101
|
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.
Collapse
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
| |
Collapse
|
102
|
Mancini E, Sanchez SE, Romanowski A, Schlaen RG, Sanchez-Lamas M, Cerdán PD, Yanovsky MJ. Acute Effects of Light on Alternative Splicing in Light-Grown Plants. Photochem Photobiol 2015; 92:126-33. [DOI: 10.1111/php.12550] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 10/06/2015] [Indexed: 02/03/2023]
Affiliation(s)
| | - Sabrina E. Sanchez
- Fundación Instituto Leloir (IIBBA-CONICET); Buenos Aires Argentina
- Molecular and Computational Biology Section; University of Southern California; Los Angeles CA
| | - Andres Romanowski
- Fundación Instituto Leloir (IIBBA-CONICET); Buenos Aires Argentina
- Departamento de Ciencia y Tecnologia Bernal; Universidad Nacional de Quilmes; Buenos Aires Argentina
| | - Ruben G. Schlaen
- Fundación Instituto Leloir (IIBBA-CONICET); Buenos Aires Argentina
| | | | - Pablo D. Cerdán
- Fundación Instituto Leloir (IIBBA-CONICET); Buenos Aires Argentina
| | | |
Collapse
|
103
|
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.
Collapse
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:
| |
Collapse
|
104
|
Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis. Proc Natl Acad Sci U S A 2015; 112:E4802-10. [PMID: 26261339 DOI: 10.1073/pnas.1513609112] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The circadian clock in Arabidopsis exerts a critical role in timing multiple biological processes and stress responses through the regulation of up to 80% of the transcriptome. As a key component of the clock, the Myb-like transcription factor CIRCADIAN CLOCK ASSOCIATED1 (CCA1) is able to initiate and set the phase of clock-controlled rhythms and has been shown to regulate gene expression by binding directly to the evening element (EE) motif found in target gene promoters. However, the precise molecular mechanisms underlying clock regulation of the rhythmic transcriptome, specifically how clock components connect to clock output pathways, is poorly understood. In this study, using ChIP followed by deep sequencing of CCA1 in constant light (LL) and diel (LD) conditions, more than 1,000 genomic regions occupied by CCA1 were identified. CCA1 targets are enriched for a myriad of biological processes and stress responses, providing direct links to clock-controlled pathways and suggesting that CCA1 plays an important role in regulating a large subset of the rhythmic transcriptome. Although many of these target genes are evening expressed and contain the EE motif, a significant subset is morning phased and enriched for previously unrecognized motifs associated with CCA1 function. Furthermore, this work revealed several CCA1 targets that do not cycle in either LL or LD conditions. Together, our results emphasize an expanded role for the clock in regulating a diverse category of genes and key pathways in Arabidopsis and provide a comprehensive resource for future functional studies.
Collapse
|
105
|
The spliceosome assembly factor GEMIN2 attenuates the effects of temperature on alternative splicing and circadian rhythms. Proc Natl Acad Sci U S A 2015; 112:9382-7. [PMID: 26170331 DOI: 10.1073/pnas.1504541112] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mechanisms by which poikilothermic organisms ensure that biological processes are robust to temperature changes are largely unknown. Temperature compensation, the ability of circadian rhythms to maintain a relatively constant period over the broad range of temperatures resulting from seasonal fluctuations in environmental conditions, is a defining property of circadian networks. Temperature affects the alternative splicing (AS) of several clock genes in fungi, plants, and flies, but the splicing factors that modulate these effects to ensure clock accuracy throughout the year remain to be identified. Here we show that GEMIN2, a spliceosomal small nuclear ribonucleoprotein assembly factor conserved from yeast to humans, modulates low temperature effects on a large subset of pre-mRNA splicing events. In particular, GEMIN2 controls the AS of several clock genes and attenuates the effects of temperature on the circadian period in Arabidopsis thaliana. We conclude that GEMIN2 is a key component of a posttranscriptional regulatory mechanism that ensures the appropriate acclimation of plants to daily and seasonal changes in temperature conditions.
Collapse
|
106
|
Pan WJ, Wang X, Deng YR, Li JH, Chen W, Chiang JY, Yang JB, Zheng L. Nondestructive and intuitive determination of circadian chlorophyll rhythms in soybean leaves using multispectral imaging. Sci Rep 2015; 5:11108. [PMID: 26059057 PMCID: PMC4461922 DOI: 10.1038/srep11108] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 04/21/2015] [Indexed: 12/29/2022] Open
Abstract
The circadian clock, synchronized by daily cyclic environmental cues, regulates diverse aspects of plant growth and development and increases plant fitness. Even though much is known regarding the molecular mechanism of circadian clock, it remains challenging to quantify the temporal variation of major photosynthesis products as well as their metabolic output in higher plants in a real-time, nondestructive and intuitive manner. In order to reveal the spatial-temporal scenarios of photosynthesis and yield formation regulated by circadian clock, multispectral imaging technique has been employed for nondestructive determination of circadian chlorophyll rhythms in soybean leaves. By utilizing partial least square regression analysis, the determination coefficients R(2), 0.9483 for chlorophyll a and 0.8906 for chlorophyll b, were reached, respectively. The predicted chlorophyll contents extracted from multispectral data showed an approximately 24-h rhythm which could be entrained by external light conditions, consistent with the chlorophyll contents measured by chemical analyses. Visualization of chlorophyll map in each pixel offers an effective way to analyse spatial-temporal distribution of chlorophyll. Our results revealed the potentiality of multispectral imaging as a feasible nondestructive universal assay for examining clock function and robustness, as well as monitoring chlorophyll a and b and other biochemical components in plants.
Collapse
Affiliation(s)
- Wen-Juan Pan
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei 230009, China
| | - Xia Wang
- School of Medical Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yong-Ren Deng
- Department of Computer Science and Engineering, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Jia-Hang Li
- Department of Computer Science and Engineering, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Wei Chen
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei 230009, China
| | - John Y. Chiang
- Department of Computer Science and Engineering, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
- Department of Healthcare Administration and Medical Informatics, Kaohsiung 80708, Taiwan
| | - Jian-Bo Yang
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Lei Zheng
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei 230009, China
- School of Medical Engineering, Hefei University of Technology, Hefei 230009, China
| |
Collapse
|
107
|
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.
Collapse
|
108
|
Nakamichi N. Adaptation to the local environment by modifications of the photoperiod response in crops. PLANT & CELL PHYSIOLOGY 2015; 56:594-604. [PMID: 25432974 PMCID: PMC4387313 DOI: 10.1093/pcp/pcu181] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 11/12/2014] [Indexed: 05/02/2023]
Abstract
Flowering plants produce a meristem at the shoot tip where specialized tissue generates shoot apical meristems at the appropriate time to differentiate into reproductive structures, pollinate and efficiently generate seeds. The complex set of molecular and phenological events culminating in development of a flowering meristem is referred to as 'flowering time'. Flowering time affects plant productivity because plants dedicate energy to produce flowers and seeds rather than vegetative tissue once the molecular decision to initiate flowering has been taken. Thus, initiation of flowering time is an important decision in plants, especially in annual plants including crops. Humans have introduced crops into latitudes and climate areas far from their origin or natural ecosystem, requiring in many cases modification of native flowering times. Recent molecular-genetic studies shed light on the genetic basis related to such introductions. In this review, recent progress regarding crop introductions and their genetic bases are summarized, as well as the potential of other agricultural plants to be introduced into different climatic zones.
Collapse
Affiliation(s)
- Norihito Nakamichi
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8602 Japan Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602 Japan Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama, 332-0022 Japan
| |
Collapse
|
109
|
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.
Collapse
Affiliation(s)
- Mikael Johansson
- Molecular Cell Physiology, Faculty for Biology, Bielefeld University, Germany
| | - Dorothee Staiger
- Molecular Cell Physiology, Faculty for Biology, Bielefeld University, Germany
| |
Collapse
|
110
|
Chi W, He B, Mao J, Jiang J, Zhang L. Plastid sigma factors: Their individual functions and regulation in transcription. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:770-8. [PMID: 25596450 DOI: 10.1016/j.bbabio.2015.01.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/02/2015] [Accepted: 01/06/2015] [Indexed: 11/18/2022]
Abstract
Sigma factors are the predominant factors involved in transcription regulation in bacteria. These factors can recruit the core RNA polymerase to promoters with specific DNA sequences and initiate gene transcription. The plastids of higher plants originating from an ancestral cyanobacterial endosymbiont also contain sigma factors that are encoded by a small family of nuclear genes. Although all plastid sigma factors contain sequences conserved in bacterial sigma factors, a considerable number of distinct traits have been acquired during evolution. The present review summarises recent advances concerning the regulation of the structure, function and activity of plastid sigma factors since their discovery nearly 40 years ago. We highlight the specialised roles and overlapping redundant functions of plastid sigma factors according to their promoter selectivity. We also focus on the mechanisms that modulate the activity of sigma factors to optimise plastid function in response to developmental cues and environmental signals. This article is part of a Special Issue entitled: Chloroplast Biogenesis.
Collapse
Affiliation(s)
- Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Baoye He
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Juan Mao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jingjing Jiang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Lixin Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| |
Collapse
|
111
|
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.
Collapse
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,
| |
Collapse
|
112
|
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.
Collapse
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
| |
Collapse
|
113
|
Mizuno T, Yamashino T. The plant circadian clock looks like a traditional Japanese clock rather than a modern Western clock. PLANT SIGNALING & BEHAVIOR 2015; 10:e1087630. [PMID: 26382718 PMCID: PMC4854355 DOI: 10.1080/15592324.2015.1087630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 08/22/2015] [Indexed: 06/05/2023]
Abstract
Life cycle adaptation to seasonal changes in photoperiod and ambient temperature is a major determinant of the ecological success behind the widespread domestication of flowering plants. The circadian clock plays a role in the underlying mechanism for adaptation through generating endogenous rhythms that allow plants to adapt and adjust to both the 24 h diurnal rotation and 365 d seasonal revolution. Nevertheless, the mechanism by which the circadian clock tracks seasonal changes in photoperiod and temperature is a longstanding subject in the field. Recently, we have begun to understand the question of how the light and ambient temperature signals feed into the circadian clock transcriptional circuitry in day-night cycles in order to track seasonal changes in photoperiod and ambient temperature. (1-4) Our results collectively indicate that the evening complex (EC) nighttime repressor consisting of LUX-ELF3-ELF4 plays a crucial role in this respect. Here, we discuss about these recent studies to add further implications.
Collapse
Affiliation(s)
- Takeshi Mizuno
- Laboratory of Molecular and Functional Genomics; School of Agriculture; Nagoya University; Nagoya, Japan
| | - Takafumi Yamashino
- Laboratory of Molecular and Functional Genomics; School of Agriculture; Nagoya University; Nagoya, Japan
| |
Collapse
|
114
|
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.
Collapse
Affiliation(s)
- Jae Sung Shim
- Department of Biology, University of Washington , Seattle, Washington 98195-1800, United States
| | | |
Collapse
|
115
|
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.
Collapse
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
| |
Collapse
|
116
|
Atkins KA, Dodd AN. Circadian regulation of chloroplasts. CURRENT OPINION IN PLANT BIOLOGY 2014; 21:43-50. [PMID: 25026538 DOI: 10.1016/j.pbi.2014.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/20/2014] [Accepted: 06/23/2014] [Indexed: 05/08/2023]
Abstract
Circadian rhythms produce a biological measure of time that increases plant performance. The mechanisms that underlie this increase in productivity require investigation to provide information that will underpin future crop improvement. There is a growing body of evidence that a sophisticated signalling network interconnects the circadian oscillator and chloroplasts. We consider this in the context of circadian signalling to chloroplasts and the relationship between retrograde signalling and circadian regulation. We place circadian signalling to chloroplasts by sigma factors within an evolutionary context. We describe selected recent developments in the integration of light and circadian signals that control chloroplast gene expression.
Collapse
Affiliation(s)
- Kelly A Atkins
- School of Biological Sciences, Bristol Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Antony N Dodd
- School of Biological Sciences, Bristol Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK; Cabot Institute, University of Bristol, Bristol BS8 1UJ, UK.
| |
Collapse
|
117
|
FBH1 affects warm temperature responses in the Arabidopsis circadian clock. Proc Natl Acad Sci U S A 2014; 111:14595-600. [PMID: 25246594 DOI: 10.1073/pnas.1416666111] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In Arabidopsis, the circadian clock allows the plant to coordinate daily external signals with internal processes, conferring enhanced fitness and growth vigor. Although external cues such as temperature can entrain the clock, an important feature of the clock is the ability to maintain a relatively constant period over a range of physiological temperatures; this ability is referred to as "temperature compensation." However, how temperature actually is perceived and integrated into the clock molecular circuitry remains largely unknown. In an effort to identify additional regulators of the circadian clock, including putative components that could modulate the clock response to changes in environmental signals, we identified in a previous large-scale screen a transcription factor that interacts with and regulates the promoter activity of a core clock gene. In this report, we characterized this transcription factor, flowering basic helix-loop-helix 1 (FBH1) that binds in vivo to the promoter of the key clock gene circadian clock-associated 1 (CCA1) and regulates its expression. We found that upon temperature changes, overexpression of FBH1 alters the pace of CCA1 expression by causing a period shortening and thus preventing the clock from buffering against this change in temperature. Furthermore, as is consistent with the current mechanistic model of feedback loops observed in the clock regulatory network, we also determined that CCA1 binds in vivo to the FBH1 promoter and regulates its expression. Together these results establish a role for FBH1 as a transcriptional modulator of warm temperature signals and clock responses in Arabidopsis.
Collapse
|
118
|
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.
Collapse
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
| |
Collapse
|
119
|
Barneche F, Malapeira J, Mas P. The impact of chromatin dynamics on plant light responses and circadian clock function. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2895-913. [PMID: 24520020 DOI: 10.1093/jxb/eru011] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Research on the functional properties of nucleosome structure and composition dynamics has revealed that chromatin-level regulation is an essential component of light signalling and clock function in plants, two processes that rely extensively on transcriptional controls. In particular, several types of histone post-translational modifications and chromatin-bound factors act sequentially or in combination to establish transcriptional patterns and to fine-tune the transcript abundance of a large repertoire of light-responsive genes and clock components. Cytogenetic approaches have also identified light-induced higher-order chromatin changes that dynamically organize the condensation of chromosomal domains into sub-nuclear foci containing silenced repeat elements. In this review, we report recently identified molecular actors that establish chromatin state dynamics in response to light signals such as photoperiod, intensity, and spectral quality. We also highlight the chromatin-dependent mechanisms that contribute to the 24-h circadian gene expression and its impact on plant physiology and development. The commonalities and contrasts of light- and clock-associated chromatin-based mechanisms are discussed, with particular emphasis on their impact on the selective regulation and rapid modulation of responsive genes.
Collapse
Affiliation(s)
- Fredy Barneche
- Environmental and Evolutionary Genomics Section, Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris, F-75005 France Inserm, U1024, Paris, F-75005 France CNRS, UMR 8197, Paris, F-75005 France
| | - Jordi Malapeira
- Center for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB, Parc de Recerca UAB, Bellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain
| | - Paloma Mas
- Center for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB, Parc de Recerca UAB, Bellaterra (Cerdanyola del Vallés), 08193 Barcelona, Spain
| |
Collapse
|
120
|
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.
Collapse
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.
| |
Collapse
|
121
|
Gyllenstrand N, Karlgren A, Clapham D, Holm K, Hall A, Gould PD, Källman T, Lagercrantz U. No time for spruce: rapid dampening of circadian rhythms in Picea abies (L. Karst). PLANT & CELL PHYSIOLOGY 2014; 55:535-50. [PMID: 24363286 DOI: 10.1093/pcp/pct199] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The identification and cloning of full-length homologs of circadian clock genes from Picea abies represent a first step to study the function and evolution of the circadian clock in gymnosperms. Phylogenetic analyses suggest that the sequences of key circadian clock genes are conserved between angiosperms and gymnosperms. though fewer homologous copies were found for most gene families in P. abies. We detected diurnal cycling of circadian clock genes in P. abies using quantitative real-time PCR; however, cycling appeared to be rapidly dampened under free-running conditions. Given the unexpected absence of transcriptional cycling during constant conditions, we employed a complementary method to assay circadian rhythmic outputs and measured delayed fluorescence in seedlings of Norway spruce. Neither of the two approaches to study circadian rhythms in Norway spruce could detect robust ∼24 h cycling behavior under constant conditions. These data suggest gene conservation but fundamental differences in clock function between gymnosperms and other plant taxa.
Collapse
Affiliation(s)
- Niclas Gyllenstrand
- Department of Plant Biology and Forest Genetics, Uppsala Biocenter, Swedish University for Agricultural Sciences, Uppsala, PO Box 7080, SE-750 07 Uppsala, Sweden
| | | | | | | | | | | | | | | |
Collapse
|
122
|
Marcolino-Gomes J, Rodrigues FA, Fuganti-Pagliarini R, Bendix C, Nakayama TJ, Celaya B, Molinari HBC, de Oliveira MCN, Harmon FG, Nepomuceno A. Diurnal oscillations of soybean circadian clock and drought responsive genes. PLoS One 2014; 9:e86402. [PMID: 24475115 PMCID: PMC3903518 DOI: 10.1371/journal.pone.0086402] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 12/09/2013] [Indexed: 01/09/2023] Open
Abstract
Rhythms produced by the endogenous circadian clock play a critical role in allowing plants to respond and adapt to the environment. While there is a well-established regulatory link between the circadian clock and responses to abiotic stress in model plants, little is known of the circadian system in crop species like soybean. This study examines how drought impacts diurnal oscillation of both drought responsive and circadian clock genes in soybean. Drought stress induced marked changes in gene expression of several circadian clock-like components, such as LCL1-, GmELF4- and PRR-like genes, which had reduced expression in stressed plants. The same conditions produced a phase advance of expression for the GmTOC1-like, GmLUX-like and GmPRR7-like genes. Similarly, the rhythmic expression pattern of the soybean drought-responsive genes DREB-, bZIP-, GOLS-, RAB18- and Remorin-like changed significantly after plant exposure to drought. In silico analysis of promoter regions of these genes revealed the presence of cis-elements associated both with stress and circadian clock regulation. Furthermore, some soybean genes with upstream ABRE elements were responsive to abscisic acid treatment. Our results indicate that some connection between the drought response and the circadian clock may exist in soybean since (i) drought stress affects gene expression of circadian clock components and (ii) several stress responsive genes display diurnal oscillation in soybeans.
Collapse
Affiliation(s)
- Juliana Marcolino-Gomes
- Embrapa Soybean, Brazilian Agricultural Research Corporation, Londrina, Paraná, Brazil
- Department of Biology, State University of Londrina, Londrina, Paraná, Brazil
| | | | | | - Claire Bendix
- Plant Gene Expression Center, ARS/USDA, Albany, California, USA and Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, California, USA
| | - Thiago Jonas Nakayama
- Department of Crop Science, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | - Brandon Celaya
- Plant Gene Expression Center, ARS/USDA, Albany, California, USA and Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, California, USA
| | - Hugo Bruno Correa Molinari
- Embrapa LABEX US Plant Biotechnology, Plant Gene Expression Center-ARS/USDA, Albany, California, United States of America
| | | | - Frank G. Harmon
- Plant Gene Expression Center, ARS/USDA, Albany, California, USA and Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, California, USA
| | - Alexandre Nepomuceno
- Embrapa Soybean, Brazilian Agricultural Research Corporation, Londrina, Paraná, Brazil
- Embrapa LABEX US Plant Biotechnology, Plant Gene Expression Center-ARS/USDA, Albany, California, United States of America
| |
Collapse
|
123
|
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: 48] [Impact Index Per Article: 4.8] [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.
Collapse
|
124
|
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.
Collapse
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,
| |
Collapse
|
125
|
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.
Collapse
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
| |
Collapse
|