Genome-wide analysis of heat shock transcription factor families in rice and Arabidopsis

Guo, Jingkang; Wu, Jian; Qian, Ji; Wang, Chao; Luo, Lei; Yuan, Yi; Wang, Yonghua; Wang, Jian

doi:10.1016/s1673-8527(08)60016-8

Cited by 227 publications

(241 citation statements)

References 52 publications

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“…In general, the rice genome encodes at least 26 Hsfs, including one variant that lacks a DNA-binding domain, a nuclear localization signal, a nuclear export signal, and an AHA-type activation domain (Guo et al 2008). Twenty-two of these 26 Hsfs were induced throughout the rice plant by heat shock treatment.…”

Section: Discussionmentioning

confidence: 99%

“…Mammals have three Hsf genes, whereas Chlamydomonas has only two Hsf genes, and only one of these (Hsf1) acts in the thermoresistance response (Morimoto 1998;Schulz-Raffelt et al 2007). Yeast and Drosophila have only a single Hsf each; however, Arabidopsis, rice, and tobacco have at least 21, 25 or 26, and 17 Hsf genes, respectively (Baniwal et al 2004;Guo et al 2008;Mishra et al 2002;Mittal et al 2009;von Koskull-Döring 2007). This high number of Hsf genes in higher plants suggests that plants have a complex and highly regulated system by which they cope with high temperatures and survive in a broader temperature range than animals or Chlamydomonas.…”

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confidence: 99%

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Generation of transgenic rice expressing heat shock protein genes under cool conditions

Yasuda

Sagehashi

Shimosaka

et al. 2013

Plant Biotechnology

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The heat shock response of rice, including expression of heat shock transcription factors (Hsfs), was investigated to elucidate the molecular regulation of its high-temperature tolerance. In silico analysis revealed that the rice genome encodes more than 19 species of Hsf genes that can be organized into three classes, A, B, and C. Rice seedlings treated with high temperature, express three class A Hsf genes (HsfA2a, HsfA2c, and HsfA2d) and two class B Hsf genes (HsfB2b and HsfB2c) at significantly elevated levels. Transgenic rice plants overexpressing these three class A Hsf genes controlled by the rice actin 1 promoter or the wheat cold response (WCR) promoter expressed the transgenes, but did not express heat shock response genes such as small HSPs, whose expression is controlled by Hsfs. Treatment with geldanamycin, an inhibitor of HSP90, elevated the expression of HSPs in the WCR::Hsf transformant. Therefore, transgenic rice co-expressing WCR::Hsfs and a dominant negative HSP90 mutant were generated in which the heat shock response could be induced under WCR promoter-activating conditions. Successful induction of the heat shock response under cool conditions in this co-expression line suggests that HSP90 controls the heat shock response via the activity of Hsf in rice cells.

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Generation of transgenic rice expressing heat shock protein genes under cool conditions

Yasuda

Sagehashi

Shimosaka

et al. 2013

Plant Biotechnology

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“…7B). HSF family members have long been associated with protein folding and stress response; thus, their role in early germination appears critical, as large numbers of proteins begin production over the germination time course (Guo et al, 2008). The identification of specific genes encoding transcription factors displaying distinct temporal expression patterns provides a way to identify putative regulators that meditate the transition from dormancy to early seedling growth after imbibition.…”

Section: Transient Changes In the Transcriptome Indicate That 3 H Maymentioning

confidence: 99%

Mapping Metabolic and Transcript Temporal Switches during Germination in Rice Highlights Specific Transcription Factors and the Role of RNA Instability in the Germination Process

et al. 2008

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Transcriptome and metabolite profiling of rice (Oryza sativa) embryo tissue during a detailed time course formed a foundation for examining transcriptional and posttranscriptional processes during germination. One hour after imbibition (HAI), independent of changes in transcript levels, rapid changes in metabolism occurred, including increases in hexose phosphates, tricarboxylic acid cycle intermediates, and g-aminobutyric acid. Later changes in the metabolome, including those involved in carbohydrate, amino acid, and cell wall metabolism, appeared to be driven by increases in transcript levels, given that the large group (over 6,000 transcripts) observed to increase from 12 HAI were enriched in metabolic functional categories. Analysis of transcripts encoding proteins located in the organelles of primary metabolism revealed that for the mitochondrial gene set, a greater proportion of transcripts peaked early, at 1 or 3 HAI, compared with the plastid set, and notably, many of these transcripts encoded proteins involved in transport functions. One group of over 2,000 transcripts displayed a unique expression pattern beginning with low levels in dry seeds, followed by a peak in expression levels at 1 or 3 HAI, before markedly declining at later time points. This group was enriched in transcription factors and signal transduction components. A subset of these transiently expressed transcription factors were further interrogated across publicly available rice array data, indicating that some were only expressed during the germination process. Analysis of the 1-kb upstream regions of transcripts displaying similar changes in abundance identified a variety of common sequence motifs, potential binding sites for transcription factors. Additionally, newly synthesized transcripts peaking at 3 HAI displayed a significant enrichment of sequence elements in the 3# untranslated region that have been previously associated with RNA instability. Overall, these analyses reveal that during rice germination, an immediate change in some metabolite levels is followed by a two-step, largescale rearrangement of the transcriptome that is mediated by RNA synthesis and degradation and is accompanied by later changes in metabolite levels.

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“…The At4g21080 (DOF4.5; Yanagisawa, 2002) promoter showed very strong chalaza-specific expression at the globular stage but then became more widespread throughout the endosperm, with the intensity of staining decreasing around the heart stage. The At4g18870 (HSF14; Guo et al, 2008) promoter also had very strong expression in the chalazal endosperm plus strong expression in the peripheral endosperm, but staining was not apparent in the micropylar domain. At around the heart stage, expression became restricted to the chalazal endosperm.…”

Section: Identification Of Promoters Driving Expression In the Early mentioning

confidence: 99%

Transcriptome Analysis of Proliferating Arabidopsis Endosperm Reveals Biological Implications for the Control of Syncytial Division, Cytokinin Signaling, and Gene Expression Regulation

et al. 2008

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During the early stages of seed development, Arabidopsis (Arabidopsis thaliana) endosperm is syncytial and proliferates rapidly through repeated rounds of mitosis without cytokinesis. This stage of endosperm development is important in determining final seed size and is a model for studying aspects of cellular and molecular biology, such as the cell cycle and genomic imprinting. However, the small size of the Arabidopsis seed makes high-throughput molecular analysis of the early endosperm technically difficult. Laser capture microdissection enabled high-resolution transcript analysis of the syncytial stage of Arabidopsis endosperm development at 4 d after pollination. Analysis of Gene Ontology representation revealed a developmental program dominated by the expression of genes associated with cell cycle, DNA processing, chromatin assembly, protein synthesis, cytoskeleton-and microtubule-related processes, and cell/organelle biogenesis and organization. Analysis of core cell cycle genes implicates particular gene family members as playing important roles in controlling syncytial cell division. Hormone marker analysis indicates predominance for cytokinin signaling during early endosperm development. Comparisons with publicly available microarray data revealed that approximately 800 putative early seed-specific genes were preferentially expressed in the endosperm. Early seed expression was confirmed for 71 genes using quantitative reverse transcription-polymerase chain reaction, with 27 transcription factors being confirmed as early seed specific. Promoter-reporter lines confirmed endosperm-preferred expression at 4 d after pollination for five transcription factors, which validates the approach and suggests important roles for these genes during early endosperm development. In summary, the data generated provide a useful resource providing novel insight into early seed development and identify new target genes for further characterization.

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Genome-wide analysis of heat shock transcription factor families in rice and Arabidopsis

Cited by 227 publications

References 52 publications

Generation of transgenic rice expressing heat shock protein genes under cool conditions

Generation of transgenic rice expressing heat shock protein genes under cool conditions

Mapping Metabolic and Transcript Temporal Switches during Germination in Rice Highlights Specific Transcription Factors and the Role of RNA Instability in the Germination Process

Transcriptome Analysis of Proliferating Arabidopsis Endosperm Reveals Biological Implications for the Control of Syncytial Division, Cytokinin Signaling, and Gene Expression Regulation

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