植物におけるタンパク質の総合アノテーションデータベースの開発〇黒谷 篤之1, Alexander A. Tokmakov2, 山田 豊1, 篠崎一雄1, 櫻井哲也1,3

1. 理化学研究所・CSRS, 2. 京都産業大学・総合, 3. 高知大学・複合☘ Abstract
近年、広範な生物種についてのゲノム解読が急速に進められており、その蓄積された塩基配列のデータ量は膨大となっている。また、これらのゲノム配列情報を有効に活用すべ
く、種々のポストゲノム解析も盛んに行われている。しかしながら、植物種におけるタンパク質全般の情報量は、動物や微生物等と比べて劣っており、植物の中で最も解析がされているシロイヌナズナであってもそのタンパク質の構造や機能についての注釈情報は、未だ不十分な状況である。そこで、我々は、植物種におけるこれらの欠落部分に対し、生物情報科学的なデータ生産手法によって情報の補充をすべく、ゲノム解読がされた代表的な6種の緑色植物、及び、31種の藻類について、これらのタンパク質配列データから、種々の構造的、機能的情報等を計算によって網羅的に求め、得られた結果を統合し、植物におけるタンパク質情報の総合アノテーションデータベースを作成した。今発表では、作成したデータベースを紹介すると共に得られたデータについての概観やその応用等について報告する。(データベースURL: http://alga-pras.riken.jp, http://plant-pras.riken.jp)☘ Data Resources &☘ Introduction

Protein Information

History of WGS Analysis in Plants%Annotated Proteins in UniProtKB

Plants Species

2012

GS20-454

Tomato40

2011

Potato2010

1st time for monocots

1st time for fruits

Soybean2009

Sorghum

20

2008

1st time for plants

2007

2006

Grape

Poplar40%

Rice

Arabidopsis

2000

0%Moss(P.patens)

1st time for tree

2005

Year2010

・ Green algae (12)・ Red algae (5)・ Glaucophyceae (1)・ Oomycetes (4)・ Diatoms (3)・ Others (6)Protein Information

20%

2004

2000

・ Dicots (3)・ Monocots (1)・ Mosses (1)・ Ferns (1)Non-redundant whole protein sequences

C. reinhardtii

Orange Algae

PlantsO. sativa

2013

1st Next Generation
Sequence Machine Land Plants

60%

G. max60

A. thaliana

Sugar beet

E. coli

2014

Protein ann. inplants is poor

80%

H. sapiens

Number of Plant Species

Pineapple

S. cerevisiae

2015

M. musculus

80

Percentage of Annotated Proteins100% PhysicochemicalProperties Structural
Properties Post-Translational
Modification Functional
Annotation/Region

Protein Sequence,Length, pI, Charged,Acidic, Basic, GRAVY,Solubility, etc.

Disorder Region, Domain
Boundary,
Transmembrane Region,
S-S bonds, Signal Peptide

STY-Phosphorylation
Site, O-/N-Glycosylation
Site, Ubiquitination Site

Pfam, UniProtKB, GO,PDB, KOG, PASS, Rosetta
Stone

2015

Database

Fig. 1 The number of whole genome sequencing (WGS) analysis in plants have been
rapidly increasing in recent years.

Fig. 2 Compared functional annotations between theFig. 3 Non-redundant whole protein sequences of 37 plant species (6 land

representative organisms. There are a lot of unannotatedproteins in plants. The information of annotated proteins
were acquired from UniProtKB.

plants and 31 algae) are prepared with the tool, such as CD-HIT, etc. Protein
information are calculated from the nr protein sequences with various
bioinformatics tools.

☘ Discovery of Candidate Genes☘ Web Interface

Including Novel Functional Region

Keyword Search
Result List

*2. Method of Conserved Region(PASS algorithm)*1. Method of Rosetta Stone

Seq 1

Seq1 (Arabidopsis)

ID Search
Alga-PrAS

blastall –i seq1 –d plants sequences ・・・

Seq2 (Soybean)

Statistical Info.

Seq3 (Soybean)

Algal-Protein Annotation Suite
31 algae, 440,000 proteins
http://alga-pras.riken.jp

Seq 1
Functional (conserved) region

Multiple Search

Plant-PrAS

Arabidopsis
Rice (msu)

Plant-Protein Annotation Suite
6 plants, 170,000 proteins
http://plant-pras.riken.jp☘ Comparative Analysis of Protein Sequences in Algae

0.3

10%
0.3
5%

5%0%

S-S Bond

STY-Phosphorylation

S-S Bond

3.0

3.0

3.0

2.5

2.5

2.5

2.5

1.0

1.0

1.0

hits / 400aa

2.5hits / 400aa

2.5hits / 400aa

2.5

1.5

STY-Phos

3.5
3.0

1.5560

2.0
1.5
1.0

0.5

0.5

0.5

0.5

0.0

0.0

0.0

0.0

2.0
1.5
1.0

2.0
1.5
1.0

2.0
1.5
1.0

 31種の藻類、及び、6種の陸上植物の各種の全タンパク質配列からタンパク質属性、構造情報、機能情報、翻訳後修飾、新規機能領域等の有用情報を備えたデータベースサイトを構築した。
 本サイトは、種間の比較解析や統計解析を容易とし、ユーザーの利便性を高めた仕様としている。
 藻類の比較配列解析において、分類間、生息環境間、単多細胞間、保存・非保存タンパク質間での相違を観察した。

0.3☘ Other Plants Databases

0.00%

3.5

3.0

0.65%

3.5

3.0

1.5

10%
0.3

3.5

3.02.015%

0.0

S-S Bond

STY-Phos

3.5

2.00%0hits / 400aa

03.5

2.0

15%

0.9

20%
0.6

0.6

Membrane25%

hits / 400aa

10%0%% Disorder

0.9

20%

15%

5%Membrane% Disorder
25%

0.9

Conservation

hits / 400aa

25%

hits / 400aa

hits / 400aa

10%hits / 400aa

Membrane% Disorder
20%

15%

3.5

Uni-/Multi-cellularhits / 400aa

Membrane

0.6560☘ Conclusion

STY-Phos

S-S Bond
3.5
3.0

hits / 400aa

Habitathits / 400aa

Classification

20%

3,531
13,391

sequences. A triplet of protein sequences is pictured: The second and third proteins arepredicted to interact because their homologs are fused in the first protein (Ed Marcotte et al.,Science, 1999). *2. Detect conserved region (more than 10 similar sequences) using BLAST
comparison with the uniprot-swissprot db. The structured fragments are identified based on
the premise that conserved sequences and are expected to have function (Kuroda et al.,Protein Science, 2000).

algae including 31 species, 440,000 proteins and 31 search items. Plant-PrAS (Plant-Protein Annotation Suite) is also
comprehensive proteome annotation database for land plants including 6 species, 170,000 proteins and 25 search
items. These databases have several search functions and useful statistical analysis.

0.9

Unannotated Proteins &PASS(+) & Pfam(-)

Fig. 5 *1. Detect protein-interacting regions using BLAST comparison with other species

Fig. 4 Alga-PrAS (Algal-Protein Annotation Suite) is 1st time comprehensive proteome annotation database for25%

Unannotated Proteins &Rosetta Stone(+) & Pfam(-)

Sequence Search

Detail Info.

% Protein disorder

Unannotated Proteins

2.5

 RIKEN Arabidopsis Genome Encyclopedia (RARGE)
http://rarge.psc.riken.jp

2.0
1.5
1.0

0.5

0.5

0.5

0.5

0.0

0.0

0.0

0.0Fig. 6 Compared protein sequences in algae with several items, such as protein disorder, membrane, S-S bond and STY-phosphorylation, and with several categories, Platform for RIKEN Metabolomics (PRIMe)
http://prime.psc.riken.jp
 Link Page of Databases in RIKEN CSRS
http://www.csrs.riken.jp/en/databasesuch as plant classification, environmental habitat, uni-cellular/multi-cellular and conservation. The category of ‘conservation’ includes the protein cluster of ‘conserved’,‘species-specific’ and ‘other’, which are conserved protein clusters involving all 31 algae species, species-specific protein clusters involving just one alga and others.

Licensed under a Creative Commons Attribution 4.0 International License. ©2017 Atsushi Kurotani （RIKEN CSRS）