201
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Chawade A, Lindlöf A, Olsson B, Olsson O. Global expression profiling of low temperature induced genes in the chilling tolerant japonica rice Jumli Marshi. PLoS One 2013; 8:e81729. [PMID: 24349120 PMCID: PMC3861252 DOI: 10.1371/journal.pone.0081729] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 10/21/2013] [Indexed: 11/21/2022] Open
Abstract
Low temperature is a key factor that limits growth and productivity of many important agronomical crops worldwide. Rice (Oryza sativa L.) is negatively affected already at temperatures below +10°C and is therefore denoted as chilling sensitive. However, chilling tolerant rice cultivars exist and can be commercially cultivated at altitudes up to 3,050 meters with temperatures reaching as low as +4°C. In this work, the global transcriptional response to cold stress (+4°C) was studied in the Nepalese highland variety Jumli Marshi (spp. japonica) and 4,636 genes were identified as significantly differentially expressed within 24 hours of cold stress. Comparison with previously published microarray data from one chilling tolerant and two sensitive rice cultivars identified 182 genes differentially expressed (DE) upon cold stress in all four rice cultivars and 511 genes DE only in the chilling tolerant rice. Promoter analysis of the 182 genes suggests a complex cross-talk between ABRE and CBF regulons. Promoter analysis of the 511 genes identified over-represented ABRE motifs but not DRE motifs, suggesting a role for ABA signaling in cold tolerance. Moreover, 2,101 genes were DE in Jumli Marshi alone. By chromosomal localization analysis, 473 of these cold responsive genes were located within 13 different QTLs previously identified as cold associated.
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Affiliation(s)
| | - Angelica Lindlöf
- CropTailor AB, Lund, Sweden
- Systems Biology Research Centre, School of Life Sciences, University of Skövde, Skövde, Sweden
| | - Björn Olsson
- Systems Biology Research Centre, School of Life Sciences, University of Skövde, Skövde, Sweden
| | - Olof Olsson
- CropTailor AB, Lund, Sweden
- Department of Pure and Applied Biochemistry, Lund University, Lund, Sweden
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202
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Keily J, MacGregor DR, Smith RW, Millar AJ, Halliday KJ, Penfield S. Model selection reveals control of cold signalling by evening-phased components of the plant circadian clock. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:247-57. [PMID: 23909712 PMCID: PMC4278413 DOI: 10.1111/tpj.12303] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 06/01/2013] [Accepted: 07/09/2013] [Indexed: 05/08/2023]
Abstract
Circadian clocks confer advantages by restricting biological processes to certain times of day through the control of specific phased outputs. Control of temperature signalling is an important function of the plant oscillator, but the architecture of the gene network controlling cold signalling by the clock is not well understood. Here we use a model ensemble fitted to time-series data and a corrected Akaike Information Criterion (AICc) analysis to extend a dynamic model to include the control of the key cold-regulated transcription factors C-REPEAT BINDING FACTORs 1-3 (CBF1, CBF2, CBF3). AICc was combined with in silico analysis of genetic perturbations in the model ensemble, and selected a model that predicted mutant phenotypes and connections between evening-phased circadian clock components and CBF3 transcriptional control, but these connections were not shared by CBF1 and CBF2. In addition, our model predicted the correct gating of CBF transcription by cold only when the cold signal originated from the clock mechanism itself, suggesting that the clock has an important role in temperature signal transduction. Our data shows that model selection could be a useful method for the expansion of gene network models.
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Affiliation(s)
- Jack Keily
- Biosciences, College of Life and Environmental Sciences, University of ExeterStocker Road, Exeter, EX4 4QD, UK
- † These authors contributed equally to the work
| | - Dana R MacGregor
- Biosciences, College of Life and Environmental Sciences, University of ExeterStocker Road, Exeter, EX4 4QD, UK
- † These authors contributed equally to the work
| | - Robert W Smith
- Department of Biological Sciences, University of EdinburghCH Waddington Building, Mayfield Road, Edinburgh, EH9 3JD, UK
| | - Andrew J Millar
- Department of Biological Sciences, University of EdinburghCH Waddington Building, Mayfield Road, Edinburgh, EH9 3JD, UK
| | - Karen J Halliday
- Department of Biological Sciences, University of EdinburghCH Waddington Building, Mayfield Road, Edinburgh, EH9 3JD, UK
| | - Steven Penfield
- Biosciences, College of Life and Environmental Sciences, University of ExeterStocker Road, Exeter, EX4 4QD, UK
- * For correspondence (e-mail )
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203
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Hotta CT, Nishiyama MY, Souza GM. Circadian rhythms of sense and antisense transcription in sugarcane, a highly polyploid crop. PLoS One 2013; 8:e71847. [PMID: 23936527 PMCID: PMC3735537 DOI: 10.1371/journal.pone.0071847] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 07/05/2013] [Indexed: 12/04/2022] Open
Abstract
Commercial sugarcane (Saccharum hybrid) is a highly polyploid and aneuploid grass that stores large amounts of sucrose in its stem. We have measured circadian rhythms of sense and antisense transcription in a commercial cultivar (RB855453) using a custom oligoarray with 14,521 probes that hybridize to sense transcripts (SS) and 7,380 probes that hybridize to antisense transcripts (AS).We estimated that 32% of SS probes and 22% AS probes were rhythmic. This is a higher proportion of rhythmic probes than the usually found in similar experiments in other plant species. Orthologs and inparalogs of Arabidopsis thaliana, sugarcane, rice, maize and sorghum were grouped in ortholog clusters. When ortholog clusters were used to compare probes among different datasets, sugarcane also showed a higher proportion of rhythmic elements than the other species. Thus, it is possible that a higher proportion of transcripts are regulated by the sugarcane circadian clock. Thirty-six percent of the identified AS/SS pairs had significant correlated time courses and 64% had uncorrelated expression patterns. The clustering of transcripts with similar function, the anticipation of daily environmental changes and the temporal compartmentation of metabolic processes were some properties identified in the circadian sugarcane transcriptome. During the day, there was a dominance of transcripts associated with photosynthesis and carbohydrate metabolism, including sucrose and starch synthesis. During the night, there was dominance of transcripts associated with genetic processing, such as histone regulation and RNA polymerase, ribosome and protein synthesis. Finally, the circadian clock also regulated hormone signalling pathways: a large proportion of auxin and ABA signalling components were regulated by the circadian clock in an unusual biphasic distribution.
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Affiliation(s)
- Carlos Takeshi Hotta
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Milton Yutaka Nishiyama
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Glaucia Mendes Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- * E-mail:
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204
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Subset of heat-shock transcription factors required for the early response of Arabidopsis to excess light. Proc Natl Acad Sci U S A 2013; 110:14474-9. [PMID: 23918368 DOI: 10.1073/pnas.1311632110] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sunlight provides energy for photosynthesis and is essential for nearly all life on earth. However, too much or too little light or rapidly fluctuating light conditions cause stress to plants. Rapid changes in the amount of light are perceived as a change in the reduced/oxidized (redox) state of photosynthetic electron transport components in chloroplasts. However, how this generates a signal that is relayed to changes in nuclear gene expression is not well understood. We modified redox state in the reference plant, Arabidopsis thaliana, using either excess light or low light plus the herbicide DBMIB (2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone), a well-known inhibitor of photosynthetic electron transport. Modification of redox state caused a change in expression of a common set of about 750 genes, many of which are known stress-responsive genes. Among the most highly enriched promoter elements in the induced gene set were heat-shock elements (HSEs), known motifs that change gene expression in response to high temperature in many systems. We show that HSEs from the promoter of the ASCORBATE PEROXIDASE 2 (APX2) gene were necessary and sufficient for APX2 expression in conditions of excess light, or under low light plus the herbicide. We tested APX2 expression phenotypes in overexpression and loss-of-function mutants of 15 Arabidopsis A-type heat-shock transcription factors (HSFs), and identified HSFA1D, HSFA2, and HSFA3 as key factors regulating APX2 expression in diverse stress conditions. Excess light regulates both the subcellular location of HSFA1D and its biochemical properties, making it a key early component of the excess light stress network of plants.
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205
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Pacín M, Legris M, Casal JJ. COP1 re-accumulates in the nucleus under shade. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:631-41. [PMID: 23647163 DOI: 10.1111/tpj.12226] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Revised: 04/25/2013] [Accepted: 04/29/2013] [Indexed: 05/23/2023]
Abstract
Shade-avoider plants typically respond to shade-light signals by increasing the rate of stem growth. CONSTITTUTIVE PHOTOMORPHOGENESIS 1 (COP1) is an E3 ligase involved in the ubiquitin labelling of proteins targeted for degradation. In dark-grown seedlings, COP1 accumulates in the nucleus and light exposure causes COP1 migration to the cytosol. Here, we show that in Arabidopsis thaliana, COP1 accumulates in the nucleus under natural or simulated shade, despite the presence of far-red light. In plants grown under white light, the transfer to shade-light conditions triggers an unexpectedly rapid re-accumulation of COP1 in the nucleus. The partial simulation of shade by lowering either blue or red light levels (maintaining far-red light) caused COP1 nuclear re-accumulation. Hypocotyl growth of wild-type seedlings is more sensitive to afternoon shade than to morning shade. A residual response to shade was observed in the cop1 mutant background, but these seedlings showed inverted sensitivity as they responded to morning shade and not to afternoon shade. COP1 overexpression exaggerated the wild-type pattern by enhancing afternoon sensitivity and making morning shade inhibitory of growth. COP1 nuclear re-accumulation also responded more strongly to afternoon shade than to morning shade. These results are consistent with a signalling role of COP1 in shade avoidance. We propose a function of COP1 in setting the daily patterns of sensitivity to shade in the fluctuating light environments of plant canopies.
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Affiliation(s)
- Manuel Pacín
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires and CONICET, 1417, Buenos Aires, Argentina
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206
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Phase-resetting mechanism of the circadian clock in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A 2013; 110:13666-71. [PMID: 23898163 DOI: 10.1073/pnas.1220004110] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although the circadian clock is a self-sustaining oscillator having a periodicity of nearly 1 d, its period length is not necessarily 24 h. Therefore, daily adjustment of the clock (i.e., resetting) is an essential mechanism for the circadian clock to adapt to daily environmental changes. One of the major cues for this resetting mechanism is light. In the unicellular green alga Chlamydomonas reinhardtii, the circadian clock is reset by blue/green and red light. However, the underlying molecular mechanisms remain largely unknown. In this study, using clock protein-luciferase fusion reporters, we found that the level of RHYTHM OF CHLOROPLAST 15 (ROC15), a clock component in C. reinhardtii, decreased rapidly after light exposure in a circadian-phase-independent manner. Blue, green, and red light were able to induce this process, with red light being the most effective among them. Expression analyses and inhibitor experiments suggested that this process was regulated mainly by a proteasome-dependent protein degradation pathway. In addition, we found that the other clock gene, ROC114, encoding an F-box protein, was involved in this process. Furthermore, we demonstrated that a roc15 mutant showed defects in the phase-resetting of the circadian clock by light. Taken together, these data strongly suggest that the light-induced degradation of ROC15 protein is one of the triggers for resetting the circadian clock in C. reinhardtii. Our data provide not only a basis for understanding the molecular mechanisms of light-induced phase-resetting in C. reinhardtii, but also insights into the phase-resetting mechanisms of circadian clocks in plants.
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207
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Abstract
Large-scale biology among plant species, as well as comparative genomics of circadian clock architecture and clock-regulated output processes, have greatly advanced our understanding of the endogenous timing system in plants.
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208
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Cox RS, Nishikata K, Shimoyama S, Yoshida Y, Matsui M, Makita Y, Toyoda T. PromoterCAD: Data-driven design of plant regulatory DNA. Nucleic Acids Res 2013; 41:W569-74. [PMID: 23766287 PMCID: PMC3692106 DOI: 10.1093/nar/gkt518] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Synthetic promoters can control the timing, location and amount of gene expression for any organism. PromoterCAD is a web application for designing synthetic promoters with altered transcriptional regulation. We use a data-first approach, using published high-throughput expression and motif data from for Arabidopsis thaliana to guide DNA design. We demonstrate data mining tools for finding motifs related to circadian oscillations and tissue-specific expression patterns. PromoterCAD is built on the LinkData open platform for data publication and rapid web application development, allowing new data to be easily added, and the source code modified to add new functionality. PromoterCAD URL: http://promotercad.org. LinkData URL: http://linkdata.org.
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Affiliation(s)
- Robert Sidney Cox
- Bioinformatics and Systems Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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209
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Hanumappa M, Preece J, Elser J, Nemeth D, Bono G, Wu K, Jaiswal P. WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks. RICE (NEW YORK, N.Y.) 2013; 6:14. [PMID: 24280312 PMCID: PMC4883732 DOI: 10.1186/1939-8433-6-14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 05/22/2013] [Indexed: 05/29/2023]
Abstract
BACKGROUND Next-generation sequencing and 'omics' platforms are used extensively in plant biology research to unravel new genomes and study their interactions with abiotic and biotic agents in the growth environment. Despite the availability of a large and growing number of genomic data sets, there are only limited resources providing highly-curated and up-to-date metabolic and regulatory networks for plant pathways. RESULTS Using PathVisio, a pathway editor tool associated with WikiPathways, we created a gene interaction network of 430 rice (Oryza sativa) genes involved in the seed development process by curating interactions reported in the published literature. We then applied an InParanoid-based homology search to these genes and used the resulting gene clusters to identify 351 Arabidopsis thaliana genes. Using this list of homologous genes, we constructed a seed development network in Arabidopsis by processing the gene list and the rice network through a Perl utility software called Pathway GeneSWAPPER developed by us. In order to demonstrate the utility of these networks in generating testable hypotheses and preliminary analysis prior to more in-depth downstream analysis, we used the expression viewer and statistical analysis features of PathVisio to analyze publicly-available and published microarray gene expression data sets on diurnal photoperiod response and the seed development time course to discover patterns of coexpressed genes found in the rice and Arabidopsis seed development networks. These seed development networks described herein, along with other plant pathways and networks, are freely available on the plant pathways portal at WikiPathways (http://plants.wikipathways.org). CONCLUSION In collaboration with the WikiPathways project we present a community curation and analysis platform for plant biologists where registered users can freely create, edit, share and monitor pathways supported by published literature. We describe the curation and annotation of a seed development network in rice, and the projection of a similar, gene homology-based network in Arabidopsis. We also demonstrate the utility of the Pathway GeneSWAPPER (PGS) application in saving valuable time and labor when a reference network in one species compiled in GPML format is used to project a similar network in another species based on gene homology.
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Affiliation(s)
- Mamatha Hanumappa
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902 USA
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902 USA
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902 USA
| | - Denise Nemeth
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902 USA
| | - Gina Bono
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902 USA
| | - Kenny Wu
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902 USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902 USA
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210
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Locascio A, Blázquez MA, Alabadí D. Dynamic regulation of cortical microtubule organization through prefoldin-DELLA interaction. Curr Biol 2013; 23:804-9. [PMID: 23583555 DOI: 10.1016/j.cub.2013.03.053] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 03/06/2013] [Accepted: 03/22/2013] [Indexed: 12/23/2022]
Abstract
Plant morphogenesis relies on specific patterns of cell division and expansion. It is well established that cortical microtubules influence the direction of cell expansion, but less is known about the molecular mechanisms that regulate microtubule arrangement. Here we show that the phytohormones gibberellins (GAs) regulate microtubule orientation through physical interaction between the nuclear-localized DELLA proteins and the prefoldin complex, a cochaperone required for tubulin folding. In the presence of GA, DELLA proteins are degraded, and the prefoldin complex stays in the cytoplasm and is functional. In the absence of GA, the prefoldin complex is localized to the nucleus, which severely compromises α/β-tubulin heterodimer availability, affecting microtubule organization. The physiological relevance of this molecular mechanism was confirmed by the observation that the daily rhythm of plant growth was accompanied by coordinated oscillation of DELLA accumulation, prefoldin subcellular localization, and cortical microtubule reorientation.
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Affiliation(s)
- Antonella Locascio
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
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211
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Jeong J, Choi G. Phytochrome-interacting factors have both shared and distinct biological roles. Mol Cells 2013; 35:371-80. [PMID: 23708772 PMCID: PMC3887866 DOI: 10.1007/s10059-013-0135-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 05/03/2013] [Indexed: 12/21/2022] Open
Abstract
Phytochromes are plant photoreceptors that perceive red and far-red light. Upon the perception of light in Arabidopsis, light-activated phytochromes enter the nucleus and act on a set of interacting proteins, modulating their activities and thereby altering the expression levels of ∼10% of the organism's entire gene complement. Phytochromeinteracting factors (PIFs) belonging to Arabidopsis basic helix-loop-helix (bHLH) subgroup 15 are key interacting proteins that play negative roles in light responses. Their activities are post-translationally countered by light-activated phytochromes, which promote the degradation of PIFs and directly or indirectly inhibit their binding to DNA. The PIFs share a high degree of similarity, but examinations of pif single and multiple mutants have indicated that they have shared and distinct functions in various developmental and physiological processes. These are believed to stem from differences in both intrinsic protein properties and their gene expression patterns. In an effort to clarify the basis of these shared and distinct functions, we compared recently published genome-wide ChIP data, developmental gene expression maps, and responses to various stimuli for the various PIFs. Based on our observations, we propose that the biological roles of PIFs stem from their shared and distinct DNA binding targets and specific gene expression patterns.
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Affiliation(s)
- Jinkil Jeong
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305–701,
Korea
| | - Giltsu Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305–701,
Korea
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212
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Emerging design principles in the Arabidopsis circadian clock. Semin Cell Dev Biol 2013; 24:393-8. [DOI: 10.1016/j.semcdb.2013.03.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 03/22/2013] [Accepted: 03/25/2013] [Indexed: 01/09/2023]
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213
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Schmal C, Reimann P, Staiger D. A circadian clock-regulated toggle switch explains AtGRP7 and AtGRP8 oscillations in Arabidopsis thaliana. PLoS Comput Biol 2013; 9:e1002986. [PMID: 23555221 PMCID: PMC3610657 DOI: 10.1371/journal.pcbi.1002986] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Accepted: 01/29/2013] [Indexed: 12/25/2022] Open
Abstract
The circadian clock controls many physiological processes in higher plants and causes a large fraction of the genome to be expressed with a 24h rhythm. The transcripts encoding the RNA-binding proteins AtGRP7 (Arabidopsis thaliana Glycine Rich Protein 7) and AtGRP8 oscillate with evening peaks. The circadian clock components CCA1 and LHY negatively affect AtGRP7 expression at the level of transcription. AtGRP7 and AtGRP8, in turn, negatively auto-regulate and reciprocally cross-regulate post-transcriptionally: high protein levels promote the generation of an alternative splice form that is rapidly degraded. This clock-regulated feedback loop has been proposed to act as a molecular slave oscillator in clock output. While mathematical models describing the circadian core oscillator in Arabidopsis thaliana were introduced recently, we propose here the first model of a circadian slave oscillator. We define the slave oscillator in terms of ordinary differential equations and identify the model's parameters by an optimization procedure based on experimental results. The model successfully reproduces the pertinent experimental findings such as waveforms, phases, and half-lives of the time-dependent concentrations. Furthermore, we obtain insights into possible mechanisms underlying the observed experimental dynamics: the negative auto-regulation and reciprocal cross-regulation via alternative splicing could be responsible for the sharply peaking waveforms of the AtGRP7 and AtGRP8 mRNA. Moreover, our results suggest that the AtGRP8 transcript oscillations are subordinated to those of AtGRP7 due to a higher impact of AtGRP7 protein on alternative splicing of its own and of the AtGRP8 pre-mRNA compared to the impact of AtGRP8 protein. Importantly, a bifurcation analysis provides theoretical evidence that the slave oscillator could be a toggle switch, arising from the reciprocal cross-regulation at the post-transcriptional level. In view of this, transcriptional repression of AtGRP7 and AtGRP8 by LHY and CCA1 induces oscillations of the toggle switch, leading to the observed high-amplitude oscillations of AtGRP7 mRNA. The circadian clock organizes the day in the life of a plant by causing 24h rhythms in gene expression. For example, the core clockwork of the model plant Arabidopsis thaliana causes the transcripts encoding the RNA-binding proteins AtGRP7 and AtGRP8 to undergo high amplitude oscillations with a peak at the end of the day. AtGRP7 and AtGRP8, in turn, negatively auto-regulate and reciprocally cross-regulate their own expression by causing alternative splicing of their pre-mRNAs, followed by rapid degradation of the alternatively spliced transcripts. This has led to the suggestion that they represent molecular slave oscillators downstream of the core clock. Using a mathematical model we obtain insights into possible mechanisms underlying the experimentally observed dynamics, e.g. a higher impact of AtGRP7 protein compared to the impact of AtGRP8 protein on the alternative splicing explains the experimentally observed phases of their transcript. Previously, components that reciprocally repress their own transcription (double negative loops) have been shown to potentially act as a toggle switch between two states. We provide theoretical evidence that the slave oscillator could be a bistable toggle switch as well, operating at the post-transcriptional level.
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Affiliation(s)
- Christoph Schmal
- Condensed Matter Theory, Faculty of Physics, Bielefeld University, Bielefeld, Germany.
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214
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McClung CR. Beyond Arabidopsis: the circadian clock in non-model plant species. Semin Cell Dev Biol 2013; 24:430-6. [PMID: 23466287 DOI: 10.1016/j.semcdb.2013.02.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Revised: 02/13/2013] [Accepted: 02/15/2013] [Indexed: 01/26/2023]
Abstract
Circadian clocks allow plants to temporally coordinate many aspects of their biology with the diurnal cycle derived from the rotation of Earth on its axis. Although there is a rich history of the study of clocks in many plant species, in recent years much progress in elucidating the architecture and function of the plant clock has emerged from studies of the model plant, Arabidopsis thaliana. There is considerable interest in extending this knowledge of the circadian clock into diverse plant species in order to address its role in topics as varied as agricultural productivity and the responses of individual species and plant communities to global climate change and environmental degradation. The analysis of circadian clocks in the green lineage provides insight into evolutionary processes in plants and throughout the eukaryotes.
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Affiliation(s)
- C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Class of 1978 Life Sciences Center, Hanover, NH 03755, USA.
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215
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Chow BY, Kay SA. Global approaches for telling time: omics and the Arabidopsis circadian clock. Semin Cell Dev Biol 2013; 24:383-92. [PMID: 23435351 DOI: 10.1016/j.semcdb.2013.02.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/08/2013] [Accepted: 02/12/2013] [Indexed: 12/31/2022]
Abstract
The circadian clock is an endogenous timer that anticipates and synchronizes biological processes to the environment. Traditional genetic approaches identified the underlying principles and genetic components, but new discoveries have been greatly impeded by the embedded redundancies that confer necessary robustness to the clock architecture. To overcome this, global (omic) techniques have provided a new depth of information about the Arabidopsis clock. Our understanding of the factors, regulation, and mechanistic connectivity between clock genes and with output processes has substantially broadened through genomic (cDNA libraries, yeast one-hybrid, protein binding microarrays, and ChIP-seq), transcriptomic (microarrays, RNA-seq), proteomic (mass spectrometry and chemical libraries), and metabolomic (mass spectrometry) approaches. This evolution in research will undoubtedly enhance our understanding of how the circadian clock optimizes growth and fitness.
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Affiliation(s)
- Brenda Y Chow
- Section of Cell and Developmental Biology and Center for Chronobiology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, United States.
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216
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Hong S, Kim SA, Guerinot ML, McClung CR. Reciprocal interaction of the circadian clock with the iron homeostasis network in Arabidopsis. PLANT PHYSIOLOGY 2013; 161:893-903. [PMID: 23250624 PMCID: PMC3561027 DOI: 10.1104/pp.112.208603] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 12/17/2012] [Indexed: 05/18/2023]
Abstract
In plants, iron (Fe) uptake and homeostasis are critical for survival, and these processes are tightly regulated at the transcriptional and posttranscriptional levels. Circadian clocks are endogenous oscillating mechanisms that allow an organism to anticipate environmental changes to coordinate biological processes both with one another and with the environmental day/night cycle. The plant circadian clock controls many physiological processes through rhythmic expression of transcripts. In this study, we examined the expression of three Fe homeostasis genes (IRON REGULATED TRANSPORTER1 [IRT1], BASIC HELIX LOOP HELIX39, and FERRITIN1) in Arabidopsis (Arabidopsis thaliana) using promoter:LUCIFERASE transgenic lines. Each of these promoters showed circadian regulation of transcription. The circadian clock monitors a number of clock outputs and uses these outputs as inputs to modulate clock function. We show that this is also true for Fe status. Fe deficiency results in a lengthened circadian period. We interrogated mutants impaired in the Fe homeostasis response, including irt1-1, which lacks the major high-affinity Fe transporter, and fit-2, which lacks Fe deficiency-induced TRANSCRIPTION FACTOR1, a basic helix-loop-helix transcription factor necessary for induction of the Fe deficiency response. Both mutants exhibit symptoms of Fe deficiency, including lengthened circadian period. To determine which components are involved in this cross talk between the circadian and Fe homeostasis networks, we tested clock- or Fe homeostasis-related mutants. Mutants defective in specific clock gene components were resistant to the change in period length under different Fe conditions observed in the wild type, suggesting that these mutants are impaired in cross talk between Fe homeostasis and the circadian clock.
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217
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Regularization of non-homogeneous dynamic Bayesian networks with global information-coupling based on hierarchical Bayesian models. Mach Learn 2013. [DOI: 10.1007/s10994-012-5326-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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218
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Pizarro A, Hayer K, Lahens NF, Hogenesch JB. CircaDB: a database of mammalian circadian gene expression profiles. Nucleic Acids Res 2012. [PMID: 23180795 PMCID: PMC3531170 DOI: 10.1093/nar/gks1161] [Citation(s) in RCA: 238] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
CircaDB (http://circadb.org) is a new database of circadian transcriptional profiles from time course expression experiments from mice and humans. Each transcript's expression was evaluated by three separate algorithms, JTK_Cycle, Lomb Scargle and DeLichtenberg. Users can query the gene annotations using simple and powerful full text search terms, restrict results to specific data sets and provide probability thresholds for each algorithm. Visualizations of the data are intuitive charts that convey profile information more effectively than a table of probabilities. The CircaDB web application is open source and available at http://github.com/itmat/circadb.
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Affiliation(s)
- Angel Pizarro
- The Institute for Translational Medicine and Therapeutics, University of Pennsylvania, 3400 Civic Center Boulevard, Building 421, Philadelphia, PA 19104, USA.
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219
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The rice B-box zinc finger gene family: genomic identification, characterization, expression profiling and diurnal analysis. PLoS One 2012; 7:e48242. [PMID: 23118960 PMCID: PMC3485221 DOI: 10.1371/journal.pone.0048242] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 09/25/2012] [Indexed: 11/30/2022] Open
Abstract
Background The B-box (BBX) -containing proteins are a class of zinc finger proteins that contain one or two B-box domains and play important roles in plant growth and development. The Arabidopsis BBX gene family has recently been re-identified and renamed. However, there has not been a genome-wide survey of the rice BBX (OsBBX) gene family until now. Methodology/Principal Findings In this study, we identified 30 rice BBX genes through a comprehensive bioinformatics analysis. Each gene was assigned a uniform nomenclature. We described the chromosome localizations, gene structures, protein domains, phylogenetic relationship, whole life-cycle expression profile and diurnal expression patterns of the OsBBX family members. Based on the phylogeny and domain constitution, the OsBBX gene family was classified into five subfamilies. The gene duplication analysis revealed that only chromosomal segmental duplication contributed to the expansion of the OsBBX gene family. The expression profile of the OsBBX genes was analyzed by Affymetrix GeneChip microarrays throughout the entire life-cycle of rice cultivar Zhenshan 97 (ZS97). In addition, microarray analysis was performed to obtain the expression patterns of these genes under light/dark conditions and after three phytohormone treatments. This analysis revealed that the expression patterns of the OsBBX genes could be classified into eight groups. Eight genes were regulated under the light/dark treatments, and eleven genes showed differential expression under at least one phytohormone treatment. Moreover, we verified the diurnal expression of the OsBBX genes using the data obtained from the Diurnal Project and qPCR analysis, and the results indicated that many of these genes had a diurnal expression pattern. Conclusions/Significance The combination of the genome-wide identification and the expression and diurnal analysis of the OsBBX gene family should facilitate additional functional studies of the OsBBX genes.
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220
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Jiao Y, Rosa BA, Oh S, Montgomery BL, Qin W, Chen J. Detection and decomposition: treatment-induced cyclic gene expression disruption in high-throughput time-series datasets. J Bioinform Comput Biol 2012; 10:1271002. [PMID: 23075209 DOI: 10.1142/s0219720012710023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Higher organisms possess many genes which cycle under normal conditions, to allow the organism to adapt to expected environmental conditions throughout the course of a day. However, treatment-induced disruption of regular cyclic gene expression patterns presents a significant challenge in novel gene discovery experiments because these disruptions can induce strong differential regulation events for genes that are not involved in an adaptive response to the treatment. To address this cycle disruption problem, we reviewed the state-of-art periodic pattern detection algorithms and a pattern decomposition algorithm (PRIISM), which is a knowledge-based Fourier analysis algorithm designed to distinguish the cyclic patterns from the rest gene expression patterns, and discussed potential future improvements.
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Affiliation(s)
- Yuhua Jiao
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.
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221
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Katiyar A, Smita S, Lenka SK, Rajwanshi R, Chinnusamy V, Bansal KC. Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis. BMC Genomics 2012. [PMID: 23050870 DOI: 10.1186/1471-2164-13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND The MYB gene family comprises one of the richest groups of transcription factors in plants. Plant MYB proteins are characterized by a highly conserved MYB DNA-binding domain. MYB proteins are classified into four major groups namely, 1R-MYB, 2R-MYB, 3R-MYB and 4R-MYB based on the number and position of MYB repeats. MYB transcription factors are involved in plant development, secondary metabolism, hormone signal transduction, disease resistance and abiotic stress tolerance. A comparative analysis of MYB family genes in rice and Arabidopsis will help reveal the evolution and function of MYB genes in plants. RESULTS A genome-wide analysis identified at least 155 and 197 MYB genes in rice and Arabidopsis, respectively. Gene structure analysis revealed that MYB family genes possess relatively more number of introns in the middle as compared with C- and N-terminal regions of the predicted genes. Intronless MYB-genes are highly conserved both in rice and Arabidopsis. MYB genes encoding R2R3 repeat MYB proteins retained conserved gene structure with three exons and two introns, whereas genes encoding R1R2R3 repeat containing proteins consist of six exons and five introns. The splicing pattern is similar among R1R2R3 MYB genes in Arabidopsis. In contrast, variation in splicing pattern was observed among R1R2R3 MYB members of rice. Consensus motif analysis of 1kb upstream region (5' to translation initiation codon) of MYB gene ORFs led to the identification of conserved and over-represented cis-motifs in both rice and Arabidopsis. Real-time quantitative RT-PCR analysis showed that several members of MYBs are up-regulated by various abiotic stresses both in rice and Arabidopsis. CONCLUSION A comprehensive genome-wide analysis of chromosomal distribution, tandem repeats and phylogenetic relationship of MYB family genes in rice and Arabidopsis suggested their evolution via duplication. Genome-wide comparative analysis of MYB genes and their expression analysis identified several MYBs with potential role in development and stress response of plants.
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Affiliation(s)
- Amit Katiyar
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
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Katiyar A, Smita S, Lenka SK, Rajwanshi R, Chinnusamy V, Bansal KC. Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis. BMC Genomics 2012; 13:544. [PMID: 23050870 PMCID: PMC3542171 DOI: 10.1186/1471-2164-13-544] [Citation(s) in RCA: 333] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 10/01/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The MYB gene family comprises one of the richest groups of transcription factors in plants. Plant MYB proteins are characterized by a highly conserved MYB DNA-binding domain. MYB proteins are classified into four major groups namely, 1R-MYB, 2R-MYB, 3R-MYB and 4R-MYB based on the number and position of MYB repeats. MYB transcription factors are involved in plant development, secondary metabolism, hormone signal transduction, disease resistance and abiotic stress tolerance. A comparative analysis of MYB family genes in rice and Arabidopsis will help reveal the evolution and function of MYB genes in plants. RESULTS A genome-wide analysis identified at least 155 and 197 MYB genes in rice and Arabidopsis, respectively. Gene structure analysis revealed that MYB family genes possess relatively more number of introns in the middle as compared with C- and N-terminal regions of the predicted genes. Intronless MYB-genes are highly conserved both in rice and Arabidopsis. MYB genes encoding R2R3 repeat MYB proteins retained conserved gene structure with three exons and two introns, whereas genes encoding R1R2R3 repeat containing proteins consist of six exons and five introns. The splicing pattern is similar among R1R2R3 MYB genes in Arabidopsis. In contrast, variation in splicing pattern was observed among R1R2R3 MYB members of rice. Consensus motif analysis of 1kb upstream region (5' to translation initiation codon) of MYB gene ORFs led to the identification of conserved and over-represented cis-motifs in both rice and Arabidopsis. Real-time quantitative RT-PCR analysis showed that several members of MYBs are up-regulated by various abiotic stresses both in rice and Arabidopsis. CONCLUSION A comprehensive genome-wide analysis of chromosomal distribution, tandem repeats and phylogenetic relationship of MYB family genes in rice and Arabidopsis suggested their evolution via duplication. Genome-wide comparative analysis of MYB genes and their expression analysis identified several MYBs with potential role in development and stress response of plants.
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Affiliation(s)
- Amit Katiyar
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
- National Bureau of Plant Genetic Resources, Indian Agricultural Research Institute Campus, New Delhi, 110012, India
| | - Shuchi Smita
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
- National Bureau of Plant Genetic Resources, Indian Agricultural Research Institute Campus, New Delhi, 110012, India
| | - Sangram Keshari Lenka
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
- Department of Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Ravi Rajwanshi
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
- Department of Biotechnology, Assam University, Silchar, Assam, 788011, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Kailash Chander Bansal
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
- National Bureau of Plant Genetic Resources, Indian Agricultural Research Institute Campus, New Delhi, 110012, India
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Nomoto Y, Kubozono S, Yamashino T, Nakamichi N, Mizuno T. Circadian Clock- and PIF4-Controlled Plant Growth: A Coincidence Mechanism Directly Integrates a Hormone Signaling Network into the Photoperiodic Control of Plant Architectures in Arabidopsis thaliana. ACTA ACUST UNITED AC 2012; 53:1950-64. [DOI: 10.1093/pcp/pcs137] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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224
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Transcriptional repressor PRR5 directly regulates clock-output pathways. Proc Natl Acad Sci U S A 2012; 109:17123-8. [PMID: 23027938 DOI: 10.1073/pnas.1205156109] [Citation(s) in RCA: 222] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The circadian clock is an endogenous time-keeping mechanism that enables organisms to adapt to external daily cycles. The clock coordinates biological activities with these cycles, mainly through genome-wide gene expression. However, the exact mechanism underlying regulation of circadian gene expression is poorly understood. Here we demonstrated that an Arabidopsis PSEUDO-RESPONSE REGULATOR 5 (PRR5), which acts in the clock genetic circuit, directly regulates expression timing of key transcription factors involved in clock-output pathways. A transient expression assay and ChIP-quantitative PCR assay using mutated PRR5 indicated that PRR5 associates with target DNA through binding at the CCT motif in vivo. ChIP followed by deep sequencing coupled with genome-wide expression profiling revealed the direct-target genes of PRR5. PRR5 direct-targets include genes encoding transcription factors involved in flowering-time regulation, hypocotyl elongation, and cold-stress responses. PRR5-target gene expression followed a circadian rhythm pattern with low, basal expression from noon until midnight, when PRR9, PRR7, and PRR5 were expressed. ChIP-quantitative PCR assays indicated that PRR7 and PRR9 bind to the direct-targets of PRR5. Genome-wide expression profiling using a prr9 prr7 prr5 triple mutant suggests that PRR5, PRR7, and PRR9 repress these targets. Taken together, our results illustrate a genetic network in which PRR5, PRR7, and PRR9 directly regulate expression timing of key transcription factors to coordinate physiological processes with daily cycles.
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225
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Abstract
Endogenous circadian rhythms regulate many aspects of an organism's behavior, physiology and development. These daily oscillations synchronize with the environment to generate robust rhythms, resulting in enhanced fitness and growth vigor in plants. Collective studies over the years have focused on understanding the transcription-based oscillator in Arabidopsis. Recent advances combining mechanistic data with genome-wide approaches have contributed significantly to a more comprehensive understanding of the molecular interactions within the oscillator, and with clock-controlled pathways. This review focuses on the regulatory mechanisms within the oscillator, highlighting key connections between new and existing components, and direct mechanistic links to downstream pathways that control overt rhythms in the whole plant.
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Affiliation(s)
- Dawn H. Nagel
- Section of Cell and Developmental Biology, Division of Biological Sciences; University of California San Diego, La Jolla, CA 92093, USA
- Center for Chronobiology; University of California San Diego, La Jolla, CA 92093, USA
| | - Steve A. Kay
- Section of Cell and Developmental Biology, Division of Biological Sciences; University of California San Diego, La Jolla, CA 92093, USA
- Center for Chronobiology; University of California San Diego, La Jolla, CA 92093, USA
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226
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Seung D, Risopatron JPM, Jones BJ, Marc J. Circadian clock-dependent gating in ABA signalling networks. PROTOPLASMA 2012; 249:445-57. [PMID: 21773710 DOI: 10.1007/s00709-011-0304-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 07/01/2011] [Indexed: 05/08/2023]
Abstract
Plant growth and development are intimately attuned to fluctuations in environmental variables such as light, temperature and water availability. A broad range of signalling and dynamic response mechanisms allows them to adjust their physiology so that growth and reproductive capacity are optimised for the prevailing conditions. Many of the response mechanisms are mediated by the plant hormones. The hormone abscisic acid (ABA) plays a dominant role in fundamental processes such as seed dormancy and germination, regulation of stomatal movements and enhancing drought tolerance in response to the osmotic stresses that result from water deficit, salinity and freezing. Whereas plants maintain a constant vigilance, there is emerging evidence that the capacity to respond is gated by the circadian clock so that it varies with diurnal fluctuations in light, temperature and water status. Clock regulation enables plants to anticipate regular diurnal fluctuations and thereby presumably to maximise metabolic efficiency. Circadian clock-dependent gating appears to regulate the ABA signalling network at numerous points, including metabolism, transport, perception and activity of the hormone. In this review, we summarise the basic principles and recent progress in elucidating the molecular mechanisms of circadian gating of the ABA response network and how it can affect fundamental processes in plant growth and development.
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Affiliation(s)
- David Seung
- School of Biological Sciences, The University of Sydney, Sydney, Australia
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227
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Campoli C, Shtaya M, Davis SJ, von Korff M. Expression conservation within the circadian clock of a monocot: natural variation at barley Ppd-H1 affects circadian expression of flowering time genes, but not clock orthologs. BMC PLANT BIOLOGY 2012; 12:97. [PMID: 22720803 PMCID: PMC3478166 DOI: 10.1186/1471-2229-12-97] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 05/09/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND The circadian clock is an endogenous mechanism that coordinates biological processes with daily changes in the environment. In plants, circadian rhythms contribute to both agricultural productivity and evolutionary fitness. In barley, the photoperiod response regulator and flowering-time gene Ppd-H1 is orthologous to the Arabidopsis core-clock gene PRR7. However, relatively little is known about the role of Ppd-H1 and other components of the circadian clock in temperate crop species. In this study, we identified barley clock orthologs and tested the effects of natural genetic variation at Ppd-H1 on diurnal and circadian expression of clock and output genes from the photoperiod-response pathway. RESULTS Barley clock orthologs HvCCA1, HvGI, HvPRR1, HvPRR37 (Ppd-H1), HvPRR73, HvPRR59 and HvPRR95 showed a high level of sequence similarity and conservation of diurnal and circadian expression patterns, when compared to Arabidopsis. The natural mutation at Ppd-H1 did not affect diurnal or circadian cycling of barley clock genes. However, the Ppd-H1 mutant was found to be arrhythmic under free-running conditions for the photoperiod-response genes HvCO1, HvCO2, and the MADS-box transcription factor and vernalization responsive gene Vrn-H1. CONCLUSION We suggest that the described eudicot clock is largely conserved in the monocot barley. However, genetic differentiation within gene families and differences in the function of Ppd-H1 suggest evolutionary modification in the angiosperm clock. Our data indicates that natural variation at Ppd-H1 does not affect the expression level of clock genes, but controls photoperiodic output genes. Circadian control of Vrn-H1 in barley suggests that this vernalization responsive gene is also controlled by the photoperiod-response pathway. Structural and functional characterization of the barley circadian clock will set the basis for future studies of the adaptive significance of the circadian clock in Triticeae species.
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Affiliation(s)
- Chiara Campoli
- Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, D50829, Cologne, Germany
| | - Munqez Shtaya
- An-Najah National University, P. O. Box 7, Nablus, Palestinian Territories
| | - Seth J Davis
- Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, D50829, Cologne, Germany
| | - Maria von Korff
- Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, D50829, Cologne, Germany
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228
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Rosa BA, Jiao Y, Oh S, Montgomery BL, Qin W, Chen J. Frequency-based time-series gene expression recomposition using PRIISM. BMC SYSTEMS BIOLOGY 2012; 6:69. [PMID: 22703599 PMCID: PMC3464900 DOI: 10.1186/1752-0509-6-69] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 06/15/2012] [Indexed: 11/30/2022]
Abstract
Background Circadian rhythm pathways influence the expression patterns of as much as 31% of the Arabidopsis genome through complicated interaction pathways, and have been found to be significantly disrupted by biotic and abiotic stress treatments, complicating treatment-response gene discovery methods due to clock pattern mismatches in the fold change-based statistics. The PRIISM (Pattern Recomposition for the Isolation of Independent Signals in Microarray data) algorithm outlined in this paper is designed to separate pattern changes induced by different forces, including treatment-response pathways and circadian clock rhythm disruptions. Results Using the Fourier transform, high-resolution time-series microarray data is projected to the frequency domain. By identifying the clock frequency range from the core circadian clock genes, we separate the frequency spectrum to different sections containing treatment-frequency (representing up- or down-regulation by an adaptive treatment response), clock-frequency (representing the circadian clock-disruption response) and noise-frequency components. Then, we project the components’ spectra back to the expression domain to reconstruct isolated, independent gene expression patterns representing the effects of the different influences. By applying PRIISM on a high-resolution time-series Arabidopsis microarray dataset under a cold treatment, we systematically evaluated our method using maximum fold change and principal component analyses. The results of this study showed that the ranked treatment-frequency fold change results produce fewer false positives than the original methodology, and the 26-hour timepoint in our dataset was the best statistic for distinguishing the most known cold-response genes. In addition, six novel cold-response genes were discovered. PRIISM also provides gene expression data which represents only circadian clock influences, and may be useful for circadian clock studies. Conclusion PRIISM is a novel approach for overcoming the problem of circadian disruptions from stress treatments on plants. PRIISM can be integrated with any existing analysis approach on gene expression data to separate circadian-influenced changes in gene expression, and it can be extended to apply to any organism with regular oscillations in gene expression patterns across a large portion of the genome.
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Affiliation(s)
- Bruce A Rosa
- Department of Biology, Lakehead University, ON, Canada
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229
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Chapman EJ, Greenham K, Castillejo C, Sartor R, Bialy A, Sun TP, Estelle M. Hypocotyl transcriptome reveals auxin regulation of growth-promoting genes through GA-dependent and -independent pathways. PLoS One 2012; 7:e36210. [PMID: 22590525 PMCID: PMC3348943 DOI: 10.1371/journal.pone.0036210] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 03/28/2012] [Indexed: 12/24/2022] Open
Abstract
Many processes critical to plant growth and development are regulated by the hormone auxin. Auxin responses are initiated through activation of a transcriptional response mediated by the TIR1/AFB family of F-box protein auxin receptors as well as the AUX/IAA and ARF families of transcriptional regulators. However, there is little information on how auxin regulates a specific cellular response. To begin to address this question, we have focused on auxin regulation of cell expansion in the Arabidopsis hypocotyl. We show that auxin-mediated hypocotyl elongation is dependent upon the TIR1/AFB family of auxin receptors and degradation of AUX/IAA repressors. We also use microarray studies of elongating hypocotyls to show that a number of growth-associated processes are activated by auxin including gibberellin biosynthesis, cell wall reorganization and biogenesis, and others. Our studies indicate that GA biosynthesis is required for normal response to auxin in the hypocotyl but that the overall transcriptional auxin output consists of PIF-dependent and -independent genes. We propose that auxin acts independently from and interdependently with PIF and GA pathways to regulate expression of growth-associated genes in cell expansion.
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Affiliation(s)
- Elisabeth J. Chapman
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Kathleen Greenham
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Cristina Castillejo
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Ryan Sartor
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Agniezska Bialy
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Tai-ping Sun
- Biology Department, Duke University, Durham, North Carolina, United States of America
| | - Mark Estelle
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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230
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Sellaro R, Pacín M, Casal JJ. Diurnal dependence of growth responses to shade in Arabidopsis: role of hormone, clock, and light signaling. MOLECULAR PLANT 2012; 5:619-28. [PMID: 22311777 DOI: 10.1093/mp/ssr122] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We investigated the diurnal dependence of the hypocotyl-growth responses to shade under sunlight-night cycles in Arabidopsis thaliana. Afternoon shade events promoted hypocotyl growth, while morning shade was ineffective. The lhy-D, elf3, lux, pif4 pif5, toc1, and quadruple della mutants retained the response to afternoon shade and the lack of response to morning shade while the lhy cca1 mutant responded to both morning and afternoon shade. The phyB mutant, plants overexpressing the multidrug resistance-like membrane protein ABCB19, and the iaa17/axr3 loss-of-function mutant failed to respond to shade. Transient exposure of sunlight-grown seedlings to synthetic auxin in the afternoon caused a stronger promotion of hypocotyl growth than morning treatments. The promotion of hypocotyl growth by afternoon shade or afternoon auxin required light perceived by phytochrome A or cryptochromes during the previous hours of the photoperiod. Although the ELF4-ELF3-LUX complex, PIF4, PIF5, and DELLA are key players in the generation of diurnal hypocotyl-growth patterns, they exert a minor role in the control of the diurnal pattern of growth responses to shade. We conclude that the strong diurnal dependency of hypocotyl-growth responses to shade relates to the balance between the antagonistic actions of LHY-CCA1 and a light-derived signal.
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Affiliation(s)
- Romina Sellaro
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires and Consejo Nacional de Investigaciones Científicas y Técnicas, Av. San Martín 4453, 1417 Buenos Aires, Argentina
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231
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Fustin JM, Doi M, Yamada H, Komatsu R, Shimba S, Okamura H. Rhythmic nucleotide synthesis in the liver: temporal segregation of metabolites. Cell Rep 2012; 1:341-9. [PMID: 22832226 DOI: 10.1016/j.celrep.2012.03.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 02/13/2012] [Accepted: 03/01/2012] [Indexed: 10/28/2022] Open
Abstract
The synthesis of nucleotides in the body is centrally controlled by the liver, via salvage or de novo synthesis. We reveal a pervasive circadian influence on hepatic nucleotide metabolism, from rhythmic gene expression of rate-limiting enzymes to oscillating nucleotide metabolome in wild-type (WT) mice. Genetic disruption of the hepatic clock leads to aberrant expression of these enzymes, together with anomalous nucleotide rhythms, such as constant low levels of ATP with an excess in uric acid, the degradation product of purines. These results clearly demonstrate that the hepatic circadian clock orchestrates nucleotide synthesis and degradation. This circadian metabolome timetable, obtained using state-of-the-art capillary electrophoresis time-of-flight mass spectrometry, will guide further investigations in nucleotide metabolism-related disorders.
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Affiliation(s)
- Jean-Michel Fustin
- Department of System Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimo-Adachi-cho, Kyoto 606-8501, Japan
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232
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Huang W, Pérez-García P, Pokhilko A, Millar AJ, Antoshechkin I, Riechmann JL, Mas P. Mapping the Core of the Arabidopsis Circadian Clock Defines the Network Structure of the Oscillator. Science 2012; 336:75-9. [DOI: 10.1126/science.1219075] [Citation(s) in RCA: 368] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In many organisms, the circadian clock is composed of functionally coupled morning and evening oscillators. In Arabidopsis, oscillator coupling relies on a core loop in which the evening oscillator component TIMING OF CAB EXPRESSION 1 (TOC1) was proposed to activate a subset of morning-expressed oscillator genes. Here, we show that TOC1 does not function as an activator but rather as a general repressor of oscillator gene expression. Repression occurs through TOC1 rhythmic association to the promoters of the oscillator genes. Hormone-dependent induction of TOC1 and analysis of RNA interference plants show that TOC1 prevents the activation of morning-expressed genes at night. Our study overturns the prevailing model of the Arabidopsis circadian clock, showing that the morning and evening oscillator loops are connected through the repressing activity of TOC1.
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Khurana N, Chauhan H, Khurana P. Expression analysis of a heat-inducible, Myo-inositol-1-phosphate synthase (MIPS) gene from wheat and the alternatively spliced variants of rice and Arabidopsis. PLANT CELL REPORTS 2012; 31:237-51. [PMID: 21971746 DOI: 10.1007/s00299-011-1160-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2011] [Revised: 08/30/2011] [Accepted: 09/21/2011] [Indexed: 05/08/2023]
Abstract
Molecular dissection and a deeper analysis of the heat stress response mechanism in wheat have been poorly understood so far. This study delves into the molecular basis of action of TaMIPS, a heat stress-inducible enzyme that was identified through PCR-select subtraction technology, which is named here as TaMIPS2. MIPS (L-Myo-inositol-phosphate synthase) is important for the normal growth and development in plants. Expression profiling showed that TaMIPS2 is expressed during different developing seed stages upon heat stress. Also, the transcript levels increase in unfertilized ovaries and significant amounts are present during the recovery period providing evidence that MIPS is crucial for its role in heat stress recovery and flower development. Alternatively spliced forms from rice and Arabidopsis were also identified and their expression analysis revealed that apart from heat stress, some of the spliced variants were also inducible by drought, NaCl, Cold, ABA, BR, SA and mannitol. In silico promoter analysis revealed various cis-elements that could contribute for the differential regulation of MIPS in different plant systems. Phylogenetic analysis indicated that MIPS are highly conserved among monocots and dicots and TaMIPS2 grouped specifically with monocots. Comparative analyses was undertaken by different experimental approaches, i.e., semi-quantitative RT-PCR, quantitative RT-PCR, Genevestigator as a reference expression tool and motif analysis to predict the possible function of TaMIPS2 in regulating the different aspects of plant development under abiotic stress in wheat.
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Affiliation(s)
- Neetika Khurana
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
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234
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Abstract
Plants are more sensitive to light in the day than at night due to the circadian clock. The protein that acts downstream from the clock to modulate blue light signalling in stomata comes as a surprise; it is FT, which is thought to be the long-distance regulator of flowering.
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Affiliation(s)
- Katharine E Hubbard
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
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235
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HSP90 functions in the circadian clock through stabilization of the client F-box protein ZEITLUPE. Proc Natl Acad Sci U S A 2011; 108:16843-8. [PMID: 21949396 DOI: 10.1073/pnas.1110406108] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The autoregulatory loops of the circadian clock consist of feedback regulation of transcription/translation circuits but also require finely coordinated cytoplasmic and nuclear proteostasis. Although protein degradation is important to establish steady-state levels, maturation into their active conformation also factors into protein homeostasis. HSP90 facilitates the maturation of a wide range of client proteins, and studies in metazoan clocks implicate HSP90 as an integrator of input or output. Here we show that the Arabidopsis circadian clock-associated F-box protein ZEITLUPE (ZTL) is a unique client for cytoplasmic HSP90. The HSP90-specific inhibitor geldanamycin and RNAi-mediated depletion of cytoplasmic HSP90 reduces levels of ZTL and lengthens circadian period, consistent with ztl loss-of-function alleles. Transient transfection of artificial microRNA targeting cytoplasmic HSP90 genes similarly lengthens period. Proteolytic targets of SCF(ZTL), TOC1 and PRR5, are stabilized in geldanamycin-treated seedlings, whereas the levels of closely related clock proteins, PRR3 and PRR7, are unchanged. An in vitro holdase assay, typically used to demonstrate chaperone activity, shows that ZTL can be effectively bound, and aggregation prevented, by HSP90. GIGANTEA, a unique stabilizer of ZTL, may act in the same pathway as HSP90, possibly linking these two proteins to a similar mechanism. Our findings establish maturation of ZTL by HSP90 as essential for proper function of the Arabidopsis circadian clock. Unlike metazoan systems, HSP90 functions here within the core oscillator. Additionally, F-box proteins as clients may place HSP90 in a unique and more central role in proteostasis.
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Marín-de la Rosa N, Alabadí D, Blázquez MÁ, Arana MV. Integrating circadian and gibberellin signaling in Arabidopsis: possible links between the circadian clock and the AtGID1 transcription. PLANT SIGNALING & BEHAVIOR 2011; 6:1411-3. [PMID: 21852756 PMCID: PMC3258079 DOI: 10.4161/psb.6.9.17209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The circadian clock acts as central coordinator of plant activity, and it regulates key traits for plant fitness such as flowering time, gas exchange, growth, and stress responses. In the May issue of the Proceedings of the National Academy of Science we describe the circadian regulation of gibberellin (GA) signaling, through transcriptional control of GA receptor genes (GID1a and GID1b). We show that, in short day photocycles, the expression of GA receptors oscillates in seedlings, yielding a window of strong GA activity at the end of the night that overlaps with the period of maximum growth. This clock-mediated control of GA signaling is not only crucial for the establishment of rhythmic patterns of growth but also affects the expression of many circadian-controlled genes that participate in a wide range of biological processes. Here we propose a possible mechanism that might operate for the transcriptional control of GID1 expression by the circadian clock.
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Affiliation(s)
| | - David Alabadí
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC); Valencia, Spain
| | | | - María Verónica Arana
- Instituto Nacional de Tecnología Agropecuaria; EEA Bariloche and CONICET; Rio Negro, Argentina
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237
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Jończyk M, Sobkowiak A, Siedlecki P, Biecek P, Trzcinska-Danielewicz J, Tiuryn J, Fronk J, Sowiński P. Rhythmic diel pattern of gene expression in juvenile maize leaf. PLoS One 2011; 6:e23628. [PMID: 21858187 PMCID: PMC3157397 DOI: 10.1371/journal.pone.0023628] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 07/21/2011] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Numerous biochemical and physiological parameters of living organisms follow a circadian rhythm. Although such rhythmic behavior is particularly pronounced in plants, which are strictly dependent on the daily photoperiod, data on the molecular aspects of the diurnal cycle in plants is scarce and mostly concerns the model species Arabidopsis thaliana. Here we studied the leaf transcriptome in seedlings of maize, an important C4 crop only distantly related to A. thaliana, throughout a cycle of 10 h darkness and 14 h light to look for rhythmic patterns of gene expression. RESULTS Using DNA microarrays comprising ca. 43,000 maize-specific probes we found that ca. 12% of all genes showed clear-cut diel rhythms of expression. Cluster analysis identified 35 groups containing from four to ca. 1,000 genes, each comprising genes of similar expression patterns. Perhaps unexpectedly, the most pronounced and most common (concerning the highest number of genes) expression maxima were observed towards and during the dark phase. Using Gene Ontology classification several meaningful functional associations were found among genes showing similar diel expression patterns, including massive induction of expression of genes related to gene expression, translation, protein modification and folding at dusk and night. Additionally, we found a clear-cut tendency among genes belonging to individual clusters to share defined transcription factor-binding sequences. CONCLUSIONS Co-expressed genes belonging to individual clusters are likely to be regulated by common mechanisms. The nocturnal phase of the diurnal cycle involves gross induction of fundamental biochemical processes and should be studied more thoroughly than was appreciated in most earlier physiological studies. Although some general mechanisms responsible for the diel regulation of gene expression might be shared among plants, details of the diurnal regulation of gene expression seem to differ between taxa.
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Affiliation(s)
- Maciej Jończyk
- Department of Plant Molecular Ecophysiology, Institute of Plant Experimental Biology and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Alicja Sobkowiak
- Plant Biochemistry and Physiology Department, Plant Breeding and Acclimatization Institute - National Research Institute, Radzików, Poland
| | - Paweł Siedlecki
- Department of Plant Molecular Biology, Institute of Plant Experimental Biology and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Przemysław Biecek
- Institute of Applied Mathematics and Mechanics, Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Warsaw, Poland
| | - Joanna Trzcinska-Danielewicz
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jerzy Tiuryn
- Institute of Informatics, Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Warsaw, Poland
| | - Jan Fronk
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Paweł Sowiński
- Department of Plant Molecular Ecophysiology, Institute of Plant Experimental Biology and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- Plant Biochemistry and Physiology Department, Plant Breeding and Acclimatization Institute - National Research Institute, Radzików, Poland
- * E-mail:
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Takase T, Nishiyama Y, Tanihigashi H, Ogura Y, Miyazaki Y, Yamada Y, Kiyosue T. LOV KELCH PROTEIN2 and ZEITLUPE repress Arabidopsis photoperiodic flowering under non-inductive conditions, dependent on FLAVIN-BINDING KELCH REPEAT F-BOX1. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 67:608-21. [PMID: 21518052 DOI: 10.1111/j.1365-313x.2011.04618.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
LOV KELCH PROTEIN2 (LKP2), ZEITLUPE (ZTL)/LOV KELCH PROTEIN1 (LKP1) and FLAVIN-BINDING KELCH REPEAT F-BOX1 (FKF1) constitute a family of Arabidopsis F-box proteins that regulate the circadian clock. Over-expression of LKP2 or ZTL causes arrhythmicity of multiple clock outputs under constant light and in constant darkness. Here, we show the significance of LKP2 and ZTL in the photoperiodic control of flowering time in Arabidopsis. In plants over-expressing LKP2, CO and FT expression was down-regulated under long-day conditions. LKP2 and ZTL physically interacted with FKF1, which was recruited from the nucleus into cytosolic speckles. LKP2 and ZTL inhibited the interaction of FKF1 with CYCLING DOF FACTOR 1, a ubiquitination substrate for FKF1 that is localized in the nucleus. The Kelch repeat regions of LKP2 and ZTL were sufficient for their physical interaction with FKF1 and translocation of FKF1 to the cytoplasm. Over-expression of LKP2 Kelch repeats induced late flowering under long-day conditions. lkp2 ztl double mutant plants flowered earlier than wild-type plants under short-day (non-inductive) conditions, and both CO and FT expression levels were up-regulated in the double mutant plants. The early flowering of lkp2 ztl was dependent on FKF1. LKP2, ZTL or both affected the accumulation of FKF1 protein during the early light period. These results indicate that an important role of LKP2 and ZTL in the photoperiodic pathway is repression of flowering under non-inductive conditions, and this is dependent on FKF1.
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Affiliation(s)
- Tomoyuki Takase
- Department of Life Science, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
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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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Nusinow DA, Helfer A, Hamilton EE, King JJ, Imaizumi T, Schultz TF, Farré EM, Kay SA. The ELF4-ELF3-LUX complex links the circadian clock to diurnal control of hypocotyl growth. Nature 2011; 475:398-402. [PMID: 21753751 PMCID: PMC3155984 DOI: 10.1038/nature10182] [Citation(s) in RCA: 615] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 05/06/2011] [Indexed: 02/07/2023]
Abstract
The circadian clock is required for adaptive responses to daily and seasonal changes in environmental conditions. Light and the circadian clock interact to consolidate the phase of hypocotyl cell elongation to peak at dawn under diurnal cycles in Arabidopsis thaliana. Here we identify a protein complex (called the evening complex)--composed of the proteins encoded by EARLY FLOWERING 3 (ELF3), ELF4 and the transcription-factor-encoding gene LUX ARRHYTHMO (LUX; also known as PHYTOCLOCK 1)--that directly regulates plant growth. ELF3 is both necessary and sufficient to form a complex between ELF4 and LUX, and the complex is diurnally regulated, peaking at dusk. ELF3, ELF4 and LUX are required for the proper expression of the growth-promoting transcription factors encoded by PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and PIF5 (also known as PHYTOCHROME INTERACTING FACTOR 3-LIKE 6) under diurnal conditions. LUX targets the complex to the promoters of PIF4 and PIF5 in vivo. Mutations in PIF4 and/or PIF5 are epistatic to the loss of the ELF4-ELF3-LUX complex, suggesting that regulation of PIF4 and PIF5 is a crucial function of the complex. Therefore, the evening complex underlies the molecular basis for circadian gating of hypocotyl growth in the early evening.
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Affiliation(s)
- Dmitri A Nusinow
- Section of Cell & Developmental Biology, Division of Biological Sciences, University of California San Diego 9500 Gilman Drive, La Jolla, California 92093-0130, USA
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241
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Filichkin SA, Breton G, Priest HD, Dharmawardhana P, Jaiswal P, Fox SE, Michael TP, Chory J, Kay SA, Mockler TC. Global profiling of rice and poplar transcriptomes highlights key conserved circadian-controlled pathways and cis-regulatory modules. PLoS One 2011; 6:e16907. [PMID: 21694767 PMCID: PMC3111414 DOI: 10.1371/journal.pone.0016907] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 01/15/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Circadian clocks provide an adaptive advantage through anticipation of daily and seasonal environmental changes. In plants, the central clock oscillator is regulated by several interlocking feedback loops. It was shown that a substantial proportion of the Arabidopsis genome cycles with phases of peak expression covering the entire day. Synchronized transcriptome cycling is driven through an extensive network of diurnal and clock-regulated transcription factors and their target cis-regulatory elements. Study of the cycling transcriptome in other plant species could thus help elucidate the similarities and differences and identify hubs of regulation common to monocot and dicot plants. METHODOLOGY/PRINCIPAL FINDINGS Using a combination of oligonucleotide microarrays and data mining pipelines, we examined daily rhythms in gene expression in one monocotyledonous and one dicotyledonous plant, rice and poplar, respectively. Cycling transcriptomes were interrogated under different diurnal (driven) and circadian (free running) light and temperature conditions. Collectively, photocycles and thermocycles regulated about 60% of the expressed nuclear genes in rice and poplar. Depending on the condition tested, up to one third of oscillating Arabidopsis-poplar-rice orthologs were phased within three hours of each other suggesting a high degree of conservation in terms of rhythmic gene expression. We identified clusters of rhythmically co-expressed genes and searched their promoter sequences to identify phase-specific cis-elements, including elements that were conserved in the promoters of Arabidopsis, poplar, and rice. CONCLUSIONS/SIGNIFICANCE Our results show that the cycling patterns of many circadian clock genes are highly conserved across poplar, rice, and Arabidopsis. The expression of many orthologous genes in key metabolic and regulatory pathways is diurnal and/or circadian regulated and phased to similar times of day. Our results confirm previous findings in Arabidopsis of three major classes of cis-regulatory modules within the plant circadian network: the morning (ME, GBOX), evening (EE, GATA), and midnight (PBX/TBX/SBX) modules. Identification of identical overrepresented motifs in the promoters of cycling genes from different species suggests that the core diurnal/circadian cis-regulatory network is deeply conserved between mono- and dicotyledonous species.
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Affiliation(s)
- Sergei A. Filichkin
- Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Ghislain Breton
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Henry D. Priest
- Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Palitha Dharmawardhana
- Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Samuel E. Fox
- Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Todd P. Michael
- The Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Joanne Chory
- Plant Biology Laboratory, The Salk Institute for Biological Studies and Howard Hughes Medical Institute, La Jolla, California, United States of America
| | - Steve A. Kay
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Todd C. Mockler
- Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
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242
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Abstract
Circadian clocks are endogenous timekeeping mechanisms that allow organisms to anticipate rhythmic, daily environmental changes. Temporal coordination of transcription results in a set of gene expression patterns with peak levels occurring at precise times of the day. An intriguing question is how a single clock can generate different oscillatory rhythms, and it has been proposed that hormone signaling might act in plants as a relay mechanism to modulate the amplitude and the phase of output rhythms. Here we show that the circadian clock gates gibberellin (GA) signaling through transcriptional regulation of the GA receptors, resulting in higher stability of DELLA proteins during daytime and higher GA sensitivity at night. Oscillation of GA signaling appears to be particularly critical for rhythmic growth, given that constitutive expression of the GA receptor expands the daily growth period in seedlings, and complete loss of DELLA function causes continuous, arrhythmic hypocotyl growth. Moreover, transcriptomic analysis of a pentuple della KO mutant indicates that the GA pathway mediates the rhythmic expression of many clock-regulated genes related to biotic and abiotic stress responses and cell wall modification. Thus, gating of GA sensitivity by the circadian clock represents an additional layer of regulation that might provide extra robustness to the diurnal growth rhythm and constitute a regulatory module that coordinates the circadian clock with additional endogenous and environmental signals.
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243
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Circadian clock-associated 1 and late elongated hypocotyl regulate expression of the C-repeat binding factor (CBF) pathway in Arabidopsis. Proc Natl Acad Sci U S A 2011; 108:7241-6. [PMID: 21471455 DOI: 10.1073/pnas.1103741108] [Citation(s) in RCA: 268] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The C-Repeat Binding Factor (CBF) cold-response pathway has a prominent role in cold acclimation, the process whereby certain plants increase tolerance to freezing in response to low nonfreezing temperatures. In Arabidopsis, the CBF pathway is characterized by rapid induction of the C-Repeat Binding Factor 1 (CBF1), CBF2, and CBF3 genes, which encode transcriptional activators, followed by induction of the CBF-targeted genes known as the "CBF regulon." Expression of the CBF regulon results in an increase in freezing tolerance. Previous studies established that CBF1, CBF2, and CBF3 are subject to circadian regulation and that their cold induction is gated by the circadian clock. Here we present the results of genetic analysis and ChIP experiments indicating that both these forms of regulation involve direct positive action of two transcription factors that are core components of the clock, i.e., Circadian Clock-Associated 1 (CCA1) and Late Elongated Hypocotyl (LHY). In plants carrying the cca1-11/lhy-21 double mutation, cold induction of CBF1, CBF2, and CBF3 was greatly impaired, and circadian regulation of CBF1 and CBF3 was essentially eliminated; circadian regulation of CBF2 continued, although with significantly reduced amplitude. Circadian regulation and cold induction of three CBF regulon genes, i.e., COld-regulated Gene15a (COR15A), COR47, and COR78, also were greatly diminished in plants carrying the cca1-11/lhy-21 double mutation. Furthermore, the cca1-11/lhy-21 double mutation resulted in impaired freezing tolerance in both nonacclimated and cold-acclimated plants. These results indicate that CCA1/LHY-mediated output from the circadian clock contributes to plant cold tolerance through regulation of the CBF cold-response pathway.
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244
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Ashelford K, Eriksson ME, Allen CM, D'Amore R, Johansson M, Gould P, Kay S, Millar AJ, Hall N, Hall A. Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis. Genome Biol 2011; 12:R28. [PMID: 21429190 PMCID: PMC3129678 DOI: 10.1186/gb-2011-12-3-r28] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 02/16/2011] [Accepted: 03/23/2011] [Indexed: 11/23/2022] Open
Abstract
Map based cloning in Arabidopsis thaliana can be a difficult and time-consuming process, specifically if the phenotype is subtle and scoring labour intensive. Here, we have re-sequenced the 120-Mb genome of a novel Arabidopsis clock mutant early bird (ebi-1) in Wassilewskija (Ws-2). We demonstrate the utility of sequencing a backcrossed line in limiting the number of SNPs considered. We identify a SNP in the gene AtNFXL-2 as the likely cause of the ebi-1 phenotype.
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Affiliation(s)
- Kevin Ashelford
- School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
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245
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Transcriptome phase distribution analysis reveals diurnal regulated biological processes and key pathways in rice flag leaves and seedling leaves. PLoS One 2011; 6:e17613. [PMID: 21407816 PMCID: PMC3047585 DOI: 10.1371/journal.pone.0017613] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Accepted: 02/01/2011] [Indexed: 12/04/2022] Open
Abstract
Plant diurnal oscillation is a 24-hour period based variation. The correlation between diurnal genes and biological pathways was widely revealed by microarray analysis in different species. Rice (Oryza sativa) is the major food staple for about half of the world's population. The rice flag leaf is essential in providing photosynthates to the grain filling. However, there is still no comprehensive view about the diurnal transcriptome for rice leaves. In this study, we applied rice microarray to monitor the rhythmically expressed genes in rice seedling and flag leaves. We developed a new computational analysis approach and identified 6,266 (10.96%) diurnal probe sets in seedling leaves, 13,773 (24.08%) diurnal probe sets in flag leaves. About 65% of overall transcription factors were identified as flag leaf preferred. In seedling leaves, the peak of phase distribution was from 2:00am to 4:00am, whereas in flag leaves, the peak was from 8:00pm to 2:00am. The diurnal phase distribution analysis of gene ontology (GO) and cis-element enrichment indicated that, some important processes were waken by the light, such as photosynthesis and abiotic stimulus, while some genes related to the nuclear and ribosome involved processes were active mostly during the switch time of light to dark. The starch and sucrose metabolism pathway genes also showed diurnal phase. We conducted comparison analysis between Arabidopsis and rice leaf transcriptome throughout the diurnal cycle. In summary, our analysis approach is feasible for relatively unbiased identification of diurnal transcripts, efficiently detecting some special periodic patterns with non-sinusoidal periodic patterns. Compared to the rice flag leaves, the gene transcription levels of seedling leaves were relatively limited to the diurnal rhythm. Our comprehensive microarray analysis of seedling and flag leaves of rice provided an overview of the rice diurnal transcriptome and indicated some diurnal regulated biological processes and key functional pathways in rice.
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Hwang H, Cho MH, Hahn BS, Lim H, Kwon YK, Hahn TR, Bhoo SH. Proteomic identification of rhythmic proteins in rice seedlings. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:470-9. [PMID: 21300183 DOI: 10.1016/j.bbapap.2011.01.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 01/20/2011] [Accepted: 01/27/2011] [Indexed: 01/04/2023]
Abstract
Many aspects of plant metabolism that are involved in plant growth and development are influenced by light-regulated diurnal rhythms as well as endogenous clock-regulated circadian rhythms. To identify the rhythmic proteins in rice, periodically grown (12h light/12h dark cycle) seedlings were harvested for three days at six-hour intervals. Continuous dark-adapted plants were also harvested for two days. Among approximately 3000 reproducible protein spots on each gel, proteomic analysis ascertained 354 spots (~12%) as light-regulated rhythmic proteins, in which 53 spots showed prolonged rhythm under continuous dark conditions. Of these 354 ascertained rhythmic protein spots, 74 diurnal spots and 10 prolonged rhythmic spots under continuous dark were identified by MALDI-TOF MS analysis. The rhythmic proteins were functionally classified into photosynthesis, central metabolism, protein synthesis, nitrogen metabolism, stress resistance, signal transduction and unknown. Comparative analysis of our proteomic data with the public microarray database (the Plant DIURNAL Project) and RT-PCR analysis of rhythmic proteins showed differences in rhythmic expression phases between mRNA and protein, suggesting that the clock-regulated proteins in rice are modulated by not only transcriptional but also post-transcriptional, translational, and/or post-translational processes.
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Affiliation(s)
- Heeyoun Hwang
- Graduate School of Biotechnology and Plant Metabolism Research Center, Kyung Hee University, Yongin 446-701, Republic of Korea
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Lu SX, Knowles SM, Webb CJ, Celaya RB, Cha C, Siu JP, Tobin EM. The Jumonji C domain-containing protein JMJ30 regulates period length in the Arabidopsis circadian clock. PLANT PHYSIOLOGY 2011; 155:906-15. [PMID: 21139085 PMCID: PMC3032475 DOI: 10.1104/pp.110.167015] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 12/02/2010] [Indexed: 05/18/2023]
Abstract
Histone methylation plays an essential role in regulating chromatin structure and gene expression. Jumonji C (JmjC) domain-containing proteins are generally known as histone demethylases. Circadian clocks regulate a large number of biological processes, and recent studies suggest that chromatin remodeling has evolved as an important mechanism for regulating both plant and mammalian circadian systems. Here, we analyzed a subgroup of JmjC domain-containing proteins and identified Arabidopsis (Arabidopsis thaliana) JMJ30 as a novel clock component involved in controlling the circadian period. Analysis of loss- and gain-of-function mutants of JMJ30 indicates that this evening-expressed gene is a genetic regulator of period length in the Arabidopsis circadian clock. Furthermore, two key components of the central oscillator of plants, transcription factors CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL, bind directly to the JMJ30 promoter to repress its expression, suggesting that JMJ30 regulates the pace of the circadian clock in close association with the central oscillator. JMJ30 represents, to our knowledge, the first JmjC domain-containing protein involved in circadian function, and we envision that this provides a possible molecular connection between chromatin remodeling and the circadian clock.
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Affiliation(s)
| | | | | | | | | | | | - Elaine M. Tobin
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095
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Abstract
An internal time-keeping mechanism has been observed in almost every organism studied from archaea to humans. This circadian clock provides a competitive advantage in fitness and survival ( 18, 30, 95, 129, 137 ). Researchers have uncovered the molecular composition of this internal clock by combining enzymology, molecular biology, genetics, and modeling approaches. However, understanding the mechanistic link between the clock and output responses has been elusive. In three model organisms, Arabidopsis thaliana, Drosophila melanogaster, and Mus musculus, whole-genome expression arrays have enabled researchers to investigate how maintaining a time-keeping mechanism connects to an adaptive advantage. Here, we review the impacts transcriptomics have had on our understanding of the clock and how this molecular clock connects with system-level circadian responses. We explore the discoveries made possible by high-throughput RNA assays, the network approaches used to investigate these large transcript datasets, and potential future directions.
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Affiliation(s)
- Colleen J Doherty
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, USA.
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Wang Z, Wang T. Dynamic proteomic analysis reveals diurnal homeostasis of key pathways in rice leaves. Proteomics 2010; 11:225-38. [DOI: 10.1002/pmic.201000065] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Revised: 10/13/2010] [Accepted: 10/18/2010] [Indexed: 12/19/2022]
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