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Mittal D, Enoki Y, Lavania D, Singh A, Sakurai H, Grover A. Binding affinities and interactions among different heat shock element types and heat shock factors in rice (Oryza sativa L.). FEBS J 2011; 278:3076-85. [PMID: 21729241 DOI: 10.1111/j.1742-4658.2011.08229.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Binding of heat shock factors (Hsfs) to heat shock elements (HSEs) leads to transcriptional regulation of heat shock genes. Genome-wide, 953 rice genes contain perfect-type, 695 genes gap-type and 1584 genes step-type HSE sequences in their 1-kb promoter region. The rice genome contains 13 class A, eight class B and four class C Hsfs (OsHsfs) and has OsHsf26 (which is of variant type) genes. Chemical cross-linking analysis of in vitro synthesized OsHsf polypeptides showed formation of homotrimers of OsHsfA2c, OsHsfA9 and OsHsfB4b proteins. Binding analysis of polypeptides with oligonucleotide probes containing perfect-, gap-, and step-type HSE sequences showed that OsHsfA2c, OsHsfA9 and OsHsfB4b differentially recognize various model HSEs as a function of varying reaction temperatures. The homomeric form of OsHsfA2c and OsHsfB4b proteins was further noted by the bimolecular fluorescence complementation approach in onion epidermal cells. In yeast two-hybrid assays, OsHsfB4b showed homomeric interaction as well as distinct heteromeric interactions with OsHsfA2a, OsHsfA7, OsHsfB4c and OsHsf26. Transactivation activity was noted in OsHsfA2c, OsHsfA2d, OsHsfA9, OsHsfC1a and OsHsfC1b in yeast cells. These differential patterns pertaining to binding with HSEs and protein-protein interactions may have a bearing on the cellular functioning of OsHsfs under a range of different physiological and environmental conditions.
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Affiliation(s)
- Dheeraj Mittal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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152
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Chauhan H, Khurana N, Agarwal P, Khurana P. Heat shock factors in rice (Oryza sativa L.): genome-wide expression analysis during reproductive development and abiotic stress. Mol Genet Genomics 2011; 286:171-87. [PMID: 21792744 DOI: 10.1007/s00438-011-0638-8] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 07/05/2011] [Indexed: 11/28/2022]
Abstract
Plants respond to heat stress by enhancing the expression of genes encoding heat shock protein (HSPs) genes through activation of heat shock factors (HSFs) which interact with heat shock elements present in the promoter of HSP genes. Plant HSFs have been divided into three conserved classes viz A, B and C. In the present study, a detailed analysis has been done of all rice HSFs, along with their spliced variants. Their chromosomal localization reveals that six HSFs are segmentally duplicated and four pairs of these segmentally duplicated HSF encoding genes show pseudo-functionalization. Expression profiling through microarray and quantitative real-time PCR showed that eight OsHsfs express at a higher level during seed development, while six HSFs are up-regulated in all the abiotic stresses studied. The expression of OsHsfA2a gene in particular was greatly stimulated by heat stress in both root and shoot tissues and also during panicle and seed development. OsHsfA3 was found more responsive to cold and drought stress, while OsHsfA7 and OsHsfA9 showed developing seed-specific expression. This study also revealed that spliced variants generally accumulated at a higher level in all the tissues examined. Different hormones/elicitors like ABA, brassinosteroids and salicylic acid also alter OsHsf gene expression. Calcium in combination with heat stress elevated further the level of HSF transcripts. Expression analysis by both microarray and real-time RT-PCR revealed a unique stable constitutive expression of OsHsfA1 across all the tissues and stresses. A detailed in silico analysis involving identification of unidentified domains has been done by MEME-motif tool in their full-length proteins as well as in DNA-binding domains. Analysis of 1 kb putative promoter region revealed presence of tissue-specific, abiotic stress and hormone-related cis-acting elements, correlating with expression under stress conditions.
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Affiliation(s)
- Harsh Chauhan
- Department of Plant Molecular Biology, University of Delhi, South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110 021, India
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153
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Lenka SK, Katiyar A, Chinnusamy V, Bansal KC. Comparative analysis of drought-responsive transcriptome in Indica rice genotypes with contrasting drought tolerance. PLANT BIOTECHNOLOGY JOURNAL 2011; 9:315-27. [PMID: 20809928 DOI: 10.1111/j.1467-7652.2010.00560.x] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Genetic improvement in drought tolerance in rice is the key to save water for sustainable agriculture. Drought tolerance is a complex trait and involves interplay of a vast array of genes. Several genotypes of rice have evolved features that impart tolerance to drought and other abiotic stresses. Comparative analysis of drought stress-responsive transcriptome between drought-tolerant (DT) landraces/genotypes and drought-sensitive modern rice cultivars will unravel novel genetic regulatory mechanisms involved in stress tolerance. Here, we report transcriptome analysis in a highly DT rice landrace, Nagina 22 (N22), versus a high-yielding but drought-susceptible rice variety IR64. Both genotypes exhibited a diverse global transcriptional response under normal and drought conditions. Gene ontology (GO) analysis suggested that drought tolerance of N22 was attributable to the enhanced expression of several enzyme-encoding genes. Drought susceptibility of IR64 was attributable to significant down-regulation of regulatory components that confer drought tolerance. Pathway analysis unravelled significant up-regulation of several components of carbon fixation, glycolysis/gluconeogenesis and flavonoid biosynthesis and down-regulation of starch and sucrose metabolism in both the cultivars under drought. However, significant up-regulation of α-linolenic acid metabolic pathway observed in N22 under drought appears to be in good agreement with high drought tolerance of this genotype. Consensus cis-motif profiling of drought-induced co-expressed genes led to the identification of novel cis-motifs. Taken together, the results of the comparative transcriptome analysis led to the identification of specific genotype-dependent genes responsible for drought tolerance in the rice landrace N22.
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Affiliation(s)
- Sangram K Lenka
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, India
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154
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Lin YX, Jiang HY, Chu ZX, Tang XL, Zhu SW, Cheng BJ. Genome-wide identification, classification and analysis of heat shock transcription factor family in maize. BMC Genomics 2011; 12:76. [PMID: 21272351 PMCID: PMC3039612 DOI: 10.1186/1471-2164-12-76] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2010] [Accepted: 01/27/2011] [Indexed: 11/15/2022] Open
Abstract
Background Heat shock response in eukaryotes is transcriptionally regulated by conserved heat shock transcription factors (Hsfs). Hsf genes are represented by a large multigene family in plants and investigation of the Hsf gene family will serve to elucidate the mechanisms by which plants respond to stress. In recent years, reports of genome-wide structural and evolutionary analysis of the entire Hsf gene family have been generated in two model plant systems, Arabidopsis and rice. Maize, an important cereal crop, has represented a model plant for genetics and evolutionary research. Although some Hsf genes have been characterized in maize, analysis of the entire Hsf gene family were not completed following Maize (B73) Genome Sequencing Project. Results A genome-wide analysis was carried out in the present study to identify all Hsfs maize genes. Due to the availability of complete maize genome sequences, 25 nonredundant Hsf genes, named ZmHsfs were identified. Chromosomal location, protein domain and motif organization of ZmHsfs were analyzed in maize genome. The phylogenetic relationships, gene duplications and expression profiles of ZmHsf genes were also presented in this study. Twenty-five ZmHsfs were classified into three major classes (class A, B, and C) according to their structural characteristics and phylogenetic comparisons, and class A was further subdivided into 10 subclasses. Moreover, phylogenetic analysis indicated that the orthologs from the three species (maize, Arabidopsis and rice) were distributed in all three classes, it also revealed diverse Hsf gene family expression patterns in classes and subclasses. Chromosomal/segmental duplications played a key role in Hsf gene family expansion in maize by investigation of gene duplication events. Furthermore, the transcripts of 25 ZmHsf genes were detected in the leaves by heat shock using quantitative real-time PCR. The result demonstrated that ZmHsf genes exhibit different expression levels in heat stress treatment. Conclusions Overall, data obtained from our investigation contributes to a better understanding of the complexity of the maize Hsf gene family and provides the first step towards directing future experimentation designed to perform systematic analysis of the functions of the Hsf gene family.
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Affiliation(s)
- Yong-Xiang Lin
- Key Lab of Crop Biology, School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, China
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155
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Mangelsen E, Kilian J, Harter K, Jansson C, Wanke D, Sundberg E. Transcriptome analysis of high-temperature stress in developing barley caryopses: early stress responses and effects on storage compound biosynthesis. MOLECULAR PLANT 2011; 4:97-115. [PMID: 20924027 DOI: 10.1093/mp/ssq058] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
High-temperature stress, like any abiotic stress, impairs the physiology and development of plants, including the stages of seed setting and ripening. We used the Affymetrix 22K Barley1 GeneChip microarray to investigate the response of developing barley (Hordeum vulgare) seeds, termed caryopses, after 0.5, 3, and 6 h of heat stress exposure; 958 induced and 1122 repressed genes exhibited spatial and temporal expression patterns that provide a detailed insight into the caryopses' early heat stress responses. Down-regulation of genes related to storage compound biosynthesis and cell growth provides evidence for a rapid impairment of the caryopsis' development. Increased levels of sugars and amino acids were indicative for both production of compatible solutes and feedback-induced accumulation of substrates for storage compound biosynthesis. Metadata analysis identified embryo and endosperm as primary locations of heat stress responses, indicating a strong impact of short-term heat stress on central developmental functions of the caryopsis. A comparison with heat stress responses in Arabidopsis shoots and drought stress responses in barley caryopses identified both conserved and presumably heat- and caryopsis-specific stress-responsive genes. Summarized, our data provide an important basis for further investigation of gene functions in order to aid an improved heat tolerance and reduced losses of yield in barley as a model for cereal crops.
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Affiliation(s)
- Elke Mangelsen
- Department of Plant Biology and Forest Genetics, The Swedish University of Agricultural Sciences (SLU), PO Box 7080, SE-75007 Uppsala, Sweden.
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156
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Calcium and secondary CPK signaling in plants in response to herbivore attack. Biochem Biophys Res Commun 2010; 400:455-60. [DOI: 10.1016/j.bbrc.2010.08.134] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 08/29/2010] [Indexed: 01/14/2023]
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157
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Kanchiswamy CN, Takahashi H, Quadro S, Maffei ME, Bossi S, Bertea C, Zebelo SA, Muroi A, Ishihama N, Yoshioka H, Boland W, Takabayashi J, Endo Y, Sawasaki T, Arimura GI. Regulation of Arabidopsis defense responses against Spodoptera littoralis by CPK-mediated calcium signaling. BMC PLANT BIOLOGY 2010; 10:97. [PMID: 20504319 PMCID: PMC3095362 DOI: 10.1186/1471-2229-10-97] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Accepted: 05/26/2010] [Indexed: 05/20/2023]
Abstract
BACKGROUND Plant Ca2+ signals are involved in a wide array of intracellular signaling pathways after pest invasion. Ca2+-binding sensory proteins such as Ca2+-dependent protein kinases (CPKs) have been predicted to mediate the signaling following Ca2+ influx after insect herbivory. However, until now this prediction was not testable. RESULTS To investigate the roles CPKs play in a herbivore response-signaling pathway, we screened the characteristics of Arabidopsis CPK mutants damaged by a feeding generalist herbivore, Spodoptera littoralis. Following insect attack, the cpk3 and cpk13 mutants showed lower transcript levels of plant defensin gene PDF1.2 compared to wild-type plants. The CPK cascade was not directly linked to the herbivory-induced signaling pathways that were mediated by defense-related phytohormones such as jasmonic acid and ethylene. CPK3 was also suggested to be involved in a negative feedback regulation of the cytosolic Ca2+ levels after herbivory and wounding damage. In vitro kinase assays of CPK3 protein with a suite of substrates demonstrated that the protein phosphorylates transcription factors (including ERF1, HsfB2a and CZF1/ZFAR1) in the presence of Ca2+. CPK13 strongly phosphorylated only HsfB2a, irrespective of the presence of Ca2+. Furthermore, in vivo agroinfiltration assays showed that CPK3-or CPK13-derived phosphorylation of a heat shock factor (HsfB2a) promotes PDF1.2 transcriptional activation in the defense response. CONCLUSIONS These results reveal the involvement of two Arabidopsis CPKs (CPK3 and CPK13) in the herbivory-induced signaling network via HsfB2a-mediated regulation of the defense-related transcriptional machinery. This cascade is not involved in the phytohormone-related signaling pathways, but rather directly impacts transcription factors for defense responses.
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Affiliation(s)
- Chidananda Nagamangala Kanchiswamy
- Global COE Program: Evolution and Biodiversity, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
- Center for Ecological Research, Kyoto University, Otsu 520-2113, Japan
- Plant Physiology Unit, Department of Plant Biology and Innovation Centre, University of Turin, 10135 Turin, Italy
| | - Hirotaka Takahashi
- Current Address: Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
- Cell-free Science and Technology Research Center, Ehime University, Matsuyama 790-8577, Japan
| | - Stefano Quadro
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745, Germany
| | - Massimo E Maffei
- Plant Physiology Unit, Department of Plant Biology and Innovation Centre, University of Turin, 10135 Turin, Italy
| | - Simone Bossi
- Plant Physiology Unit, Department of Plant Biology and Innovation Centre, University of Turin, 10135 Turin, Italy
| | - Cinzia Bertea
- Plant Physiology Unit, Department of Plant Biology and Innovation Centre, University of Turin, 10135 Turin, Italy
| | - Simon Atsbaha Zebelo
- Plant Physiology Unit, Department of Plant Biology and Innovation Centre, University of Turin, 10135 Turin, Italy
| | - Atsushi Muroi
- Global COE Program: Evolution and Biodiversity, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
- Center for Ecological Research, Kyoto University, Otsu 520-2113, Japan
| | - Nobuaki Ishihama
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Hirofumi Yoshioka
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Wilhelm Boland
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745, Germany
| | - Junji Takabayashi
- Center for Ecological Research, Kyoto University, Otsu 520-2113, Japan
| | - Yaeta Endo
- Cell-free Science and Technology Research Center, Ehime University, Matsuyama 790-8577, Japan
| | - Tatsuya Sawasaki
- Cell-free Science and Technology Research Center, Ehime University, Matsuyama 790-8577, Japan
| | - Gen-ichiro Arimura
- Global COE Program: Evolution and Biodiversity, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
- Center for Ecological Research, Kyoto University, Otsu 520-2113, Japan
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158
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Wang Z, Zhang Q. Genome-wide identification and evolutionary analysis of the animal specific ETS transcription factor family. Evol Bioinform Online 2009; 5:119-31. [PMID: 20011068 PMCID: PMC2789578 DOI: 10.4137/ebo.s2948] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The ETS proteins are a family of transcription factors (TFs) that regulate a variety of biological processes. We made genome-wide analyses to explore the classification of the ETS gene family. We identified 207 ETS genes which encode 321 ETS TFs from ten animal species. Of the 321 ETS TFs, 155 contain only an ETS domain, about 50% contain a ETS_PEA3_N or a SAM_PNT domain in addition to an ETS domain, the rest (only four) contain a second ETS domain or a second ETS_PEA3_N domain or an another domain (AT_hook or DNA_pol_B). A Neighbor-Joining phylogenetic tree was constructed using the amino acid sequences of the ETS domain of the ETS TFs. The results revealed that the ETS genes of the ten species can be divided into two distinct groups. Group I contains one nematode ETS gene and 18 vertebrate animal ETS genes. Group II contains the majority of the ETS TFs and can be further divided into eleven subgroups. The sequence motifs outside the DNA-binding domain and the conservation of the exon-intron structural patterns of the ETS TFs in human, cattle, and chicken further support the phylogenetic classification among these ETS TFs. Extensive duplication of the ETS genes was found in the genome of each species. The duplicated ETS genes account for ~69% of the total of ETS genes. Furthermore, we also found there are ETS gene clusters in all of the ten animal species. Statistical analysis of the Gene Ontology annotations of the ETS genes showed that the ETS proteins tend to be related to RNA biosynthetic process, biopolymer metabolic process and macromolecule metabolic process expected from the common GO categories of transcriptional factors. We also discussed the functional conservation and diversification of ETS TFs.
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Affiliation(s)
- Zhipeng Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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159
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Mittal D, Chakrabarti S, Sarkar A, Singh A, Grover A. Heat shock factor gene family in rice: genomic organization and transcript expression profiling in response to high temperature, low temperature and oxidative stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2009; 47:785-95. [PMID: 19539489 DOI: 10.1016/j.plaphy.2009.05.003] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Revised: 05/05/2009] [Accepted: 05/19/2009] [Indexed: 05/04/2023]
Abstract
Binding of heat shock factors (HSFs) with heat shock element sequence is critical for the transcriptional induction of heat shock genes. Rice genome sequence shows 26 OsHsf genes out of which 25 possess various important domains noted in HSFs i.e. DNA binding domain (DBD), oligomerization domain (OD), nuclear localization signal (NLS), nuclear export signal (NES) and AHA type activation domain. OsHsf entry LOC_Os06g226100 has the oligomerization domain but lacks the above other domains. Also, there are no ESTs or full-length cDNA noted for this entry in database. Expression profiling showed that 22 OsHsf genes are induced by high temperature. Induction of 10 and 14 OsHsf genes was also noted against low temperature stress and oxidative stress, respectively. All OsHsf genes induced by oxidative stress were also induced by high temperature. On the other hand, induction of 6 and 1 OsHsf genes was noted to be exclusive to high and low temperature stresses, respectively. Seven OsHsf genes showed induced expression in response to all the three stresses examined. While in silico promoter analysis showed that OsHsf genes contain upstream regulatory elements corresponding to different abiotic stresses, there was lack of correlation noted between the in silico profiling of the elements and their corresponding transcript expression patterns. Apart from stress inducibility, EST database suggests that various OsHsf genes are developmentally regulated in diverse tissue types.
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Affiliation(s)
- Dheeraj Mittal
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi-110021, India
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160
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Howell KA, Narsai R, Carroll A, Ivanova A, Lohse M, Usadel B, Millar AH, Whelan J. Mapping metabolic and transcript temporal switches during germination in rice highlights specific transcription factors and the role of RNA instability in the germination process. PLANT PHYSIOLOGY 2009; 149:961-80. [PMID: 19074628 PMCID: PMC2633829 DOI: 10.1104/pp.108.129874] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 12/03/2008] [Indexed: 05/20/2023]
Abstract
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 gamma-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, large-scale 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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Affiliation(s)
- Katharine A Howell
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
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161
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Day RC, Herridge RP, Ambrose BA, Macknight RC. Transcriptome analysis of proliferating Arabidopsis endosperm reveals biological implications for the control of syncytial division, cytokinin signaling, and gene expression regulation. PLANT PHYSIOLOGY 2008; 148:1964-84. [PMID: 18923020 PMCID: PMC2593665 DOI: 10.1104/pp.108.128108] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Accepted: 10/06/2008] [Indexed: 05/18/2023]
Abstract
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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Affiliation(s)
- Robert C Day
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
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