-Yamaguchi K, "ABAmediated transcriptional regulation in response to osmotic
stress in plants" Journal of Plant Research 124 509-525 (2011)

Honsel A, Kojima M, Haas R, Frank W, Sakakibara H, Herschbach C, Rennenberg H, "Sulphur limitation and early sulphur
deficiency responses in poplar: significance of gene expression, metabolites, and plant hormones" Journal of Experimental Botany 63 1873-1893 (2011)

793

Fukazawa J, Nakata M, Ito T, Matsushita A, Yamaguchi S,
Takahashi Y, "bZIP transcription factor RSG controls the feedback regulation of NtGA20ox1 via intracellular localizationand epigenetic mechanism" Plant Signaling & Behavior 6 2628 (2011)

Ide Y, Kusano M, Oikawa A, Fukushima A, Tomatsu H, Saito
K, Hirai MY, Fujiwara T, "Effects of molybdenum deficiency
and defects in molybdate transporter MOT1 on transcript accumulation and nitrogen/sulphur metabolism in Arabidopsis
thaliana" Journal of Experimental Botany 62 1483-1497 (2011)

794

Inubushi k, Sakakibara H, Kojima M, Hattori H, Okumura Y,
Nimura M, Ohishi K, "Role of underground conditions in theoccurrence of carnation stunting and proliferation syndrome,and relationship between the symptoms and endogenous
phytohormones" Journal of the Japanese Society for Horticultural Science 80 182-189 (2011)

795

Ishida J, Yoshida S, Ito M, Namba S, Shirasu K, "Agrobacterium
rhizogenes-mediated transformation of the parasitic plant
Phtheirospermum japonicum" PLoS One 6 e25802 (2011)

796

Ito S, Umehara M, Hanada A, Kitahata N, Hayase H, Yamaguchi S, Asami T, "Effects of triazole derivatives on strigolactone
levels and growth retardation in rice" PLoS One 6 e21723(2011)

797

Iwamoto M, Kiyota S, Hanada A, Yamaguchi S, Takano M,"The multiple contributions of phytochromes to the control ofinternode elongation in rice" Plant Physiology 157 1187-1195(2011)

798

Iwase A, Mitsuda N, Koyama T, Hiratsu K, Kojima M, Arai T,
Inoue Y, Seki M, Sakakibara H, Sugimoto K, Ohme-Takagi M,"The AP2/ERF transcription factor WIND1 controls cell dedifferentiation in Arabidopsis" Current Biology 21 508-514(2011)

799

Iwase A, Ohme-Takagi M, Sugimoto K, "WIND1: A key molecular switch for plant cell dedifferentiation" Plant Signaling& Behavior 6 1943-1945 (2011)

800

Izawa T, Mihara M, Suzuki Y, Gupta M, Itoh H, Nagano A, Motoyama R, Sawada Y, Yano M, Hirai MY, Makino A, Nagamura
Y, "Os-GIGANTEA confers robust diurnal rhythms on the global transcriptome of rice in the field" The Plant Cell 23 17411755 (2011)

801

Kamiya T, Yamagami M, Hirai MY, Fujiwara T, "Establishmentof an in planta magnesium monitoring system using CAX3
promoter-luciferase in Arabidopsis" Journal of Experimental
Botany 63 355-363 (2011)

PSC Publications 2000 – 2012

802

803

Kawashima C, Matthewman C, Huang S, Lee B, Yoshimoto
N, Koprivova A, Rubio-Somoza I, Todesco M, Rathjen T, Saito
K, Takahashi H, Dalmay T, Kopriva S, "Interplay of SLIM1 andmiR395 in the regulation of sulfate assimilation in Arabidopsis" The Plant Journal 66 863-76 (2011)

804

Kiba T, Kudo T, Kojima M, Sakakibara H, "Hormonal control ofnitrogen acquisition: roles of auxin, abscisic acid, and cytokinin" Journal of Experimental Botany 62 1399-1409 (2011)

805

Kikuchi J, Ogata Y, Shinozaki K, "ECOMICS: Ecosystem TransOMICS Tools and Methods for Complex Environmental Samples and Datasets" Journal of Ecosystem & Ecography S2 001(2011)

806

807

808

809

810

Hayashi T, Iida K, Hanamata S, Iida H, Shinozaki K, Kuchitsu K,"Involvement of the putative Ca2+-permeable mechanosensitive channels, NtMCA1 and NtMCA2, in Ca2+ uptake, Ca2+-dependent cell proliferation and mechanical stress-induced gene
expression in tobacco (Nicotiana tabacum) BY-2 cells" Journalof Plant Research 125 555-568 (2011)

Katsumata T, Fukazawa J, Magome H, Jikumaru Y, Kamiya Y,
Natsume M, Kawaide H, Yamaguchi S, "Involvement of the
CYP78A subfamily of cytochrome P450 monooxygenases inprotonema growth and gametophore formation in the moss
Physcomitrella patens" Bioscience Biotechnology and Biochemistry 75 331-336 (2011)

Kim J, Mizoi J, Yoshida T, Fujita Y, Nakajima J, Ohori T, Todaka D, Nakashima K, Hirayama T, Shinozaki K, ShinozakiYamaguchi K, "An ABRE promoter sequence is involved in osmotic stress-responsive expression of the DREB2A gene, which
encodes a transcription factor regulating drought-inducible
genes in Arabidopsis" Plant and Cell Physiology 52 2136-2146(2011)

815

816

817

818

819

Kimura K, Tran LS, Funane K, "Loss of poly- γ -glutamic Acid
Synthesis of Bacillus subtilis (natto) Due to IS4Bsu1 Translocation to swrA Gene" Food Science and Technology Research 17447-451 (2011)
Kobayashi M, Kouzu N, Inami A, Toyooka K, Konishi Y, Matsuoka K, Matoh T, "Characterization of Arabidopsis CTP:3deoxy-D-manno-2-octulosonate cytidylyltransferase (CMPKDO synthetase), the enzyme that activates KDO duringrhamnogalacturonan II biosynthesis" Plant and Cell Physiology
52 1832-1843 (2011)
Kodaira K, Qin F, Tran LS, Maruyama K, Kidokoro S, Fujita Y,
Shinozaki K, Yamaguchi-Shinozaki K, "Arabidopsis Cys2/His2
Zinc-Finger Proteins AZF1 and AZF2 Negatively Regulate Abscisic Acid-Repressive and Auxin-Inducible Genes under Abiotic
Stress Conditions" Plant Physiology 157 742-756 (2011)
Kodama Y, "A bright green-colored bimolecular fluorescencecomplementation assay in living plant cells" Plant Biotechnology 28 95-98 (2011)

820

821

822

811

Kodama Y, Suetsugu N, Wada M, "Novel protein-protein interaction family proteins involved in chloroplast movement
response" Plant Signaling & Behavior 6 483-490 (2011)812

Kuromori T, Ito T, Sugimoto E, Shinozaki K, "Arabidopsis mutant of AtABCG26, an ABC transporter gene, is defective inpollen maturation" Journal of Plant Physiology 168 2001-2005(2011)

823

Kuromori T, Sugimoto E, Shinozaki K, "Arabidopsis mutants of
AtABCG22, an ABC transporter gene, increase water transpiration and drought susceptibility" The Plant Journal 67 885894 (2011)

824

813

814

Kurusu T, Yamanaka T, Nakano M, Takiguchi A, Ogasawara Y,

Kusano M, Fukushima A, Redestig H, Saito K, "Metabolomic
approaches toward understanding nitrogen metabolism inplants" Journal of Experimental Botany 62 1439-1453 (2011)
Kusano M, Par J, Jonas G, Fukushima A, Michael S, Johan T,
Thomas M, "Metabolite signature during short-day induced
growth cessation in Populus" Frontiers in Plant Physiology 2
1-11 (2011)
Kusano M, Redestig H, Tadayoshi H, Oikawa A, Matsuda F,
Fukushima A, Arita M, Shin W, Megumu Y, Kyoko H, Hiroshi E,
Saito K, "Covering chemical diversity of genetically-modified
tomatoes using metabolomics for objective substantial equivalence assessment" PLoS One 6 e16989 (2011)
Kusano M, Tabuchi M, Fukushima A, Funayama K, Diaz C,
Kobayashi M, Hayashi N, Tsuchiya Y, Takahashi H, Kamata A,
Yamaya T, Saito K, "Metabolomics data reveal a crucial role ofcytosolic glutamine synthetase 1;1 in coordinating metabolicbalance in rice" The Plant Journal 66 456-466 (2011)
Kusano M, Tohge T, Fukushima A, Kobayashi M, Hayashi N,
Otsuki H, Kondou Y, Goto H, Kawashima M, Matsuda F, Niida R,
Matsui M, Saito K, Fernie A, "Metabolomics reveals comprehensive reprogramming involving two independent metabolic
responses of Arabidopsis to UV-B light" The Plant Journal 67
354-369 (2011)
Lackman P, Gonzalez-Guzman M, Tilleman S, Carqueijeiro I,
Cuellar Perez A, Moses T, Seo M, Kanno Y, Hakkinen S, Van
Montagu M, Thevelein J, Maaheimo H, Oksman-Caldentey
K, Rodriguez P, Rischer H, Goossens A, "Jasmonate signaling
involves the abscisic acid receptor PYL4 to regulate metabolic
reprogramming in Arabidopsis and tobacco" Proceedingsof the National Academy of Sciences of the United States ofAmerica 108 5891-5896 (2011)

837

Okamoto M, Kushiro T, Jikumaru Y, Abrams S, Kamiya Y,
Seki M, Nambara E, "ABA 9'-hydroxylation is catalyzed by
CYP707A in Arabidopsis" Phytochemistry 72 717-722 (2011)

838

Okamoto M, Seki M, "Expression profile and 5'-terminal structure of Arabidopsis antisense transcripts expressed in seeds"
Plant Signaling & Behavior 6 691-693 (2011)839

Okazaki Y, Kamide Y, Hirai MY, Saito K, "Plant lipidomics
based on hydrophilic interaction chromatography coupled toion trap time-of-flight mass spectrometry" Metabolomics doi:
10.1007/s11306-011-0318-z (2011)

840

Osanai T, Oikawa A, Azuma M, Tanaka K, Saito K, Hirai MY,
Ikeuchi M, "Genetic engineering of group 2 σ factor SigE
widely activates expressions of sugar catabolic genes in Synechocystis species PCC 6803" The Journal of Biological Chemistry 286 30962-30971 (2011)

841

Ou B, Yin K, Liu S, Yan Y, Gu T, Man Jennifer H, Zhang L,
Miao J, Kondou Y, Matsui M, Gu H, Qu L, "A High-Throughput
Screening System for Arabidopsis Transcription Factors and Its
Application to Med25-Dependent Transcriptional Regulation"
Molecular Plant 4 1-10 (2011)842

Nemoto K, Seto T, Takahashi H, Nozawa A, Seki M, Shinozaki K,
Endo Y, Sawasaki T, "Autophosphorylation profiling of Arabidopsis protein kinases using the cell-free system" Phytochemistry 72 1136-1144 (2011)

Pei-Chi L, Pomeanz M, Jikumaru Y, Kang S, Hah C, Fujioka S,
Kamiya Y, Jyan-Chyn J, "The Arabidopsis tandem zinc finger
protein AtTZF1 affects ABA- and GA-mediated growth, stressand gene expression responses" The Plant Journal 65 253-268(2011)

843

Nishimura T, Toyooka K, Sato M, Matsumoto S, Lucas M,
Strnad M, Baluska F, Koshiba T, "Immunohistochemical observation of indole-3-acetic acid at the IAA synthetic maize coleoptile tips" Plant Signaling & Behavior 6 1-10 (2011)

Peng L, Fukao Y, Myouga F, Motohashi R, Shinozaki K, Shikanai T, "A Chaperonin Subunit with Unique Structures Is Essential for Folding of a Specific Substrate" PLoS Biology 9e1001040 (2011)844

Qin F, Kodaira K, Maruyama K, Mizoi J, Tran LS, Fujita Y,
Morimoto K, Shinozaki K, Shinozaki-Yamaguchi K, "SPINDLY, a negative regulator of Gibberellic Acid signaling, is involvedin the plant abiotic stress response" Plant Physiology 157
1900-1913 (2011)845

Qin F, Shinozaki K, Shinozaki-Yamaguchi K, "Achievements
and challenges in understanding plant abiotic stress responses
and tolerance" Plant and Cell Physiology 52 1569-1582 (2011)

846

Redestig H, Kobayashi M, Saito K, Kusano M, "Exploring matrix effects and quantification performance in metabolomics
experiments using artificial biological gradients" Analytical
Chemistry 83 5645-5651 (2011)

847

Redestig H, Kusano M, Ebana K, Kobayashi M, Oikawa A,
Okazaki Y, Matsuda F, Arita M, Fujita N, Saito K, "Exploring
molecular backgrounds of quality traits in rice by predictivemodels based on high-coverage metabolomics" BMC Systems
Biology 5 1-11 (2011)

848

Robert-Seilaniantz A, MacLean D, Jikumaru Y, Hill L, Yamaguchi S, Kamiya Y, Jones J, "The microRNA miR393 re-directs
secondary metabolite biosynthesis away from camalexin andtowards glucosinolates" The Plant Journal 67 218-231 (2011)

849

Saika H, Oikawa A, Matsuda F, Onodera H, Saito K, Toki S,"Application of gene targeting to designed mutation breeding of high-tryptophan rice" Plant Physiology 156 1269-1277(2011)

108 18512-18517 (2011)

825

826

Matsuda F, Nakabayashi R, Sawada Y, Suzuki M, Hirai MY,
Kanaya S, Saito K, "Mass spectra-based framework for automated structural elucidation of metabolome data to explore
phytochemical diversity" Frontiers in Plant Science 2 40 (2011)
Minamisawa N, Sato M, Cho K, Ueno H, Katsuaki T, Kajikawa
M, Yamato K, Ohyama K, Toyooka K, Kim G, Horiguchi G,
Takano H, Ueda T, Tsukaya H, "ANGUSTIFOLIA, a plant homolog of CtBP/BARS, functions outside the nucleus" The Plant
Journal 68 788-799 (2011)

827

Mito T, Seki M, Shinozaki K, Takagi-Ohme M, Matsui K, "Generation of chimeric repressors that confer salt tolerance inArabidopsis and rice" Plant Biotechnology Journal 9 736-746(2011)

828

Monda K, Negi J, Iio A, Kusumi k, Kojima M, Hashimoto M,
Sakakibara H, Iba K, "Environmental regulation of stomatal
response in the Arabidopsis Cvi-0 ecotype" Planta 234 555-563(2011)

829

830

831

832

Nanjo Y, Maruyama K, Yasue H, Shinozaki-Yamaguchi K, Shinozaki K, Komatsu S, "Transcriptional responses to flooding
stress in roots including hypocotyl of soybean seedlings" Plant
Molecular Biology 77 129-144 (2011)

Nishiyama R, Watanabe Y, Fujita Y, Le DT, Kojima M, Werner
T, Vankova R, Yamaguchi-Shinozaki K, Shinozaki K, Kakimoto
T, Sakakibara H, Schmulling T, Tran LS, "Analysis of Cytokinin
Mutants and Regulation of Cytokinin Metabolic Genes Reveals
Important Regulatory Roles of Cytokinins in Drought, Salt andAbscisic Acid Responses, and Abscisic Acid Biosynthesis" The
Plant Cell 23 2169-2183 (2011)

Le DT, Nishiyama R, Watanabe Y, Mochida K, YamaguchiShinozaki K, Shinozaki K, Tran LS, "Genome-Wide Expression
Profiling of Soybean Two-Component System Genes in Soybean Root and Shoot Tissues under Dehydration Stress" DNA
Research 18 17-29 (2011)

833

Le DT, Nishiyama R, Watanabe Y, Mochida K, YamaguchiShinozaki K, Shinozaki K, Tran LS, "Genome-Wide Survey andExpression Analysis of the Plant-Specific NAC Transcription
Factor Family in Soybean During Development and Dehydration Stress" DNA Research 18 263-276 (2011)

Ogawa d, Abe K, Miyao A, Kojima M, Sakakibara H, Mizutani
M, Morita H, Toda Y, Hobo T, Sato Y, Hattori T, Hirochika H,
Takeda S, "RSS1 regulates the cell cycle and maintains meristematic activity under stress conditions in rice" Nature Communications 2 1-11 (2011)

834

Oikawa A, Fujita N, Horie R, Saito K, Tawaraya K, "Solid-phaseextraction for metabolomic analysis of high-salinity samples
by capillary electrophoresis-mass spectrometry" Journal of
Separation Science 34 1063-1068 (2011)

835

Oikawa A, Kamide Y, Hirai MY, Saito K, "Metabolomics of asingle vacuole reveals metabolic dynamism in an alga Chara
australis" Plant Physiology 157 544-551 (2011)

836

Oikawa A, Otsuka T, Jikumaru Y, Yamaguchi S, Matsuda F,
Nakabayashi R, Takashina T, Isuzugawa K, Saito K, Shiratake
K, "Effects of freeze-drying of samples on metabolite levels in
metabolome analyses" Journal of Separation Science 34 35613567 (2011)

Lomin S, Sakakibara K, Romanov G, Sakakibara H, "Ligandbinding properties and subcellular localization of maize cytokinin receptors" Journal of Experimental Botany 62 5149-5159(2011)
Mashiguchi K, Tanaka K, Sakai T, Sugawara S, Kawaide H,
Natsume M, Hanada A, Yaeno T, Shirasu K, Yao H, McSteenP, Zhao Y, Hayashi K, Kamiya Y, Kasahara H, "The main auxin
biosynthesis pathway in Arabidopsis" Proceedings of the National Academy of Sciences of the United States of America

PSC Publications 2000 – 2012

850

851

852

853

854

Sakakibara K, Hanada K, "An evolutionary view of functional
diversity in family 1 glycosyltransferases" The Plant Journal 66
182-193 (2011)
Sakamoto T, Inui YT, Uraguchi S, Yoshizumi T, Matsunaga S,
Matsui M, Umeda M, Fukui K, Fujiwara T, "Condensin II Alleviates DNA Damage and Is Essential for Tolerance of Boron
Overload Stress in Arabidopsis" The Plant Cell 23 3533-3546(2011)
Sakurai N, Ara T, Ogata Y, Sano R, Ohno T, Sugiyama K, Hiruta
A, Yamazaki K, Yano K, Aoki K, Aharoni A, Hamada K, Yokoyama K, Kawamura S, Otsuka H, Tokimatsu T, Kanehisa
M, Suzuki H, Saito K, Shibata D, "KaPPA-View4: A metabolic
pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data" Nucleic Acids Research 39 D677D684 (2011)
Sakurai T, Kondou Y, Akiyama K, Kurotani A, Higuchi M,
Ichikawa T, Kuroda H, Kusano M, Mori M, Saitou T, Sakakibara
H, Sugano S, Suzuki M, Takahashi H, Takahashi S, Takatsuji H,
Yokotani N, Yoshizumi T, Saito K, Shinozaki K, Oda K, Hirochika H, Matsui M, "RiceFox: A Database of Arabidopsis mutant lines overexpressing rice full-length cDNA that contains awide range of trait information to facilitate analysis of genefunction" Plant Cell Physiology 52 265-273 (2011)
Sasaki E, Takahashi C, Asami T, Shimada Y, "AtCAST, a Tool for
Exploring Gene Expression Similarities among DNA Microarray
Experiments Using Networks" Plant Cell Physiology 52 169180 (2011)

855

Sawai S, Saito K, "Triterpenoid biosynthesis and engineeringin plants" Frontiers in Plant Science 2 25 (2011)856

Scalbert A, Andres-Lacueva C, Arita M, Kroon P, Manach C,
Urpi-Sarda M, Wishart D, "Databases on Food Phytochemicals
and Their Health-Promoting Effects" Journal of Agriculturaland Food Chemistry 59 4331-4348 (2011)

857

858

859

860

861

862

Seki H, Sawai S, Ohyama K, Mizutani M, Ohnishi T, Sudo H,
Fukushima E, Akashi T, Aoki T, Saito K, Muranaka T, "Triterpene functional genomics in licorice for identification of
CYP72A154 involved in the biosynthesis of glycyrrhizin" The
Plant Cell 23 4112-4123 (2011)
Sekiyama Y, Chikayama E, Kikuchi J, "Evaluation of a semipolar solvent system as a step toward heteronuclear multidimensional NMR-based metabolomics for 13C-labeled bacteria,
plants, and animals" Analytical Chemistry 83 719-726 (2011)
Seo M, Koshiba T, "Transport of ABA from the site of biosynthesis to the site of action" Journal of Plant Research 124 501507 (2011)

863

864

865

Skirycz A, Claeys H, De Bodt S, Oikawa A, Shimoda S, Andriankaja M, Maleux K, Eloy N, Frederik C, Yoo S, Saito K, Inze D,

873

Stoz H, Jikumaru Y, Shimada Y, Sasaki E, Stingl N, Mueller M,
Kamiya Y, "Jasmonate-dependent and COI1-independent defense responses against Sclerotinia sclerotiorum in Arabidopsis
thaliana: Auxin is Part of COI1-independent defense signaling" Plant and Cell Physiology 52 1941-1956 (2011)874

Stoz H, Sawada Y, Shimada Y, Hirai MY, Sasaki E, Krischke M,
Brown P, Saito K, Kamiya Y, "Role of camalexin, indole glucosinolates, and side chain modification of glucosinolate-derived
isothiocyanates in defense of Arabidopsis against Sclerotinia
sclerotiorum" The Plant Journal 67 81-93 (2011)
Suzuki A, Suriyagoda L, Shigeyama T, Tominaga A, Sasaki M,
Hiratsuka Y, Yoshinaga A, Arima S, Agarie S, Sakai T, Inada
S, Jikumaru Y, Kamiya Y, Uchiumi T, Abe M, Hashiguchi M,
Akashi R, Sato S, Kaneko T, Tabata S, Hrsch A, "Lotus japonicus
nodulation is photomorphogenetically controlled by sensing
the red/far red (R/FR) ratio through jasmonic acid (JA) signaling" PNAS 108 16837-16842 (2011)

866

Takahashi H, Kopriva S, Giordano M, Saito K, Hell R, "Sulfur
assimilation in photosynthetic organisms: molecular functions
and regulations of transporters and assimilatory enzymes"
Annual Review of Plant Biology 62 157-84 (2011)

867

Takase T, Ishikawa H, Murakami H, Kikuchi J, Sato-Nara K,
Suzuki H, "The Circadian clock modulates water dynamics andaquaporin expression in Arabidopsis roots" Plant Cell Physiology 52 373-383 (2011)

868

869

870

871

Shin R, "Transcriptional Regulatory Components Responding
to Macronutrient Limitation" Journal of Plant Biology 54 286293 (2011)
Shin R, Jez J, Basra A, Zhang B, Schachtman D, "14-3-3 Proteins fine-tune plant nutrient metabolism" FEBS Letters 585
143-147 (2011)"Pause-and-stop: the effects of osmotic stress on cell proliferation during early leaf development in Arabidopsis and a rolefor ethylene signaling in cell cycle arrest" The Plant Cell 23
1876-1888 (2011)

872

Takeda S, Hanano K, Kariya A, Shimizu S, Zhao L, Matsui M,
Tasaka M, Aida M, "CUP-SHAPED COTYLEDON1 transcription
factor activates the expression of LSH4 and LSH3, two members of the ALOG gene family, in shoot organ boundary cells"
The Plant Journal 66 1066-1077 (2011)
Takeuchi K, Gyohda A, Tominaga M, Kawamatsu M, Hatakeyama A, Ishii N, Shimaya K, Nishimura T, Riemann M, Nick P,
Hashimoto M, Komano T, Endo A, Okamoto T, Jikumaru Y,
Kamiya Y, Terakawa T, Koshiba T, "RSOsPR10 expression in response to environmental stresses is regulated antagonisticallyby jasmonate/ethylene and salicylic Acid signaling pathways inrice roots" Plant and Cell Physiology 52 1686-1696 (2011)
Tanaka N, Itoh H, Sentoku N, Kojima M, Sakakibara H, Izawa
T, Itoh J, Nagato Y, "The COP1 ortholog PPS regulates thejuvenile-adult and vegetative-reproductive phase changes inrice" The Plant Cell 23 2143-2154 (2011)
Thierry D, Sedijani P, Kondou Y, Matsui M, de Jong G, Samsen
G, Wiese-Klinkenberg A, Primavesi L, Paul M, Schluepmann
H, "Growth arrest by trehalose-6-phosphate: an astonishingcase of primary metabolite control over growth by way of
the SnRK1 signaling pathway" Plant Physiology 157 160-174(2011)
To T, Kim J, Matsui A, Kurihara Y, Morosawa T, Ishida J, Tanaka
M, Endo T, Kakutani T, Toyoda T, Kimura H, Yokoyama S, Shinozaki K, Seki M, "Arabidopsis HDA6 regulates locus-directed
heterochromatin silencing in cooperation with MET1" PLoS
Genetics 7 e1002055 (2011)875

To T, Nakaminami K, Kim J, Morosawa T, Ishida J, Tanaka M,
Yokoyama S, Shinozaki K, Seki M, "Arabidopsis HDA6 is required for freezing tolerance" Biochemical and BiophysicalResearch Communications 406 414-419 (2011)
Tohge T, Kusano M, Fukushima A, Saito K, Fernie A, "Transcriptional and metabolic programs following exposure ofplants to UV-B irradiation" Plant Signaling & Behavior 6 19871992 (2011)
Tominaga R, Ishida T, Wada T, "Chapter tow - new insights
into the mechanism of development of Arabidopsis root hairs
and trichomes" International Review of Cell and Molecular
Biology 286 67-106 (2011)

Biological Chemistry 286 43577-43586 (2011)886

Yamazaki M, Saito K, "Molecular genetic study on the anthocyanin chemotypes of Perilla frutescens var. crispa" Natural
Product Communications 6 423-427 (2011)

887

Yasumitsu H, Mochida K, Yasuda C, Isobe M, Kawsar S, Fujii Y,
Matsumoto R, Kanaly R, Ozeki Y, "Antiproliferative effects ofgalectin-1 from Rana catesbeiana eggs on human leukemia
cells and its binding proteins in human cells" In Vitro Cellular
Developmental Biology: Animal 47 728-734 (2011)

888

Yokotani N, Higuchi M, Kondou Y, Ichikawa T, Iwabuchi M,
Hirochika H, Matsui M, Oda K, "A novel chloroplast protein,
CEST induces tolerance to multiple environmental stresses andreduces photooxidative damage in transgenic Arabidopsis"
Journal of Experimental Botany 62 557-569 (2011)889

Yoshida T, Ohama N, Nakajima J, Kidokoro S, Mizoi J, Nakashima K, Maruyama K, Kim J, Seki M, Todaka D, Osakabe
Y, Sakuma Y, Schoffl F, Shinozaki K, Shinozaki-Yamaguchi K, "Arabidopsis HsfA1 transcription factors function as the main
positive regulators in heat shock-responsive gene expression"
Molecular Genetics and Genomics 286 321-332 (2011)

876

Tominaga R, Iwata M, Nukumizu Y, Wada T, "Analysis of IIId,
IIIe and IVa group basic-helix-loop-helix proteins expressed in
Arabidopsis root epidermis" Plant Science 181 471-478 (2011)877

Toyokura K, Watanabe K, Oikawa A, Kusano M, Tameshige T,
Tatematsu K, Matsumoto N, Tsugeki R, Saito K, Okada K, "Succinic semialdehyde dehydrogenase is involved in the robust
patterning of Arabidopsis leaves along the adaxial-abaxial
axis" Plant Cell Physiology 52 1340-1353 (2011)

878

Ueda M, Matsui K, Ishiguro S, Kato T, Tabata S, Kobayashi M,
Seki M, Shinozaki K, Okada K, "Arabidopsis RPT2a encoding
the 26S proteasome subunit is required for various aspects ofroot meristem maintenance, and regulates gametogenesis redundantly with its homolog, RPT2b" Plant and Cell Physiology
52 1628-1640 (2011)890

Yoshimitsu Y, Tanaka K, Fukuda W, Asami T, Yoshida S, Hayashi
K, Kamiya Y, Jikumaru Y, Shigeta T, Nakamura Y, Matsuo T,
Okamoto S, "Transcription of DWARF4 Plays a Crucial Rolein Auxin-Regulated Root Elongation in Addition to Brassinosteroid Homeostasis in Arabidopsis Thaliana" PLoS One 6
e23851 (2011)879

Umezawa T, "Systems biology approaches to abscisic acid signaling" Journal of Plant Research 124 539-548 (2011)

891

880

Virapom V, Yamazaki M, Saito K, Denduangboripant J, Chayamarit K, Chuanasa T, Sukrong S, "Correlation of camptothecinproducing ability and phylogenetic relationship in the genus
Ophiorrhiza" Planta Medica 77 759-64 (2011)

Zhang Z, Ogawa M, Fleet C, Zentella R, Hu J, Heo J, Lim J, Kamiya Y, Yamaguchi S, Sun T, "SCARECROW-LIKE 3 promotes
gibberellin signaling by antagonizing master growth repressor
DELLA in Arabidopsis" Proceedings of the National Academyof Sciences of the United States of America 108 2160-2165(2011)

881

892

Wang J, Ma X, Kojima M, Sakakibara H, Hou B, "N-Glucosyltransferase UGT76C2 is involved in cytokinin homeostasis andcytokinin response in Arabidopsis thaliana" Plant Cell Physiology 52 2200-2213 (2011)

Zhao C, Hanada A, Yamaguchi S, Kamiya Y, Beers E, "The Arabidopsis Myb genes MYR1 and MYR2 are redundant negative
regulators of flowering time under decreased light intensity"
The Plant Journal 66 502-515 (2011)

882

893

Wang Y, Wu J, Nakamichi N, Sakakibara H, Nam H, Wu S,"LIGHT-REGULATED WD1 and PSEUDO-RESPONSE REGULATOR9 form a positive feedback regulatory loop in the Arabidopsis circadian clock" The Plant Cell 23 486-498 (2011)

883

Won C, Sheng X, Mashiguchi K, Zheng Z, Dai X, Cheng Y, Kasahara H, Kamiya Y, Chory J, Zhao Y, "Conversion of tryptophan
to indole-3-acetic acid by TRYPTOPHAN AMINOTRANSFERASES OF ARABIDOPSIS and YUCCAs in Arabidopsis" Proceedingsof the National Academy of Sciences of the United States ofAmerica 108 18518-18523 (2011)

Zhu Z, An F, Feng Y, Li P, Xue L, A M, Jiang Z, Kim J, To T, Li
W, Zhang X, Yu Q, Dong Z, Chen W, Seki M, Zhou J, Hongwei
G, "Derepression of ethylene-stabilized transcription factors(EIN3/EIL1) mediates jasmonate and ethylene signaling synergy in Arabidopsis" Proceedings of the National Academyof Sciences of the United States of America 108 12539-12544(2011)

894

Afendi F, Okada T, Yamazaki M, Hirai-Morita A, Nakamura Y,
Nakamura K, Ikeda S, Takahashi H, Altaf-Ul-Amin M, Darusman L, Saito K, Kanaya S, "KNApSAcK Family Databases: Integrated metabolite-plant species databases for multifaceted
plant research" Plant Cell Physiology 53 e1 (2012)

895

Arita M, "From metabolic reactions to networks and pathways" Methods in Molecular Biology 804 93-106 (2012)

896

Bunsupa S, Katayama K, Ikeura E, Oikawa A, Toyooka K, Saito
K, Yamazaki M, "Lysine decarboxylase catalyzes the first stepof quinolizidine alkaloid biosynthesis and coevolved withalkaloid production in Leguminosae" The Plant Cell 24 12021216 (2012)

884

885

Wu G, Wang X, Li X, Kamiya Y, Otegui M, Chory J, "Methylation of a Phosphatase Specifies Dephosphorylation and
Degradation of Activated Brassinosteroid Receptors" Science
Signaling 4 ra29 (2011)
Yamada K, Kanai M, Osakabe Y, Ohiraki H, Shinozaki K,
Shinozaki-Yamaguchi K, "Monosaccharide absorption activityof Arabidopsis roots depends on expression profiles of transporter genes under high salinity conditions" The Journal of

PSC Publications 2000 – 2012

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Choudhary SP, Kanwar M, Bhardwaj R, Yu J-Q, Tran L-SP,"Chromium stress mitigation by polyamine-brassinosteroid
application involves phytohormonal and physiological strategies in Raphanus sativus L." PLoS One 7 e33210 (2012)
Choudhary S, Oral H, Bhardwaj R, Yu J, Tran LS, "Interaction ofbrassinosteroids and polyamines enhances copper stress tolerance in Raphanus sativus" Journal of Experimental Botany 63
5659-5675 (2012)

909

910

Kadota Y, Shirasu K, "The HSP90 complex of plants" Biochimica et Biophysica Acta 1823 689-697 (2012)911

Kanaya T, Hase K, Takahashi D, Fukuda S, Hoshino K, Sasaki I,
Hemmi H, Knoop KA, Kumar N, Sato M, Katsuno T, Yokosuka
O, Toyooka K, Nakai K, Sakamoto A, Kitahara Y, Jinnohara T,
McSorley SJ, Kaisho T, Williams IR, Ohno H. "The Ets Transcription Factor Spi-B Is Essential for the Differentiation of Intestinal Microfold (M) Cells" Nature Immunology 13 729-736(2012)

Choudhary S, Yu J, Yamaguchi-Shinozaki K, Shinozaki K, Tran
LS, "Benefits of brassinosteroid crosstalk" Trends in Plant Science 17 594-605 (2012)
Date Y, Iikura T, Yamazawa A, Moriya S, Kikuchi J, "Metabolic
Sequences of Anaerobic Fermentation on Glucose-Based Feeding Substrates Based on Correlation Analyses of Microbial andMetabolite Profiling" Journal of Proteome Research 11 56025610 (2012)
Date Y, Sakata K, Kikuchi J, "Chemical profiling of complex
biochemical mixtures from various seaweeds" Polymer Journal
44 888-894 (2012)
Endo A, Tatematsu K, Hanada K, Duermeyer L, Okamoto M,
Sakakibara K, Saito K, Toyoda T, Kawakami N, Kamiya Y, Seki
M, Nambara E, "Tissue-specific transcriptome analysis reveals
cell wall metabolism, flavonol biosynthesis, and defense responses are activated in the endosperm of germinating Arabidopsis thaliana seeds" Plant and Cell Physiology 53 16-27(2012)
Everroad R, Yoshida S, Tsuboi Y, Date Y, Kikuchi J, Moriya S,"Concentration of metabolites from low-density planktonic
communities for environmental metabolomics using nuclear
magnetic resonance spectroscopy" Journal of Visualized Experiments 62 e3163 (2012)
Frey A, Effroy D, Lefebvre V, Seo M, Perreau F, Berger A,
Sechet J, To A, North H, Marion-Poll A, "Epoxycarotenoid
cleavage by NCED5 fine-tunes ABA accumulation and affects
seed dormancy and drought tolerance with other NCED family members" The Plant Journal 70 501-512 (2012)
Fujita M, Fujita Y, Iuchi S, Yamada K, Kobayashi Y, Urano K,
Kobayashi M, Shinozaki-Yamaguchi K, Shinozaki K, "Naturalvariation in a polyamine transporter determines paraquat tolerance in Arabidopsis" Proceedings of the National Academyof Sciences of the United States of America 109 6343-6347(2012)
Fukushima A, Nishizawa T, Hayakumo M, Hikosaka S, Saito K,
Goto E, Kusano M, "Exploring Tomato Gene Functions Basedon Coexpression Modules Using Graph Clustering and Differential Coexpression Approaches" Plant Physiology 158 14871502 (2012)
Goh T, Kasahara H, Mimura T, Kamiya Y, Fukaki H, "Multiple
AUX/IAA-ARF modules regulate lateral root formation: therole of Arabidopsis SHY2/IAA3-mediated auxin signalling"
Philosophical Transactions of the Royal Society B 367 14611468 (2012)
Ha S, Vankova R, Yamaguchi-Shinozaki K, Shinozaki K, Tran
LS, "Cytokinins: metabolism and function in plant adaptation
to environmental stresses" Trends in Plant Science 17 172-179

Ishida T, Yoshimura M, Miura K, Sugimoto K, "MMS21/HPY2
and SIZ1, two Arabidopsis SUMO E3 ligases, have distinct functions in development" PLoS One 7 e46897 (2012)

912

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918

Kanno Y, Hanada A, Chiba Y, Ichikawa T, Nakazawa M, Matsui
M, Koshiba T, Kamiya Y, Seo M, "Identification of an abscisicacid transporter by functional screening using the receptor
complex as a sensor" Proceedings of the National Academy of
Sciences of the United States of America 109 9653-9658 (2012)
Kim J, Mizoi J, Kidokoro S, Maruyama K, Nakajima J, Nakashima K, Mitsuda N, Takiguchi Y, Takagi-Ohme M, Kondou Y,
Matsui M, Shinozaki K, Shinozaki-Yamaguchi K, "Arabidopsis
GROWTH-REGULATING FACTOR7 functions as a transcriptional repressor of abscisic acid- and osmotic stress-responsive
genes, including DREB2A" The Plant Cell 24 3393-3405 (2012)
Kim J, Nam J, John K, Kusano M, Oikawa A, Saito K, Lee C,"GC-TOF-MS- and CE-TOF-MS-based Metabolic Profiling ofCheonggukjang (Fast-fermented Bean Paste) during Fermentation and its correlation with Metabolic Pathways" Journalof Agricultural and Food Chemistry 60 9746-9753 (2012)
Kim J, To T, Ishida J, Matsui A, Kimura H, Seki M, "Transition ofchromatin status during the process of recovery from drought
stress in Arabidopsis thaliana" Plant and Cell Physiology 53
847-856 (2012)
Kim J, To T, Seki M, "An epigenetic integrator: new insights
into genome regulation, environmental stress responses anddevelopmental controls by HISTONE DEACETYLASE 6" Plant
and Cell Physiology 53 794-800 (2012)
Kimbara J, Yoshida M, Ito H, Hosoi K, Kusano M, Kobayashi M,
Ariizumi T, Asamizu E, Ezura H, "A novel class of sticky peel
and light green mutations causes cuticle deficiency in leaves
and fruits of tomato (Solanum lycopersicum)" Planta 236
1559-70 (2012)
Kobayashi K, Baba S, Obayashi T, Sato M, Toyooka K, Keranen
M, Aro E, Fukaki H, Ohta H, Sugimoto K, Masuda T, "Regulation of Root Greening by Light and Auxin/Cytokinin Signalingin Arabidopsis" The Plant Cell 24 1081-1095 (2012)

Moriya S, Kikuchi J, "Exploring the conformational space ofamorphous cellulose using NMR chemical shifts" Carbohydrate Polymers 90 1197-1203 (2012)

sawa T, Tanaka M, Toyoda T, Seki M, Ecker J, "Surveillance of
3' Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis" G3: Genes, Genomes, Genetics 2 487-498 (2012)(2012)

922

Kurusu T, Nishikawa D, Yamazaki Y, Gotoh M, Nakano M,
Hamada H, Yamanaka T, Iida K, Nakagawa Y, Saji H, Shinozaki
K, Iida H, Kuchitsu K, "Plasma membrane protein OsMCA1 is
involved in regulation of hypo-osmotic shock-induced Ca2+
influx and modulates generation of reactive oxygen species incultured rice cells" BMC Plant Biology 12 11 (2012)

923

Kusano M, Fukushima A, Naoko F, Okazaki Y, Kobayashi M,
Naoko O, Kaworu E, Saito K, "Deciphering starch quality ofrice kernels using metabolite profiling and pedigree network
analysis" Molecular Plant 5 442-451 (2012)
Kusano M, Saito K, "Role of Metabolomics in Crop Improvement" Journal of Plant Biochemistry and Biotechnology 21
24-31 (2012)

924

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934

Nakabayashi K, Bartsch M, Xiang Y, Miatton E, Pellenghar S,
Yano R, Seo M, Soppe W, "The time required for dormancy
release in Arabidopsis is determined by DELAY OF GERMINATION1 protein levels in freshly harvested seeds" The Plant Cell
24 2826-2838 (2012)

935

Nakagami H, Sugiyama N, Ishihama Y, Shirasu K, "Shotguns
in the front line: Phosphoproteomics in plants" Plant and Cell
Physiology 53 118-124 (2012)

936

Nakaminami K, Matsui A, Shinozaki K, Seki M, "RNA regulation in plant abiotic stress responses" Biochimica et Biophysica
Acta 1819 149-153 (2012)

937

Nakashima K, Takasaki H, Mizoi J, Shinozaki K, ShinozakiYamaguchi K, "NAC transcription factors in plant abiotic stressresponses" Biochimica et Biophysica Acta 1819 97-103 (2012)

938

Nam Y-J, Tran L-SP, Kojima M, Sakakibara H, Nishiyama R, Shin
R, "Regulatory Roles of Cytokinins and Cytokinin Signaling in
Response to Potassium Deficiency in Arabidopsis" PLoS One 7
e47797 (2012)939

Nelissen H, Rymen B, Jikumaru Y, Demuynck K, Lijsebettens M,
Kamiya Y, Inze D, Beemster G, "A local maximum in gibberellin levels regulates maize leaf growth by spatial control of cell
division" Current Biology 22 1183-1187 (2012)

940

Nishimura T, Matano N, Morishima T, Kakinuma C, Hayashi
K, Komano T, Kubo M, Hasebe M, Kasahara H, Kamiya Y, Koshiba T, "Identification of IAA Transport Inhibitors Including
Compounds Affecting Cellular PIN Trafficking by Two Chemical Screening Approaches Using Maize Coleoptile Systems"
Plant and Cell Physiology 53 1671-1682 (2012)

941

Nishiyama R, Le DT, Watanabe Y, Matsui A, Tanaka M, Seki
M, Yamaguchi-Shinozaki K, Shinozaki K, Tran L-SP, "Transcriptome Analyses of a Salt-Tolerant Cytokinin-Deficient Mutant
Reveal Differential Regulation of Salt Stress Response by Cytokinin Deficiency" PLoS One 7 e32124 (2012)

942

Maruyama M, Hayashi S, Nishimura N, Ishide M, Kobayashi K,
Yagi Y, Asami T, Nakamura T, Shinozaki K, Hirayama T, "Isolation of Arabidopsis ahg11, a weak ABA hypersensitive mutant defective in nad4 RNA editing" Journal of Experimental
Botany 63 5301-5310 (2012)

Ogata Y, Chikayama E, Morioka Y, Everroad RC, Shino A, Matsushima A, Haruna H, Moriya S, Toyoda T, Kikuchi J, "ECOMICS: A Web-Based Toolkit for Investigating the Biomolecular
Web in Ecosystems Using a Trans-omics Approach" PLoS One
7 e30263 (2012)

943

Matsuda F, Okazaki Y, Oikawa A, Kusano M, Nakabayashi R,
Kikuchi J, Yonemaru J, Ebana K, Yano M, Saito K, "Dissectionof genotype-phenotype associations in rice grains using metabolome quantitative trait loci analysis" The Plant Journal 70
624-636 (2012)

Ogawa Y, Sakurai N, Oikawa A, Kai K, Morishita Y, Mori K,
Moriya K, Fujii F, Aoki K, Suzuki H, Ohta D, Saito K, Daisuke S,"High-throughput Cryopreservation of Plant Cell Cultures for
Functional Genomics" Plant and Cell Physiology 53 943-952(2012)

944

Oikawa A, Saito K, "Metabolite analyses of single cells" The
Plant Journal 70 30-38 (2012)

945

Okushita K, Chikayama E, Kikuchi J, "Solubilization Mechanism and Characterization of the Structural Change of Bacterial Cellulose in Regenerated States through Ionic Liquid
Treatment" Biomacromolecules 13 1323-1330 (2012)

946

Okushita K, Komatsu T, Chikayama E, Kikuchi J, "Statistical ap-

Le DT, Aldrich DL, Valliyodan B, Watanabe Y, Ha CV, Nishiyama
R, Guttikonda SK, Quach TN, Gutierrez-Gonzalez JJ, Tran
L-SP, Nguyen HT, "Evaluation of Candidate Reference Genes
for Normalization of Quantitative RT-PCR in Soybean Tissues
under Various Abiotic Stress Conditions" PLoS One 7 e46487(2012)

926

Le DT, Nishiyama R, Watanabe Y, Vankova R, Tanaka M, Seki
M, Ham LH, Yamaguchi-Shinozaki K, Shinozaki K, Tran L-SP,"Identification and expression analysis of cytokinin metabolic
genes in soybean under normal and drought conditions in relation to cytokinin levels" PLoS One 7 e42411 (2012)

927

Lin S, Yoshimoto M, Lyu P, Tang C, Arita M, "Phylogenomic
and Domain Analysis of Iterative Polyketide Synthases inAspergillus Species" Evolutionary bioinformatics 8 373-387(2012)

928

Ma Y, Qin F, Tran L-SP, "Contribution of genomics to genediscovery in plant abiotic stress responses" Molecular Plant 51176-1178 (2012)

929

930

931

Maruyama K, Todaka D, Mizoi J, Yoshida T, Kidokoro S, Matsukura S, Takasaki H, Sakurai T, Yamamoto Y, Yoshihara K, Kojima M, Sakakibara H, Shinozaki K, Shinozaki-Yamaguchi K,"Identification of cis-acting promoter elements in cold- anddehydration-induced transcriptional pathways in Arabidopsis,
rice, and soybean" DNA Research 19 37-49 (2012)

919

Komaki S, Sugimoto K, "Control of the plant cell cycle by developmental and environmental cues" Plant and Cell Physiology 53 953-964 (2012)

920

Kumar R, Tran L-SP, Neelakandan AK, Nguyen HT, "Higher
plant cytochrome b5 polypeptides modulate fatty acid desaturation" PLoS One 7 e31370 (2012)

932

Mizoi J, Shinozaki K, Shinozaki-Yamaguchi K, "AP2/ERF familytranscription factors in plant abiotic stress responses" Biochimica et Biophysica Acta 1819 86-96 (2012)

921

Kurihara Y, Schmitz R, Nery J, Schultz M, Kurihara E, Moro-

933

Mori T, Chikayama E, Tsuboi Y, Ishida N, Shisa N, Noritake Y,

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954

Osakabe Y, Kawaoka A, Nishikubo N, Osakabe K, "Responses
to environmental stresses in woody plants: key to survive andlongevity" Journal of Plant Research 125 1-10 (2012)
Peng C, Lin S, Peng S, Lyu P, Arita M, Tang C, "Feature Identification of Compensatory Gene Pairs without Sequence
Homology in Yeast" Comparative and functional genomics
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Plackett A, Powers S, Fernandez-Garcia N, Urbanova T, Takebayashi Y, Seo M, Jikumaru Y, Benlloch R, Nilsson O, RuizRivero O, Phillips A, Wilson Z, Thomas S, Hedden P, "Analysisof the developmental roles of the Arabidopsis gibberellin
20-oxidases demonstrates that GA20ox1, -2, and -3 are thedominant paralogs" The Plant Cell 24 941-960 (2012)
Rymen B, Sugimoto K, "Tuning growth to the environmental
demands" Current Opinion in Plant Biology 15 683-690 (2012)
Sakakibara K, Fukushima A, Nakabayashi R, Hanada K, Matsuda F, Sugawara S, Inoue E, Kuromori T, Ito T, Shinozaki K,
Wangwattana B, Yamazaki M, Saito K, "Two glycosyltransferases involved in anthocyanin modification delineated by transcriptome independent component analysis in Arabidopsis
thaliana" The Plant Journal 69 154-167 (2012)
Sakurai N, Ogata Y, Ara T, Sano R, Akimoto N, Hiruta A, Suzuki
H, Kajiwara M, Widyastuti U, Suharsono S, Yokota A, Akashi K,
Kikuchi J, Shibata D, "Development of KaPPA-View4 for omics
studies on Jatropha and a database system KaPPA-Loader forconstruction of local omics databases" Plant Biotechnology 29
131-135 (2012)
Schneider K, Breuer C, Kawamura A, Jikumaru Y, Hanada A,
Fujioka S, Ichikawa T, Kondou Y, Matsui M, Kamiya Y, Yamaguchi S, Sugimoto K, "Arabidopsis PIZZA has the capacity toacylate brassinosteroids" PLoS One 7 e46805 (2012)
Seo M, Jikumaru Y, Kamiya Y, "Profiling of hormones and related metabolites in seed dormancy and germination studies"
Methods in Molecular Biology 773 99-111 (2012)

955

Shigeyama T, Tominaga A, Arima S, Sakai T, Inada S, Jikumaru
Y, Kamiya Y, Uchiumi T, Abe M, Hashiguchi M, Akashi R, Hirsch
A, Suzuki A, "Additional cause for reduced JA-Ile in the rootof a Lotus japonicus phyB mutant" Plant Signaling & Behavior
7 746-748 (2012)

956

Shimamura M, Itouga M, Tsubota H, "Evolution of apolar
sporocytes in marchantialean liverworts: implications frommolecular phylogeny" Journal of Plant Research 125 197-206(2012)

957

Takahashi H, Ozawa A, Nemoto K, Nozawa A, Seki M, Shinozaki K, Takeda H, Endo Y, Sawasaki T, "Genome-wide biochemical analysis of Arabidopsis protein phosphatase using awheat cell-free system" FEBS Letters 586 3134-3141 (2012)

958

Tanaka H, Osakabe Y, Katsura S, Mizuno S, Maruyama K, Kusakabe K, Mizoi J, Shinozaki K, Shinozaki-Yamaguchi K, "Abiotic stress-inducible receptor-like kinases negatively control
ABA signaling in Arabidopsis" The Plant Journal 70 599-613(2012)

959

Toh S, Kamiya Y, Kawakami N, Nambara E, McCourt P, Tsuchiya Y, "Thermoinhibition Uncovers a Role for Strigolactones in
Arabidopsis Seed Germination" Plant Cell Physiology 53 107117 (2012)

fold conserved across plant pathogenic oomycete species"
PLoS Pathogens 8 e1002400 (2012)

972

Xu Z, Lee K, Dong T, Jeong J, Jin J, Kanno Y, Kim D, Kim S,
Seo M, Bressan R, Yun D, Hwang I, "A vacuolar β -glucosidase
homolog that possesses glucose-conjugated abscisic acidhydrolyzing activity plays an important role in osmotic stressresponses in Arabidopsis" The Plant Cell 24 2184-2199 (2012)

973

Yamaguchi M, Takechi K, Myouga F, Imura S, Sato H, Takio S,
Shinozaki K, Takano H, "Loss of the Plastid Envelope Protein
AtLrgB Causes Spontaneous Chlorotic Cell Death in Arabidopsis thaliana" Plant and Cell Physiology 53 125-134 (2012)960

Tokmakov A, Kurotani A, Takagi T, Toyama M, Shirouzu M,
Fukami Y, Yokoyama S, "Multiple post-translational modifications affect heterologous protein synthesis" The Journal of
Biological Chemistry 287 27106-27116 (2012)

961

Tokunaga H, Kojima M, Kuroha T, Ishida T, Sugimoto K, Kiba T,
Sakakibara H, "Arabidopsis lonely guy (LOG) multiple mutants
reveal a central role of the LOG-dependent pathway in cytokinin activation" The Plant Journal 69 355-365 (2012)

962

974

Tominaga R, Iwata M, Nukumizu Y, Sano R, Wada T, "A fulllength R-like basic-helix-loop-helix transcription factor is required for anthocyanin upregulation whereas the N-terminal
region regulates epidermal hair formation" Plant Science 183
115-122 (2012)

Yamamura M, Noda S, Hattori T, Shino A, Kikuchi J, Takabe K,
Suzuki S, Shibata D, Umezawa T, "Characterization of lignocellulose of Erianthus ravennae in relation to enzymatic saccharification efficiency" Plant Biotechnology 29 1-11 (2012)

975

Tominaga R, Nukumizu Y, Wada T, "Amino acid substitution
converts WEREWOLF function from an activator to a repressorof Arabidopsis non-hair cell development" Plant Science 183
37-42 (2012)

Yanagawa Y, "Ubiquitin/proteasome-mediated proteolysis is
involved in the response to flooding stress in soybean roots,
independent of oxygen limitation" Plant Science 185-186 250258 (2012)

976

Yazawa k, Jiang C, Kojima M, Sakakibara H, Takatsuji H, "Reduction of abscisic acid levels or inhibition of abscisic acid signaling in rice during the early phase of Magnaporthe oryzae
infection decreases its susceptibility to the fungus" Physiological and Molecular Plant Pathology 78 1-7 (2012)

977

Yoshimoto K, Noutoshi Y, Hayashi K, Shirasu K, Takahashi T,
Motose H, "A Chemical Biology Approach Reveals an Opposite Action between Thermospermine and Auxin in Xylem
Development in Arabidopsis thaliana" Plant Cell Physiology
53 1-40 (2012)

978Breuer C, Morohashi K, Kawamura A, Takahashi N. Ishida T,
Umeda M, Grotewold E, Sugimoto K, "Transcriptional repression of the APC/C activator CCS52A1 promotes active termination of cell growth" The EMBO Journal 31 4488-4501 (2012)

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Kobayashi K, Narise T, Sonoike K, Hashimoto H, Sato N, Kondo
M, Nishimura M, Sato M, Toyooka K, Sugimoto K, Wada H,
Masuda T, Ohta H, "Role of galactolipid biosynthesis in coordinated development of photosynthetic complexes andthylakoid membranes during chloroplast biogenesis in Arabidopsis" The Plant Journal 73 250-261 (2013)

963

964

Tominaga T, Sano K, Kikuchi J, Mitomo H, Ijiro K, Osada Y,"Hydrophilic Double-Network Polymers that Sustain High Mechanical Modulus under 80% Humidity" ACS Macro Letters 1
432-436 (2012)

965

Ueno S, Moriguchi Y, Uchiyama K, Ujino-Ihara T, Futamura
N, Sakurai T, Shinohara K, Tsumura Y, "A second generation
framework for the analysis of microsatellites in expressedsequence tags and the development of EST-SSR markers fora conifer, Cryptomeria japonica" BMC Genomics 13 136-151(2012)

966

Uraji M, Katagiri T, Okuma E, Ye W, Hossain M, Masuda C,
Miura A, Nakamura Y, Mori I, Shinozaki K, Murata Y, "Cooperative function of PLDδ and PLDα 1 in Abscisic Acid-induced
stomatal closure in Arabidopsis" Plant Physiology 159 450-460(2012)

967

Utsumi Y, Tanaka M, Morosawa T, Kurotani A, Yoshida T,
Mochida K, Matsui A, Umemura Y, Ishitani M, Shinozaki K,
Sakurai T, Seki M, "Transcriptome analysis using a high-density
oligomicroarray under drought stress in various genotypes of
cassava: an important tropical crop" DNA Research 19 335-345(2012)

968

Vergara L, Everroad R, Andraca G, Kikuchi J, Makihara H,"Plant host differences between Cossus redtenbacheri and
Cossus insularis: insights from mechanical tests and molecularphylogeny" Bulletin of Insectology 65 217-222 (2012)969

Wada M, Takahashi H, Altaf-Ul-Amin M, Nakamura K, Hirai
MY, Ohta D, Kanaya K, "Prediction of operon-like gene clusters in the Arabidopsis thaliana genome based on co-expression analysis of neighboring genes" Gene 503 56-64 (2012)

970

Watanabe T, Shino A, Akashi K, Kikuchi J, "Spectroscopic investigation of tissue-specific biomass profiling for Jatropha
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971

Win Y, Krasileva K, Kamoun S, Shirasu K, Staskawicz B, Banfield M, "Sequence divergent RXLR effectors share a structural

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