101
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Hernando CE, Romanowski A, Yanovsky MJ. Transcriptional and post-transcriptional control of the plant circadian gene regulatory network. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:84-94. [PMID: 27412912 DOI: 10.1016/j.bbagrm.2016.07.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/30/2016] [Accepted: 07/03/2016] [Indexed: 11/16/2022]
Abstract
The circadian clock drives rhythms in multiple physiological processes allowing plants to anticipate and adjust to periodic changes in environmental conditions. These physiological rhythms are associated with robust oscillations in the expression of thousands of genes linked to the control of photosynthesis, cell elongation, biotic and abiotic stress responses, developmental processes such as flowering, and the clock itself. Given its pervasive effects on plant physiology, it is not surprising that circadian clock genes have played an important role in the domestication of crop plants and in the improvement of crop productivity. Therefore, identifying the principles governing the dynamics of the circadian gene regulatory network in plants could strongly contribute to further speed up crop improvement. Here we provide an historical as well as a current description of our knowledge of the molecular mechanisms underlying circadian rhythms in plants. This work focuses on the transcriptional and post-transcriptional regulatory layers that control the very core of the circadian clock, and some of its complex interactions with signaling pathways that help synchronize plant growth and development to daily and seasonal changes in the environment. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- C Esteban Hernando
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Av. Patricias Argentinas 435, C1405BWE Ciudad de Buenos Aires, Argentina.
| | - Andrés Romanowski
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Av. Patricias Argentinas 435, C1405BWE Ciudad de Buenos Aires, Argentina.
| | - Marcelo J Yanovsky
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Av. Patricias Argentinas 435, C1405BWE Ciudad de Buenos Aires, Argentina.
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102
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Millar AJ. The Intracellular Dynamics of Circadian Clocks Reach for the Light of Ecology and Evolution. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:595-618. [PMID: 26653934 DOI: 10.1146/annurev-arplant-043014-115619] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A major challenge for biology is to extend our understanding of molecular regulation from the simplified conditions of the laboratory to ecologically relevant environments. Tractable examples are essential to make these connections for complex, pleiotropic regulators and, to go further, to link relevant genome sequences to field traits. Here, I review the case for the biological clock in higher plants. The gene network of the circadian clock drives pervasive, 24-hour rhythms in metabolism, behavior, and physiology across the eukaryotes and in some prokaryotes. In plants, the scope of chronobiology is now extending from the most tractable, intracellular readouts to the clock's many effects at the whole-organism level and across the life cycle, including biomass and flowering. I discuss five research areas where recent progress might be integrated in the future, to understand not only circadian functions in natural conditions but also the evolution of the clock's molecular mechanisms.
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Affiliation(s)
- Andrew J Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, United Kingdom;
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103
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Kamioka M, Takao S, Suzuki T, Taki K, Higashiyama T, Kinoshita T, Nakamichi N. Direct Repression of Evening Genes by CIRCADIAN CLOCK-ASSOCIATED1 in the Arabidopsis Circadian Clock. THE PLANT CELL 2016; 28:696-711. [PMID: 26941090 PMCID: PMC4826007 DOI: 10.1105/tpc.15.00737] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 02/11/2016] [Accepted: 02/26/2016] [Indexed: 05/18/2023]
Abstract
The circadian clock is a biological timekeeping system that provides organisms with the ability to adapt to day-night cycles. Timing of the expression of four members of the Arabidopsis thaliana PSEUDO-RESPONSE REGULATOR(PRR) family is crucial for proper clock function, and transcriptional control of PRRs remains incompletely defined. Here, we demonstrate that direct regulation of PRR5 by CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) determines the repression state of PRR5 in the morning. Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) analyses indicated that CCA1 associates with three separate regions upstream of PRR5 CCA1 and its homolog LATE ELONGATED HYPOCOTYL (LHY) suppressed PRR5 promoter activity in a transient assay. The regions bound by CCA1 in the PRR5 promoter gave rhythmic patterns with troughs in the morning, when CCA1 and LHY are at high levels. Furthermore,ChIP-seq revealed that CCA1 associates with at least 449 loci with 863 adjacent genes. Importantly, this gene set contains genes that are repressed but upregulated incca1 lhy double mutants in the morning. This study shows that direct binding by CCA1 in the morning provides strong repression of PRR5, and repression by CCA1 also temporally regulates an evening-expressed gene set that includes PRR5.
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Affiliation(s)
- Mari Kamioka
- School of Agriculture, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan
| | - Saori Takao
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan
| | - Takamasa Suzuki
- Exploratory Research for Advanced Technology (ERATO) Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8602, Japan College of Bioscience and Biotechnology, Chub University, Kasugai 487-8501, Japan Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8602, Japan
| | - Kyomi Taki
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8602, Japan
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan Exploratory Research for Advanced Technology (ERATO) Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8602, Japan Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8602, Japan
| | - Toshinori Kinoshita
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8602, Japan
| | - Norihito Nakamichi
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8602, Japan
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104
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De Caluwé J, Xiao Q, Hermans C, Verbruggen N, Leloup JC, Gonze D. A Compact Model for the Complex Plant Circadian Clock. FRONTIERS IN PLANT SCIENCE 2016; 7:74. [PMID: 26904049 PMCID: PMC4742534 DOI: 10.3389/fpls.2016.00074] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 01/16/2016] [Indexed: 05/23/2023]
Abstract
The circadian clock is an endogenous timekeeper that allows organisms to anticipate and adapt to the daily variations of their environment. The plant clock is an intricate network of interlocked feedback loops, in which transcription factors regulate each other to generate oscillations with expression peaks at specific times of the day. Over the last decade, mathematical modeling approaches have been used to understand the inner workings of the clock in the model plant Arabidopsis thaliana. Those efforts have produced a number of models of ever increasing complexity. Here, we present an alternative model that combines a low number of equations and parameters, similar to the very earliest models, with the complex network structure found in more recent ones. This simple model describes the temporal evolution of the abundance of eight clock gene mRNA/protein and captures key features of the clock on a qualitative level, namely the entrained and free-running behaviors of the wild type clock, as well as the defects found in knockout mutants (such as altered free-running periods, lack of entrainment, or changes in the expression of other clock genes). Additionally, our model produces complex responses to various light cues, such as extreme photoperiods and non-24 h environmental cycles, and can describe the control of hypocotyl growth by the clock. Our model constitutes a useful tool to probe dynamical properties of the core clock as well as clock-dependent processes.
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Affiliation(s)
- Joëlle De Caluwé
- Unité de Chronobiologie Théorique, Faculté des Sciences, Université Libre de BruxellesBrussels, Belgium
| | - Qiying Xiao
- Laboratory of Plant Physiology and Molecular Genetics, Faculté des Sciences, Université Libre de BruxellesBrussels, Belgium
| | - Christian Hermans
- Laboratory of Plant Physiology and Molecular Genetics, Faculté des Sciences, Université Libre de BruxellesBrussels, Belgium
| | - Nathalie Verbruggen
- Laboratory of Plant Physiology and Molecular Genetics, Faculté des Sciences, Université Libre de BruxellesBrussels, Belgium
| | - Jean-Christophe Leloup
- Unité de Chronobiologie Théorique, Faculté des Sciences, Université Libre de BruxellesBrussels, Belgium
| | - Didier Gonze
- Unité de Chronobiologie Théorique, Faculté des Sciences, Université Libre de BruxellesBrussels, Belgium
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105
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Yon F, Joo Y, Cortés Llorca L, Rothe E, Baldwin IT, Kim SG. Silencing Nicotiana attenuata LHY and ZTL alters circadian rhythms in flowers. THE NEW PHYTOLOGIST 2016; 209:1058-66. [PMID: 26439540 PMCID: PMC5147715 DOI: 10.1111/nph.13681] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/22/2015] [Indexed: 05/20/2023]
Abstract
The rhythmic opening/closing and volatile emissions of flowers are known to attract pollinators at specific times. That these rhythms are maintained under constant light or dark conditions suggests a circadian clock involvement. Although a forward and reverse genetic approach has led to the identification of core circadian clock components in Arabidopsis thaliana, the involvement of these clock components in floral rhythms has remained untested, probably because of the weak diurnal rhythms in A. thaliana flowers. Here, we addressed the role of these core clock components in the flowers of the wild tobacco Nicotiana attenuata, whose flowers open at night, emit benzyl acetone (BA) scents and move vertically through a 140° arc. We first measured N. attenuata floral rhythms under constant light conditions. The results suggest that the circadian clock controls flower opening, BA emission and pedicel movement, but not flower closing. We generated transgenic N. attenuata lines silenced in the homologous genes of Arabidopsis LATE ELONGATED HYPOCOTYL (LHY) and ZEITLUPE (ZTL), which are known to be core clock components. Silencing NaLHY and NaZTL strongly altered floral rhythms in different ways, indicating that conserved clock components in N. attenuata coordinate these floral rhythms.
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Affiliation(s)
- Felipe Yon
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Youngsung Joo
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Lucas Cortés Llorca
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Eva Rothe
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Ian T. Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Sang-Gyu Kim
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
- Center for Genome Engineering, Institute for Basic Science, Yuseong-gu, Daejeon 305-811, South Korea
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106
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Liu TL, Newton L, Liu MJ, Shiu SH, Farré EM. A G-Box-Like Motif Is Necessary for Transcriptional Regulation by Circadian Pseudo-Response Regulators in Arabidopsis. PLANT PHYSIOLOGY 2016; 170:528-39. [PMID: 26586835 PMCID: PMC4704597 DOI: 10.1104/pp.15.01562] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 11/17/2015] [Indexed: 05/18/2023]
Abstract
PSEUDO-RESPONSE REGULATORs (PRRs) play overlapping and distinct roles in maintaining circadian rhythms and regulating diverse biological processes, including the photoperiodic control of flowering, growth, and abiotic stress responses. PRRs act as transcriptional repressors and associate with chromatin via their conserved C-terminal CCT (CONSTANS, CONSTANS-like, and TIMING OF CAB EXPRESSION 1 [TOC1/PRR1]) domains by a still-poorly understood mechanism. Here, we identified genome-wide targets of PRR9 using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) and compared them with PRR7, PRR5, and TOC1/PRR1 ChIP-seq data. We found that PRR binding sites are located within genomic regions of low nucleosome occupancy and high DNase I hypersensitivity. Moreover, conserved noncoding regions among Brassicaceae species are enriched around PRR binding sites, indicating that PRRs associate with functionally relevant cis-regulatory regions. The PRRs shared a significant number of binding regions, and our results indicate that they coordinately restrict the expression of target genes to around dawn. A G-box-like motif was overrepresented at PRR binding regions, and we showed that this motif is necessary for mediating transcriptional regulation of CIRCADIAN CLOCK ASSOCIATED 1 and PRR9 by the PRRs. Our results further our understanding of how PRRs target specific promoters and provide an extensive resource for studying circadian regulatory networks in plants.
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Affiliation(s)
- Tiffany L Liu
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Linsey Newton
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Ming-Jung Liu
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Eva M Farré
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
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107
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Choudhary MK, Nomura Y, Shi H, Nakagami H, Somers DE. Circadian Profiling of the Arabidopsis Proteome Using 2D-DIGE. FRONTIERS IN PLANT SCIENCE 2016; 7:1007. [PMID: 27462335 PMCID: PMC4940426 DOI: 10.3389/fpls.2016.01007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 06/27/2016] [Indexed: 05/18/2023]
Abstract
Clock-generated biological rhythms provide an adaptive advantage to an organism, resulting in increased fitness and survival. To better elucidate the plant response to the circadian system, we surveyed protein oscillations in Arabidopsis seedlings under constant light. Using large-scale two-dimensional difference in gel electrophoresis (2D-DIGE) the abundance of more than 1000 proteins spots was reproducibly resolved quantified and profiled across a circadian time series. A comparison between phenol-extracted samples and RuBisCO-depleted extracts identified 71 and 40 rhythmically-expressed proteins, respectively, and between 30 and 40% of these derive from non-rhythmic transcripts. These included proteins influencing transcriptional regulation, translation, metabolism, photosynthesis, protein chaperones, and stress-mediated responses. The phasing of maximum expression for the cyclic proteins was similar for both datasets, with a nearly even distribution of peak phases across the time series. STRING clustering analysis identified two interaction networks with a notable number of oscillating proteins: plastid-based and cytosolic chaperones and 10 proteins involved in photosynthesis. The oscillation of the ABA receptor, PYR1/RCAR11, with peak expression near dusk adds to a growing body of evidence that intimately ties ABA signaling to the circadian system. Taken together, this study provides new insights into the importance of post-transcriptional circadian control of plant physiology and metabolism.
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Affiliation(s)
- Mani K. Choudhary
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and TechnologyPohang, South Korea
| | - Yuko Nomura
- Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Hua Shi
- Department of Molecular Genetics, Ohio State UniversityColumbus, OH, USA
| | - Hirofumi Nakagami
- Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - David E. Somers
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and TechnologyPohang, South Korea
- Department of Molecular Genetics, Ohio State UniversityColumbus, OH, USA
- *Correspondence: David E. Somers
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108
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Huang H, Alvarez S, Bindbeutel R, Shen Z, Naldrett MJ, Evans BS, Briggs SP, Hicks LM, Kay SA, Nusinow DA. Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry. Mol Cell Proteomics 2016; 15:201-217. [PMID: 26545401 DOI: 10.6019/pxd002606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Indexed: 05/21/2023] Open
Abstract
Many species possess an endogenous circadian clock to synchronize internal physiology with an oscillating external environment. In plants, the circadian clock coordinates growth, metabolism and development over daily and seasonal time scales. Many proteins in the circadian network form oscillating complexes that temporally regulate myriad processes, including signal transduction, transcription, protein degradation and post-translational modification. In Arabidopsis thaliana, a tripartite complex composed of EARLY FLOWERING 4 (ELF4), EARLY FLOWERING 3 (ELF3), and LUX ARRHYTHMO (LUX), named the evening complex, modulates daily rhythms in gene expression and growth through transcriptional regulation. However, little is known about the physical interactions that connect the circadian system to other pathways. We used affinity purification and mass spectrometry (AP-MS) methods to identify proteins that associate with the evening complex in A. thaliana. New connections within the circadian network as well as to light signaling pathways were identified, including linkages between the evening complex, TIMING OF CAB EXPRESSION1 (TOC1), TIME FOR COFFEE (TIC), all phytochromes and TANDEM ZINC KNUCKLE/PLUS3 (TZP). Coupling genetic mutation with affinity purifications tested the roles of phytochrome B (phyB), EARLY FLOWERING 4, and EARLY FLOWERING 3 as nodes connecting the evening complex to clock and light signaling pathways. These experiments establish a hierarchical association between pathways and indicate direct and indirect interactions. Specifically, the results suggested that EARLY FLOWERING 3 and phytochrome B act as hubs connecting the clock and red light signaling pathways. Finally, we characterized a clade of associated nuclear kinases that regulate circadian rhythms, growth, and flowering in A. thaliana. Coupling mass spectrometry and genetics is a powerful method to rapidly and directly identify novel components and connections within and between complex signaling pathways.
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Affiliation(s)
- He Huang
- From the ‡Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, Missouri, 63132
| | - Sophie Alvarez
- From the ‡Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, Missouri, 63132
| | - Rebecca Bindbeutel
- From the ‡Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, Missouri, 63132
| | - Zhouxin Shen
- §University of California San Diego, Division of Biological Sciences, Cell and Developmental Biology Section, 9500 Gilman Drive, La Jolla, California 92093-0116
| | - Michael J Naldrett
- From the ‡Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, Missouri, 63132
| | - Bradley S Evans
- From the ‡Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, Missouri, 63132
| | - Steven P Briggs
- §University of California San Diego, Division of Biological Sciences, Cell and Developmental Biology Section, 9500 Gilman Drive, La Jolla, California 92093-0116
| | - Leslie M Hicks
- ¶The University of North Carolina at Chapel Hill, Department of Chemistry, Chapel Hill, North Carolina 27599
| | - Steve A Kay
- ‖University of Southern California, Molecular and Computational Biology Section, Los Angeles, California 90089
| | - Dmitri A Nusinow
- From the ‡Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, Missouri, 63132;
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109
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Adams S, Manfield I, Stockley P, Carré IA. Revised Morning Loops of the Arabidopsis Circadian Clock Based on Analyses of Direct Regulatory Interactions. PLoS One 2015; 10:e0143943. [PMID: 26625126 PMCID: PMC4666590 DOI: 10.1371/journal.pone.0143943] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 11/11/2015] [Indexed: 11/24/2022] Open
Abstract
The network structure of the plant circadian clock is complex and direct regulatory interactions between individual components have proven particularly difficult to predict from genetic analyses. Here, we systematically investigate in vivo binding interactions between the morning-specific transcription factor, LATE ELONGATED HYPOCOTYL (LHY) and the promoters of other components of the network. We then demonstrate the functionality of these interactions by testing the responsiveness of the target gene to an ethanol-induced change in expression level of the LHY protein. We uncover novel, negative autoregulatory feedback loops from LHY and the closely related CIRCADIAN CLOCK ASSOCIATED-1 (CCA1) onto their own and each other’s expression. Furthermore we show that LHY acts as a repressor of all other clock components, including PSEUDO-RESPONSE REGULATORs (PRRs) 9 and 7, which were previously thought to be positive regulatory targets. These experimental results lead to a substantial revision of the morning loops of the clock.
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Affiliation(s)
- Sally Adams
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Ian Manfield
- Astbury Centre, University of Leeds, Leeds, United Kingdom
| | - Peter Stockley
- Astbury Centre, University of Leeds, Leeds, United Kingdom
| | - Isabelle A. Carré
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- * E-mail:
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110
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Huang H, Alvarez S, Bindbeutel R, Shen Z, Naldrett MJ, Evans BS, Briggs SP, Hicks LM, Kay SA, Nusinow DA. Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry. Mol Cell Proteomics 2015; 15:201-17. [PMID: 26545401 PMCID: PMC4762519 DOI: 10.1074/mcp.m115.054064] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Indexed: 11/30/2022] Open
Abstract
Many species possess an endogenous circadian clock to synchronize internal physiology with an oscillating external environment. In plants, the circadian clock coordinates growth, metabolism and development over daily and seasonal time scales. Many proteins in the circadian network form oscillating complexes that temporally regulate myriad processes, including signal transduction, transcription, protein degradation and post-translational modification. In Arabidopsis thaliana, a tripartite complex composed of EARLY FLOWERING 4 (ELF4), EARLY FLOWERING 3 (ELF3), and LUX ARRHYTHMO (LUX), named the evening complex, modulates daily rhythms in gene expression and growth through transcriptional regulation. However, little is known about the physical interactions that connect the circadian system to other pathways. We used affinity purification and mass spectrometry (AP-MS) methods to identify proteins that associate with the evening complex in A. thaliana. New connections within the circadian network as well as to light signaling pathways were identified, including linkages between the evening complex, TIMING OF CAB EXPRESSION1 (TOC1), TIME FOR COFFEE (TIC), all phytochromes and TANDEM ZINC KNUCKLE/PLUS3 (TZP). Coupling genetic mutation with affinity purifications tested the roles of phytochrome B (phyB), EARLY FLOWERING 4, and EARLY FLOWERING 3 as nodes connecting the evening complex to clock and light signaling pathways. These experiments establish a hierarchical association between pathways and indicate direct and indirect interactions. Specifically, the results suggested that EARLY FLOWERING 3 and phytochrome B act as hubs connecting the clock and red light signaling pathways. Finally, we characterized a clade of associated nuclear kinases that regulate circadian rhythms, growth, and flowering in A. thaliana. Coupling mass spectrometry and genetics is a powerful method to rapidly and directly identify novel components and connections within and between complex signaling pathways.
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Affiliation(s)
- He Huang
- From the ‡Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, Missouri, 63132
| | - Sophie Alvarez
- From the ‡Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, Missouri, 63132
| | - Rebecca Bindbeutel
- From the ‡Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, Missouri, 63132
| | - Zhouxin Shen
- §University of California San Diego, Division of Biological Sciences, Cell and Developmental Biology Section, 9500 Gilman Drive, La Jolla, California 92093-0116
| | - Michael J Naldrett
- From the ‡Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, Missouri, 63132
| | - Bradley S Evans
- From the ‡Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, Missouri, 63132
| | - Steven P Briggs
- §University of California San Diego, Division of Biological Sciences, Cell and Developmental Biology Section, 9500 Gilman Drive, La Jolla, California 92093-0116
| | - Leslie M Hicks
- ¶The University of North Carolina at Chapel Hill, Department of Chemistry, Chapel Hill, North Carolina 27599
| | - Steve A Kay
- ‖University of Southern California, Molecular and Computational Biology Section, Los Angeles, California 90089
| | - Dmitri A Nusinow
- From the ‡Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, Missouri, 63132;
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111
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Capovilla G, Pajoro A, Immink RGH, Schmid M. Role of alternative pre-mRNA splicing in temperature signaling. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:97-103. [PMID: 26190743 DOI: 10.1016/j.pbi.2015.06.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/18/2015] [Accepted: 06/20/2015] [Indexed: 05/20/2023]
Abstract
Developmental plasticity enables plants to respond rapidly to changing environmental conditions, such as temperature fluctuations. Understanding how plants measure temperature and integrate this information into developmental programs at the molecular level will be essential to breed thermo-tolerant crop varieties. Recent studies identified alternative splicing (AS) as a possible 'molecular thermometer', allowing plants to quickly adjust the abundance of functional transcripts to environmental perturbations. In this review, recent advances regarding the effects of temperature-responsive AS on plant development will be discussed, with emphasis on the circadian clock and flowering time control. The challenge for the near future will be to understand the molecular mechanisms by which temperature can influence AS regulation.
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Affiliation(s)
- Giovanna Capovilla
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72074 Tübingen, Germany
| | - Alice Pajoro
- Plant Research International, Bioscience, 6708 PB Wageningen, The Netherlands; Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Richard G H Immink
- Plant Research International, Bioscience, 6708 PB Wageningen, The Netherlands; Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Markus Schmid
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72074 Tübingen, Germany; Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, S-901 87 Umea, Sweden.
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112
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Litthauer S, Battle MW, Lawson T, Jones MA. Phototropins maintain robust circadian oscillation of PSII operating efficiency under blue light. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015. [PMID: 26215041 DOI: 10.1111/tpj.12947] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The circadian system allows plants to coordinate metabolic and physiological functions with predictable environmental variables such as dusk and dawn. This endogenous oscillator is comprised of biochemical and transcriptional rhythms that are synchronized with a plant's surroundings via environmental signals, including light and temperature. We have used chlorophyll fluorescence techniques to describe circadian rhythms of PSII operating efficiency (Fq'/Fm') in the chloroplasts of Arabidopsis thaliana. These Fq'/Fm' oscillations appear to be influenced by transcriptional feedback loops previously described in the nucleus, and are induced by rhythmic changes in photochemical quenching over circadian time. Our work reveals that a family of blue photoreceptors, phototropins, maintain robust rhythms of Fq'/Fm' under constant blue light. As phototropins do not influence circadian gene expression in the nucleus our imaging methodology highlights differences between the modulation of circadian outputs in distinct subcellular compartments.
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Affiliation(s)
- Suzanne Litthauer
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Martin W Battle
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Tracy Lawson
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Matthew A Jones
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
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113
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Jones MA, Hu W, Litthauer S, Lagarias JC, Harmer SL. A Constitutively Active Allele of Phytochrome B Maintains Circadian Robustness in the Absence of Light. PLANT PHYSIOLOGY 2015; 169:814-25. [PMID: 26157113 PMCID: PMC4577416 DOI: 10.1104/pp.15.00782] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 07/06/2015] [Indexed: 05/18/2023]
Abstract
The sensitivity of the circadian system to light allows entrainment of the clock, permitting coordination of plant metabolic function and flowering time across seasons. Light affects the circadian system via both photoreceptors, such as phytochromes and cryptochromes, and sugar production by photosynthesis. In the present study, we introduce a constitutively active version of phytochrome B-Y276H (YHB) into both wild-type and phytochrome null backgrounds of Arabidopsis (Arabidopsis thaliana) to distinguish the effects of photoreceptor signaling on clock function from those of photosynthesis. We find that the YHB mutation is sufficient to phenocopy red light input into the circadian mechanism and to sustain robust rhythms in steady-state mRNA levels even in plants grown without light or exogenous sugars. The pace of the clock is insensitive to light intensity in YHB plants, indicating that light input to the clock is constitutively activated by this allele. Mutation of YHB so that it is retained in the cytoplasm abrogates its effects on clock function, indicating that nuclear localization of phytochrome is necessary for its clock regulatory activity. We also demonstrate a role for phytochrome C as part of the red light sensing network that modulates phytochrome B signaling input into the circadian system. Our findings indicate that phytochrome signaling in the nucleus plays a critical role in sustaining robust clock function under red light, even in the absence of photosynthesis or exogenous sources of energy.
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Affiliation(s)
- Matthew Alan Jones
- School of Biological Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, United Kingdom (M.A.J., S.L.); andDepartment of Plant Biology, College of Biological Sciences (M.A.J., S.L.H.) and Department of Molecular and Cellular Biology (W.H., J.C.L.), University of California, Davis, California 95616
| | - Wei Hu
- School of Biological Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, United Kingdom (M.A.J., S.L.); andDepartment of Plant Biology, College of Biological Sciences (M.A.J., S.L.H.) and Department of Molecular and Cellular Biology (W.H., J.C.L.), University of California, Davis, California 95616
| | - Suzanne Litthauer
- School of Biological Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, United Kingdom (M.A.J., S.L.); andDepartment of Plant Biology, College of Biological Sciences (M.A.J., S.L.H.) and Department of Molecular and Cellular Biology (W.H., J.C.L.), University of California, Davis, California 95616
| | - J Clark Lagarias
- School of Biological Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, United Kingdom (M.A.J., S.L.); andDepartment of Plant Biology, College of Biological Sciences (M.A.J., S.L.H.) and Department of Molecular and Cellular Biology (W.H., J.C.L.), University of California, Davis, California 95616
| | - Stacey Lynn Harmer
- School of Biological Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, United Kingdom (M.A.J., S.L.); andDepartment of Plant Biology, College of Biological Sciences (M.A.J., S.L.H.) and Department of Molecular and Cellular Biology (W.H., J.C.L.), University of California, Davis, California 95616
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114
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Bendix C, Marshall CM, Harmon FG. Circadian Clock Genes Universally Control Key Agricultural Traits. MOLECULAR PLANT 2015; 8:1135-52. [PMID: 25772379 DOI: 10.1016/j.molp.2015.03.003] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 02/26/2015] [Accepted: 03/04/2015] [Indexed: 05/17/2023]
Abstract
Circadian clocks are endogenous timers that enable plants to synchronize biological processes with daily and seasonal environmental conditions in order to allocate resources during the most beneficial times of day and year. The circadian clock regulates a number of central plant activities, including growth, development, and reproduction, primarily through controlling a substantial proportion of transcriptional activity and protein function. This review examines the roles that alleles of circadian clock genes have played in domestication and improvement of crop plants. The focus here is on three groups of circadian clock genes essential to clock function in Arabidopsis thaliana: PSEUDO-RESPONSE REGULATORs, GIGANTEA, and the evening complex genes early flowering 3, early flowering 4, and lux arrhythmo. homologous genes from each group underlie quantitative trait loci that have beneficial influences on key agricultural traits, especially flowering time but also yield, biomass, and biennial growth habit. Emerging insights into circadian clock regulation of other fundamental plant processes, including responses to abiotic and biotic stresses, are discussed to highlight promising avenues for further crop improvement.
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Affiliation(s)
- Claire Bendix
- Plant Gene Expression Center, USDA-ARS, Albany, CA 94710, USA; Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Carine M Marshall
- Plant Gene Expression Center, USDA-ARS, Albany, CA 94710, USA; Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Frank G Harmon
- Plant Gene Expression Center, USDA-ARS, Albany, CA 94710, USA; Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA.
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115
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Circadian clock gene LATE ELONGATED HYPOCOTYL directly regulates the timing of floral scent emission in Petunia. Proc Natl Acad Sci U S A 2015; 112:9775-80. [PMID: 26124104 DOI: 10.1073/pnas.1422875112] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Flowers present a complex display of signals to attract pollinators, including the emission of floral volatiles. Volatile emission is highly regulated, and many species restrict emissions to specific times of the day. This rhythmic emission of scent is regulated by the circadian clock; however, the mechanisms have remained unknown. In Petunia hybrida, volatile emissions are dominated by products of the floral volatile benzenoid/phenylpropanoid (FVBP) metabolic pathway. Here we demonstrate that the circadian clock gene P. hybrida LATE ELONGATED HYPOCOTYL (LHY; PhLHY) regulates the daily expression patterns of the FVBP pathway genes and floral volatile production. PhLHY expression peaks in the morning, antiphasic to the expression of P. hybrida GIGANTEA (PhGI), the master scent regulator ODORANT1 (ODO1), and many other evening-expressed FVBP genes. Overexpression phenotypes of PhLHY in Arabidopsis caused an arrhythmic clock phenotype, which resembles those of LHY overexpressors. In Petunia, constitutive expression of PhLHY depressed the expression levels of PhGI, ODO1, evening-expressed FVBP pathway genes, and FVBP emission in flowers. Additionally, in the Petunia lines in which PhLHY expression was reduced, the timing of peak expression of PhGI, ODO1, and the FVBP pathway genes advanced to the morning. Moreover, PhLHY protein binds to cis-regulatory elements called evening elements that exist in promoters of ODO1 and other FVBP genes. Thus, our results imply that PhLHY directly sets the timing of floral volatile emission by restricting the expression of ODO1 and other FVBP genes to the evening in Petunia.
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116
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Townsley BT, Covington MF, Ichihashi Y, Zumstein K, Sinha NR. BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction. FRONTIERS IN PLANT SCIENCE 2015; 6:366. [PMID: 26052336 DOI: 10.3389/fpls.2015.00366/abstract] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/08/2015] [Indexed: 05/26/2023]
Abstract
Next Generation Sequencing (NGS) is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq) has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing the terminal breathing of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing (BrAD-seq) reduces sample handling and requires far fewer enzymatic steps than most available methods to produce high quality strand-specific RNA-seq libraries. The method we present is optimized for 3-prime Digital Gene Expression (DGE) libraries and can easily extend to full transcript coverage shotgun (SHO) type strand-specific libraries and is modularized to accommodate a diversity of RNA and DNA input materials. BrAD-seq offers a highly streamlined and inexpensive option for RNA-seq libraries.
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Affiliation(s)
- Brad T Townsley
- Department of Plant Biology, University of California, Davis Davis, CA, USA
| | | | - Yasunori Ichihashi
- Department of Plant Biology, University of California, Davis Davis, CA, USA
| | - Kristina Zumstein
- Department of Plant Biology, University of California, Davis Davis, CA, USA
| | - Neelima R Sinha
- Department of Plant Biology, University of California, Davis Davis, CA, USA
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117
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Mi G, Di Y. The level of residual dispersion variation and the power of differential expression tests for RNA-Seq data. PLoS One 2015; 10:e0120117. [PMID: 25849826 PMCID: PMC4388866 DOI: 10.1371/journal.pone.0120117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 02/04/2015] [Indexed: 11/19/2022] Open
Abstract
RNA-Sequencing (RNA-Seq) has been widely adopted for quantifying gene expression changes in comparative transcriptome analysis. For detecting differentially expressed genes, a variety of statistical methods based on the negative binomial (NB) distribution have been proposed. These methods differ in the ways they handle the NB nuisance parameters (i.e., the dispersion parameters associated with each gene) to save power, such as by using a dispersion model to exploit an apparent relationship between the dispersion parameter and the NB mean. Presumably, dispersion models with fewer parameters will result in greater power if the models are correct, but will produce misleading conclusions if not. This paper investigates this power and robustness trade-off by assessing rates of identifying true differential expression using the various methods under realistic assumptions about NB dispersion parameters. Our results indicate that the relative performances of the different methods are closely related to the level of dispersion variation unexplained by the dispersion model. We propose a simple statistic to quantify the level of residual dispersion variation from a fitted dispersion model and show that the magnitude of this statistic gives hints about whether and how much we can gain statistical power by a dispersion-modeling approach.
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Affiliation(s)
- Gu Mi
- Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
| | - Yanming Di
- Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America
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118
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Time-dependent sequestration of RVE8 by LNK proteins shapes the diurnal oscillation of anthocyanin biosynthesis. Proc Natl Acad Sci U S A 2015; 112:5249-53. [PMID: 25848001 DOI: 10.1073/pnas.1420792112] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Circadian clocks sustain 24-h rhythms in physiology and metabolism that are synchronized with the day/night cycle. In plants, the regulatory network responsible for the generation of rhythms has been broadly investigated over the past years. However, little is known about the intersecting pathways that link the environmental signals with rhythms in cellular metabolism. Here, we examine the role of the circadian components REVEILLE8/LHY-CCA1-LIKE5 (RVE8/LCL5) and NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED genes (LNK) shaping the diurnal oscillation of the anthocyanin metabolic pathway. Around dawn, RVE8 up-regulates anthocyanin gene expression by directly associating to the promoters of a subset of anthocyanin biosynthetic genes. The up-regulation is overcome at midday by the repressing activity of LNK proteins, as inferred by the increased anthocyanin gene expression in lnk1/lnk2 double mutant plants. Chromatin immunoprecipitation assays using LNK and RVE8 misexpressing plants show that RVE8 binding to target promoters is precluded in LNK overexpressing plants and conversely, binding is enhanced in the absence of functional LNKs, which provides a mechanism by which LNKs antagonize RVE8 function in the regulation of anthocyanin accumulation. Based on their previously described transcriptional coactivating function, our study defines a switch in the regulatory activity of RVE8-LNK interaction, from a synergic coactivating role of evening-expressed clock genes to a repressive antagonistic function modulating anthocyanin biosynthesis around midday.
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119
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Nozue K, Tat AV, Kumar Devisetty U, Robinson M, Mumbach MR, Ichihashi Y, Lekkala S, Maloof JN. Shade avoidance components and pathways in adult plants revealed by phenotypic profiling. PLoS Genet 2015; 11:e1004953. [PMID: 25874869 PMCID: PMC4398415 DOI: 10.1371/journal.pgen.1004953] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 12/11/2014] [Indexed: 01/01/2023] Open
Abstract
Shade from neighboring plants limits light for photosynthesis; as a consequence, plants have a variety of strategies to avoid canopy shade and compete with their neighbors for light. Collectively the response to foliar shade is called the shade avoidance syndrome (SAS). The SAS includes elongation of a variety of organs, acceleration of flowering time, and additional physiological responses, which are seen throughout the plant life cycle. However, current mechanistic knowledge is mainly limited to shade-induced elongation of seedlings. Here we use phenotypic profiling of seedling, leaf, and flowering time traits to untangle complex SAS networks. We used over-representation analysis (ORA) of shade-responsive genes, combined with previous annotation, to logically select 59 known and candidate novel mutants for phenotyping. Our analysis reveals shared and separate pathways for each shade avoidance response. In particular, auxin pathway components were required for shade avoidance responses in hypocotyl, petiole, and flowering time, whereas jasmonic acid pathway components were only required for petiole and flowering time responses. Our phenotypic profiling allowed discovery of seventeen novel shade avoidance mutants. Our results demonstrate that logical selection of mutants increased success of phenotypic profiling to dissect complex traits and discover novel components.
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Affiliation(s)
- Kazunari Nozue
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - An V. Tat
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Upendra Kumar Devisetty
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Matthew Robinson
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Maxwell R. Mumbach
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Yasunori Ichihashi
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Saradadevi Lekkala
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Julin N. Maloof
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
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120
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Johansson M, Staiger D. Time to flower: interplay between photoperiod and the circadian clock. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:719-30. [PMID: 25371508 DOI: 10.1093/jxb/eru441] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Plants precisely time the onset of flowering to ensure reproductive success. A major factor in seasonal control of flowering time is the photoperiod. The length of the daily light period is measured by the circadian clock in leaves, and a signal is conveyed to the shoot apex to initiate floral transition accordingly. In the last two decades, the molecular players in the photoperiodic pathway have been identified in Arabidopsis thaliana. Moreover, the intricate connections between the circadian clockwork and components of the photoperiodic pathway have been unravelled. In particular, the molecular basis of time-of-day-dependent sensitivity to floral stimuli, as predicted by Bünning and Pittendrigh, has been elucidated. This review covers recent insights into the molecular mechanisms underlying clock regulation of photoperiodic responses and the integration of the photoperiodic pathway into the flowering time network in Arabidopsis. Furthermore, examples of conservation and divergence in photoperiodic flower induction in other plant species are discussed.
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Affiliation(s)
- Mikael Johansson
- Molecular Cell Physiology, Faculty for Biology, Bielefeld University, Germany
| | - Dorothee Staiger
- Molecular Cell Physiology, Faculty for Biology, Bielefeld University, Germany
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121
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Romanowski A, Yanovsky MJ. Circadian rhythms and post-transcriptional regulation in higher plants. FRONTIERS IN PLANT SCIENCE 2015; 6:437. [PMID: 26124767 PMCID: PMC4464108 DOI: 10.3389/fpls.2015.00437] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 05/28/2015] [Indexed: 05/06/2023]
Abstract
The circadian clock of plants allows them to cope with daily changes in their environment. This is accomplished by the rhythmic regulation of gene expression, in a process that involves many regulatory steps. One of the key steps involved at the RNA level is post-transcriptional regulation, which ensures a correct control on the different amounts and types of mRNA that will ultimately define the current physiological state of the plant cell. Recent advances in the study of the processes of regulation of pre-mRNA processing, RNA turn-over and surveillance, regulation of translation, function of lncRNAs, biogenesis and function of small RNAs, and the development of bioinformatics tools have helped to vastly expand our understanding of how this regulatory step performs its role. In this work we review the current progress in circadian regulation at the post-transcriptional level research in plants. It is the continuous interaction of all the information flow control post-transcriptional processes that allow a plant to precisely time and predict daily environmental changes.
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Affiliation(s)
| | - Marcelo J. Yanovsky
- *Correspondence: Marcelo J. Yanovsky, Laboratorio de Genómica Comparativa del Desarrollo Vegetal, Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina,
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122
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Townsley BT, Covington MF, Ichihashi Y, Zumstein K, Sinha NR. BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction. FRONTIERS IN PLANT SCIENCE 2015; 6:366. [PMID: 26052336 PMCID: PMC4441129 DOI: 10.3389/fpls.2015.00366] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/08/2015] [Indexed: 05/18/2023]
Abstract
Next Generation Sequencing (NGS) is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq) has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing the terminal breathing of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing (BrAD-seq) reduces sample handling and requires far fewer enzymatic steps than most available methods to produce high quality strand-specific RNA-seq libraries. The method we present is optimized for 3-prime Digital Gene Expression (DGE) libraries and can easily extend to full transcript coverage shotgun (SHO) type strand-specific libraries and is modularized to accommodate a diversity of RNA and DNA input materials. BrAD-seq offers a highly streamlined and inexpensive option for RNA-seq libraries.
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Affiliation(s)
| | | | | | | | - Neelima R. Sinha
- *Correspondence: Neelima R. Sinha, Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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123
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Xing H, Wang P, Cui X, Zhang C, Wang L, Liu X, Yuan L, Li Y, Xie Q, Xu X. LNK1 and LNK2 recruitment to the evening element require morning expressed circadian related MYB-like transcription factors. PLANT SIGNALING & BEHAVIOR 2015; 10:e1010888. [PMID: 25848708 PMCID: PMC4622603 DOI: 10.1080/15592324.2015.1010888] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/10/2015] [Accepted: 01/15/2015] [Indexed: 05/25/2023]
Abstract
Transcriptional feedback loops in Arabidopsis circadian clock is composed of more repressive components, while the knowledge of activation mechanism remains limited. We recently reported 2 members from a family of NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED genes, LNK1 and LNK2, dynamically interact with morning-phased transcriptional factors, like CIRCADIAN CLOCK ASSOCIATED1 (CCA1), LATE ELONGATED HYPOCOTYL (LHY), REVEILLE8 (RVE8) and RVE4, and function as coactivators for the expression of TIMING OF CAB EXPRESSION1 (TOC1) and PSEUDO-RESPONSE REGULATOR5 (PRR5) via transcriptional factors RVE8 and RVE4. Here we provide evidence that both LNK1 and LNK2 play critical role in the transcriptional activation of PRR5, LNK1 may contribute more than LNK2 did under experimental conditions. We also identified that both LNK1 and LNK2 recruitment to the evening element of PRR5 promoter via LNK1-RVE8 or LNK2-RVE8 proteins complex through electrophoretic mobility shift assay. Therefore LNK1 and LNK2 function as coactivator of dawn-phased MYB-like transcription factors, such as RVE8 in morning complex to regulate the target genes expression.
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Affiliation(s)
- Hongya Xing
- Hebei Key Laboratory of Molecular and Cellular Biology; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; College of Life Sciences; Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling; Shijiazhuang, China
| | - Peng Wang
- Hebei Key Laboratory of Molecular and Cellular Biology; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; College of Life Sciences; Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling; Shijiazhuang, China
| | - Xuan Cui
- Hebei Key Laboratory of Molecular and Cellular Biology; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; College of Life Sciences; Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling; Shijiazhuang, China
| | - Chenguang Zhang
- Hebei Key Laboratory of Molecular and Cellular Biology; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; College of Life Sciences; Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling; Shijiazhuang, China
| | - Lingbao Wang
- Hebei Key Laboratory of Molecular and Cellular Biology; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; College of Life Sciences; Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling; Shijiazhuang, China
| | - Xian Liu
- Hebei Key Laboratory of Molecular and Cellular Biology; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; College of Life Sciences; Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling; Shijiazhuang, China
| | - Li Yuan
- Hebei Key Laboratory of Molecular and Cellular Biology; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; College of Life Sciences; Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling; Shijiazhuang, China
| | - Yue Li
- Hebei Key Laboratory of Molecular and Cellular Biology; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; College of Life Sciences; Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling; Shijiazhuang, China
| | - Qiguang Xie
- Hebei Key Laboratory of Molecular and Cellular Biology; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; College of Life Sciences; Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling; Shijiazhuang, China
| | - Xiaodong Xu
- Hebei Key Laboratory of Molecular and Cellular Biology; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; College of Life Sciences; Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling; Shijiazhuang, China
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124
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Shim JS, Imaizumi T. Circadian clock and photoperiodic response in Arabidopsis: from seasonal flowering to redox homeostasis. Biochemistry 2014; 54:157-70. [PMID: 25346271 PMCID: PMC4303289 DOI: 10.1021/bi500922q] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Many of the developmental responses
and behaviors in plants that
occur throughout the year are controlled by photoperiod; among these,
seasonal flowering is the most characterized. Molecular genetic and
biochemical analyses have revealed the mechanisms by which plants
sense changes in day length to regulate seasonal flowering. In Arabidopsis thaliana, induction of the expression of a florigen,
FLOWERING LOCUS T (FT) protein, is a major output of the photoperiodic
flowering pathway. The circadian clock coordinates the expression
profiles and activities of the components in this pathway. Light-dependent
control of CONSTANS (CO) transcription factor activity is a crucial
part of the induction of the photoperiodic expression of FT. CO protein is stabilized only in the long day afternoon, which
is when FT is induced. In this review, we summarize
recent progress in the determination of the molecular architecture
of the circadian clock and mechanisms underlying photoperiodic flowering.
In addition, we introduce the molecular mechanisms of other biological
processes, such as hypocotyl growth and reactive oxygen species production,
which are also controlled by alterations in photoperiod.
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Affiliation(s)
- Jae Sung Shim
- Department of Biology, University of Washington , Seattle, Washington 98195-1800, United States
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125
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Mizuno T, Kitayama M, Oka H, Tsubouchi M, Takayama C, Nomoto Y, Yamashino T. The EC night-time repressor plays a crucial role in modulating circadian clock transcriptional circuitry by conservatively double-checking both warm-night and night-time-light signals in a synergistic manner in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2014; 55:2139-51. [PMID: 25332490 DOI: 10.1093/pcp/pcu144] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
During the last decade, significant research progress has been made in Arabidopsis thaliana in defining the molecular mechanisms behind the plant circadian clock. The circadian clock must have the ability to integrate both external light and ambient temperature signals into its transcriptional circuitry to regulate its function properly. We previously showed that transcription of a set of clock genes including LUX (LUX ARRHYTHMO), GI (GIGANTEA), LNK1 (NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED GENE 1), PRR9 (PSEUDO-RESPONSE REGULATOR 9) and PRR7 is commonly regulated through the evening complex (EC) night-time repressor in response to both moderate changes in temperature (Δ6°C) and differences in steady-state growth-compatible temperature (16-28°C). Here, we further show that a night-time-light signal also feeds into the circadian clock transcriptional circuitry through the EC night-time repressor, so that the same set of EC target genes is up-regulated in response to a night-time-light pulse. This light-induced event is dependent on phytochromes, but not cryptochromes. Interestingly, both the warm-night and night-time-light signals negatively modulate the activity of the EC night-time repressor in a synergistic manner. In other words, an exponential burst of transcription of the EC target genes is observed only when these signals are simultaneously fed into the repressor. Taken together, we propose that the EC night-time repressor plays a crucial role in modulating the clock transcriptional circuitry to keep track properly of seasonal changes in photo- and thermal cycles by conservatively double-checking the external light and ambient temperature signals.
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Affiliation(s)
- Takeshi Mizuno
- Laboratory of Molecular and Functional Genomics, School of Agriculture, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Miki Kitayama
- Laboratory of Molecular and Functional Genomics, School of Agriculture, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Haruka Oka
- Laboratory of Molecular and Functional Genomics, School of Agriculture, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Mayuka Tsubouchi
- Laboratory of Molecular and Functional Genomics, School of Agriculture, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Chieko Takayama
- Laboratory of Molecular and Functional Genomics, School of Agriculture, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Yuji Nomoto
- Laboratory of Molecular and Functional Genomics, School of Agriculture, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Takafumi Yamashino
- Laboratory of Molecular and Functional Genomics, School of Agriculture, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
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Berns MC, Nordström K, Cremer F, Tóth R, Hartke M, Simon S, Klasen JR, Bürstel I, Coupland G. Evening expression of arabidopsis GIGANTEA is controlled by combinatorial interactions among evolutionarily conserved regulatory motifs. THE PLANT CELL 2014; 26:3999-4018. [PMID: 25361953 PMCID: PMC4247573 DOI: 10.1105/tpc.114.129437] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/11/2014] [Accepted: 10/12/2014] [Indexed: 05/18/2023]
Abstract
Diurnal patterns of gene transcription are often conferred by complex interactions between circadian clock control and acute responses to environmental cues. Arabidopsis thaliana GIGANTEA (GI) contributes to photoperiodic flowering, circadian clock control, and photoreceptor signaling, and its transcription is regulated by the circadian clock and light. We used phylogenetic shadowing to identify three evolutionarily constrained regions (conserved regulatory modules [CRMs]) within the GI promoter and show that CRM2 is sufficient to confer a similar transcriptional pattern as the full-length promoter. Dissection of CRM2 showed that one subfragment (CRM2-A) contributes light inducibility, while another (CRM2-B) exhibits a diurnal response. Mutational analysis showed that three ABA RESPONSE ELEMENT LIKE (ABREL) motifs in CRM2-A and three EVENING ELEMENTs (EEs) in CRM2-B are essential in combination to confer a high amplitude diurnal pattern of expression. Genome-wide analysis identified characteristic spacing patterns of EEs and 71 A. thaliana promoters containing three EEs. Among these promoters, that of FLAVIN BINDING KELCH REPEAT F-BOX1 was analyzed in detail and shown to harbor a CRM functionally related to GI CRM2. Thus, combinatorial interactions among EEs and ABRELs confer diurnal patterns of transcription via an evolutionarily conserved module present in GI and other evening-expressed genes.
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Affiliation(s)
- Markus C Berns
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Karl Nordström
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Frédéric Cremer
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Réka Tóth
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Martin Hartke
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Samson Simon
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Jonas R Klasen
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Ingmar Bürstel
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - George Coupland
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
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127
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Fogelmark K, Troein C. Rethinking transcriptional activation in the Arabidopsis circadian clock. PLoS Comput Biol 2014; 10:e1003705. [PMID: 25033214 PMCID: PMC4102396 DOI: 10.1371/journal.pcbi.1003705] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 05/19/2014] [Indexed: 12/19/2022] Open
Abstract
Circadian clocks are biological timekeepers that allow living cells to time their activity in anticipation of predictable daily changes in light and other environmental factors. The complexity of the circadian clock in higher plants makes it difficult to understand the role of individual genes or molecular interactions, and mathematical modelling has been useful in guiding clock research in model organisms such as Arabidopsis thaliana. We present a model of the circadian clock in Arabidopsis, based on a large corpus of published time course data. It appears from experimental evidence in the literature that most interactions in the clock are repressive. Hence, we remove all transcriptional activation found in previous models of this system, and instead extend the system by including two new components, the morning-expressed activator RVE8 and the nightly repressor/activator NOX. Our modelling results demonstrate that the clock does not need a large number of activators in order to reproduce the observed gene expression patterns. For example, the sequential expression of the PRR genes does not require the genes to be connected as a series of activators. In the presented model, transcriptional activation is exclusively the task of RVE8. Predictions of how strongly RVE8 affects its targets are found to agree with earlier interpretations of the experimental data, but generally we find that the many negative feedbacks in the system should discourage intuitive interpretations of mutant phenotypes. The dynamics of the clock are difficult to predict without mathematical modelling, and the clock is better viewed as a tangled web than as a series of loops. Like most living organisms, plants are dependent on sunlight, and evolution has endowed them with an internal clock by which they can predict sunrise and sunset. The clock consists of many genes that control each other in a complex network, leading to daily oscillations in protein levels. The interactions between genes can be positive or negative, causing target genes to be turned on or off. By constructing mathematical models that incorporate our knowledge of this network, we can interpret experimental data by comparing with results from the models. Any discrepancy between experimental data and model predictions will highlight where we are lacking in understanding. We compiled more than 800 sets of measured data from published articles about the clock in the model organism thale cress (Arabidopsis thaliana). Using these data, we constructed a mathematical model which compares favourably with previous models for simulating the clock. We used our model to investigate the role of positive interactions between genes, whether they are necessary for the function of the clock and if they can be identified in the model.
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Affiliation(s)
- Karl Fogelmark
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Carl Troein
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
- * E-mail:
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128
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Xie Q, Wang P, Liu X, Yuan L, Wang L, Zhang C, Li Y, Xing H, Zhi L, Yue Z, Zhao C, McClung CR, Xu X. LNK1 and LNK2 are transcriptional coactivators in the Arabidopsis circadian oscillator. THE PLANT CELL 2014; 26:2843-57. [PMID: 25012192 PMCID: PMC4145118 DOI: 10.1105/tpc.114.126573] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 06/08/2014] [Accepted: 06/20/2014] [Indexed: 05/18/2023]
Abstract
Transcriptional feedback loops are central to the architecture of eukaryotic circadian clocks. Models of the Arabidopsis thaliana circadian clock have emphasized transcriptional repressors, but recently, Myb-like REVEILLE (RVE) transcription factors have been established as transcriptional activators of central clock components, including PSEUDO-RESPONSE REGULATOR5 (PRR5) and TIMING OF CAB EXPRESSION1 (TOC1). We show here that NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED1 (LNK1) and LNK2, members of a small family of four LNK proteins, dynamically interact with morning-expressed oscillator components, including RVE4 and RVE8. Mutational disruption of LNK1 and LNK2 function prevents transcriptional activation of PRR5 by RVE8. The LNKs lack known DNA binding domains, yet LNK1 acts as a transcriptional activator in yeast and in planta. Chromatin immunoprecipitation shows that LNK1 is recruited to the PRR5 and TOC1 promoters in planta. We conclude that LNK1 is a transcriptional coactivator necessary for expression of the clock genes PRR5 and TOC1 through recruitment to their promoters via interaction with bona fide DNA binding proteins such as RVE4 and RVE8.
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Affiliation(s)
- Qiguang Xie
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
| | - Peng Wang
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
| | - Xian Liu
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
| | - Li Yuan
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
| | - Lingbao Wang
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
| | - Chenguang Zhang
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
| | - Yue Li
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
| | - Hongya Xing
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
| | - Liya Zhi
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
| | - Zhiliang Yue
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
| | - Chunsheng Zhao
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
| | - C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755-3563
| | - Xiaodong Xu
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
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129
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Chow BY, Sanchez SE, Breton G, Pruneda-Paz JL, Krogan NT, Kay SA. Transcriptional regulation of LUX by CBF1 mediates cold input to the circadian clock in Arabidopsis. Curr Biol 2014; 24:1518-24. [PMID: 24954045 DOI: 10.1016/j.cub.2014.05.029] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 04/11/2014] [Accepted: 05/13/2014] [Indexed: 11/27/2022]
Abstract
Circadian clocks allow organisms to anticipate daily changes in the environment to enhance overall fitness. Transcription factors (TFs) play a prominent role in the molecular mechanism but are incompletely described possibly due to functional redundancy, gene family proliferation, and/or lack of context-specific assays. To overcome these, we performed a high-throughput yeast one-hybrid screen using the LUX ARRYHTHMO (LUX) gene promoter as bait against an Arabidopsis TF library. LUX is a unique gene because its mutation causes severe clock defects and transcript maintains high-amplitude cycling in the cold. We report the well-characterized cold-inducible C-repeat (CRT)/drought-responsive element (DRE) binding factor CBF1/DREB1b is a transcriptional regulator of LUX. We show that CBF1 binds the CRT in the LUX promoter, and both genes overlap in temporal and spatial expression. CBF1 overexpression causes upregulation of LUX and also alters other clock gene transcripts. LUX promoter regions including the CRT and Evening Element (EE) are sufficient for high-amplitude transcriptional cycling in the cold, and cold-acclimated lux seedlings are sensitive to freezing stress. Our data show cold signaling is integrated into the clock by CBF-mediated regulation of LUX expression, thereby defining a new transcriptional mechanism for temperature input to the circadian clock.
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Affiliation(s)
- Brenda Y Chow
- University of Southern California, Molecular and Computational Biology, Department of Biology Dana and David Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
| | - Sabrina E Sanchez
- University of Southern California, Molecular and Computational Biology, Department of Biology Dana and David Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
| | - Ghislain Breton
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jose L Pruneda-Paz
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Naden T Krogan
- American University, Department of Biology, Washington, DC 20016, USA
| | - Steve A Kay
- University of Southern California, Molecular and Computational Biology, Department of Biology Dana and David Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA.
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130
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Skeffington AW, Graf A, Duxbury Z, Gruissem W, Smith AM. Glucan, Water Dikinase Exerts Little Control over Starch Degradation in Arabidopsis Leaves at Night. PLANT PHYSIOLOGY 2014; 165:866-879. [PMID: 24781197 PMCID: PMC4044853 DOI: 10.1104/pp.114.237016] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 04/28/2014] [Indexed: 05/20/2023]
Abstract
The first step on the pathway of starch degradation in Arabidopsis (Arabidopsis thaliana) leaves at night is the phosphorylation of starch polymers, catalyzed by glucan, water dikinase (GWD). It has been suggested that GWD is important for the control of starch degradation, because its transcript levels undergo strong diel fluctuations, its activity is subject to redox regulation in vitro, and starch degradation is strongly decreased in gwd mutant plants. To test this suggestion, we analyzed changes in GWD protein abundance in relation to starch levels in wild-type plants, in transgenic plants in which GWD transcripts were strongly reduced by induction of RNA interference, and in transgenic plants overexpressing GWD. We found that GWD protein levels do not vary over the diel cycle and that the protein has a half-life of 2 d. Overexpression of GWD does not accelerate starch degradation in leaves, and starch degradation is not inhibited until GWD levels are reduced by 70%. Surprisingly, this degree of reduction also inhibits starch synthesis in the light. To discover the importance of redox regulation, we generated transgenic plants expressing constitutively active GWD. These plants retained normal control of degradation. We conclude that GWD exerts only a low level of control over starch degradation in Arabidopsis leaves.
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Affiliation(s)
- Alastair W Skeffington
- John Innes Centre, Norwich NR4 7UH, United Kingdom (A.W.S., A.G., Z.D., A.M.S.); andDepartment of Biology, Eidgenössisch Technische Hochschule Zürich, CH-8092 Zurich, Switzerland (A.G., W.G.)
| | - Alexander Graf
- John Innes Centre, Norwich NR4 7UH, United Kingdom (A.W.S., A.G., Z.D., A.M.S.); andDepartment of Biology, Eidgenössisch Technische Hochschule Zürich, CH-8092 Zurich, Switzerland (A.G., W.G.)
| | - Zane Duxbury
- John Innes Centre, Norwich NR4 7UH, United Kingdom (A.W.S., A.G., Z.D., A.M.S.); andDepartment of Biology, Eidgenössisch Technische Hochschule Zürich, CH-8092 Zurich, Switzerland (A.G., W.G.)
| | - Wilhelm Gruissem
- John Innes Centre, Norwich NR4 7UH, United Kingdom (A.W.S., A.G., Z.D., A.M.S.); andDepartment of Biology, Eidgenössisch Technische Hochschule Zürich, CH-8092 Zurich, Switzerland (A.G., W.G.)
| | - Alison M Smith
- John Innes Centre, Norwich NR4 7UH, United Kingdom (A.W.S., A.G., Z.D., A.M.S.); andDepartment of Biology, Eidgenössisch Technische Hochschule Zürich, CH-8092 Zurich, Switzerland (A.G., W.G.)
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131
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Hsu PY, Harmer SL. Wheels within wheels: the plant circadian system. TRENDS IN PLANT SCIENCE 2014; 19:240-9. [PMID: 24373845 PMCID: PMC3976767 DOI: 10.1016/j.tplants.2013.11.007] [Citation(s) in RCA: 238] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/20/2013] [Accepted: 11/20/2013] [Indexed: 05/18/2023]
Abstract
Circadian clocks integrate environmental signals with internal cues to coordinate diverse physiological outputs so that they occur at the most appropriate season or time of day. Recent studies using systems approaches, primarily in Arabidopsis, have expanded our understanding of the molecular regulation of the central circadian oscillator and its connections to input and output pathways. Similar approaches have also begun to reveal the importance of the clock for key agricultural traits in crop species. In this review, we discuss recent developments in the field, including a new understanding of the molecular architecture underlying the plant clock; mechanistic links between clock components and input and output pathways; and our growing understanding of the importance of clock genes for agronomically important traits.
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Affiliation(s)
- Polly Yingshan Hsu
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Stacey L Harmer
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA.
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132
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McClung CR. Wheels within wheels: new transcriptional feedback loops in the Arabidopsis circadian clock. F1000PRIME REPORTS 2014; 6:2. [PMID: 24592314 PMCID: PMC3883422 DOI: 10.12703/p6-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The circadian clock allows organisms to temporally coordinate their biology with the diurnal oscillation of the environment, which enhances plant performance. Accordingly, a fuller understanding of the circadian clock mechanism may contribute to efforts to optimize plant performance. One recurring theme in clock mechanism is coupled transcription-translation feedback loops. To date, the majority of plant transcription factors constituting these loops, including the central oscillator components CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), LATE ELONGATED HYPOCOTYL (LHY), and TIMING OF CAB2 EXPRESSION 1 (TOC1), and the related PSEUDO-RESPONSE REGULATORS (PRRs), are transcriptional repressors, leading to a model of the clock emphasizing repressive interactions. Recent work, however, has revealed that a subset of the REVEILLE (RVE) family of Myb transcription factors closely related to CCA1 and LHY are transcriptional activators in novel feedback transcription-translation feedback loops. Other recently identified transcriptional activators that contribute to clock function include LIGHT-REGULATED WD 1 (LWD1) and LWD2 and night light-inducible and clock-regulated transcription factors NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED1 (LNK1) and LNK2. Collectively, these advances permit a substantial reconfiguration of the clock model.
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133
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Mizuno T, Takeuchi A, Nomoto Y, Nakamichi N, Yamashino T. The LNK1 night light-inducible and clock-regulated gene is induced also in response to warm-night through the circadian clock nighttime repressor in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2014; 9:e28505. [PMID: 24690904 PMCID: PMC4091318 DOI: 10.4161/psb.28505] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Ambient temperature has two fundamental impacts on the Arabidopsis circadian clock system in the processes referred to as temperature compensation and entrainment, respectively. These temperature-related longstanding problems have not yet been fully clarified. Recently, we provided evidence that temperature signals feed into the clock transcriptional circuitry through the evening complex (EC) nighttime repressor composed of LUX-ELF3-ELF4, and that the transcription of PRR9, PRR7, GI and LUX is commonly regulated through the nighttime repressor in response to both moderate changes in temperature (∆6 °C) and differences in steady-state growth-compatible temperature (16 °C to 28 °C). These temperature-associated characteristics of the core clock genes might be relevant to the fundamental oscillator functions. Here, we further show that the recently identified LNK1 night light-inducible and clock-controlled gene, which actually has a robust peak at daytime, is induced also by warm-night through the EC nighttime repressor in a manner very similar to PRR7, which is also night light-inducible daytime gene. Based on these findings, a hypothetical view is proposed with regard to the temperature entrainment of the central oscillator.
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Affiliation(s)
- Takeshi Mizuno
- Laboratory of Molecular and Functional Genomics; School of Agriculture; Nagoya University; Furocho, Chikusa-ku, Nagoya, Japan
| | - Aya Takeuchi
- Laboratory of Molecular and Functional Genomics; School of Agriculture; Nagoya University; Furocho, Chikusa-ku, Nagoya, Japan
| | - Yuji Nomoto
- Laboratory of Molecular and Functional Genomics; School of Agriculture; Nagoya University; Furocho, Chikusa-ku, Nagoya, Japan
| | - Norihito Nakamichi
- Laboratory of Molecular and Functional Genomics; School of Agriculture; Nagoya University; Furocho, Chikusa-ku, Nagoya, Japan
- Institute of Transformative Bio-Molecules; Nagoya University; Furocho, Chikusa-ku, Nagoya, Japan
| | - Takafumi Yamashino
- Laboratory of Molecular and Functional Genomics; School of Agriculture; Nagoya University; Furocho, Chikusa-ku, Nagoya, Japan
- Correspondence to: Takafumi Yamashino,
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134
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Chew YH, Smith RW, Jones HJ, Seaton DD, Grima R, Halliday KJ. Mathematical models light up plant signaling. THE PLANT CELL 2014; 26:5-20. [PMID: 24481073 PMCID: PMC3963593 DOI: 10.1105/tpc.113.120006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 12/13/2014] [Accepted: 01/13/2014] [Indexed: 05/08/2023]
Abstract
Plants respond to changes in the environment by triggering a suite of regulatory networks that control and synchronize molecular signaling in different tissues, organs, and the whole plant. Molecular studies through genetic and environmental perturbations, particularly in the model plant Arabidopsis thaliana, have revealed many of the mechanisms by which these responses are actuated. In recent years, mathematical modeling has become a complementary tool to the experimental approach that has furthered our understanding of biological mechanisms. In this review, we present modeling examples encompassing a range of different biological processes, in particular those regulated by light. Current issues and future directions in the modeling of plant systems are discussed.
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Affiliation(s)
- Yin Hoon Chew
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
- SynthSys, Edinburgh EH9 3JD, United Kingdom
| | - Robert W. Smith
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
| | - Harriet J. Jones
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
- SynthSys, Edinburgh EH9 3JD, United Kingdom
| | - Daniel D. Seaton
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
- SynthSys, Edinburgh EH9 3JD, United Kingdom
| | - Ramon Grima
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
- SynthSys, Edinburgh EH9 3JD, United Kingdom
| | - Karen J. Halliday
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
- SynthSys, Edinburgh EH9 3JD, United Kingdom
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135
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Abstract
The circadian clock of Arabidopsis, a popular model organism for plants, is more complex than expected, with negative feedback loops based on the repression of gene expression having a less exclusive role than previously thought.
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Affiliation(s)
- Sabrina E Sanchez
- is at the Instituto de Investigaciones Bioquímicas de Buenos Aires , Leloir Institute , Buenos Aires , Argentina
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