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NUCLEAR FACTOR Y, Subunit A (NF-YA) Proteins Positively Regulate Flowering and Act Through FLOWERING LOCUS T. PLoS Genet 2016; 12:e1006496. [PMID: 27977687 PMCID: PMC5157953 DOI: 10.1371/journal.pgen.1006496] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 11/18/2016] [Indexed: 12/12/2022] Open
Abstract
Photoperiod dependent flowering is one of several mechanisms used by plants to initiate the developmental transition from vegetative growth to reproductive growth. The NUCLEAR FACTOR Y (NF-Y) transcription factors are heterotrimeric complexes composed of NF-YA and histone-fold domain (HFD) containing NF-YB/NF-YC, that initiate photoperiod-dependent flowering by cooperatively interacting with CONSTANS (CO) to drive the expression of FLOWERING LOCUS T (FT). This involves NF-Y and CO binding at distal CCAAT and proximal “CORE” elements, respectively, in the FT promoter. While this is well established for the HFD subunits, there remains some question over the potential role of NF-YA as either positive or negative regulators of this process. Here we provide strong support, in the form of genetic and biochemical analyses, that NF-YA, in complex with NF-YB/NF-YC proteins, can directly bind the distal CCAAT box in the FT promoter and are positive regulators of flowering in an FT-dependent manner. For plants to have reproductive success, they must time their flowering with the most beneficial biotic and abiotic environmental conditions—after all, reproductive success would likely be low if flowers developed when pollinators were not present or freezing temperatures were on the horizon. Proper timing mechanisms for flowering vary significantly between different species, but can be connected to a variety of environmental cues, including water availability, temperature, and day length. Numerous labs have studied the molecular aspects of these timing mechanisms and discovered that many of these pathways converge on the gene FLOWERING LOCUS T (FT). This means that understanding precisely how this gene is regulated can teach us a lot about many plant species in both natural and agricultural settings. In the current study, we focus on day length as an essential cue for flowering in the plant species Arabidopsis thaliana. We further unravel the complexity of FT regulation by clarifying the roles of NUCLEAR FACTOR Y genes in day length perception.
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152
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Xu JJ, Zhang XF, Xue HW. Rice aleurone layer specific OsNF-YB1 regulates grain filling and endosperm development by interacting with an ERF transcription factor. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:6399-6411. [PMID: 27803124 PMCID: PMC5181583 DOI: 10.1093/jxb/erw409] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Grain yield and quality of rice mainly depend on grain filling and endosperm development. Here we report that a rice NUCLEAR FACTOR Y (NF-Y) transcription factor, OsNF-YB1, is specifically expressed in the aleurone layer of developing endosperm and regulates grain filling and endosperm development. Knockdown of OsNF-YB1 expression by RNAi significantly retarded grain filling, leading to small grains with chalky endosperm as well as altered starch quality. Whereas OsNF-YB1 shows subcellular localization in both the cytosol and the nucleus in roots, it was specifically targeted to the nucleus of aleurone layer cells, which was facilitated by interacting with OsNF-YC proteins preferentially expressed in the aleurone layer. RNA sequencing analysis revealed that genes related to membrane transport and ATP biosynthesis were enriched in the down-regulated category in OsNF-YB1 RNAi plants, which is consistent with the crucial role of OsNF-YB1 in rice grain filling and endosperm development. Identification of the genome-wide targets of OsNF-YB1 by ChIP sequencing showed that OsNF-YB1 directly regulates genes involved in the transport of nutrients such as sugar and amino acids. Interestingly, different from the binding sites reported for other NF-Y complexes, the GCC box, the binding motif of ERF transcription factors, was enriched in the binding peaks of OsNF-YB1. Indeed, further analyses confirmed the interaction of OsERF#115 with OsNF-YB1, and OsERF#115 directly binds to the GCC box. It is proposed that OsNF-YB1 specifically regulate the transcription of downstream genes during rice endosperm development by forming protein complexes consisting of OsNF-YB1, OsNF-YC and ERF, providing informative insights into the molecular functional mechanisms of the NF-Y factor.
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Affiliation(s)
- Jing-Jing Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032 Shanghai, China
| | - Xiao-Fan Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032 Shanghai, China
| | - Hong-Wei Xue
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032 Shanghai, China
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153
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Weber B, Zicola J, Oka R, Stam M. Plant Enhancers: A Call for Discovery. TRENDS IN PLANT SCIENCE 2016; 21:974-987. [PMID: 27593567 DOI: 10.1016/j.tplants.2016.07.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/18/2016] [Accepted: 07/28/2016] [Indexed: 05/12/2023]
Abstract
Higher eukaryotes typically contain many different cell types, displaying different cellular functions that are influenced by biotic and abiotic cues. The different functions are characterized by specific gene expression patterns mediated by regulatory sequences such as transcriptional enhancers. Recent genome-wide approaches have identified thousands of enhancers in animals, reviving interest in enhancers in gene regulation. Although the regulatory roles of plant enhancers are as crucial as those in animals, genome-wide approaches have only very recently been applied to plants. Here we review characteristics of enhancers at the DNA and chromatin level in plants and other species, their similarities and differences, and techniques widely used for genome-wide discovery of enhancers in animal systems that can be implemented in plants.
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Affiliation(s)
- Blaise Weber
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Johan Zicola
- Max Planck Institute for Plant Breeding Research, Department Plant Developmental Biology, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Rurika Oka
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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154
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Swain S, Myers ZA, Siriwardana CL, Holt BF. The multifaceted roles of NUCLEAR FACTOR-Y in Arabidopsis thaliana development and stress responses. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:636-644. [PMID: 27989935 DOI: 10.1016/j.bbagrm.2016.10.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 01/03/2023]
Abstract
NUCLEAR FACTOR-Y (NF-Y) is a heterotrimeric transcription factor (TF) consisting of evolutionarily distinct NF-YA, NF-YB and NF-YC subunits. The functional NF-Y heterotrimer binds to CCAAT elements in eukaryotic gene promoters and influences their expression. The genome of the model organism Arabidopsis thaliana encodes 10 distinct NF-YA, NF-YB, and NF-YC proteins, allowing for enormous combinatorial and functional diversity. Two decades of research have elucidated the importance of NF-Ys in plant growth, development and stress responses; however, the molecular mechanisms of action remain largely unexplored. Intriguingly, recent evidence suggests that NF-Ys are frequently associated with other groups of TFs, expanding the potential NF-Y combinatorial complexity. Further, information regarding the regulation of individual NF-Y subunits at the transcriptional and post-transcriptional level is beginning to emerge. In this review, we will identify developing trends within the NF-Y field and discuss recent progress towards a better understanding of NF-Y function, molecular action, and regulation in the context of Arabidopsis. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.
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Affiliation(s)
- Swadhin Swain
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States
| | - Zachary A Myers
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States
| | - Chamindika L Siriwardana
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States
| | - Ben F Holt
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States.
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155
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Brambilla V, Fornara F. Y flowering? Regulation and activity of CONSTANS and CCT-domain proteins in Arabidopsis and crop species. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:655-660. [PMID: 27793713 DOI: 10.1016/j.bbagrm.2016.10.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/09/2016] [Accepted: 10/20/2016] [Indexed: 12/21/2022]
Abstract
Changes in day length regulate the proper timing of flowering in several plant species. The genetic architecture of this process is based on CCT-domain proteins, many of which interact with NF-Y subunits to regulate transcription of target genes. In the model plant Arabidopsis thaliana, the CONSTANS CCT-domain protein is a central photoperiodic sensor. We will discuss how the diurnal rhythms of its transcription and protein accumulation are generated, and how the protein engages into multiple complexes to control production of a systemic flowering signal. Regulatory parallels will be drawn between Arabidopsis and major crops that indicate conservation of some CCT/NF-Y modules during plant evolution. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.
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Affiliation(s)
- Vittoria Brambilla
- Department of Agricultural and Environmental Sciences - Production, Territory, Agroenergy, University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - Fabio Fornara
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy.
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156
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Książkiewicz M, Rychel S, Nelson MN, Wyrwa K, Naganowska B, Wolko B. Expansion of the phosphatidylethanolamine binding protein family in legumes: a case study of Lupinus angustifolius L. FLOWERING LOCUS T homologs, LanFTc1 and LanFTc2. BMC Genomics 2016; 17:820. [PMID: 27769166 PMCID: PMC5073747 DOI: 10.1186/s12864-016-3150-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 10/08/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Arabidopsis FLOWERING LOCUS T (FT) gene, a member of the phosphatidylethanolamine binding protein (PEBP) family, is a major controller of flowering in response to photoperiod, vernalization and light quality. In legumes, FT evolved into three, functionally diversified clades, FTa, FTb and FTc. A milestone achievement in narrow-leafed lupin (Lupinus angustifolius L.) domestication was the loss of vernalization responsiveness at the Ku locus. Recently, one of two existing L. angustifolius homologs of FTc, LanFTc1, was revealed to be the gene underlying Ku. It is the first recorded involvement of an FTc homologue in vernalization. The evolutionary basis of this phenomenon in lupin has not yet been deciphered. RESULTS Bacterial artificial chromosome (BAC) clones carrying LanFTc1 and LanFTc2 genes were localized in different mitotic chromosomes and constituted sequence-specific landmarks for linkage groups NLL-10 and NLL-17. BAC-derived superscaffolds containing LanFTc genes revealed clear microsyntenic patterns to genome sequences of nine legume species. Superscaffold-1 carrying LanFTc1 aligned to regions encoding one or more FT-like genes whereas superscaffold-2 mapped to a region lacking such a homolog. Comparative mapping of the L. angustifolius genome assembly anchored to linkage map localized superscaffold-1 in the middle of a 15 cM conserved, collinear region. In contrast, superscaffold-2 was found at the edge of a 20 cM syntenic block containing highly disrupted collinearity at the LanFTc2 locus. 118 PEBP-family full-length homologs were identified in 10 legume genomes. Bayesian phylogenetic inference provided novel evidence supporting the hypothesis that whole-genome and tandem duplications contributed to expansion of PEBP-family genes in legumes. Duplicated genes were subjected to strong purifying selection. Promoter analysis of FT genes revealed no statistically significant sequence similarity between duplicated copies; only RE-alpha and CCAAT-box motifs were found at conserved positions and orientations. CONCLUSIONS Numerous lineage-specific duplications occurred during the evolution of legume PEBP-family genes. Whole-genome duplications resulted in the origin of subclades FTa, FTb and FTc and in the multiplication of FTa and FTb copy number. LanFTc1 is located in the region conserved among all main lineages of Papilionoideae. LanFTc1 is a direct descendant of ancestral FTc, whereas LanFTc2 appeared by subsequent duplication.
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Affiliation(s)
- Michał Książkiewicz
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - Sandra Rychel
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Matthew N Nelson
- Natural Capital and Plant Health, Royal Botanic Gardens Kew, Wakehurst Place, Ardingly, West Sussex, RH17 6TN, UK.,School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Katarzyna Wyrwa
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Barbara Naganowska
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Bogdan Wolko
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
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157
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Song YH. The Effect of Fluctuations in Photoperiod and Ambient Temperature on the Timing of Flowering: Time to Move on Natural Environmental Conditions. Mol Cells 2016; 39:715-721. [PMID: 27788575 PMCID: PMC5104878 DOI: 10.14348/molcells.2016.0237] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 10/17/2016] [Indexed: 11/27/2022] Open
Abstract
Plants have become physiologically adapted to a seasonally shifting environment by evolving many sensory mechanisms. Seasonal flowering is a good example of adaptation to local environmental demands and is crucial for maximizing reproductive fitness. Photoperiod and temperature are major environmental stimuli that control flowering through expression of a floral inducer, FLOWERING LOCUS T (FT) protein. Recent discoveries made using the model plant Arabidopsis thaliana have shown that the functions of photoreceptors are essential for the timing of FT gene induction, via modulation of the transcriptional activator CONSTANS (CO) at transcriptional and posttranslational levels in response to seasonal variations. The activation of FT transcription by the fine-tuned CO protein enables plants to switch from vegetative growth to flowering under inductive environmental conditions. The present review briefly summarizes our current understanding of the molecular mechanisms by which the information of environmental stimuli is sensed and transduced to trigger FT induction in leaves.
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Affiliation(s)
- Young Hun Song
- Department of Life Sciences, Ajou University, Suwon 16499,
Korea
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158
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Myers ZA, Kumimoto RW, Siriwardana CL, Gayler KK, Risinger JR, Pezzetta D, Holt III BF. NUCLEAR FACTOR Y, Subunit C (NF-YC) Transcription Factors Are Positive Regulators of Photomorphogenesis in Arabidopsis thaliana. PLoS Genet 2016; 12:e1006333. [PMID: 27685091 PMCID: PMC5042435 DOI: 10.1371/journal.pgen.1006333] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 08/30/2016] [Indexed: 01/10/2023] Open
Abstract
Recent reports suggest that NF-Y transcription factors are positive regulators of skotomorphogenesis in Arabidopsis thaliana. Three NF-YC genes (NF-YC3, NF-YC4, and NF-YC9) are known to have overlapping functions in photoperiod dependent flowering and previous studies demonstrated that they interact with basic leucine zipper (bZIP) transcription factors. This included ELONGATED HYPOCOTYL 5 (HY5), which has well-demonstrated roles in photomorphogenesis. Similar to hy5 mutants, we report that nf-yc3 nf-yc4 nf-yc9 triple mutants failed to inhibit hypocotyl elongation in all tested light wavelengths. Surprisingly, nf-yc3 nf-yc4 nf-yc9 hy5 mutants had synergistic defects in light perception, suggesting that NF-Ys represent a parallel light signaling pathway. As with other photomorphogenic transcription factors, nf-yc3 nf-yc4 nf-yc9 triple mutants also partially suppressed the short hypocotyl and dwarf rosette phenotypes of CONSTITUTIVE PHOTOMORPHOGENIC 1 (cop1) mutants. Thus, our data strongly suggest that NF-Y transcription factors have important roles as positive regulators of photomorphogenesis, and in conjunction with other recent reports, implies that the NF-Y are multifaceted regulators of early seedling development. Light perception is critically important for the fitness of plants in both natural and agricultural settings. Plants not only use light for photosynthesis, but also as a cue for proper development. As a seedling emerges from soil it must determine the light environment and adopt an appropriate growth habit. When blue and red wavelengths are the dominant sources of light, plants will undergo photomorphogenesis. Photomorphogenesis describes a number of developmental responses initiated by light in a seedling, and includes shortened stems and establishing the ability to photosynthesize. The genes regulating photomorphogenesis have been studied extensively, but a complete picture remains elusive. Here we describe the finding that NUCLEAR FACTOR-Y (NF-Y) genes are positive regulators of photomorphogenesis—i.e., in plants where NF-Y genes are mutated, they display some characteristics of dark grown plants, even though they are in the light. Our data suggests that the roles of NF-Y genes in light perception do not fit in easily with those of other described pathways. Thus, studying these genes promises to help develop a more complete picture of how light drives plant development.
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Affiliation(s)
- Zachary A. Myers
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Roderick W. Kumimoto
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Chamindika L. Siriwardana
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Krystal K. Gayler
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
| | | | - Daniela Pezzetta
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Ben F. Holt III
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
- * E-mail:
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159
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Liu X, Hu P, Huang M, Tang Y, Li Y, Li L, Hou X. The NF-YC-RGL2 module integrates GA and ABA signalling to regulate seed germination in Arabidopsis. Nat Commun 2016; 7:12768. [PMID: 27624486 PMCID: PMC5027291 DOI: 10.1038/ncomms12768] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 07/30/2016] [Indexed: 12/18/2022] Open
Abstract
The antagonistic crosstalk between gibberellic acid (GA) and abscisic acid (ABA) plays a pivotal role in the modulation of seed germination. However, the molecular mechanism of such phytohormone interaction remains largely elusive. Here we show that three Arabidopsis NUCLEAR FACTOR-Y C (NF-YC) homologues NF-YC3, NF-YC4 and NF-YC9 redundantly modulate GA- and ABA-mediated seed germination. These NF-YCs interact with the DELLA protein RGL2, a key repressor of GA signalling. The NF-YC–RGL2 module targets ABI5, a gene encoding a core component of ABA signalling, via specific CCAAT elements and collectively regulates a set of GA- and ABA-responsive genes, thus controlling germination. These results suggest that the NF-YC–RGL2–ABI5 module integrates GA and ABA signalling pathways during seed germination. Crosstalk between gibberellic acid (GA) and abscisic acid (ABA) regulates seed germination. Here the authors show that NF-YC transcription factors can interact with the RGL2 DELLA protein to regulate expression of ABI5 and therefore modulate ABA- and GA-responsive gene expression.
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Affiliation(s)
- Xu Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Pengwei Hu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.,Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Mingkun Huang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Tang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yuge Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ling Li
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xingliang Hou
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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160
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Takeshima R, Hayashi T, Zhu J, Zhao C, Xu M, Yamaguchi N, Sayama T, Ishimoto M, Kong L, Shi X, Liu B, Tian Z, Yamada T, Kong F, Abe J. A soybean quantitative trait locus that promotes flowering under long days is identified as FT5a, a FLOWERING LOCUS T ortholog. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5247-58. [PMID: 27422993 PMCID: PMC5014162 DOI: 10.1093/jxb/erw283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
FLOWERING LOCUS T (FT) is an important floral integrator whose functions are conserved across plant species. In soybean, two orthologs, FT2a and FT5a, play a major role in initiating flowering. Their expression in response to different photoperiods is controlled by allelic combinations at the maturity loci E1 to E4, generating variation in flowering time among cultivars. We determined the molecular basis of a quantitative trait locus (QTL) for flowering time in linkage group J (Chromosome 16). Fine-mapping delimited the QTL to a genomic region of 107kb that harbors FT5a We detected 15 DNA polymorphisms between parents with the early-flowering (ef) and late-flowering (lf) alleles in the promoter region, an intron, and the 3' untranslated region of FT5a, although the FT5a coding regions were identical. Transcript abundance of FT5a was higher in near-isogenic lines for ef than in those for lf, suggesting that different transcriptional activities or mRNA stability caused the flowering time difference. Single-nucleotide polymorphism (SNP) calling from re-sequencing data for 439 cultivated and wild soybean accessions indicated that ef is a rare haplotype that is distinct from common haplotypes including lf The ef allele at FT5a may play an adaptive role at latitudes where early flowering is desirable.
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Affiliation(s)
- Ryoma Takeshima
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Takafumi Hayashi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Jianghui Zhu
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Chen Zhao
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Meilan Xu
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Naoya Yamaguchi
- Hokkaido Research Organization Tokachi Agricultural Experiment Station, Memuro, Hokkaido 082-0081, Japan
| | - Takashi Sayama
- National Institute of Agrobiological Sciences, Kannondai, Ibaraki 305-8602, Japan
| | - Masao Ishimoto
- National Institute of Agrobiological Sciences, Kannondai, Ibaraki 305-8602, Japan
| | - Lingping Kong
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Xinyi Shi
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Baohui Liu
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 1001014, China
| | - Tetsuya Yamada
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Fanjiang Kong
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Jun Abe
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
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161
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Ren C, Zhang Z, Wang Y, Li S, Liang Z. Genome-wide identification and characterization of the NF-Y gene family in grape (vitis vinifera L.). BMC Genomics 2016; 17:605. [PMID: 27516172 PMCID: PMC4982312 DOI: 10.1186/s12864-016-2989-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/02/2016] [Indexed: 12/13/2022] Open
Abstract
Background Nuclear factor Y (NF-Y) transcription factor is composed of three distinct subunits: NF-YA, NF-YB and NF-YC. Many members of NF-Y family have been reported to be key regulators in plant development, phytohormone signaling and drought tolerance. However, the function of the NF-Y family is less known in grape (Vitis vinifera L.). Results A total of 34 grape NF-Y genes that distributed unevenly on grape (V. vinifera) chromosomes were identified in this study. Phylogenetic analysis was performed to predict functional similarities between Arabidopsis thaliana and grape NF-Y genes. Comparison of the structures of grape NF-Y genes (VvNF-Ys) revealed their functional conservation and alteration. Furthermore, we investigated the expression profiles of VvNF-Ys in response to various stresses, phytohormone treatments, and in leaves and grape berries with various sugar contents at different developmental stages. The relationship between VvNF-Y transcript levels and sugar content was examined to select candidates for exogenous sugar treatments. Quantitative real-time PCR (qPCR) indicated that many VvNF-Ys responded to different sugar stimuli with variations in transcript abundance. qPCR and publicly available microarray data suggest that VvNF-Ys exhibit distinct expression patterns in different grape organs and developmental stages, and a number of VvNF-Ys may participate in responses to multiple abiotic and biotic stresses, phytohormone treatments and sugar accumulation or metabolism. Conclusions In this study, we characterized 34 VvNF-Ys based on their distributions on chromosomes, gene structures, phylogenetic relationship with Arabidopsis NF-Y genes, and their expression patterns. The potential roles of VvNF-Ys in sugar accumulation or metabolism were also investigated. Altogether, the data provide significant insights on VvNF-Ys, and lay foundations for further functional studies of NF-Y genes in grape. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2989-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chong Ren
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zhan Zhang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, People's Republic of China.
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, People's Republic of China.
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162
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Brkljacic J, Grotewold E. Combinatorial control of plant gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:31-40. [PMID: 27427484 DOI: 10.1016/j.bbagrm.2016.07.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 07/05/2016] [Accepted: 07/07/2016] [Indexed: 01/02/2023]
Abstract
Combinatorial gene regulation provides a mechanism by which relatively small numbers of transcription factors can control the expression of a much larger number of genes with finely tuned temporal and spatial patterns. This is achieved by transcription factors assembling into complexes in a combinatorial fashion, exponentially increasing the number of genes that they can target. Such an arrangement also increases the specificity and affinity for the cis-regulatory sequences required for accurate target gene expression. Superimposed on this transcription factor combinatorial arrangement is the increasing realization that histone modification marks expand the regulatory information, which is interpreted by histone readers and writers that are part of the regulatory apparatus. Here, we review the progress in these areas from the perspective of plant combinatorial gene regulation, providing examples of different regulatory solutions and comparing them to other metazoans. 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)
- Jelena Brkljacic
- Center for Applied Plant Sciences (CAPS),The Ohio State University, Columbus, OH 43210, USA
| | - Erich Grotewold
- Center for Applied Plant Sciences (CAPS),The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
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163
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Hanemian M, Barlet X, Sorin C, Yadeta KA, Keller H, Favery B, Simon R, Thomma BPHJ, Hartmann C, Crespi M, Marco Y, Tremousaygue D, Deslandes L. Arabidopsis CLAVATA1 and CLAVATA2 receptors contribute to Ralstonia solanacearum pathogenicity through a miR169-dependent pathway. THE NEW PHYTOLOGIST 2016; 211:502-15. [PMID: 26990325 DOI: 10.1111/nph.13913] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 01/22/2016] [Indexed: 05/21/2023]
Abstract
Bacterial wilt caused by Ralstonia solanacearum is one of the most destructive bacterial plant diseases. Although many molecular determinants involved in R. solanacearum adaptation to hosts and pathogenesis have been described, host components required for disease establishment remain poorly characterized. Phenotypical analysis of Arabidopsis mutants for leucine-rich repeat (LRR)-receptor-like proteins revealed that mutations in the CLAVATA1 (CLV1) and CLAVATA2 (CLV2) genes confer enhanced disease resistance to bacterial wilt. We further investigated the underlying mechanisms using genetic, transcriptomic and molecular approaches. The enhanced resistance of both clv1 and clv2 mutants to the bacteria did not require the well characterized CLV signalling modules involved in shoot meristem homeostasis, and was conditioned by neither salicylic acid nor ethylene defence-related hormones. Gene expression microarray analysis performed on clv1 and clv2 revealed deregulation of genes encoding nuclear transcription factor Y subunit alpha (NF-YA) transcription factors whose post-transcriptional regulation is known to involve microRNAs from the miR169 family. Both clv mutants showed a defect in miR169 accumulation. Conversely, overexpression of miR169 abrogated the resistance phenotype of clv mutants. We propose that CLV1 and CLV2, two receptors involved in CLV3 perception during plant development, contribute to bacterial wilt through a signalling pathway involving the miR169/NF-YA module.
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Affiliation(s)
- Mathieu Hanemian
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, UMR441, Chemin de Borde Rouge, F-31326, Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, UMR2594, Chemin de Borde Rouge, F-31326, Castanet-Tolosan, France
| | - Xavier Barlet
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, UMR441, Chemin de Borde Rouge, F-31326, Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, UMR2594, Chemin de Borde Rouge, F-31326, Castanet-Tolosan, France
| | - Céline Sorin
- CNRS, Institut des Sciences du Végétal, Saclay Plant Sciences, UPR2355, 91198, Gif-sur-Yvette, France
| | - Koste A Yadeta
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Harald Keller
- INRA, Univ. Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Bruno Favery
- INRA, Univ. Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Rüdiger Simon
- Institut für Entwicklungsgenetik, Heinrich-Heine-Universität, Universitätstr. 1, 40225, Düsseldorf, Germany
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Caroline Hartmann
- Université Paris Diderot, 5 rue Thomas Mann, 75205, Paris Cedex 13, France
| | - Martin Crespi
- CNRS, Institut des Sciences du Végétal, Saclay Plant Sciences, UPR2355, 91198, Gif-sur-Yvette, France
| | - Yves Marco
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, UMR441, Chemin de Borde Rouge, F-31326, Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, UMR2594, Chemin de Borde Rouge, F-31326, Castanet-Tolosan, France
| | - Dominique Tremousaygue
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, UMR441, Chemin de Borde Rouge, F-31326, Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, UMR2594, Chemin de Borde Rouge, F-31326, Castanet-Tolosan, France
| | - Laurent Deslandes
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, UMR441, Chemin de Borde Rouge, F-31326, Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, UMR2594, Chemin de Borde Rouge, F-31326, Castanet-Tolosan, France
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164
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Binding Sites in the EFG1 Promoter for Transcription Factors in a Proposed Regulatory Network: A Functional Analysis in the White and Opaque Phases of Candida albicans. G3-GENES GENOMES GENETICS 2016; 6:1725-37. [PMID: 27172219 PMCID: PMC4889668 DOI: 10.1534/g3.116.029785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In Candida albicans the transcription factor Efg1, which is differentially expressed in the white phase of the white-opaque transition, is essential for expression of the white phenotype. It is one of six transcription factors included in a proposed interactive transcription network regulating white-opaque switching and maintenance of the alternative phenotypes. Ten sites were identified in the EFG1 promoter that differentially bind one or more of the network transcription factors in the white and/or opaque phase. To explore the functionality of these binding sites in the differential expression of EFG1, we generated targeted deletions of each of the 10 binding sites, combinatorial deletions, and regional deletions using a Renillareniformis luciferase reporter system. Individually targeted deletion of only four of the 10 sites had minor effects consistent with differential expression of EFG1, and only in the opaque phase. Alternative explanations are considered.
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165
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Liu C, Wang C, Wang G, Becker C, Zaidem M, Weigel D. Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution. Genome Res 2016; 26:1057-68. [PMID: 27225844 PMCID: PMC4971768 DOI: 10.1101/gr.204032.116] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 05/24/2016] [Indexed: 12/31/2022]
Abstract
The three-dimensional packing of the genome plays an important role in regulating gene expression. We have used Hi-C, a genome-wide chromatin conformation capture (3C) method, to analyze Arabidopsis thaliana chromosomes dissected into subkilobase segments, which is required for gene-level resolution in this species with a gene-dense genome. We found that the repressive H3K27me3 histone mark is overrepresented in the promoter regions of genes that are in conformational linkage over long distances. In line with the globally dispersed distribution of RNA polymerase II in A. thaliana nuclear space, actively transcribed genes do not show a strong tendency to associate with each other. In general, there are often contacts between 5' and 3' ends of genes, forming local chromatin loops. Such self-loop structures of genes are more likely to occur in more highly expressed genes, although they can also be found in silent genes. Silent genes with local chromatin loops are highly enriched for the histone variant H3.3 at their 5' and 3' ends but depleted of repressive marks such as heterochromatic histone modifications and DNA methylation in flanking regions. Our results suggest that, different from animals, a major theme of genome folding in A. thaliana is the formation of structural units that correspond to gene bodies.
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Affiliation(s)
- Chang Liu
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany
| | - Congmao Wang
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Institute of Digital Agriculture, Zhejiang Academy of Agriculture Sciences, Hangzhou 310029, China
| | - George Wang
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Claude Becker
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Maricris Zaidem
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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166
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Rodriguez-Granados NY, Ramirez-Prado JS, Veluchamy A, Latrasse D, Raynaud C, Crespi M, Ariel F, Benhamed M. Put your 3D glasses on: plant chromatin is on show. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3205-21. [PMID: 27129951 DOI: 10.1093/jxb/erw168] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The three-dimensional organization of the eukaryotic nucleus and its chromosomal conformation have emerged as important features in the complex network of mechanisms behind gene activity and genome connectivity dynamics, which can be evidenced in the regionalized chromosomal spatial distribution and the clustering of diverse genomic regions with similar expression patterns. The development of chromatin conformation capture (3C) techniques has permitted the elucidation of commonalities between the eukaryotic phyla, as well as important differences among them. The growing number of studies in the field performed in plants has shed light on the structural and regulatory features of these organisms. For instance, it has been proposed that plant chromatin can be arranged into different conformations such as Rabl, Rosette-like, and Bouquet, and that both short- and long-range chromatin interactions occur in Arabidopsis. In this review, we compile the current knowledge about chromosome architecture characteristics in plants, as well as the molecular events and elements (including long non-coding RNAs, histone and DNA modifications, chromatin remodeling complexes, and transcription factors) shaping the genome three-dimensional conformation. Furthermore, we discuss the developmental outputs of genome topology-mediated gene expression regulation. It is becoming increasingly clear that new tools and techniques with higher resolution need to be developed and implemented in Arabidopsis and other model plants in order to better understand chromosome architecture dynamics, from an integrative perspective with other fields of plant biology such as development, stress biology, and finally agriculture.
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Affiliation(s)
- Natalia Y Rodriguez-Granados
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Juan S Ramirez-Prado
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Alaguraj Veluchamy
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| | - Federico Ariel
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| | - Moussa Benhamed
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
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167
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Xu F, Li T, Xu PB, Li L, Du SS, Lian HL, Yang HQ. DELLA proteins physically interact with CONSTANS to regulate flowering under long days in Arabidopsis. FEBS Lett 2016; 590:541-9. [PMID: 26801684 DOI: 10.1002/1873-3468.12076] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 12/25/2015] [Accepted: 01/15/2016] [Indexed: 12/20/2022]
Abstract
Proper timing of flowering is essential for reproduction of plants. Although it is well known that both light and gibberellin (GA) signaling play critical roles in promoting flowering in Arabidopsis thaliana, whether and how they are integrated to regulate flowering remain largely unknown. Here, we show through biochemical studies that DELLA proteins physically interact with CONSTANS (CO). Furthermore, the interaction of CO with NF-YB2 is inhibited by the DELLA protein, RGA. Our findings suggest that regulation of flowering by GA signaling in leaves under long days is mediated, at least in part, through repression of DELLA proteins on CO, providing a molecular link between DELLA proteins, key components in GA signaling pathway, and CO, a critical flowering activator in photoperiod signaling pathway.
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Affiliation(s)
- Feng Xu
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture and School of Agriculture and Biology, Shanghai Jiaotong University, China
| | - Ting Li
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture and School of Agriculture and Biology, Shanghai Jiaotong University, China
| | - Peng-Bo Xu
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture and School of Agriculture and Biology, Shanghai Jiaotong University, China
| | - Ling Li
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture and School of Agriculture and Biology, Shanghai Jiaotong University, China
| | - Sha-Sha Du
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong-Li Lian
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture and School of Agriculture and Biology, Shanghai Jiaotong University, China
| | - Hong-Quan Yang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
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168
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Liu W, Stewart CN. Plant synthetic promoters and transcription factors. Curr Opin Biotechnol 2016; 37:36-44. [DOI: 10.1016/j.copbio.2015.10.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/06/2015] [Indexed: 10/22/2022]
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169
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Wang J, Meng X, Chen H, Yuan C, Li X, Zhou Y, Chen M. Exploring the mechanisms of genome-wide long-range interactions: interpreting chromosome organization. Brief Funct Genomics 2016; 15:385-95. [PMID: 26769147 DOI: 10.1093/bfgp/elv062] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Developments in chromosome conformation capture (3C) technologies have revealed that the three-dimensional organization of a genome leads widely separated functional elements to reside in close proximity. However, the mechanisms responsible for mediating long-range interactions are still not completely known. In this review, we firstly evaluate and compare the current seven 3C-based methods, summarize their advantages and discuss their limitations to our current understanding of genome structure. Then, software packages available to perform the analysis of 3C-based data are described. Moreover, we review the insights into the two main mechanisms of long-range interactions, which regulate gene expression by bringing together promoters and distal regulatory elements and by creating structural domains that contain functionally related genes with similar expression landscape. At last, we summarize what is known about the mediating factors involved in stimulation/repression of long-range interactions, such as transcription factors and noncoding RNAs.
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170
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Hu T, Ye J, Tao P, Li H, Zhang J, Zhang Y, Ye Z. The tomato HD-Zip I transcription factor SlHZ24 modulates ascorbate accumulation through positive regulation of the D-mannose/L-galactose pathway. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:16-29. [PMID: 26610866 DOI: 10.1111/tpj.13085] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/12/2015] [Accepted: 11/16/2015] [Indexed: 05/03/2023]
Abstract
Ascorbate (AsA) is an antioxidant that can scavenge the reactive oxygen species (ROS) produced when plants encounter stressful conditions. Here, it was revealed by a yeast one-hybrid assay that a tomato (Solanum lycopersicum) HD-Zip I family transcription factor, SlHZ24, binds to the promoter of an AsA biosynthetic gene encoding GDP-D-mannose pyrophosphorylase 3 (SlGMP3). Both the transient expression system and electrophoretic mobility shift assay (EMSA) showed that SlHZ24 binds to a regulatory cis-element in the SlGMP3 promoter, and further overexpression of SlHZ24 in transgenic tomato lines resulted in increased AsA levels. In contrast, suppressing expression of the gene using RNA interference (RNAi) had the opposite effect. These data suggest that SlHZ24 can positively regulate the accumulation of AsA, and in support of this it was shown that SlGMP3 expression increased in the SlHZ24-overexpressing lines and declined in SlHZ24-RNAi lines. SlHZ24 also affected the expression of other genes in the D-mannose/L-galactose pathway, such as genes encoding GDP-mannose-3',5'-epimerase 2 (SlGME2), GDP-L-galactose phosphorylase (SlGGP) and SlGMP4. The EMSA indicated that SlHZ24 bound to the promoters of SlGME2 and SlGGP, suggesting multi-targeted regulation of AsA biosynthesis. Finally, SlHZ24-overexpressing plants showed less sensitivity to oxidative stress; we therefore conclude that SlHZ24 promotes AsA biosynthesis, which in turn enhances oxidative stress tolerance.
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Affiliation(s)
- Tixu Hu
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Ye
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Peiwen Tao
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hanxia Li
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junhong Zhang
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuyang Zhang
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhibiao Ye
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
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171
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Yu Y, Liu Z, Wang L, Kim SG, Seo PJ, Qiao M, Wang N, Li S, Cao X, Park CM, Xiang F. WRKY71 accelerates flowering via the direct activation of FLOWERING LOCUS T and LEAFY in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:96-106. [PMID: 26643131 DOI: 10.1111/tpj.13092] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 11/19/2015] [Accepted: 11/23/2015] [Indexed: 05/03/2023]
Abstract
Flowering is crucial for achieving reproductive success. A large number of well-delineated factors affecting flowering are involved in complex genetic networks in Arabidopsis thaliana. However, the underlying part played by the WRKY transcription factors in this process is not yet clear. Here, we report that WRKY71 is able to accelerate flowering in Arabidopsis. An activation-tagged mutant WRKY71-1D and a constitutive over-expresser of WRKY71 both flowered earlier than the wild type (WT). In contrast, both the RNA interference-based multiple WRKY knock-out mutant (w71w8 + 28RNAi) and the dominant repression line (W71-SRDX) flowered later. Gene expression analysis showed that the transcript abundance of the flowering time integrator gene FLOWERING LOCUS T (FT) and the floral meristem identity genes LEAFY (LFY), APETALA1 (AP1) and FRUITFULL (FUL) were greater in WRKY71-1D than in the WT, but lower in w71w8 + 28RNAi and W71-SRDX. Further, WRKY71 was shown to bind to the W-boxes in the FT and LFY promoters in vitro and in vivo. The suggestion is that WRKY71 activity hastens flowering via the direct activation of FT and LFY.
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Affiliation(s)
- Yanchong Yu
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Zhenhua Liu
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Long Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Sang-Gyu Kim
- Molecular Signaling Laboratory, Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
| | - Pil J Seo
- Molecular Signaling Laboratory, Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
| | - Meng Qiao
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Nan Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Shuo Li
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chung-Mo Park
- Molecular Signaling Laboratory, Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
| | - Fengning Xiang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Sciences, Shandong University, Jinan, 250100, China
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172
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Zhao H, Wu D, Kong F, Lin K, Zhang H, Li G. The Arabidopsis thaliana Nuclear Factor Y Transcription Factors. FRONTIERS IN PLANT SCIENCE 2016; 7:2045. [PMID: 28119722 PMCID: PMC5222873 DOI: 10.3389/fpls.2016.02045] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 12/21/2016] [Indexed: 05/03/2023]
Abstract
Nuclear factor Y (NF-Y) is an evolutionarily conserved trimeric transcription factor complex present in nearly all eukaryotes. The heterotrimeric NF-Y complex consists of three subunits, NF-YA, NF-YB, and NF-YC, and binds to the CCAAT box in the promoter regions of its target genes to regulate their expression. Yeast and mammal genomes generally have single genes with multiple splicing isoforms that encode each NF-Y subunit. By contrast, plant genomes generally have multi-gene families encoding each subunit and these genes are differentially expressed in various tissues or stages. Therefore, different subunit combinations can lead to a wide variety of NF-Y complexes in various tissues, stages, and growth conditions, indicating the potentially diverse functions of this complex in plants. Indeed, many recent studies have proved that the NF-Y complex plays multiple essential roles in plant growth, development, and stress responses. In this review, we highlight recent progress on NF-Y in Arabidopsis thaliana, including NF-Y protein structure, heterotrimeric complex formation, and the molecular mechanism by which NF-Y regulates downstream target gene expression. We then focus on its biological functions and underlying molecular mechanisms. Finally, possible directions for future research on NF-Y are also presented.
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173
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Li L, Li X, Liu Y, Liu H. Flowering responses to light and temperature. SCIENCE CHINA-LIFE SCIENCES 2015; 59:403-8. [PMID: 26687726 DOI: 10.1007/s11427-015-4910-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 05/20/2015] [Indexed: 11/27/2022]
Abstract
Light and temperature signals are the most important environmental cues regulating plant growth and development. Plants have evolved various strategies to prepare for, and adapt to environmental changes. Plants integrate environmental cues with endogenous signals to regulate various physiological processes, including flowering time. There are at least five distinct pathways controlling flowering in the model plant Arabidopsis thaliana: the photoperiod pathway, the vernalization/thermosensory pathway, the autonomous floral initiation, the gibberellins pathway, and the age pathway. The photoperiod and temperature/ vernalization pathways mainly perceive external signals from the environment, while the autonomous and age pathways transmit endogenous cues within plants. In many plant species, floral transition is precisely controlled by light signals (photoperiod) and temperature to optimize seed production in specific environments. The molecular mechanisms by which light and temperature control flowering responses have been revealed using forward and reverse genetic approaches. Here we focus on the recent advances in research on flowering responses to light and temperature.
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Affiliation(s)
- Li Li
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xu Li
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yawen Liu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Hongtao Liu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
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174
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Nguyen KT, Park J, Park E, Lee I, Choi G. The Arabidopsis RING Domain Protein BOI Inhibits Flowering via CO-dependent and CO-independent Mechanisms. MOLECULAR PLANT 2015; 8:1725-36. [PMID: 26298008 DOI: 10.1016/j.molp.2015.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/24/2015] [Accepted: 08/12/2015] [Indexed: 05/25/2023]
Abstract
BOTRYTIS SUSCEPTIBLE1 INTERACTOR (BOI) and its three homologs (BOIs) are RING domain-containing proteins that repress flowering. Here, we investigated how BOIs repress flowering. Genetic analysis of the boiQ quadruple mutant indicates that BOIs repress flowering mainly through FLOWERING LOCUS T (FT). BOIs repress the expression of FT by CONSTANS (CO)-dependent and -independent mechanisms: in the CO-dependent mechanism, BOIs bind to CO, inhibit the targeting of CO to the FT locus, and thus repress the expression of FT; in the CO-independent mechanism, BOIs target the FT locus via a mechanism that requires DELLAs but not CO. This dual repression of FT makes BOIs strong repressors of flowering in both CO-dependent and CO-independent pathways in Arabidopsis thaliana. Our finding that BOIs inhibit CO targeting further suggests that, in addition to modulating CO mRNA expression and CO protein stability, flowering regulation can also modulate the targeting of CO to FT.
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Affiliation(s)
- Khoa Thi Nguyen
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
| | - Jeongmoo Park
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
| | - Eunae Park
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
| | - Ilha Lee
- School of Biological Sciences, Seoul National University, Seoul 151-747, Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea.
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175
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Burgess DG, Xu J, Freeling M. Advances in understanding cis regulation of the plant gene with an emphasis on comparative genomics. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:141-7. [PMID: 26247124 DOI: 10.1016/j.pbi.2015.07.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/26/2015] [Accepted: 07/07/2015] [Indexed: 05/07/2023]
Abstract
The plant gene model remains largely an extrapolation from animals, with the cis functional unit, the gene, cast as a dynamic looping structure. Molecular genetics with model plants continues to make advances; highlighted here are quantitative-occupancy results from the Arabidopsis thaliana (Arabidopsis) Phytochrome-Interacting bHLH transcription Factors (PIF) quartet. Compared to this complex snapshot, results from chromatin occupancy and other Encyclopedia of DNA Elements (ENCODE)-like approaches increase our transcription factor-motif cognate library, but regulation cannot by itself be inferred from binding. Complementary published Arabidopsis conserved noncoding sequence lists are compared, evaluated, merged, and released. Comparative genomic approaches have identified a cis modifier of a gene's expression-hypothetically, a transposon-based 'rheostat'-that works in all cells, times and places.
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Affiliation(s)
- Diane G Burgess
- Department of Plant and Microbial Biology, University of California, Berkeley 94720, United States.
| | - Jie Xu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, China
| | - Michael Freeling
- Department of Plant and Microbial Biology, University of California, Berkeley 94720, United States
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176
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Bratzel F, Turck F. Molecular memories in the regulation of seasonal flowering: from competence to cessation. Genome Biol 2015; 16:192. [PMID: 26374394 PMCID: PMC4571075 DOI: 10.1186/s13059-015-0770-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Plants commit to flowering based on endogenous and exogenous information that they can remember across mitotic cell divisions. Here, we review how signal perception and epigenetic memory converge at key integrator genes, and we show how variation in their regulatory circuits supports the diversity of plant lifestyles.
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Affiliation(s)
- Fabian Bratzel
- Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, Carl von Linne Weg 10, 50829, Cologne, Germany
| | - Franziska Turck
- Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, Carl von Linne Weg 10, 50829, Cologne, Germany.
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177
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Winter CM, Yamaguchi N, Wu MF, Wagner D. Transcriptional programs regulated by both LEAFY and APETALA1 at the time of flower formation. PHYSIOLOGIA PLANTARUM 2015; 155:55-73. [PMID: 26096587 PMCID: PMC5757833 DOI: 10.1111/ppl.12357] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 06/09/2015] [Indexed: 05/24/2023]
Abstract
Two key regulators of the switch to flower formation and of flower patterning in Arabidopsis are the plant-specific helix-turn-helix transcription factor LEAFY (LFY) and the MADS box transcription factor APETALA1 (AP1). The interactions between these two transcriptional regulators are complex. AP1 is both a direct target of LFY and can act in parallel with LFY. Available genetic and molecular evidence suggests that LFY and AP1 together orchestrate the switch to flower formation and early events during flower morphogenesis by altering transcriptional programs. However, very little is known about target genes regulated by both transcription factors. Here, we performed a meta-analysis of public datasets to identify genes that are likely to be regulated by both LFY and AP1. Our analyses uncovered known and novel direct LFY and AP1 targets with a role in the control of onset of flower formation. It also identified additional families of proteins and regulatory pathways that may be under transcriptional control by both transcription factors. In particular, several of these genes are linked to response to hormones, to transport and to development. Finally, we show that the gibberellin catabolism enzyme ELA1, which was recently shown to be important for the timing of the switch to flower formation, is positively feedback-regulated by AP1. Our study contributes to the elucidation of the regulatory network that leads to formation of a vital plant organ system, the flower.
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Affiliation(s)
- Cara M. Winter
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Nobutoshi Yamaguchi
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Miin-Feng Wu
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
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178
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Zhang T, Zhang D, Liu Y, Luo C, Zhou Y, Zhang L. Overexpression of a NF-YB3 transcription factor from Picea wilsonii confers tolerance to salinity and drought stress in transformed Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 94:153-64. [PMID: 26093308 DOI: 10.1016/j.plaphy.2015.05.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 04/16/2015] [Accepted: 05/02/2015] [Indexed: 05/04/2023]
Abstract
Nuclear factor Y (NF-Y) is a highly conserved transcription factor comprising NF-YA, NF-YB and NF-YC subunits. To date, the roles of NF-Y subunit in plant still remain elusive. In this study, a subunit NF-YB (PwNF-YB3), was isolated from Picea wilsonii Mast. and its role was studied. PwNF-YB3 transcript was detected in all vegetative and reproductive tissues with higher levels in stem and root and was greatly induced by salinity, heat and PEG but not by cold and ABA treatment. Over-expression of PwNF-YB3 in Arabidopsis showed a significant acceleration in the onset of flowering and resulted in more vigorous seed germination and significant tolerance for seedlings under salinity, drought and osmotic stress compared with wild type plants. Transcription levels of salinity-responsive gene (SOS3) and drought-induced gene (CDPK1) were substantially higher in transgenic Arabidopsis than in wild-type plants. Importantly, CBF pathway markers (COR15B, KIN1, LEA76), but not ABA pathway markers CBF4, were greatly induced under condition of drought. The nuclear localization showed that NF-YB3 acted as a transcription factor. Taken together, the data provide evidence that PwNF-YB3 positively confers significant tolerance to salt, osmotic and drought stress in transformed Arabidopsis plants probably through modulating gene regulation in CBF-dependent pathway.
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Affiliation(s)
- Tong Zhang
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing 100083, PR China
| | - Dun Zhang
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing 100083, PR China
| | - Yajing Liu
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing 100083, PR China
| | - Chaobing Luo
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing 100083, PR China
| | - Yanni Zhou
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing 100083, PR China
| | - Lingyun Zhang
- Key Laboratory of Forest Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing 100083, PR China.
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179
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Abstract
Methods that use high-throughput sequencing have begun to reveal features of the three-dimensional structure of genomes at a resolution that goes far beyond that of traditional microscopy. Integration of these methods with other molecular tools has advanced our knowledge of both global and local chromatin packing in plants, and has revealed how patterns of chromatin packing correlate with the genomic and epigenomic landscapes. This update reports recent progress made in this area in plants, and suggests new research directions.
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Affiliation(s)
- Chang Liu
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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180
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Charlier JB, Polese C, Nouet C, Carnol M, Bosman B, Krämer U, Motte P, Hanikenne M. Zinc triggers a complex transcriptional and post-transcriptional regulation of the metal homeostasis gene FRD3 in Arabidopsis relatives. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3865-78. [PMID: 25900619 PMCID: PMC4473987 DOI: 10.1093/jxb/erv188] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In Arabidopsis thaliana, FRD3 (FERRIC CHELATE REDUCTASE DEFECTIVE 3) plays a central role in metal homeostasis. FRD3 is among a set of metal homeostasis genes that are constitutively highly expressed in roots and shoots of Arabidopsis halleri, a zinc hyperaccumulating and hypertolerant species. Here, we examined the regulation of FRD3 by zinc in both species to shed light on the evolutionary processes underlying the evolution of hyperaccumulation in A. halleri. We combined gene expression studies with the use of β-glucuronidase and green fluorescent protein reporter constructs to compare the expression profile and transcriptional and post-transcriptional regulation of FRD3 in both species. The AtFRD3 and AhFRD3 genes displayed a conserved expression profile. In A. thaliana, alternative transcription initiation sites from two promoters determined transcript variants that were differentially regulated by zinc supply in roots and shoots to favour the most highly translated variant under zinc-excess conditions. In A. halleri, a single transcript variant with higher transcript stability and enhanced translation has been maintained. The FRD3 gene thus undergoes complex transcriptional and post-transcriptional regulation in Arabidopsis relatives. Our study reveals that a diverse set of mechanisms underlie increased gene dosage in the A. halleri lineage and illustrates how an environmental challenge can alter gene regulation.
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Affiliation(s)
- Jean-Benoit Charlier
- Functional Genomics and Plant Molecular Imaging, Center for Protein Engineering (CIP), Department of Life Sciences, University of Liège, B-4000 Liège, Belgium
| | - Catherine Polese
- Functional Genomics and Plant Molecular Imaging, Center for Protein Engineering (CIP), Department of Life Sciences, University of Liège, B-4000 Liège, Belgium
| | - Cécile Nouet
- Functional Genomics and Plant Molecular Imaging, Center for Protein Engineering (CIP), Department of Life Sciences, University of Liège, B-4000 Liège, Belgium
| | - Monique Carnol
- Laboratory of Plant and Microbial Ecology, Department of Biology, Ecology, Evolution, University of Liège, B-4000 Liège, Belgium
| | - Bernard Bosman
- Laboratory of Plant and Microbial Ecology, Department of Biology, Ecology, Evolution, University of Liège, B-4000 Liège, Belgium
| | - Ute Krämer
- Department of Plant Physiology, Ruhr University Bochum, D-44801 Bochum, Germany
| | - Patrick Motte
- Functional Genomics and Plant Molecular Imaging, Center for Protein Engineering (CIP), Department of Life Sciences, University of Liège, B-4000 Liège, Belgium PhytoSYSTEMS, University of Liège, B-4000 Liège, Belgium
| | - Marc Hanikenne
- Functional Genomics and Plant Molecular Imaging, Center for Protein Engineering (CIP), Department of Life Sciences, University of Liège, B-4000 Liège, Belgium PhytoSYSTEMS, University of Liège, B-4000 Liège, Belgium
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181
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Simon S, Rühl M, de Montaigu A, Wötzel S, Coupland G. Evolution of CONSTANS Regulation and Function after Gene Duplication Produced a Photoperiodic Flowering Switch in the Brassicaceae. Mol Biol Evol 2015; 32:2284-301. [PMID: 25972346 PMCID: PMC4540966 DOI: 10.1093/molbev/msv110] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Environmental control of flowering allows plant reproduction to occur under optimal conditions and facilitates adaptation to different locations. At high latitude, flowering of many plants is controlled by seasonal changes in day length. The photoperiodic flowering pathway confers this response in the Brassicaceae, which colonized temperate latitudes after divergence from the Cleomaceae, their subtropical sister family. The CONSTANS (CO) transcription factor of Arabidopsis thaliana, a member of the Brassicaceae, is central to the photoperiodic flowering response and shows characteristic patterns of transcription required for day-length sensing. CO is believed to be widely conserved among flowering plants; however, we show that it arose after gene duplication at the root of the Brassicaceae followed by divergence of transcriptional regulation and protein function. CO has two close homologs, CONSTANS-LIKE1 (COL1) and COL2, which are related to CO by tandem duplication and whole-genome duplication, respectively. The single CO homolog present in the Cleomaceae shows transcriptional and functional features similar to those of COL1 and COL2, suggesting that these were ancestral. We detect cis-regulatory and codon changes characteristic of CO and use transgenic assays to demonstrate their significance in the day-length-dependent activation of the CO target gene FLOWERING LOCUS T. Thus, the function of CO as a potent photoperiodic flowering switch evolved in the Brassicaceae after gene duplication. The origin of CO may have contributed to the range expansion of the Brassicaceae and suggests that in other families CO genes involved in photoperiodic flowering arose by convergent evolution.
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Affiliation(s)
- Samson Simon
- Department of Plant Developmental Biology, Max-Planck-Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Mark Rühl
- Department of Plant Developmental Biology, Max-Planck-Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Amaury de Montaigu
- Department of Plant Developmental Biology, Max-Planck-Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Stefan Wötzel
- Department of Plant Developmental Biology, Max-Planck-Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - George Coupland
- Department of Plant Developmental Biology, Max-Planck-Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
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182
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He Y. Enabling photoperiodic control of flowering by timely chromatin silencing of the florigen gene. Nucleus 2015; 6:179-82. [PMID: 25950625 DOI: 10.1080/19491034.2015.1038000] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Many plants synchronize their flowering times with changing seasons to maximize reproductive success. A key seasonal cue is the change in day length (photoperiod), that induces the production of a systemic flowering signaling molecule called florigen. A major florigen component is FLOWERING LOCUS T (FT) or its orthologs. In the long-day plant Arabidopsis thaliana, FT expression is well known to be activated by the photoperiod pathway output specifically near dusk in long days; however, underappreciated is the importance of FT silencing at other times of the day, in enabling Arabidopsis to respond only to long days in flowering. We have recently reported that a plant-specific chromatin-silencing complex called EMF1c represses FT expression at times other than around dusk in long days to prevent its temporal ectopic expression from "spoiling" the long-day floral induction in Arabidopsis. Here I further discuss in other day-length sensitive plants the potential involvement of a chromatin mechanism similar to the Arabidopsis EMF1c-mediated silencing, in repressing the expression of FT orthologs to enable diverse photoperiodic control of flowering.
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Key Words
- CO, CONSTANS
- EMF1, EMBRYONIC FLOWER 1
- EMF1c
- FT
- FT, FLOWERING LOCUS T
- H2Aub, Histone 2A monoubiquitination
- H3K27me3, Histone 3 lysine-27 trimethylation
- Histone 3 lysine-27 trimethylation
- LHP1, LIKE HETEROCHROMATIN PROTEIN 1
- NF-Y, nuclear factor Y
- PRC1
- PRC1, Polycomb repressive complex 1
- PRC2, Polycomb repressive complex 2
- PcG, Polycomb group
- chromatin silencing
- flowering time
- photoperiod pathway
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Affiliation(s)
- Yuehui He
- a Shanghai Center for Plant Stress Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences ; Shanghai , China
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183
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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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184
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Golembeski GS, Imaizumi T. Photoperiodic Regulation of Florigen Function in Arabidopsis thaliana. THE ARABIDOPSIS BOOK 2015; 13:e0178. [PMID: 26157354 PMCID: PMC4489636 DOI: 10.1199/tab.0178] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
One mechanism through which flowering in response to seasonal change is brought about is by sensing the fluctuation in day-length; the photoperiod. Flowering induction occurs through the production of the florigenic protein FLOWERING LOCUS T (FT) and its movement from the phloem companion cells in the leaf vasculature into the shoot apex, where meristematic reprogramming occurs. FT activation in response to photoperiod condition is accomplished largely through the activity of the transcription factor CONSTANS (CO). Regulation of CO expression and protein stability, as well as the timing of other components via the circadian clock, is a critical mechanism by which plants are able to respond to photoperiod to initiate the floral transition. Modulation of FT expression in response to external and internal stimuli via components of the flowering network is crucial to mediate a fluid flowering response to a variety of environmental parameters. In addition, the regulated movement of FT protein from the phloem to the shoot apex, and interactions that determine floral meristem cell fate, constitute novel mechanisms through which photoperiodic information is translated into flowering time.
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Affiliation(s)
- Greg S. Golembeski
- University of Washington, Department of Biology, Seattle, WA, 98195-1800
| | - Takato Imaizumi
- University of Washington, Department of Biology, Seattle, WA, 98195-1800
- Address correspondence to
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185
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Song YH, Shim JS, Kinmonth-Schultz HA, Imaizumi T. Photoperiodic flowering: time measurement mechanisms in leaves. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:441-64. [PMID: 25534513 PMCID: PMC4414745 DOI: 10.1146/annurev-arplant-043014-115555] [Citation(s) in RCA: 395] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Many plants use information about changing day length (photoperiod) to align their flowering time with seasonal changes to increase reproductive success. A mechanism for photoperiodic time measurement is present in leaves, and the day-length-specific induction of the FLOWERING LOCUS T (FT) gene, which encodes florigen, is a major final output of the pathway. Here, we summarize the current understanding of the molecular mechanisms by which photoperiodic information is perceived in order to trigger FT expression in Arabidopsis as well as in the primary cereals wheat, barley, and rice. In these plants, the differences in photoperiod are measured by interactions between circadian-clock-regulated components, such as CONSTANS (CO), and light signaling. The interactions happen under certain day-length conditions, as previously predicted by the external coincidence model. In these plants, the coincidence mechanisms are governed by multilayered regulation with numerous conserved as well as unique regulatory components, highlighting the breadth of photoperiodic regulation across plant species.
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Affiliation(s)
- Young Hun Song
- Department of Biology, University of Washington, Seattle, Washington 98195-1800;
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186
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Feng ZJ, He GH, Zheng WJ, Lu PP, Chen M, Gong YM, Ma YZ, Xu ZS. Foxtail Millet NF-Y Families: Genome-Wide Survey and Evolution Analyses Identified Two Functional Genes Important in Abiotic Stresses. FRONTIERS IN PLANT SCIENCE 2015; 6:1142. [PMID: 26734043 PMCID: PMC4687410 DOI: 10.3389/fpls.2015.01142] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 12/01/2015] [Indexed: 05/19/2023]
Abstract
It was reported that Nuclear Factor Y (NF-Y) genes were involved in abiotic stress in plants. Foxtail millet (Setaria italica), an elite stress tolerant crop, provided an impetus for the investigation of the NF-Y families in abiotic responses. In the present study, a total of 39 NF-Y genes were identified in foxtail millet. Synteny analyses suggested that foxtail millet NF-Y genes had experienced rapid expansion and strong purifying selection during the process of plant evolution. De novo transcriptome assembly of foxtail millet revealed 11 drought up-regulated NF-Y genes. SiNF-YA1 and SiNF-YB8 were highly activated in leaves and/or roots by drought and salt stresses. Abscisic acid (ABA) and H2O2 played positive roles in the induction of SiNF-YA1 and SiNF-YB8 under stress treatments. Transient luciferase (LUC) expression assays revealed that SiNF-YA1 and SiNF-YB8 could activate the LUC gene driven by the tobacco (Nicotiana tobacam) NtERD10, NtLEA5, NtCAT, NtSOD, or NtPOD promoter under normal or stress conditions. Overexpression of SiNF-YA1 enhanced drought and salt tolerance by activating stress-related genes NtERD10 and NtCAT1 and by maintaining relatively stable relative water content (RWC) and contents of chlorophyll, superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and malondialdehyde (MDA) in transgenic lines under stresses. SiNF-YB8 regulated expression of NtSOD, NtPOD, NtLEA5, and NtERD10 and conferred relatively high RWC and chlorophyll contents and low MDA content, resulting in drought and osmotic tolerance in transgenic lines under stresses. Therefore, SiNF-YA1 and SiNF-YB8 could activate stress-related genes and improve physiological traits, resulting in tolerance to abiotic stresses in plants. All these results will facilitate functional characterization of foxtail millet NF-Ys in future studies.
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Affiliation(s)
- Zhi-Juan Feng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of AgricultureBeijing, China
- Institute of Vegetables, Zhejiang Academy of AgricultureHangzhou, Zhejiang, China
| | - Guan-Hua He
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of AgricultureBeijing, China
| | - Wei-Jun Zheng
- College of Agronomy, Northwest A&F UniversityYangling, Shaanxi, China
| | - Pan-Pan Lu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of AgricultureBeijing, China
| | - Ming Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of AgricultureBeijing, China
| | - Ya-Ming Gong
- Institute of Vegetables, Zhejiang Academy of AgricultureHangzhou, Zhejiang, China
| | - You-Zhi Ma
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of AgricultureBeijing, China
- *Correspondence: You-Zhi Ma
| | - Zhao-Shi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of AgricultureBeijing, China
- Zhao-Shi Xu
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187
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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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188
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Romera-Branchat M, Andrés F, Coupland G. Flowering responses to seasonal cues: what's new? CURRENT OPINION IN PLANT BIOLOGY 2014; 21:120-127. [PMID: 25072635 DOI: 10.1016/j.pbi.2014.07.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 06/30/2014] [Accepted: 07/07/2014] [Indexed: 05/20/2023]
Abstract
Seasonal cues of day length or winter cold trigger flowering of many species. Forward and reverse genetic approaches are revealing the mechanisms by which these responses are conferred. Homologues of the Arabidopsis thaliana protein FLOWERING LOCUS T (FT) are widely used to mediate seasonal responses to day length and act as graft-transmissible promoters or repressors of flowering. Winter cold in A. thaliana promotes flowering by repressing transcription of the MADS box gene FLOWERING LOCUS C (FLC). The mechanism by which this occurs involves a complex interplay of different forms of long noncoding RNAs induced at the FLC locus during cold and changes in the chromatin of FLC. In perennial relatives of A. thaliana, flowering also requires the age-dependent downregulation of miRNA156 before winter.
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Affiliation(s)
| | - Fernando Andrés
- 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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189
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Heyndrickx KS, Van de Velde J, Wang C, Weigel D, Vandepoele K. A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana. THE PLANT CELL 2014; 26:3894-910. [PMID: 25361952 PMCID: PMC4247581 DOI: 10.1105/tpc.114.130591] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 10/07/2014] [Accepted: 10/12/2014] [Indexed: 05/19/2023]
Abstract
Understanding the mechanisms underlying gene regulation is paramount to comprehend the translation from genotype to phenotype. The two are connected by gene expression, and it is generally thought that variation in transcription factor (TF) function is an important determinant of phenotypic evolution. We analyzed publicly available genome-wide chromatin immunoprecipitation experiments for 27 TFs in Arabidopsis thaliana and constructed an experimental network containing 46,619 regulatory interactions and 15,188 target genes. We identified hub targets and highly occupied target (HOT) regions, which are enriched for genes involved in development, stimulus responses, signaling, and gene regulatory processes in the currently profiled network. We provide several lines of evidence that TF binding at plant HOT regions is functional, in contrast to that in animals, and not merely the result of accessible chromatin. HOT regions harbor specific DNA motifs, are enriched for differentially expressed genes, and are often conserved across crucifers and dicots, even though they are not under higher levels of purifying selection than non-HOT regions. Distal bound regions are under purifying selection as well and are enriched for a chromatin state showing regulation by the Polycomb repressive complex. Gene expression complexity is positively correlated with the total number of bound TFs, revealing insights in the regulatory code for genes with different expression breadths. The integration of noncanonical and canonical DNA motif information yields new hypotheses on cobinding and tethering between specific TFs involved in flowering and light regulation.
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Affiliation(s)
- Ken S Heyndrickx
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Jan Van de Velde
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Congmao Wang
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Klaas Vandepoele
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
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190
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Wang CQ, Guthrie C, Sarmast MK, Dehesh K. BBX19 interacts with CONSTANS to repress FLOWERING LOCUS T transcription, defining a flowering time checkpoint in Arabidopsis. THE PLANT CELL 2014; 26:3589-602. [PMID: 25228341 PMCID: PMC4213167 DOI: 10.1105/tpc.114.130252] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The timely transition of vegetative to reproductive development is coordinated through quantitative regulation of floral pathway genes in response to physiological and environmental cues. Here, we show that the circadian-controlled expression of the Arabidopsis thaliana floral transition regulators FLOWERING LOCUS T (FT) and CONSTANS (CO) is antiphasic to that of BBX19, a transcription factor with two B-Box motifs. Diminished expression of BBX19 by RNA interference accelerates flowering, and constitutive expression of BBX19 delays flowering under inductive photoperiods. This delay is not accompanied by the alteration of CO expression levels but rather by a reduction of transcript levels of FT and the FT-regulated genes SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1, LEAFY, and FRUITFUL. Similar to CO, BBX19 is expressed in vasculature. BBX19 and CO colocalize in the nucleus and interact physically in vivo. In transient assays, coinfiltration of 10-fold more CO overcomes the BBX19-mediated repression of FT activation. Substitution of the conserved Cys-25 to Ser in the BBX19 Box1 motif abolishes the BBX19-CO interaction and eliminates the negative regulation of flowering time, while the analogous C76S substitution in the Box2 motif is ineffective. Together, these results implicate BBX19 as a circadian clock output that depletes the active CO pool to accurately monitor daylength and precisely time FT expression.
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Affiliation(s)
- Chang-Quan Wang
- Department of Plant Biology, University of California, Davis, California 95616
| | - Cade Guthrie
- Department of Plant Biology, University of California, Davis, California 95616
| | | | - Katayoon Dehesh
- Department of Plant Biology, University of California, Davis, California 95616
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191
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Hou X, Zhou J, Liu C, Liu L, Shen L, Yu H. Nuclear factor Y-mediated H3K27me3 demethylation of the SOC1 locus orchestrates flowering responses of Arabidopsis. Nat Commun 2014; 5:4601. [PMID: 25105952 DOI: 10.1038/ncomms5601] [Citation(s) in RCA: 186] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Accepted: 07/07/2014] [Indexed: 12/12/2022] Open
Abstract
Nuclear factor Y (NF-Y) is a conserved heterotrimeric transcription factor complex that binds to the CCAAT motifs within the promoter region of many genes. In plants, a large number of genes code for variants of each NF-YA, B or C subunit that can assemble in a combinatorial fashion. Here, we report the discovery of an Arabidopsis NF-Y complex that exerts epigenetic control over flowering time by integrating environmental and developmental signals. We show that NF-Y interacts with CONSTANS in the photoperiod pathway and DELLAs in the gibberellin pathway, to directly regulate the transcription of SOC1, a major floral pathway integrator. This NF-Y complex binds to a unique cis-element within the SOC1 promoter to modulate trimethylated H3K27 levels, partly through a H3K27 demethylase REF6. Our findings establish NF-Y complexes as critical mediators of epigenetic marks that regulate the response to environmental or intrinsic signals in plants.
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Affiliation(s)
- Xingliang Hou
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
| | - Jiannan Zhou
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore
| | - Chang Liu
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore
| | - Lu Liu
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore
| | - Lisha Shen
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore
| | - Hao Yu
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore
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192
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Liu L, Adrian J, Pankin A, Hu J, Dong X, von Korff M, Turck F. Induced and natural variation of promoter length modulates the photoperiodic response of FLOWERING LOCUS T. Nat Commun 2014; 5:4558. [PMID: 25087553 PMCID: PMC4143923 DOI: 10.1038/ncomms5558] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 06/30/2014] [Indexed: 12/15/2022] Open
Abstract
FLOWERING LOCUS T (FT) regulates the floral transition in many plant species by integrating environmental seasonal signals and internal cues. Here we show that two interdependent regulatory regions are necessary and sufficient to convey photoperiod responsiveness to FT. While a minimal distance between the regulatory regions is required to fully suppress FT expression under short days, increased distance reduces promoter response to long days. Natural variation at FT creating promoter length differences is widespread, correlates with longitudinal and latitudinal clines and affects a promoter region physically interacting with both photoperiod control regions. Three major FT promoter variants correlate with differences in FT allele usage in F1 hybrids. We propose that FT variation in cis could be adaptive by conferring differences in FT transcriptional control ultimately translating to increased fitness. Gene expression at FLOWERING LOCUS T controls floral transition in many plants and is regulated by both environmental signals and internal cues. Liu et al. show that the distance between two regulatory sequences in the FT promoter varies with geographical location and determines responsiveness to photoperiod.
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Affiliation(s)
- Liangyu Liu
- 1] Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, Carl von Linne Weg 10, 50829 Cologne, Germany [2] Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China [3] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jessika Adrian
- 1] Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, Carl von Linne Weg 10, 50829 Cologne, Germany [2]
| | - Artem Pankin
- Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, Carl von Linne Weg 10, 50829 Cologne, Germany
| | - Jinyong Hu
- Max Planck Institute for Plant Breeding Research, Department of Plant Breeding and Genetics, Carl von Linne Weg 10, 50829 Cologne, Germany
| | - Xue Dong
- Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, Carl von Linne Weg 10, 50829 Cologne, Germany
| | - Maria von Korff
- 1] Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, Carl von Linne Weg 10, 50829 Cologne, Germany [2] Institute of Plant Genetics, Heinrich-Heine-University, Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225 Düsseldorf, Germany
| | - Franziska Turck
- Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, Carl von Linne Weg 10, 50829 Cologne, Germany
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193
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Wong ACS, Hecht VFG, Picard K, Diwadkar P, Laurie RE, Wen J, Mysore K, Macknight RC, Weller JL. Isolation and functional analysis of CONSTANS-LIKE genes suggests that a central role for CONSTANS in flowering time control is not evolutionarily conserved in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2014; 5:486. [PMID: 25278955 PMCID: PMC4166892 DOI: 10.3389/fpls.2014.00486] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 09/03/2014] [Indexed: 05/18/2023]
Abstract
The zinc finger transcription factor CONSTANS has a well-established central role in the mechanism for photoperiod sensing in Arabidopsis, integrating light and circadian clock signals to upregulate the florigen gene FT under long-day but not short-day conditions. Although CONSTANS-LIKE (COL) genes in other species have also been shown to regulate flowering time, it is not clear how widely this central role in photoperiod sensing is conserved. Legumes are a major plant group and various legume species show significant natural variation for photoperiod responsive flowering. Orthologs of several Arabidopsis genes have been shown to participate in photoperiodic flowering in legumes, but the possible function of COL genes as integrators of the photoperiod response has not yet been examined in detail. Here we characterize the COL family in the temperate long-day legume Medicago truncatula, using expression analyses, reverse genetics, transient activation assays and Arabidopsis transformation. Our results provide several lines of evidence suggesting that COL genes are unlikely to have a central role in the photoperiod response mechanism in this species.
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Affiliation(s)
- Albert C. S. Wong
- School of Biological Sciences, University of TasmaniaHobart, TAS, Australia
| | | | - Kelsey Picard
- Department of Biochemistry, University of OtagoDunedin, New Zealand
| | - Payal Diwadkar
- Department of Biochemistry, University of OtagoDunedin, New Zealand
| | | | - Jiangqi Wen
- Plant Biology Division, Samuel Roberts Noble FoundationArdmore, OK, USA
| | - Kirankumar Mysore
- Plant Biology Division, Samuel Roberts Noble FoundationArdmore, OK, USA
| | | | - James L. Weller
- School of Biological Sciences, University of TasmaniaHobart, TAS, Australia
- *Correspondence: James L. Weller, School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia e-mail:
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194
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Desvoyes B, Fernández-Marcos M, Sequeira-Mendes J, Otero S, Vergara Z, Gutierrez C. Looking at plant cell cycle from the chromatin window. FRONTIERS IN PLANT SCIENCE 2014; 5:369. [PMID: 25120553 PMCID: PMC4110626 DOI: 10.3389/fpls.2014.00369] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/11/2014] [Indexed: 05/03/2023]
Abstract
The cell cycle is defined by a series of complex events, finely coordinated through hormonal, developmental and environmental signals, which occur in a unidirectional manner and end up in producing two daughter cells. Accumulating evidence reveals that chromatin is not a static entity throughout the cell cycle. In fact, there are many changes that include nucleosome remodeling, histone modifications, deposition and exchange, among others. Interestingly, it is possible to correlate the occurrence of several of these chromatin-related events with specific processes necessary for cell cycle progression, e.g., licensing of DNA replication origins, the E2F-dependent transcriptional wave in G1, the activation of replication origins in S-phase, the G2-specific transcription of genes required for mitosis or the chromatin packaging occurring in mitosis. Therefore, an emerging view is that chromatin dynamics must be considered as an intrinsic part of cell cycle regulation. In this article, we review the main features of several key chromatin events that occur at defined times throughout the cell cycle and discuss whether they are actually controlling the transit through specific cell cycle stages.
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Affiliation(s)
| | | | | | | | | | - Crisanto Gutierrez
- *Correspondence: Crisanto Gutierrez, Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas, Universidad Autónoma de Madrid, Nicolas Cabrera 1, Cantoblanco, Madrid 28049, Spain e-mail:
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