bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics of RpaB–promoter interaction during high light stress, revealed by chromatin immunoprecipitation (ChIP) analysis in Synechococcus elongatus PCC 7942
Authors: Hanaoka Mitsumasa , Tanaka Kan 
Published: July 2008

SummaryIn cyanobacteria, a series of genes are induced by, and cause tolerance to, high light stress conditions. Some of these genes share a short, repeated sequence motif known as a high light regulatory 1 (HLR1) element in their promoter regions. Previously, RpaB, a two‐component response regulator, was shown to interact with the HLR1 element of several high light‐responsive promoters in vitro. However, how RpaB regulates target promoters in vivo remained elusive. In this study, we analyzed the role of RpaB in transcriptional regulation of high light‐responsive genes by chromatin immunoprecipitation (ChIP) analysis, which has been recently developed and utilized to study in vivo interactions between DNA‐binding proteins and the relevant target DNA. One of the advantages of this method is the ability to detect dynamic interaction patterns in response to various growth and/or environmental conditions instantaneously at the time of the analysis. Here we examined the binding patterns of RpaB under various light conditions using ChIP assays. We found that strong interactions of RpaB with target promoters were weakened in a high light‐dependent manner, and that the lower binding level of RpaB continued as long as the high light conditions were maintained. Thus, in regulation of high light‐inducible genes, we suggest that RpaB functions as a repressor under normal light conditions, and that high light conditions result in release of the repression.
Tissue‐dependent limited pleiotropy affects gene expression in barley
Authors: Potokina Elena , Druka Arnis , Luo Zewei , Moscou Matthew , Wise Roger , Waugh Robbie , Kearsey Mike 
Published: July 2008

SummaryNon‐synonymous coding mutations in a gene change the resulting protein, no matter where it is expressed, but the effects of cis‐regulatory mutations could be spatially or temporally limited – a phenomenon termed limited pleiotropy. Here, we report the genome‐wide occurrence of limited pleiotropy of cis‐regulatory mutations in barley (Hordeum vulgare L.) using Affymetrix analysis of 22 840 genes in a population of 139 doubled haploid lines derived from a cross between the cultivars Steptoe (St) and Morex (Mx). We identified robust cis‐acting expression regulators that segregate as major genes in two successive ontogenetic stages: germinating embryo tissues and seedling leaves from the embryonic axis. We show that these polymorphisms may be consistent in both tissues or may cause a dramatic change in transcript abundance in one tissue but not in another. We also show that the parental allele that increases expression can vary with the tissue, suggesting nucleotide polymorphism in enhancer sequences. Because of the limited pleiotropy of cis‐regulating mutations, the number of cis expression quantitative trait loci (cis‐eQTLs) discovered by ‘genetical genomics’ is strongly affected by the particular tissue or developmental stage studied. Given that limited pleiotropy is a common feature of cis‐regulatory mutations in barley, we predict that the phenomenon would be relevant to developmental and/or tissue‐specific interactions across wide taxonomic boundaries in both plants and animals.
Functional gene‐mining for salt‐tolerance genes with the power of Arabidopsis
Authors: Du Jin , Huang Yue‐Ping , Xi Jing , Cao Min‐Jie , Ni Wan‐Song , Chen Xi , Zhu Jian‐Kang , Oliver David J. , Xiang Cheng‐Bin 
Published: July 2008

SummaryHere we report on a functional gene‐mining method developed to isolate stress tolerance genes without any prior knowledge of the genome or genetic mapping of the source germplasms. The feasibility of this approach was demonstrated by isolating novel salt stress tolerance genes from salt cress (Thellungiella halophila), an extremophile that is adapted to a harsh saline environment and a close relative of the model plant Arabidopsis thaliana. This gene‐mining method is based on the expression of salt cress cDNA libraries in Arabidopsis. A cDNA expression library of the source germplasm, salt cress, was constructed and used to transform Arabidopsis via Agrobacterium‐mediated gene transfer. A transgenic seed library consisting of >125 000 independent lines was generated and screened for salt‐tolerant lines via a high‐throughput genetic screen. A number of salt‐tolerant lines were isolated, and the salt cress cDNAs were identified by PCR amplification and sequencing. Among the genes isolated, several novel small protein‐encoding genes were discovered. The homologs of these genes in Arabidopsis have not been experimentally analyzed, and their functions remain unknown. The function of two genes isolated by this method, ST6‐66 and ST225, and their Arabidopsis homologs, were investigated in Arabidopsis using gain‐ and loss‐of‐function analyses, and their importance in salt tolerance was demonstrated. Thus, our functional gene‐mining method was validated by these results. Our method should be applicable for the functional mining of stress tolerance genes from various germplasms. Future improvements of the method are also discussed.
Overexpression of a fatty acid amide hydrolase compromises innate immunity in Arabidopsis
Authors: Kang Li , Wang Yuh‐Shuh , Uppalapati Srinivasa Rao , Wang Keri , Tang Yuhong , Vadapalli Vatsala , Venables Barney J. , Chapman Kent D. , Blancaflor Elison B. , Mysore Kirankumar S. 
Published: July 2008

Summary N‐acylethanolamines are a group of lipid mediators that accumulate under a variety of neurological and pathological conditions in mammals. N‐acylethanolamine signaling is terminated by the action of diverse hydrolases, among which fatty acid amide hydrolase (FAAH) has been well characterized. Here, we show that transgenic Arabidopsis lines overexpressing an AtFAAH are more susceptible to the bacterial pathogens Pseudomonas syringae pv. tomato and P. syringae pv. maculicola. AtFAAH overexpressors also were highly susceptible to non‐host pathogens P. syringae pv. syringae and P. syringae pv. tabaci. AtFAAH overexpressors had lower amounts of jasmonic acid, abscisic acid and both free and conjugated salicylic acid (SA), compared with the wild‐type. Gene expression studies revealed that transcripts of a number of plant defense genes, as well as genes involved in SA biosynthesis and signaling, were lower in AtFAAH overexpressors than wild‐type plants. Our data suggest that FAAH overexpression alters phytohormone accumulation and signaling which in turn compromises innate immunity to bacterial pathogens.
HAHB4, a sunflower HD‐Zip protein, integrates signals from the jasmonic acid and ethylene pathways during wounding and biotic stress responses
Authors: Manavella Pablo A. , Dezar Carlos A. , Bonaventure Gustavo , Baldwin Ian T. , Chan Raquel L. 
Published: July 2008

SummaryThe Helianthus annuus (sunflower) HAHB4 transcription factor belongs to the HD‐Zip family and its transcript levels are strongly induced when sunflower plants are attacked by herbivores, mechanically damaged or treated with methyl‐jasmonic acid (MeJA) or ethylene (ET). Promoter fusion analysis, in Arabidopsis and in sunflower, demonstrated that induction of HAHB4 expression by these treatments is regulated at the transcriptional level. In transiently transformed sunflower plants HAHB4 expression upregulates the transcript levels of several genes involved in JA biosynthesis and defense‐related processes such as the production of green leaf volatiles and trypsin protease inhibitors (TPI). In HAHB4 sunflower overexpressing tissue, increased activities of lipoxygenase, hydroperoxide lyase and TPI are detected whereas in HAHB4‐silenced tissue these activities are reduced. Transgenic Arabidopsis thaliana and Zea mays plants ecotopically expressing HAHB4 also exhibit higher transcript levels of defense‐related genes and when Spodoptera littoralis or Spodoptera frugiperda larvae are placed on each species, respectively, larvae consumed less and gain less mass compared with larvae feeding on control plants. Arabidopsis plants ectopically expressing HAHB4 had higher amounts of JA, JA‐isoleucine and ET compared with control plants both before and after wounding, but reduced levels of salicylic acid (SA) after wounding and bacterial infection. We conclude that HAHB4 coordinates the production of phytohormones during biotic stress responses and mechanical damage, specifically by positively regulating JA and ET production and negatively regulating ET sensitivity and SA accumulation.
Molecular basis of the functional specificities of phototropin 1 and 2
Authors: Aihara Yusuke , Tabata Ryohei , Suzuki Tomomi , Shimazaki Ken‐ichiro , Nagatani Akira 
Published: July 2008

SummaryA blue‐light photoreceptor in plants, phototropin, mediates phototropism, chloroplast relocation, stomatal opening, and leaf‐flattening responses. Phototropin is divided into two functional moieties, the N‐terminal photosensory and the C‐terminal signaling moieties. Phototropin perceives light stimuli by the light, oxygen or voltage (LOV) domain in the N‐terminus; the signal is then transduced intramolecularly to the C‐terminal kinase domain. Two phototropins, phot1 and phot2, which have overlapping and distinct functions, exist in Arabidopsis thaliana. Phot1 mediates responses with higher sensitivity than phot2. Phot2 mediates specific responses, such as the chloroplast avoidance response and chloroplast dark positioning. To elucidate the molecular basis for the functional specificities of phot1 and phot2, we exchanged the N‐ and C‐terminal moieties of phot1 and phot2, fused them to GFP and expressed them under the PHOT2 promoter in the phot1 phot2 mutant background. With respect to phototropism and other responses, the chimeric phototropin consisting of phot1 N‐terminal and phot2 C‐terminal moieties (P1n/2cG) was almost as sensitive as phot1; whereas the reverse combination (P2n/1cG) functioned with lower sensitivity. Hence, the N‐terminal moiety mainly determined the sensitivity of the phototropins. Unexpectedly, both P1n/2cG and P2n/1cG mediated the chloroplast avoidance response, which is specific to phot2. Hence, chloroplast avoidance activity appeared to be suppressed specifically in the combination of N‐ and C‐terminal moieties of phot1. Unlike the chloroplast avoidance response, chloroplast dark positioning was observed for P2G and P2n/1cG but not for P1G or P1n/2cG, suggesting that a specific structure in the N‐terminal moiety of phot2 is required for this activity.
Genome‐scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5
Authors: Benhamed Moussa , Martin‐Magniette Marie‐Laure , Taconnat Ludivine , Bitton Frédérique , Servet Caroline , De Clercq Rebecca , De Meyer Björn , Buysschaert Caroline , Rombauts Stéphane , Villarroel Raimundo , Aubourg Sébastien , Beynon Jim , Bhalerao Rishikesh P. , Coupland George , Gruissem Wilhelm , Menke Frank L.H. , Weisshaar Bernd , Renou Jean‐Pierre , Zhou Dao‐Xiu , Hilson Pierre 
Published: July 2008

SummaryWe have assembled approximately 20 000 Arabidopsis thaliana promoter regions, compatible with functional studies that require cloning and with microarray applications. The promoter fragments can be captured as modular entry clones (MultiSite Gateway format) via site‐specific recombinational cloning, and transferred into vectors of choice to investigate transcriptional networks. The fragments can also be amplified by PCR and printed on glass arrays. In combination with immunoprecipitation of protein–DNA complexes (ChIP–chip), these arrays enable characterization of binding sites for chromatin‐associated proteins or the extent of chromatin modifications at genome scale. The Arabidopsis histone acetyltransferase GCN5 associated with 40% of the tested promoters. At most sites, binding did not depend on the integrity of the GCN5 bromodomain. However, the presence of the bromodomain was necessary for binding to 11% of the promoter regions, and correlated with acetylation of lysine 14 of histone H3 in these promoters. Combined analysis of ChIP–chip and transcriptomic data indicated that binding of GCN5 does not strictly correlate with gene activation. GCN5 has previously been shown to be required for light‐regulated gene expression and growth, and we found that GCN5 targets were enriched in early light‐responsive genes. Thus, in addition to its transcriptional activation function, GCN5 may play an important role in priming activation of inducible genes under non‐induced conditions.
Arabinogalactan proteins 6 and 11 are required for stamen and pollen function in Arabidopsis
Authors: Levitin Bella , Richter Dganit , Markovich Inbal , Zik Moriyah 
Published: July 2008

SummarySuccessful male reproductive function in plants is dependent on the correct development and functioning of stamens and pollen. AGP6 and AGP11 are two homologous Arabidopsis genes encoding cell wall‐associated arabinogalactan glycoproteins (AGPs). Both genes were found to be specifically expressed in stamens, pollen grains and pollen tubes, suggesting that these genes may play a role in male organ development and function. RNAi lines with reduced AGP6 and AGP11 expression were generated. These, together with lines harboring point mutations in the coding region of AGP6, were used to show that loss of function in AGP6 and AGP11 led to reduced fertility, at least partly as a result of inhibition of pollen tube growth. Our results also suggest that AGP6 and AGP11 play an additional role in the release of pollen grains from the mature anther. Thus, our study demonstrates the involvement of specific AGPs in pollen tube growth and stamen function.
Getting the most out of publicly available T‐DNA insertion lines
Authors: Ülker Bekir , Peiter Edgar , Dixon David P. , Moffat Caroline , Capper Richard , Bouché Nicolas , Edwards Robert , Sanders Dale , Knight Heather , Knight Marc R. 
Published: July 2008

SummaryIn the course of several different projects, we came to realize that there is a significant amount of untapped potential in the publicly available T‐DNA insertion lines. In addition to the GABI‐Kat lines, which were designed specifically for activation tagging, lines from the SAIL and FLAGdb collections are also useful for this purpose. As well as the 35S promoter chosen for activation tagging in GABI‐Kat lines, we found that the 1′2′ bidirectional promoter is capable of activating expression of flanking genomic sequences in both GABI‐Kat and SAIL lines. Thus these lines have added potential for activation tagging. We also show that these lines are capable of generating antisense transcripts and so have the potential to be used for suppression (loss/reduction of function) studies. By virtue of weak terminator sequences in some T‐DNA constructs, transcript read‐through from selectable markers is also possible, which again has the potential to be exploited in activation/suppression studies. Finally, we show that, by selecting and characterizing lines in which the T‐DNA insertions are present specifically within introns of a target gene, an allelic series of mutants with varying levels of reduced expression can be generated, due to differences in efficiency of intron splicing. Taken together, our analyses demonstrate that there is a wealth of untapped potential within existing insertion lines for studies on gene function, and the effective exploitation of these resources is discussed.
Quantitative analysis of heterogeneous spatial distribution of Arabidopsis leaf trichomes using micro X‐ray computed tomography
Authors: Kaminuma Eli , Yoshizumi Takeshi , Wada Takuji , Matsui Minami , Toyoda Tetsuro 
Published: July 2008

SummaryQuantitative morphological traits may be defined based on the 3D anatomy reconstructed from micro X‐ray computed tomography (μCT) images. In this study, the heterogeneous spatial distribution of trichomes (hairs) on the adaxial leaf blade surface in Arabidopsis was evaluated in terms of 3D quantitative traits, including trichome number, average nearest‐neighbour distance between trichomes, and proportion of large trichomes. The data reflect spatial heterogeneity in the radial direction, in that a greater number of trichomes were observed on the leaf blade margins relative to the non‐margins, a distribution effect caused by the CAPRICE (CPC) and GLABRA3 (GL3) genes, which have previously been shown to affect trichome density. We further determined that the proportion of large trichomes on the blade mid‐rib increases from the proximal end to the distal leaf tip in both wild‐type plants and GL3 mutants. Our results indicate that the GL3 gene affects trichome distribution, rather than trichome growth, causing trichome initiation at the proximal base rather than the distal tip. On the other hand, CPC does affect trichome growth and developmental progression. Hence, quantitative phenotyping based on μCT enables precise phenotypic description for elucidation of gene control in morphological mutants.
Exploring the nuclear proteome ofMedicago truncatulaat the switch towards seed filling
Authors: Repetto Ombretta , Rogniaux Hélène , Firnhaber Christian , Zuber Hélène , Küster Helge , Larré Colette , Thompson Richard , Gallardo Karine 
Published: July 2008

SummaryDespite its importance in determining seed composition, and hence quality, regulation of the development of legume seeds is incompletely understood. Because of the cardinal role played by the nucleus in gene expression and regulation, we have characterized the nuclear proteome ofMedicago truncatulaat the 12 days after pollination (dap) stage that marks the switch towards seed filling. Nano‐liquid chromatography–tandem mass spectrometry analysis of nuclear protein bands excised from one‐dimensional SDS‐PAGE identified 179 polypeptides (143 different proteins), providing an insight into the complexity and distinctive feature of the seed nuclear proteome and highlighting new plant nuclear proteins with possible roles in the biogenesis of ribosomal subunits (PESCADILLO‐like) or nucleocytoplasmic trafficking (dynamin‐like GTPase). The results revealed that nuclei of 12‐dap seeds store a pool of ribosomal proteins in preparation for intense protein synthesis activity, occurring subsequently during seed filling. Diverse proteins of the molecular machinery leading to the synthesis of ribosomal subunits were identified along with proteins involved in transcriptional regulation, RNA processing or transport. Some had already been shown to play a role during the early stages of seed formation whereas for others the findings are novel (e.g. the DIP2 and ES43 transcriptional regulators or the RNA silencing‐related ARGONAUTE proteins). This study also revealed the presence of chromatin‐modifying enzymes and RNA interference proteins that have roles in RNA‐directed DNA methylation and may be involved in modifying genome architecture and accessibility during seed filling and maturation.
A new method for isolating large quantities of Arabidopsis trichomes for transcriptome, cell wall and other types of analyses
Authors: Marks M. David , Betancur Lissete , Gilding Edward , Chen Fang , Bauer Stefan , Wenger Jonathan P. , Dixon Richard A. , Haigler Candace H. 
Published: July 2008

SummaryA new procedure has been developed for the isolation of wild‐type and mutant Arabidopsis trichomes. The isolated trichomes maintained enzymatic activity and were used for DNA, protein, and RNA isolation. The RNA was used to generate probes suitable for Affymetrix analysis. The validity of the Affymetrix results was confirmed by quantitative PCR analysis on a subset of genes that are preferentially expressed in trichomes or leaves. Sufficient quantities of trichomes were isolated to probe the biochemical nature of trichome cell walls. These analyses provide evidence for the presence of lignin in Arabidopsis trichome cell walls. The monosaccharide analysis and positive staining with ruthenium red indicates that the walls also contain a large portion of pectin. The 2.23‐fold ratio of pectin‐related sugars compared with potential cellulosic glucose suggests that the polysaccharides of the trichome cell walls are more like those of typical primary walls even though the wall becomes quite thick. Overall, these analyses open the door to using the Arabidopsis trichome cell wall as an excellent model to probe various questions concerning plant cell wall biosynthesis.
Multicolor bimolecular fluorescence complementation reveals simultaneous formation of alternative CBL/CIPK complexes in planta
Authors: Waadt Rainer , Schmidt Lena K. , Lohse Marc , Hashimoto Kenji , Bock Ralph , Kudla Jörg 
Published: July 2008

SummaryThe specificity of intracellular signaling and developmental patterning in biological systems relies on selective interactions between different proteins in specific cellular compartments. The identification of such protein–protein interactions is essential for unraveling complex signaling and regulatory networks. Recently, bimolecular fluorescence complementation (BiFC) has emerged as a powerful technique for the efficient detection of protein interactions in their native subcellular localization. Here we report significant technical advances in the methodology of plant BiFC. We describe a series of versatile BiFC vector sets that are fully compatible with previously generated vectors. The new vectors enable the generation of both C‐terminal and N‐terminal fusion proteins and carry optimized fluorescent protein genes that considerably improve the sensitivity of BiFC. Using these vectors, we describe a multicolor BiFC (mcBiFC) approach for the simultaneous visualization of multiple protein interactions in the same cell. Application to a protein interaction network acting in calcium‐mediated signal transduction revealed the concurrent interaction of the protein kinase CIPK24 with the calcium sensors CBL1 and CBL10 at the plasma membrane and tonoplast, respectively. We have also visualized by mcBiFC the simultaneous formation of CBL1/CIPK1 and CBL9/CIPK1 protein complexes at the plasma membrane. Thus, mcBiFC provides a useful new tool for exploring complex regulatory networks in plants.
Differences in incidence of suicide attempts during phases of bipolar I and II disorders
Authors: Valtonen Hanna M , Suominen Kirsi , Haukka Jari , Mantere Outi , Leppämäki Sami , Arvilommi Petri , Isometsä Erkki T 
Published: July 2008

Background:  Differences in the incidence of suicide attempts during various phases of bipolar disorder (BD), or the relative importance of static versus time‐varying risk factors for overall risk for suicide attempts, are unknown.Methods:  We investigated the incidence of suicide attempts in different phases of BD as a part of the Jorvi Bipolar Study (JoBS), a naturalistic, prospective, 18‐month study representing psychiatric in‐ and outpatients with DSM‐IV BD in three Finnish cities. Life charts were used to classify time spent in follow‐up in the different phases of illness among the 81 BD I and 95 BD II patients.Results:  Compared to the other phases of the illness, the incidence of suicide attempts was 37‐fold higher [95% confidence interval (CI) for relative risk (RR): 11.8–120.3] during combined mixed and depressive mixed states, and 18‐fold higher (95% CI: 6.5–50.8) during major depressive phases. In Cox’s proportional hazards regression models, combined mixed (mixed or depressive mixed) or major depressive phases and prior suicide attempts independently predicted suicide attempts. No other factor significantly modified the risks related to these time‐varying risk factors; their population‐attributable fraction was 86%.Conclusions:  The incidence of suicide attempts varies remarkably between illness phases, with mixed and depressive phases involving the highest risk by time. Time spent in high‐risk illness phases is likely the major determinant of overall risk for suicide attempts among BD patients. Studies of suicidal behavior should investigate the role of both static and time‐varying risk factors in overall risk; clinically, management of mixed and depressive phases may be crucial in reducing risk.