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Song Z, Bian Y, Xiao Y, Xu D. B-BOX proteins:Multi-layered roles of molecular cogs in light-mediated growth and development in plants. JOURNAL OF PLANT PHYSIOLOGY 2024; 299:154265. [PMID: 38754343 DOI: 10.1016/j.jplph.2024.154265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/05/2024] [Accepted: 05/05/2024] [Indexed: 05/18/2024]
Abstract
B-box containing proteins (BBXs) are a class of zinc-ligating transcription factors or regulators that play essential roles in various physiological and developmental processes in plants. They not only directly associate with target genes to regulate their transcription, but also interact with other transcription factors to mediate target genes' expression, thus forming a complex transcriptional network ensuring plants' adaptation to dynamically changing light environments. This review summarizes and highlights the molecular and biochemical properties of BBXs, as well as recent advances with a focus on their critical regulatory functions in photomorphogenesis (de-etiolation), shade avoidance, photoperiodic-mediated flowering, and secondary metabolite biosynthesis and accumulation in plants.
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Affiliation(s)
- Zhaoqing Song
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yeting Bian
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuntao Xiao
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dongqing Xu
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
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Chen J, Wang Y, Wu Y, Huang X, Qiu X, Chen J, Lin Q, Zhao H, Chen F, Gao G. Genome-wide identification and expression analysis of the PP2C gene family in Apocynum venetum and Apocynum hendersonii. BMC PLANT BIOLOGY 2024; 24:652. [PMID: 38982365 PMCID: PMC11232223 DOI: 10.1186/s12870-024-05328-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/24/2024] [Indexed: 07/11/2024]
Abstract
BACKGROUND Protein phosphatase class 2 C (PP2C) is the largest protein phosphatase family in plants. Members of the PP2C gene family are involved in a variety of physiological pathways in plants, including the abscisic acid signalling pathway, the regulation of plant growth and development, etc., and are capable of responding to a wide range of biotic and abiotic stresses, and play an important role in plant growth, development, and response to stress. Apocynum is a perennial persistent herb, divided into Apocynum venetum and Apocynum hendersonii. It mainly grows in saline soil, deserts and other harsh environments, and is widely used in saline soil improvement, ecological restoration, textiles and medicine. A. hendersonii was found to be more tolerant to adverse conditions. The main purpose of this study was to investigate the PP2C gene family and its expression pattern under salt stress and to identify important candidate genes related to salt tolerance. RESULTS In this study, 68 AvPP2C genes and 68 AhPP2C genes were identified from the genomes of A. venetum and A. hendersonii, respectively. They were classified into 13 subgroups based on their phylogenetic relationships and were further analyzed for their subcellular locations, gene structures, conserved structural domains, and cis-acting elements. The results of qRT-PCR analyses of seven AvPP2C genes and seven AhPP2C genes proved that they differed significantly in gene expression under salt stress. It has been observed that the PP2C genes in A. venetum and A. hendersonii exhibit different expression patterns. Specifically, AvPP2C2, 6, 24, 27, 41 and AhPP2C2, 6, 24, 27, 42 have shown significant differences in expression under salt stress. This indicates that these genes may play a crucial role in the salt tolerance mechanism of A. venetum and A. hendersonii. CONCLUSIONS In this study, we conducted a genome-wide analysis of the AvPP2C and AhPP2C gene families in Apocynum, which provided a reference for further understanding the functional characteristics of these genes.
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Affiliation(s)
- Jiayi Chen
- Hunan Provincial Key Laboratory of the Traditional Chinese Medicine Agricultural Biogenomics, Changsha Medical University, Changsha, 410219, China
| | - Yue Wang
- Hunan Provincial Key Laboratory of the Traditional Chinese Medicine Agricultural Biogenomics, Changsha Medical University, Changsha, 410219, China
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Yongmei Wu
- Hunan Provincial Key Laboratory of the Traditional Chinese Medicine Agricultural Biogenomics, Changsha Medical University, Changsha, 410219, China
| | - Xiaoyu Huang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Xiaojun Qiu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Jikang Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
- Yuelushan Laboratory, Changsha, 410082, P.R. China
| | - Qian Lin
- Hunan Provincial Key Laboratory of the Traditional Chinese Medicine Agricultural Biogenomics, Changsha Medical University, Changsha, 410219, China
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Haohan Zhao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
- Yuelushan Laboratory, Changsha, 410082, P.R. China
| | - Fengming Chen
- Hunan Provincial Key Laboratory of the Traditional Chinese Medicine Agricultural Biogenomics, Changsha Medical University, Changsha, 410219, China.
| | - Gang Gao
- Hunan Provincial Key Laboratory of the Traditional Chinese Medicine Agricultural Biogenomics, Changsha Medical University, Changsha, 410219, China.
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.
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Veciana N, Martín G, Leivar P, Monte E. BBX16 mediates the repression of seedling photomorphogenesis downstream of the GUN1/GLK1 module during retrograde signalling. THE NEW PHYTOLOGIST 2022; 234:93-106. [PMID: 35043407 PMCID: PMC9305768 DOI: 10.1111/nph.17975] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/05/2022] [Indexed: 05/03/2023]
Abstract
Plastid-to-nucleus retrograde signalling (RS) initiated by dysfunctional chloroplasts impact photomorphogenic development. We have previously shown that the transcription factor GLK1 acts downstream of the RS regulator GUN1 in photodamaging conditions to regulate not only the well established expression of photosynthesis-associated nuclear genes (PhANGs) but also to regulate seedling morphogenesis. Specifically, the GUN1/GLK1 module inhibits the light-induced phytochrome-interacting factor (PIF)-repressed transcriptional network to suppress cotyledon development when chloroplast integrity is compromised, modulating the area exposed to potentially damaging high light. However, how the GUN1/GLK1 module inhibits photomorphogenesis upon chloroplast damage remained undefined. Here, we report the identification of BBX16 as a novel direct target of GLK1. BBX16 is induced and promotes photomorphogenesis in moderate light and is repressed via GUN1/GLK1 after chloroplast damage. Additionally, we showed that BBX16 represents a regulatory branching point downstream of GUN1/GLK1 in the regulation of PhANG expression and seedling development upon RS activation. The gun1 phenotype in lincomycin and the gun1-like phenotype of GLK1OX are markedly suppressed in gun1bbx16 and GLK1OXbbx16. This study identified BBX16 as the first member of the BBX family involved in RS, and defines a molecular bifurcation mechanism operated by GLK1/BBX16 to optimise seedling de-etiolation, and to ensure photoprotection in unfavourable light conditions.
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Affiliation(s)
- Nil Veciana
- Centre for Research in Agricultural Genomics (CRAG) CSIC‐IRTA‐UAB‐UBCampus UAB, Bellaterra08193BarcelonaSpain
| | - Guiomar Martín
- Centre for Research in Agricultural Genomics (CRAG) CSIC‐IRTA‐UAB‐UBCampus UAB, Bellaterra08193BarcelonaSpain
| | - Pablo Leivar
- Laboratory of BiochemistryInstitut Químic de SarriàUniversitat Ramon Llull08017BarcelonaSpain
| | - Elena Monte
- Centre for Research in Agricultural Genomics (CRAG) CSIC‐IRTA‐UAB‐UBCampus UAB, Bellaterra08193BarcelonaSpain
- Consejo Superior de Investigaciones Científicas (CSIC)08028BarcelonaSpain
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Zeng L, Wang JZ, He X, Ke H, Lemos M, Gray WM, Dehesh K. A plastidial retrograde signal potentiates biosynthesis of systemic stress response activators. THE NEW PHYTOLOGIST 2022; 233:1732-1749. [PMID: 34859454 PMCID: PMC8776617 DOI: 10.1111/nph.17890] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/23/2021] [Indexed: 05/26/2023]
Abstract
Plants employ an array of intricate and hierarchical signaling cascades to perceive and transduce informational cues to synchronize and tailor adaptive responses. Systemic stress response (SSR) is a recognized complex signaling and response network quintessential to plant's local and distal responses to environmental triggers; however, the identity of the initiating signals has remained fragmented. Here, we show that both biotic (aphids and viral pathogens) and abiotic (high light and wounding) stresses induce accumulation of the plastidial-retrograde-signaling metabolite methylerythritol cyclodiphosphate (MEcPP), leading to reduction of the phytohormone auxin and the subsequent decreased expression of the phosphatase PP2C.D1. This enables phosphorylation of mitogen-activated protein kinases 3/6 and the consequential induction of the downstream events ultimately, resulting in biosynthesis of the two SSR priming metabolites pipecolic acid and N-hydroxy-pipecolic acid. This work identifies plastids as a major initiation site, and the plastidial retrograde signal MEcPP as an initiator of a multicomponent signaling cascade potentiating the biosynthesis of SSR activators, in response to biotic and abiotic triggers.
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Affiliation(s)
- Liping Zeng
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Jin-Zheng Wang
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Xiang He
- Current address: Laboratory of Allergy and Inflammation, Chengdu third people’s hospital branch of National Clinical Research Center for Respiratory Disease, Chengdu 610031, China
| | - Haiyan Ke
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Mark Lemos
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - William M. Gray
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Katayoon Dehesh
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
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Du M, Bou Daher F, Liu Y, Steward A, Tillmann M, Zhang X, Wong JH, Ren H, Cohen JD, Li C, Gray WM. Biphasic control of cell expansion by auxin coordinates etiolated seedling development. SCIENCE ADVANCES 2022; 8:eabj1570. [PMID: 35020423 PMCID: PMC8754305 DOI: 10.1126/sciadv.abj1570] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Seedling emergence is critical for food security. It requires rapid hypocotyl elongation and apical hook formation, both of which are mediated by regulated cell expansion. How these events are coordinated in etiolated seedlings is unclear. Here, we show that biphasic control of cell expansion by the phytohormone auxin underlies this process. Shortly after germination, high auxin levels restrain elongation. This provides a temporal window for apical hook formation, involving a gravity-induced auxin maximum on the eventual concave side of the hook. This auxin maximum induces PP2C.D1 expression, leading to asymmetrical H+-ATPase activity across the hypocotyl that contributes to the differential cell elongation underlying hook development. Subsequently, auxin concentrations decline acropetally and switch from restraining to promoting elongation, thereby driving hypocotyl elongation. Our findings demonstrate how differential auxin concentrations throughout the hypocotyl coordinate etiolated development, leading to successful soil emergence.
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Affiliation(s)
- Minmin Du
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Firas Bou Daher
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Yuanyuan Liu
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Andrew Steward
- Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, MN 55108, USA
| | - Molly Tillmann
- Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, MN 55108, USA
| | - Xiaoyue Zhang
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jeh Haur Wong
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Hong Ren
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Jerry D. Cohen
- Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, MN 55108, USA
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Corresponding author. (C.L.); (W.M.G.)
| | - William M. Gray
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
- Corresponding author. (C.L.); (W.M.G.)
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Direct photoresponsive inhibition of a p53-like transcription activation domain in PIF3 by Arabidopsis phytochrome B. Nat Commun 2021; 12:5614. [PMID: 34556672 PMCID: PMC8460787 DOI: 10.1038/s41467-021-25909-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/09/2021] [Indexed: 11/24/2022] Open
Abstract
Photoactivated phytochrome B (PHYB) binds to antagonistically acting PHYTOCHROME-INTERACTING transcription FACTORs (PIFs) to regulate hundreds of light responsive genes in Arabidopsis by promoting PIF degradation. However, whether PHYB directly controls the transactivation activity of PIFs remains ambiguous. Here we show that the prototypic PIF, PIF3, possesses a p53-like transcription activation domain (AD) consisting of a hydrophobic activator motif flanked by acidic residues. A PIF3mAD mutant, in which the activator motif is replaced with alanines, fails to activate PIF3 target genes in Arabidopsis, validating the functions of the PIF3 AD in vivo. Intriguingly, the N-terminal photosensory module of PHYB binds immediately adjacent to the PIF3 AD to repress PIF3’s transactivation activity, demonstrating a novel PHYB signaling mechanism through direct interference of the transactivation activity of PIF3. Our findings indicate that PHYB, likely also PHYA, controls the stability and activity of PIFs via structurally separable dual signaling mechanisms. Photoactivated phytochrome B regulates gene expression by interacting with PIF transcription factors. Here the authors show that PIF3 contains a p53-like transcription activation domain (AD) and that PHYB can directly suppress PIF3 transactivation activity by binding adjacent to the AD.
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Bursch K, Niemann ET, Nelson DC, Johansson H. Karrikins control seedling photomorphogenesis and anthocyanin biosynthesis through a HY5-BBX transcriptional module. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1346-1362. [PMID: 34160854 DOI: 10.1111/tpj.15383] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/18/2021] [Indexed: 05/15/2023]
Abstract
The butenolide molecule, karrikin (KAR), emerging in smoke of burned plant material, enhances light responses such as germination, inhibition of hypocotyl elongation, and anthocyanin accumulation in Arabidopsis. The KAR signaling pathway consists of KARRIKIN INSENSITIVE 2 (KAI2) and MORE AXILLARY GROWTH 2 (MAX2), which, upon activation, act in an SCF E3 ubiquitin ligase complex to target the downstream signaling components SUPPRESSOR OF MAX2 1 (SMAX1) and SMAX1-LIKE 2 (SMXL2) for degradation. How degradation of SMAX1 and SMXL2 is translated into growth responses remains unknown. Although light clearly influences the activity of KAR, the molecular connection between the two pathways is still poorly understood. Here, we demonstrate that the KAR signaling pathway promotes the activity of a transcriptional module consisting of ELONGATED HYPOCOTYL 5 (HY5), B-BOX DOMAIN PROTEIN 20 (BBX20), and BBX21. The bbx20 bbx21 mutant is largely insensitive to treatment with KAR2 , similar to a hy5 mutant, with regards to inhibition of hypocotyl elongation and anthocyanin accumulation. Detailed analysis of higher order mutants in combination with RNA-sequencing analysis revealed that anthocyanin accumulation downstream of SMAX1 and SMXL2 is fully dependent on the HY5-BBX module. However, the promotion of hypocotyl elongation by SMAX1 and SMXL2 is, in contrast to KAR2 treatment, only partially dependent on BBX20, BBX21, and HY5. Taken together, these results suggest that light- and KAR-dependent signaling intersect at the HY5-BBX transcriptional module.
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Affiliation(s)
- Katharina Bursch
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Berlin, 14195, Germany
| | - Ella T Niemann
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Berlin, 14195, Germany
| | - David C Nelson
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Henrik Johansson
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Berlin, 14195, Germany
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Rovira A, Sentandreu M, Nagatani A, Leivar P, Monte E. The Sequential Action of MIDA9/PP2C.D1, PP2C.D2, and PP2C.D5 Is Necessary to Form and Maintain the Hook After Germination in the Dark. FRONTIERS IN PLANT SCIENCE 2021; 12:636098. [PMID: 33767720 PMCID: PMC7985339 DOI: 10.3389/fpls.2021.636098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
During seedling etiolation after germination in the dark, seedlings have closed cotyledons and form an apical hook to protect the meristem as they break through the soil to reach the surface. Once in contact with light, the hook opens and cotyledons are oriented upward and separate. Hook development in the dark after seedling emergence from the seed follows three distinctly timed and sequential phases: formation, maintenance, and eventual opening. We previously identified MISREGULATED IN DARK9 (MIDA9) as a phytochrome interacting factor (PIF)-repressed gene in the dark necessary for hook development during etiolated growth. MIDA9 encodes the type 2C phosphatase PP2C.D1, and pp2c-d1/mida9 mutants exhibit open hooks in the dark. Recent evidence has described that PP2C.D1 and other PP2C.D members negatively regulate SMALL AUXIN UP RNA (SAUR)-mediated cell elongation. However, the fundamental question of the timing of PP2C.D1 action (and possibly other members of the PP2C.D family) during hook development remains to be addressed. Here, we show that PP2C.D1 is required immediately after germination to form the hook. pp2c.d1/mida9 shows reduced cell expansion in the outer layer of the hook and, therefore, does not establish the differential cell growth necessary for hook formation, indicating that PP2C.D1 is necessary to promote cell elongation during this early stage. Additionally, genetic analyses of single and high order mutants in PP2C.D1, PP2C.D2, and PP2C.D5 demonstrate that the three PP2C.Ds act collectively and sequentially during etiolation: whereas PP2C.D1 dominates hook formation, PP2C.D2 is necessary during the maintenance phase, and PP2C.D5 acts to prevent opening during the third phase together with PP2C.D1 and PP2C.D2. Finally, we uncover a possible connection of PP2C.D1 levels with ethylene physiology, which could help optimize hook formation during post-germinative growth in the dark.
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Affiliation(s)
- Arnau Rovira
- Plant Development and Signal Transduction Program, Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Maria Sentandreu
- Plant Development and Signal Transduction Program, Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Akira Nagatani
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Pablo Leivar
- Plant Development and Signal Transduction Program, Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, Spain
| | - Elena Monte
- Plant Development and Signal Transduction Program, Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
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Martín G, Veciana N, Boix M, Rovira A, Henriques R, Monte E. The photoperiodic response of hypocotyl elongation involves regulation of CDF1 and CDF5 activity. PHYSIOLOGIA PLANTARUM 2020; 169:480-490. [PMID: 32379360 DOI: 10.1111/ppl.13119] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/23/2020] [Accepted: 05/03/2020] [Indexed: 06/11/2023]
Abstract
Hypocotyl elongation relies on directional cell expansion, a process under light and circadian clock control. Under short photoperiods (SD), hypocotyl elongation in Arabidopsis thaliana follows a rhythmic pattern, a process in which circadian morning-to-midnight waves of the transcriptional repressors PSEUDO-RESPONSE REGULATORS (PRRs) jointly gate PHYTOCHROME-INTERACTING FACTOR (PIF) activity to dawn. Previously, we described CYCLING DOF FACTOR 5 (CDF5) as a target of this antagonistic PRR/PIF dynamic interplay. Under SD, PIFs induce CDF5 accumulation specifically at dawn, when it promotes the expression of positive cell elongation regulators such as YUCCA8 to induce growth. In contrast to SD, hypocotyl elongation under long days (LD) is largely reduced. Here, we examine whether CDF5 is an actor in this photoperiod specific regulation. We report that transcription of CDF5 is robustly induced in SD compared to LD, in accordance with PIFs accumulating to higher levels in SD, and in contrast to other members of the CDF family, whose expression is mainly clock regulated and have similar waveforms in SD and LD. Notably, when CDF5 was constitutively expressed under LD, CDF5 protein accumulated to levels comparable to SD but was inactive in promoting cell elongation. Similar results were observed for CDF1. Our findings indicate that both CDFs can promote cell elongation specifically in shorter photoperiods, however, their activity in LD is inhibited at the post-translational level. These data not only expand our understanding of the biological role of CDF transcription factors, but also identify a previously unrecognized regulatory layer in the photoperiodic response of hypocotyl elongation.
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Affiliation(s)
- Guiomar Martín
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
- Instituto Gulbenkian de Ciência (IGC), Oeiras, 2780-156, Portugal
| | - Nil Veciana
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
| | - Marc Boix
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
| | - Arnau Rovira
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
| | - Rossana Henriques
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, T23 TK30, Ireland
- Environmental Research Institute, University College Cork, Cork, T23 XE10, Ireland
| | - Elena Monte
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08028, Spain
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Leivar P, Martín G, Soy J, Dalton-Roesler J, Quail PH, Monte E. Phytochrome-imposed inhibition of PIF7 activity shapes photoperiodic growth in Arabidopsis together with PIF1, 3, 4 and 5. PHYSIOLOGIA PLANTARUM 2020; 169:452-466. [PMID: 32412656 DOI: 10.1111/ppl.13123] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/05/2020] [Accepted: 05/11/2020] [Indexed: 05/29/2023]
Abstract
Under photoperiodic conditions, Arabidopsis thaliana seedling growth is inhibited in long days (LDs), but promoted under the extended nights of short days (SDs). This behavior is partly implemented by phytochrome (phy)-imposed oscillations in the abundance of the growth-promoting, phy-interacting bHLH transcription factors PHY-INTERACTING FACTOR 1 (PIF1), PIF3, PIF4 and PIF5 (PIF quartet or PIFq). However, the observation that a pifq mutant is still stimulated to elongate when given a phy-inactivating end-of-day far-red pulse (EODFR), suggests that additional factors are involved in the phy-mediated suppression of growth during the subsequent dark period. Here, by combining growth-analysis of pif7 single- and higher-order mutants with gene expression analysis under SD, LD, SD-EODFR, and LD-EODFR, we show that PIF7 promotes growth during the dark hours of SD, by regulating growth-related gene expression. Interestingly, the relative contribution of PIF7 in promoting growth is stronger under EODFR, whereas PIF3 role is more important under SD, suggesting that PIF7 is a prominent target of phy-suppression. Indeed, we show that phy imposes phosphorylation and inactivation of PIF7 during the light hours in SD, and prevents full dephosphorylation during the night. This repression can be lifted with an EODFR, which correlates with increased PIF7-mediated gene expression and elongation. In addition, our results suggest that PIF7 function might involve heterodimerization with PIF3. Furthermore, our data indicate that a pifqpif7 quintuple mutant is largely insensitive to photoperiod for hypocotyl elongation. Collectively, the data suggest that PIF7, together with the PIFq, is required for the photoperiodic regulation of seasonal growth.
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Affiliation(s)
- Pablo Leivar
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, Spain
| | - Guiomar Martín
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Judit Soy
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Jutta Dalton-Roesler
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
- United States Department of Agriculture, Plant Gene Expression Center, Albany, CA, USA
| | - Peter H Quail
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
- United States Department of Agriculture, Plant Gene Expression Center, Albany, CA, USA
| | - Elena Monte
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
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11
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Wong JH, Spartz AK, Park MY, Du M, Gray WM. Mutation of a Conserved Motif of PP2C.D Phosphatases Confers SAUR Immunity and Constitutive Activity. PLANT PHYSIOLOGY 2019; 181:353-366. [PMID: 31311832 PMCID: PMC6716246 DOI: 10.1104/pp.19.00496] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/21/2019] [Indexed: 05/05/2023]
Abstract
The phytohormone auxin promotes the growth of plant shoots by stimulating cell expansion via plasma membrane (PM) H+-ATPase activation, which facilitates cell wall loosening and solute uptake. Mechanistic insight was recently obtained by demonstrating that auxin-induced SMALL AUXIN UP RNA (SAUR) proteins inhibit D-CLADE TYPE 2C PROTEIN PHOSPHATASE (PP2C.D) activity, thereby trapping PM H+-ATPases in the phosphorylated, activated state, but how SAURs bind PP2C.D proteins and inhibit their activity is unknown. Here, we identified a highly conserved motif near the C-terminal region of the PP2C.D catalytic domain that is required for SAUR binding in Arabidopsis (Arabidopsis thaliana). Missense mutations in this motif abolished SAUR binding but had no apparent effect on catalytic activity. Consequently, mutant PP2C.D proteins that could not bind SAURs exhibited constitutive activity, as they were immune to SAUR inhibition. In planta expression of SAUR-immune pp2c.d2 or pp2c.d5 derivatives conferred severe cell expansion defects and corresponding constitutively low levels of PM H+-ATPase phosphorylation. These growth defects were not alleviated by either auxin treatment or 35S:StrepII-SAUR19 coexpression. In contrast, a PM H+-ATPase gain-of-function mutation that results in a constitutively active H+ pump partially suppressed SAUR-immune pp2c.d5 phenotypes, demonstrating that impaired PM H+-ATPase function is largely responsible for the reduced growth of the SAUR-immune pp2c.d5 mutant. Together, these findings provide crucial genetic support for SAUR-PP2C.D regulation of cell expansion via modulation of PM H+-ATPase activity. Furthermore, SAUR-immune pp2c.d derivatives provide new genetic tools for elucidating SAUR and PP2C.D functions and manipulating plant organ growth.
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Affiliation(s)
- Jeh Haur Wong
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Angela K Spartz
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Mee Yeon Park
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Minmin Du
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - William M Gray
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
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12
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Dong J, Sun N, Yang J, Deng Z, Lan J, Qin G, He H, Deng XW, Irish VF, Chen H, Wei N. The Transcription Factors TCP4 and PIF3 Antagonistically Regulate Organ-Specific Light Induction of SAUR Genes to Modulate Cotyledon Opening during De-Etiolation in Arabidopsis. THE PLANT CELL 2019; 31:1155-1170. [PMID: 30914467 PMCID: PMC6533013 DOI: 10.1105/tpc.18.00803] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 03/11/2019] [Accepted: 03/21/2019] [Indexed: 05/19/2023]
Abstract
Light elicits different growth responses in different organs of plants. These organ-specific responses are prominently displayed during de-etiolation. While major light-responsive components and early signaling pathways in this process have been identified, this information has yet to explain how organ-specific light responses are achieved. Here, we report that members of the TEOSINTE BRANCHED1, CYCLOIDEA, and PCF (TCP) transcription factor family participate in photomorphogenesis and facilitate light-induced cotyledon opening in Arabidopsis (Arabidopsis thaliana). Chromatin immunoprecipitation sequencing and RNA sequencing analyses indicated that TCP4 targets a number of SMALL AUXIN UPREGULATED RNA (SAUR) genes that have previously been shown to exhibit organ-specific, light-responsive expression. We demonstrate that TCP4-like transcription factors, which are predominantly expressed in the cotyledons of both light- and dark-grown seedlings, activate SAUR16 and SAUR50 expression in response to light. Light regulates the binding of TCP4 to the promoters of SAUR14, SAUR16, and SAUR50 through PHYTOCHROME-INTERACTING FACTORs (PIFs). PIF3, which accumulates in etiolated seedlings and its levels rapidly decline upon light exposure, also binds to the SAUR16 and SAUR50 promoters, while suppressing the binding of TCP4 to these promoters in the dark. Our study reveals that the interplay between light-responsive factors PIFs and the developmental regulator TCP4 determines the cotyledon-specific light regulation of SAUR16 and SAUR50, which contributes to cotyledon closure and opening before and after de-etiolation.
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Affiliation(s)
- Jie Dong
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Ning Sun
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Jing Yang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhaoguo Deng
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Jingqiu Lan
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Genji Qin
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Vivian F Irish
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Haodong Chen
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Ning Wei
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520
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13
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Lee HG, Seo PJ. MYB96 recruits the HDA15 protein to suppress negative regulators of ABA signaling in Arabidopsis. Nat Commun 2019. [PMID: 30979883 DOI: 10.1038/s41467-019-09417-9411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
Unlike activation of target genes in response to abscisic acid (ABA), how MYB96 transcription factor represses ABA-repressible genes to further enhance ABA responses remains unknown. Here, we show MYB96 interacts with the histone modifier HDA15 to suppress negative regulators of early ABA signaling. The MYB96-HDA15 complex co-binds to the promoters of a subset of RHO GTPASE OF PLANTS (ROP) genes, ROP6, ROP10, and ROP11, and represses their expression by removing acetyl groups of histone H3 and H4 from the cognate regions, particularly in the presence of ABA. In support, HDA15-deficient mutants display reduced ABA sensitivity and are susceptible to drought stress with derepression of the ROP genes, as observed in the myb96-1 mutant. Biochemical and genetic analyses show that MYB96 and HDA15 are interdependent in the regulation of ROP suppression. Thus, MYB96 confers maximal ABA sensitivity by regulating both positive and negative regulators of ABA signaling through distinctive molecular mechanisms.
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Affiliation(s)
- Hong Gil Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea.
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14
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Lee HG, Seo PJ. MYB96 recruits the HDA15 protein to suppress negative regulators of ABA signaling in Arabidopsis. Nat Commun 2019; 10:1713. [PMID: 30979883 PMCID: PMC6461653 DOI: 10.1038/s41467-019-09417-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/06/2019] [Indexed: 12/18/2022] Open
Abstract
Unlike activation of target genes in response to abscisic acid (ABA), how MYB96 transcription factor represses ABA-repressible genes to further enhance ABA responses remains unknown. Here, we show MYB96 interacts with the histone modifier HDA15 to suppress negative regulators of early ABA signaling. The MYB96-HDA15 complex co-binds to the promoters of a subset of RHO GTPASE OF PLANTS (ROP) genes, ROP6, ROP10, and ROP11, and represses their expression by removing acetyl groups of histone H3 and H4 from the cognate regions, particularly in the presence of ABA. In support, HDA15-deficient mutants display reduced ABA sensitivity and are susceptible to drought stress with derepression of the ROP genes, as observed in the myb96-1 mutant. Biochemical and genetic analyses show that MYB96 and HDA15 are interdependent in the regulation of ROP suppression. Thus, MYB96 confers maximal ABA sensitivity by regulating both positive and negative regulators of ABA signaling through distinctive molecular mechanisms. MYB96 can regulate both positive and negative regulators of ABA signaling to maximize plant drought tolerance. Here, the authors show that MYB96 represses expression of ABA negative regulators in Arabidopsis by interacting with HDA15 and promoting histone deacetylation at the cognate regions.
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Affiliation(s)
- Hong Gil Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea. .,Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea.
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15
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Vaishak KP, Yadukrishnan P, Bakshi S, Kushwaha AK, Ramachandran H, Job N, Babu D, Datta S. The B-box bridge between light and hormones in plants. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2018; 191:164-174. [PMID: 30640143 DOI: 10.1016/j.jphotobiol.2018.12.021] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/23/2018] [Accepted: 12/27/2018] [Indexed: 11/29/2022]
Abstract
Plant development is meticulously modulated by interactions between the surrounding environment and the endogenous phytohormones. Light, as an external signal coordinates with the extensive networks of hormones inside the plant to execute its effects on growth and development. Several proteins in plants have been identified for their crucial roles in mediating light regulated development. Among these are the B-box (BBX) family of transcription factors characterized by the presence of zinc-finger B-box domain in their N-terminal region. In Arabidopsis there are 32 BBX proteins that are divided into five structural groups on the basis of the domains present. Several BBX proteins play important roles in seedling photomorphogenesis, neighbourhood detection and photoperiodic regulation of flowering. There is increasing evidence that besides light signaling BBX proteins also play integral roles in several hormone signaling pathways in plants. Here we attempt to comprehensively integrate the roles of multiple BBX proteins in various light and hormone signaling pathways. We further discuss the role of the BBX proteins in mediating crosstalk between the two signaling pathways to harmonize plant growth and development. Finally, we try to analyse the conservation of BBX genes across species and discuss the role of BBX proteins in regulating economically important traits in crop plants.
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Affiliation(s)
- K P Vaishak
- Plant Cell and Development Biology Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India; School of Biological Sciences, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, India
| | - Premachandran Yadukrishnan
- Plant Cell and Development Biology Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Souvika Bakshi
- Plant Cell and Development Biology Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Amit Kumar Kushwaha
- Plant Cell and Development Biology Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Harshil Ramachandran
- Plant Cell and Development Biology Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Nikhil Job
- Plant Cell and Development Biology Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Dion Babu
- Plant Cell and Development Biology Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Sourav Datta
- Plant Cell and Development Biology Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India.
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16
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Lin F, Jiang Y, Li J, Yan T, Fan L, Liang J, Chen ZJ, Xu D, Deng XW. B-BOX DOMAIN PROTEIN28 Negatively Regulates Photomorphogenesis by Repressing the Activity of Transcription Factor HY5 and Undergoes COP1-Mediated Degradation. THE PLANT CELL 2018; 30:2006-2019. [PMID: 30099385 PMCID: PMC6181009 DOI: 10.1105/tpc.18.00226] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 06/27/2018] [Accepted: 08/06/2018] [Indexed: 05/04/2023]
Abstract
Plants have evolved a delicate molecular system to fine-tune their growth and development in response to dynamically changing light environments. In this study, we found that BBX28, a B-box domain protein, negatively regulates photomorphogenic development in a dose-dependent manner in Arabidopsis thaliana BBX28 interferes with the binding of transcription factor HY5 to the promoters of its target genes through physical interactions, thereby repressing its activity and negatively affecting HY5-regulated gene expression. In darkness, BBX28 associates with CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1) and undergoes COP1-mediated degradation via the 26S proteasome system. Collectively, these results demonstrate that BBX28 acts as a key factor in the COP1-HY5 regulatory hub by maintaining proper HY5 activity to ensure normal photomorphogenic development in plants.
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Affiliation(s)
- Fang Lin
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Plant and Food Sciences, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yan Jiang
- Institute of Plant and Food Sciences, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jian Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Tingting Yan
- Institute of Plant and Food Sciences, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Liumin Fan
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Jiansheng Liang
- Institute of Plant and Food Sciences, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas 78712
| | - Dongqing Xu
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas 78712
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Plant and Food Sciences, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
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17
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A subset of plasma membrane-localized PP2C.D phosphatases negatively regulate SAUR-mediated cell expansion in Arabidopsis. PLoS Genet 2018; 14:e1007455. [PMID: 29897949 PMCID: PMC6016943 DOI: 10.1371/journal.pgen.1007455] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 06/25/2018] [Accepted: 05/30/2018] [Indexed: 02/06/2023] Open
Abstract
The plant hormone auxin regulates numerous growth and developmental processes throughout the plant life cycle. One major function of auxin in plant growth and development is the regulation of cell expansion. Our previous studies have shown that SMALL AUXIN UP RNA (SAUR) proteins promote auxin-induced cell expansion via an acid growth mechanism. These proteins inhibit the PP2C.D family phosphatases to activate plasma membrane (PM) H+-ATPases and thereby promote cell expansion. However, the functions of individual PP2C.D phosphatases are poorly understood. Here, we investigated PP2C.D-mediated control of cell expansion and other aspects of plant growth and development. The nine PP2C.D family members exhibit distinct subcellular localization patterns. Our genetic findings demonstrate that the three plasma membrane-localized members, PP2C.D2, PP2C.D5, and PP2C.D6, are the major regulators of cell expansion. These phosphatases physically interact with SAUR19 and PM H+-ATPases, and inhibit cell expansion by dephosphorylating the penultimate threonine of PM H+-ATPases. PP2C.D genes are broadly expressed and are crucial for diverse plant growth and developmental processes, including apical hook development, phototropism, and organ growth. GFP-SAUR19 overexpression suppresses the growth defects conferred by PP2C.D5 overexpression, indicating that SAUR proteins antagonize the growth inhibition conferred by the plasma membrane-localized PP2C.D phosphatases. Auxin and high temperature upregulate the expression of some PP2C.D family members, which may provide an additional layer of regulation to prevent plant overgrowth. Our findings provide novel insights into auxin-induced cell expansion, and provide crucial loss-of-function genetic support for SAUR-PP2C.D regulatory modules controlling key aspects of plant growth. The plant hormone auxin is a major regulator of cell expansion, which is a fundamental cellular process essential for plant growth and development. The acid growth theory was proposed in the 1970s to explain auxin-induced cell expansion. However, the mechanistic basis of auxin-induced cell expansion via acid growth is poorly understood. Here, we investigated the functions of the D-clade PP2C (PP2C.D) family phosphatases in auxin-induced cell expansion as well as plant growth and development. The PP2C.D protein family is composed of nine members. Our findings demonstrate that the plasma membrane-localized PP2C.D2, PP2C.D5, and PP2C.D6 family members are the major regulators in auxin-induced cell expansion. These proteins physically associate with SAUR proteins and plasma membrane H+-ATPases to negatively regulate cell expansion. PP2C.D genes are broadly expressed and are crucial for a variety of plant growth and developmental processes, particularly elongation growth, such as hypocotyl and stamen filament growth. The results of our studies provide novel insights into auxin-induced cell expansion via an acid growth mechanism.
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18
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Qiu Y, Pasoreck EK, Reddy AK, Nagatani A, Ma W, Chory J, Chen M. Mechanism of early light signaling by the carboxy-terminal output module of Arabidopsis phytochrome B. Nat Commun 2017. [PMID: 29199270 DOI: 10.1038/s41467-107-02062-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Plant phytochromes are thought to transduce light signals by mediating the degradation of phytochrome-interacting transcription factors (PIFs) through the N-terminal photosensory module, while the C-terminal module, including a histidine kinase-related domain (HKRD), does not participate in signaling. Here we show that the C-terminal module of Arabidopsis phytochrome B (PHYB) is sufficient to mediate the degradation of PIF3 specifically and to activate photosynthetic genes in the dark. The HKRD is a dimerization domain for PHYB homo and heterodimerization. A D1040V mutation, which disrupts the dimerization of HKRD and the interaction between C-terminal module and PIF3, abrogates PHYB nuclear accumulation, photobody biogenesis, and PIF3 degradation. By contrast, disrupting the interaction between PIF3 and PHYB's N-terminal module has little effect on PIF3 degradation. Together, this study demonstrates that the dimeric form of the C-terminal module plays important signaling roles by targeting PHYB to subnuclear photobodies and interacting with PIF3 to trigger its degradation.
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Affiliation(s)
- Yongjian Qiu
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | | | - Amit K Reddy
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Akira Nagatani
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Wenxiu Ma
- Department of Statistics, University of California, Riverside, CA, 92521, USA
| | - Joanne Chory
- Howard Hughes Medical Institute, Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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19
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Mechanism of early light signaling by the carboxy-terminal output module of Arabidopsis phytochrome B. Nat Commun 2017; 8:1905. [PMID: 29199270 PMCID: PMC5712524 DOI: 10.1038/s41467-017-02062-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 11/03/2017] [Indexed: 11/08/2022] Open
Abstract
Plant phytochromes are thought to transduce light signals by mediating the degradation of phytochrome-interacting transcription factors (PIFs) through the N-terminal photosensory module, while the C-terminal module, including a histidine kinase-related domain (HKRD), does not participate in signaling. Here we show that the C-terminal module of Arabidopsis phytochrome B (PHYB) is sufficient to mediate the degradation of PIF3 specifically and to activate photosynthetic genes in the dark. The HKRD is a dimerization domain for PHYB homo and heterodimerization. A D1040V mutation, which disrupts the dimerization of HKRD and the interaction between C-terminal module and PIF3, abrogates PHYB nuclear accumulation, photobody biogenesis, and PIF3 degradation. By contrast, disrupting the interaction between PIF3 and PHYB's N-terminal module has little effect on PIF3 degradation. Together, this study demonstrates that the dimeric form of the C-terminal module plays important signaling roles by targeting PHYB to subnuclear photobodies and interacting with PIF3 to trigger its degradation.
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20
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Seluzicki A, Burko Y, Chory J. Dancing in the dark: darkness as a signal in plants. PLANT, CELL & ENVIRONMENT 2017; 40:2487-2501. [PMID: 28044340 PMCID: PMC6110299 DOI: 10.1111/pce.12900] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 05/21/2023]
Abstract
Daily cycles of light and dark provide an organizing principle and temporal constraints under which life on Earth evolved. While light is often the focus of plant studies, it is only half the story. Plants continuously adjust to their surroundings, taking both dawn and dusk as cues to organize their growth, development and metabolism to appropriate times of day. In this review, we examine the effects of darkness on plant physiology and growth. We describe the similarities and differences between seedlings grown in the dark versus those grown in light-dark cycles, and the evolution of etiolated growth. We discuss the integration of the circadian clock into other processes, looking carefully at the points of contact between clock genes and growth-promoting gene-regulatory networks in temporal gating of growth. We also examine daily starch accumulation and degradation, and the possible contribution of dark-specific metabolic controls in regulating energy and growth. Examining these studies together reveals a complex and continuous balancing act, with many signals, dark included, contributing information and guiding the plant through its life cycle. The extraordinary interconnection between light and dark is manifest during cycles of day and night and during seedling emergence above versus below the soil surface.
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Affiliation(s)
- Adam Seluzicki
- Salk Institute for Biological Studies, Plant Biology Laboratory, La Jolla, CA, 92037, USA
| | - Yogev Burko
- Salk Institute for Biological Studies, Plant Biology Laboratory, La Jolla, CA, 92037, USA
- Howard Hughes Medical Institute Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Joanne Chory
- Salk Institute for Biological Studies, Plant Biology Laboratory, La Jolla, CA, 92037, USA
- Howard Hughes Medical Institute Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
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21
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Reply to Jin and Zhu: PINOID-mediated COP1 phosphorylation matters in photomorphogenesis in Arabidopsis. Proc Natl Acad Sci U S A 2017; 114:E8136-E8137. [PMID: 28912351 DOI: 10.1073/pnas.1712385114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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22
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Zhang X, Huai J, Shang F, Xu G, Tang W, Jing Y, Lin R. A PIF1/PIF3-HY5-BBX23 Transcription Factor Cascade Affects Photomorphogenesis. PLANT PHYSIOLOGY 2017; 174:2487-2500. [PMID: 28687557 PMCID: PMC5543951 DOI: 10.1104/pp.17.00418] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/01/2017] [Indexed: 05/18/2023]
Abstract
Light signaling plays an essential role in controlling higher plants' early developmental process termed as photomorphogenesis. Transcriptional regulation is a vital mechanism that is orchestrated by transcription factors and other regulatory proteins working in concert to finely tune gene expression. Although many transcription factors/regulators have been characterized in the light-signaling pathway, their interregulation remains largely unknown. Here, we show that PHYTOCHROME-INTERACTING FACTOR3 (PIF3) and PIF1 transcription factors directly bind to the regulatory regions of ELONGATED HYPOCOTYL5 (HY5) and a B-box gene BBX23 and activate their expression in Arabidopsis (Arabidopsis thaliana). We found that BBX23 and its close homolog gene BBX22 play a redundant role in regulating hypocotyl growth, and that plants overexpressing BBX23 display reduced hypocotyl elongation under red, far-red, and blue light conditions. Intriguingly, BBX23 transcription is inhibited by light, whereas its protein is degraded in darkness. Furthermore, we demonstrate that HY5 physically interacts with BBX23, and these two proteins coordinately regulate the expression of both light-induced and light-repressed genes. BBX23 is also recruited to the promoter sequences of the light-responsive genes in a partial HY5-dependent manner. Taken together, our study reveals that the transcriptional cascade consisting of PIF1/PIF3, HY5, and BBX23 controls photomorphogenesis, providing a transcriptional regulatory layer by which plants fine-tune their growth in response to changing light environment.
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Affiliation(s)
- Xinyu Zhang
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junling Huai
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Fangfang Shang
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gang Xu
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weijiang Tang
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yanjun Jing
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Dobisova T, Hrdinova V, Cuesta C, Michlickova S, Urbankova I, Hejatkova R, Zadnikova P, Pernisova M, Benkova E, Hejatko J. Light Controls Cytokinin Signaling via Transcriptional Regulation of Constitutively Active Sensor Histidine Kinase CKI1. PLANT PHYSIOLOGY 2017; 174:387-404. [PMID: 28292856 PMCID: PMC5411129 DOI: 10.1104/pp.16.01964] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/04/2017] [Indexed: 05/07/2023]
Abstract
In plants, the multistep phosphorelay (MSP) pathway mediates a range of regulatory processes, including those activated by cytokinins. The cross talk between cytokinin response and light has been known for a long time. However, the molecular mechanism underlying the interaction between light and cytokinin signaling remains elusive. In the screen for upstream regulators we identified a LONG PALE HYPOCOTYL (LPH) gene whose activity is indispensable for spatiotemporally correct expression of CYTOKININ INDEPENDENT1 (CKI1), encoding the constitutively active sensor His kinase that activates MSP signaling. lph is a new allele of HEME OXYGENASE1 (HY1) that encodes the key protein in the biosynthesis of phytochromobilin, a cofactor of photoconvertible phytochromes. Our analysis confirmed the light-dependent regulation of the CKI1 expression pattern. We show that CKI1 expression is under the control of phytochrome A (phyA), functioning as a dual (both positive and negative) regulator of CKI1 expression, presumably via the phyA-regulated transcription factors (TF) PHYTOCHROME INTERACTING FACTOR3 and CIRCADIAN CLOCK ASSOCIATED1. Changes in CKI1 expression observed in lph/hy1-7 and phy mutants correlate with misregulation of MSP signaling, changed cytokinin sensitivity, and developmental aberrations that were previously shown to be associated with cytokinin and/or CKI1 action. Besides that, we demonstrate a novel role of phyA-dependent CKI1 expression in the hypocotyl elongation and hook development during skotomorphogenesis. Based on these results, we propose that the light-dependent regulation of CKI1 provides a plausible mechanistic link underlying the well-known interaction between light- and cytokinin-controlled plant development.
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Affiliation(s)
- Tereza Dobisova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Vendula Hrdinova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Candela Cuesta
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Sarka Michlickova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Ivana Urbankova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Romana Hejatkova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Petra Zadnikova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Marketa Pernisova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Eva Benkova
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
| | - Jan Hejatko
- CEITEC - Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, CZ-62500, Brno, Czech Republic (T.D., V.H., S.M., I.U., R.H., P.Z., M.P., E.B., J.H.); and Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria (C.C., P.Z., E.B.)
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24
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Kim K, Jeong J, Kim J, Lee N, Kim ME, Lee S, Chang Kim S, Choi G. PIF1 Regulates Plastid Development by Repressing Photosynthetic Genes in the Endodermis. MOLECULAR PLANT 2016; 9:1415-1427. [PMID: 27591813 DOI: 10.1016/j.molp.2016.08.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/11/2016] [Accepted: 08/24/2016] [Indexed: 05/14/2023]
Abstract
Mutations in Phytochrome Interacting Factors (PIFs) induce a conversion of the endodermal amyloplasts necessary for gravity sensing to plastids with developed thylakoids accompanied by abnormal activation of photosynthetic genes in the dark. In this study, we investigated how PIFs regulate endodermal plastid development by performing comparative transcriptome analysis. We show that both endodermal expression of PIF1 and global expression of the PIF quartet induce transcriptional changes in genes enriched for nuclear-encoded photosynthetic genes such as LHCA and LHCB. Among the 94 shared differentially expressed genes identified from the comparative transcriptome analysis, only 14 genes are demonstrated to be direct targets of PIF1, and most photosynthetic genes are not. Using a co-expression analysis, we identified a direct target of PIF, whose expression pattern shows a strong negative correlation with many photosynthetic genes. We have named this gene REPRESSOR OF PHOTOSYNTHETIC GENES1 (RPGE1). Endodermal expression of RPGE1 rescued the elevated expression of photosynthetic genes found in the pif quadruple (pifQ) mutant and partly restored amyloplast development and hypocotyl negative gravitropism. Taken together, our results indicate that RPGE1 acts downstream of PIF1 in the endodermis to repress photosynthetic genes and regulate plastid development.
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Affiliation(s)
- Keunhwa Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Jinkil Jeong
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Jeongheon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Nayoung Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Mi Eon Kim
- Center for Gas Analysis, Division of Metrology for Quality of Life, Korea Research Institute of Standards and Science (KRISS), Daejeon 305-340, Republic of Korea
| | - Sangil Lee
- Center for Gas Analysis, Division of Metrology for Quality of Life, Korea Research Institute of Standards and Science (KRISS), Daejeon 305-340, Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Giltsu Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea.
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25
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Martin G, Soy J, Monte E. Genomic Analysis Reveals Contrasting PIFq Contribution to Diurnal Rhythmic Gene Expression in PIF-Induced and -Repressed Genes. FRONTIERS IN PLANT SCIENCE 2016; 7:962. [PMID: 27458465 PMCID: PMC4930942 DOI: 10.3389/fpls.2016.00962] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Accepted: 06/15/2016] [Indexed: 05/29/2023]
Abstract
Members of the PIF quartet (PIFq; PIF1, PIF3, PIF4, and PIF5) collectively contribute to induce growth in Arabidopsis seedlings under short day (SD) conditions, specifically promoting elongation at dawn. Their action involves the direct regulation of growth-related and hormone-associated genes. However, a comprehensive definition of the PIFq-regulated transcriptome under SD is still lacking. We have recently shown that SD and free-running (LL) conditions correspond to "growth" and "no growth" conditions, respectively, correlating with greater abundance of PIF protein in SD. Here, we present a genomic analysis whereby we first define SD-regulated genes at dawn compared to LL in the wild type, followed by identification of those SD-regulated genes whose expression depends on the presence of PIFq. By using this sequential strategy, we have identified 349 PIF/SD-regulated genes, approximately 55% induced and 42% repressed by both SD and PIFq. Comparison with available databases indicates that PIF/SD-induced and PIF/SD-repressed sets are differently phased at dawn and mid-morning, respectively. In addition, we found that whereas rhythmicity of the PIF/SD-induced gene set is lost in LL, most PIF/SD-repressed genes keep their rhythmicity in LL, suggesting differential regulation of both gene sets by the circadian clock. Moreover, we also uncovered distinct overrepresented functions in the induced and repressed gene sets, in accord with previous studies in other examined PIF-regulated processes. Interestingly, promoter analyses showed that, whereas PIF/SD-induced genes are enriched in direct PIF targets, PIF/SD-repressed genes are mostly indirectly regulated by the PIFs and might be more enriched in ABA-regulated genes.
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26
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Molecular basis for differential light responses in Arabidopsis stems and leaves. Proc Natl Acad Sci U S A 2016; 113:5774-6. [PMID: 27179007 DOI: 10.1073/pnas.1605750113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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27
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Phytochrome and retrograde signalling pathways converge to antagonistically regulate a light-induced transcriptional network. Nat Commun 2016; 7:11431. [PMID: 27150909 PMCID: PMC4859062 DOI: 10.1038/ncomms11431] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 03/23/2016] [Indexed: 02/08/2023] Open
Abstract
Plastid-to-nucleus retrograde signals emitted by dysfunctional chloroplasts impact photomorphogenic development, but the molecular link between retrograde- and photosensory-receptor signalling has remained unclear. Here, we show that the phytochrome and retrograde signalling (RS) pathways converge antagonistically to regulate the expression of the nuclear-encoded transcription factor GLK1, a key regulator of a light-induced transcriptional network central to photomorphogenesis. GLK1 gene transcription is directly repressed by PHYTOCHROME-INTERACTING FACTOR (PIF)-class bHLH transcription factors in darkness, but light-activated phytochrome reverses this activity, thereby inducing expression. Conversely, we show that retrograde signals repress this induction by a mechanism independent of PIF mediation. Collectively, our data indicate that light at moderate levels acts through the plant's nuclear-localized sensory-photoreceptor system to induce appropriate photomorphogenic development, but at excessive levels, sensed through the separate plastid-localized RS system, acts to suppress such development, thus providing a mechanism for protection against photo-oxidative damage by minimizing the tissue exposure to deleterious radiation. Retrograde signals from dysfunctional chloroplasts influence plant response to light. Here the authors show that the GUN1 retrograde signalling pathway acts antagonistically to the phytochrome-mediated red light perception pathway to control the expression of GLK1, a key transcriptional regulator of photomorphogenesis.
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28
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Molecular convergence of clock and photosensory pathways through PIF3-TOC1 interaction and co-occupancy of target promoters. Proc Natl Acad Sci U S A 2016; 113:4870-5. [PMID: 27071129 DOI: 10.1073/pnas.1603745113] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A mechanism for integrating light perception and the endogenous circadian clock is central to a plant's capacity to coordinate its growth and development with the prevailing daily light/dark cycles. Under short-day (SD) photocycles, hypocotyl elongation is maximal at dawn, being promoted by the collective activity of a quartet of transcription factors, called PIF1, PIF3, PIF4, and PIF5 (phytochrome-interacting factors). PIF protein abundance in SDs oscillates as a balance between synthesis and photoactivated-phytochrome-imposed degradation, with maximum levels accumulating at the end of the long night. Previous evidence shows that elongation under diurnal conditions (as well as in shade) is also subjected to circadian gating. However, the mechanism underlying these phenomena is incompletely understood. Here we show that the PIFs and the core clock component Timing of CAB expression 1 (TOC1) display coincident cobinding to the promoters of predawn-phased, growth-related genes under SD conditions. TOC1 interacts with the PIFs and represses their transcriptional activation activity, antagonizing PIF-induced growth. Given the dynamics of TOC1 abundance (displaying high postdusk levels that progressively decline during the long night), our data suggest that TOC1 functions to provide a direct output from the core clock that transiently constrains the growth-promoting activity of the accumulating PIFs early postdusk, thereby gating growth to predawn, when conditions for cell elongation are optimal. These findings unveil a previously unrecognized mechanism whereby a core circadian clock output signal converges immediately with the phytochrome photosensory pathway to coregulate directly the activity of the PIF transcription factors positioned at the apex of a transcriptional network that regulates a diversity of downstream morphogenic responses.
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29
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Nozue K, Tat AV, Kumar Devisetty U, Robinson M, Mumbach MR, Ichihashi Y, Lekkala S, Maloof JN. Shade avoidance components and pathways in adult plants revealed by phenotypic profiling. PLoS Genet 2015; 11:e1004953. [PMID: 25874869 PMCID: PMC4398415 DOI: 10.1371/journal.pgen.1004953] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 12/11/2014] [Indexed: 01/01/2023] Open
Abstract
Shade from neighboring plants limits light for photosynthesis; as a consequence, plants have a variety of strategies to avoid canopy shade and compete with their neighbors for light. Collectively the response to foliar shade is called the shade avoidance syndrome (SAS). The SAS includes elongation of a variety of organs, acceleration of flowering time, and additional physiological responses, which are seen throughout the plant life cycle. However, current mechanistic knowledge is mainly limited to shade-induced elongation of seedlings. Here we use phenotypic profiling of seedling, leaf, and flowering time traits to untangle complex SAS networks. We used over-representation analysis (ORA) of shade-responsive genes, combined with previous annotation, to logically select 59 known and candidate novel mutants for phenotyping. Our analysis reveals shared and separate pathways for each shade avoidance response. In particular, auxin pathway components were required for shade avoidance responses in hypocotyl, petiole, and flowering time, whereas jasmonic acid pathway components were only required for petiole and flowering time responses. Our phenotypic profiling allowed discovery of seventeen novel shade avoidance mutants. Our results demonstrate that logical selection of mutants increased success of phenotypic profiling to dissect complex traits and discover novel components.
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Affiliation(s)
- Kazunari Nozue
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - An V. Tat
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Upendra Kumar Devisetty
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Matthew Robinson
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Maxwell R. Mumbach
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Yasunori Ichihashi
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Saradadevi Lekkala
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Julin N. Maloof
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
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30
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Zhang L, Peng Y, Wei X, Dai Y, Yuan D, Lu Y, Pan Y, Zhu Z. Small RNAs as important regulators for the hybrid vigour of super-hybrid rice. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5989-6002. [PMID: 25129133 PMCID: PMC4203131 DOI: 10.1093/jxb/eru337] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Heterosis is an important biological phenomenon; however, the role of small RNA (sRNA) in heterosis of hybrid rice remains poorly described. Here, we performed sRNA profiling of F1 super-hybrid rice LYP9 and its parents using high-throughput sequencing technology, and identified 355 distinct mature microRNAs and trans-acting small interfering RNAs, 69 of which were differentially expressed sRNAs (DES) between the hybrid and the mid-parental value. Among these, 34 DES were predicted to target 176 transcripts, of which 112 encoded 94 transcription factors. Further analysis showed that 67.6% of DES expression levels were negatively correlated with their target mRNAs either in flag leaves or panicles. The target genes of DES were significantly enriched in some important biological processes, including the auxin signalling pathway, in which existed a regulatory network mediated by DES and their targets, closely associated with plant growth and development. Overall, 20.8% of DES and their target genes were significantly enriched in quantitative trait loci of small intervals related to important rice agronomic traits including growth vigour, grain yield, and plant architecture, suggesting that the interaction between sRNAs and their targets contributes to the heterotic phenotypes of hybrid rice. Our findings revealed that sRNAs might play important roles in hybrid vigour of super-hybrid rice by regulating their target genes, especially in controlling the auxin signalling pathway. The above finding provides a novel insight into the molecular mechanism of heterosis.
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Affiliation(s)
- Lei Zhang
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China
| | - Yonggang Peng
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China
| | - Xiaoli Wei
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China
| | - Yan Dai
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China
| | - Dawei Yuan
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China
| | - Yufei Lu
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China
| | - Yangyang Pan
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China
| | - Zhen Zhu
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, PR China
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31
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Pfeiffer A, Shi H, Tepperman JM, Zhang Y, Quail PH. Combinatorial complexity in a transcriptionally centered signaling hub in Arabidopsis. MOLECULAR PLANT 2014; 7:1598-1618. [PMID: 25122696 PMCID: PMC4587546 DOI: 10.1093/mp/ssu087] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/29/2014] [Indexed: 05/18/2023]
Abstract
A subfamily of four Phytochrome (phy)-Interacting bHLH transcription Factors (PIFs) collectively promote skotomorphogenic development in dark-grown seedlings. This activity is reversed upon exposure to light, by photoactivated phy molecules that induce degradation of the PIFs, thereby triggering the transcriptional changes that drive a transition to photomorphogenesis. The PIFs function both redundantly and partially differentially at the morphogenic level in this process. To identify the direct targets of PIF transcriptional regulation genome-wide, we analyzed the DNA-binding sites for all four PIFs by ChIP-seq analysis, and defined the genes transcriptionally regulated by each PIF, using RNA-seq analysis of pif mutants. Despite the absence of detectable differences in DNA-binding-motif recognition between the PIFs, the data show a spectrum of regulatory patterns, ranging from single PIF dominance to equal contributions by all four. Similarly, a broad array of promoter architectures was found, ranging from single PIF-binding sites, containing single sequence motifs, through multiple PIF-binding sites, each containing one or more motifs, with each site occupied preferentially by one to multiple PIFs. Quantitative analysis of the promoter occupancy and expression level induced by each PIF revealed an intriguing pattern. Although there is no robust correlation broadly across the target-gene population, examination of individual genes that are shared targets of multiple PIFs shows a gradation in correlation from strongly positive, through uncorrelated, to negative. This finding suggests a dual-layered mechanism of transcriptional regulation, comprising both a continuum of binding-site occupancy by each PIF and a superimposed layer of local regulation that acts differentially on each PIF, to modulate its intrinsic transcriptional activation capacity at each site, in a quantitative pattern that varies between the individual PIFs from gene to gene. These findings provide a framework for probing the mechanisms by which transcription factors with overlapping direct-target genes integrate and selectively transduce signals to their target networks.
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Affiliation(s)
- Anne Pfeiffer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; United States Department of Agriculture, Plant Gene Expression Center, Albany, CA 94710, USA
| | - Hui Shi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; United States Department of Agriculture, Plant Gene Expression Center, Albany, CA 94710, USA
| | - James M Tepperman
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; United States Department of Agriculture, Plant Gene Expression Center, Albany, CA 94710, USA
| | - Yu Zhang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; United States Department of Agriculture, Plant Gene Expression Center, Albany, CA 94710, USA
| | - Peter H Quail
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; United States Department of Agriculture, Plant Gene Expression Center, Albany, CA 94710, USA.
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32
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Gangappa SN, Botto JF. The BBX family of plant transcription factors. TRENDS IN PLANT SCIENCE 2014; 19:460-70. [PMID: 24582145 DOI: 10.1016/j.tplants.2014.01.010] [Citation(s) in RCA: 285] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 01/13/2014] [Accepted: 01/15/2014] [Indexed: 05/04/2023]
Abstract
The B-box (BBX) proteins are a class of zinc-finger transcription factors containing a B-box domain with one or two B-box motifs, and sometimes also feature a CCT (CONSTANS, CO-like, and TOC1) domain. BBX proteins are key factors in regulatory networks controlling growth and developmental processes that include seedling photomorphogenesis, photoperiodic regulation of flowering, shade avoidance, and responses to biotic and abiotic stresses. In this review we discuss the functions of BBX proteins and the role of B-box motif in mediating transcriptional regulation and protein-protein interaction in plant signaling. In addition, we provide novel insights into the molecular mechanisms of their action and the evolutionary significance of their functional divergence.
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Affiliation(s)
- Sreeramaiah N Gangappa
- Department of Biological and Environmental Sciences, Gothenburg University, Gothenburg 40530, Sweden
| | - Javier F Botto
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires 1417, Argentina.
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33
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Soy J, Leivar P, Monte E. PIF1 promotes phytochrome-regulated growth under photoperiodic conditions in Arabidopsis together with PIF3, PIF4, and PIF5. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2925-36. [PMID: 24420574 PMCID: PMC4056538 DOI: 10.1093/jxb/ert465] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Seedlings growing under diurnal conditions display maximal growth at the end of the night in short-day (SD) photoperiods. Current evidence indicates that this behaviour involves the action of PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) together with PIF4 and PIF5, through direct regulation of growth-related genes at dawn coinciding with a PIF3 accumulation peak generated by phytochrome-imposed oscillations in protein abundance. Here, to assess how alterations in PIF3 levels impact seedling growth, the night-specific accumulation of PIF3 was modulated by releasing SD-grown seedlings into continuous light, or by exposing them to a phytochrome-inactivating end-of-day far-red pulse (EOD-FRp). The data show a strong direct correlation between PIF3 accumulation, PIF3-regulated induction of growth-related genes, and hypocotyl elongation, and suggest that growth promotion in SD conditions involves factors other than PIF3, PIF4, and PIF5. Using a pif1 mutant, evidence is provided that PIF1 also contributes to inducing hypocotyl elongation during the dark period under diurnal conditions. PIF1 displayed constitutive transcript levels in SD conditions, suggesting that phytochrome-imposed oscillations in PIF1 protein abundance determine its accumulation and action during the night, similar to PIF3 and in contrast to PIF4 and PIF5, which oscillate diurnally due to a combination of circadian clock-regulated transcription and light control of protein accumulation. Furthermore, using single and higher order pif mutants, the relative contribution of each member of the PIF quartet to the regulation of morphogenesis and the expression of selected growth marker genes under SD conditions, or under SD conditions supplemented with an EOD-FRp, is defined. Collectively, the data indicate that PIF1, PIF3, PIF4, and PIF5 act together to promote and optimize growth under photoperiodic conditions.
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Affiliation(s)
- Judit Soy
- Departament de Genètica Molecular, Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Univ. Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Pablo Leivar
- Departament de Genètica Molecular, Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Univ. Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Elena Monte
- Departament de Genètica Molecular, Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Univ. Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
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Leivar P, Monte E. PIFs: systems integrators in plant development. THE PLANT CELL 2014; 26:56-78. [PMID: 24481072 PMCID: PMC3963594 DOI: 10.1105/tpc.113.120857] [Citation(s) in RCA: 384] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 01/03/2014] [Accepted: 01/14/2014] [Indexed: 05/17/2023]
Abstract
Phytochrome-interacting factors (PIFs) are members of the Arabidopsis thaliana basic helix-loop-helix family of transcriptional regulators that interact specifically with the active Pfr conformer of phytochrome (phy) photoreceptors. PIFs are central regulators of photomorphogenic development that act to promote stem growth, and this activity is reversed upon interaction with phy in response to light. Recently, significant progress has been made in defining the transcriptional networks directly regulated by PIFs, as well as the convergence of other signaling pathways on the PIFs to modulate growth. Here, we summarize and highlight these findings in the context of PIFs acting as integrators of light and other signals. We discuss progress in our understanding of the transcriptional and posttranslational regulation of PIFs that illustrates the integration of light with hormonal pathways and the circadian clock, and we review seedling hypocotyl growth as a paradigm of PIFs acting at the interface of these signals. Based on these advances, PIFs are emerging as required factors for growth, acting as central components of a regulatory node that integrates multiple internal and external signals to optimize plant development.
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Mazzella MA, Casal JJ, Muschietti JP, Fox AR. Hormonal networks involved in apical hook development in darkness and their response to light. FRONTIERS IN PLANT SCIENCE 2014; 5:52. [PMID: 24616725 PMCID: PMC3935338 DOI: 10.3389/fpls.2014.00052] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 02/04/2014] [Indexed: 05/19/2023]
Abstract
In darkness, the dicot seedlings produce an apical hook as result of differential cell division and extension at opposite sides of the hypocotyl. This hook protects the apical meristem from mechanical damage during seedling emergence from the soil. In darkness, gibberellins act via the DELLA-PIF (PHYTOCHROME INTERACTING FACTORs) pathway, and ethylene acts via the EIN3/EIL1 (ETHYLENE INSENSITIVE 3/EIN3 like 1)-HLS1 (HOOKLESS 1) pathway to control the asymmetric accumulation of auxin required for apical hook formation and maintenance. These core pathways form a network with multiple points of connection. Light perception by phytochromes and cryptochromes reduces the activity of PIFs and (COP1) CONSTITUTIVE PHOTOMORPHOGENIC 1-both required for hook formation in darkness-, lowers the levels of gibberellins, and triggers hook opening as a component of the switch between heterotrophic and photoautotrophic development. Apical hook opening is thus a suitable model to study the convergence of endogenous and exogenous signals on the control of cell division and cell growth.
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Affiliation(s)
- Maria A. Mazzella
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, “Dr. Héctor Torres” (INGEBI-CONICET)Buenos Aires, Argentina
- *Correspondence: Maria A. Mazzella, INGEBI, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, “Dr. Héctor Torres”, 2490 Vuelta de Obligado, Buenos Aires, 1428, Argentina e-mail:
| | - Jorge J. Casal
- Facultad de Agronomía, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Universidad de Buenos Aires and CONICETBuenos Aires, Argentina
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICETBuenos Aires, Argentina
| | - Jorge P. Muschietti
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, “Dr. Héctor Torres” (INGEBI-CONICET)Buenos Aires, Argentina
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos AiresBuenos Aires, Argentina
| | - Ana R. Fox
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, “Dr. Héctor Torres” (INGEBI-CONICET)Buenos Aires, Argentina
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Liu X, Chen CY, Wang KC, Luo M, Tai R, Yuan L, Zhao M, Yang S, Tian G, Cui Y, Hsieh HL, Wu K. PHYTOCHROME INTERACTING FACTOR3 associates with the histone deacetylase HDA15 in repression of chlorophyll biosynthesis and photosynthesis in etiolated Arabidopsis seedlings. THE PLANT CELL 2013; 25:1258-73. [PMID: 23548744 PMCID: PMC3663266 DOI: 10.1105/tpc.113.109710] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 02/22/2013] [Accepted: 03/15/2013] [Indexed: 05/18/2023]
Abstract
PHYTOCHROME INTERACTING FACTOR3 (PIF3) is a key basic helix-loop-helix transcription factor of Arabidopsis thaliana that negatively regulates light responses, repressing chlorophyll biosynthesis, photosynthesis, and photomorphogenesis in the dark. However, the mechanism for the PIF3-mediated transcription regulation remains largely unknown. In this study, we found that the REDUCED POTASSIUM DEPENDENCY3/HISTONE DEACETYLASE1-type histone deacetylase HDA15 directly interacted with PIF3 in vivo and in vitro. Genome-wide transcriptome analysis revealed that HDA15 acts mainly as a transcriptional repressor and negatively regulates chlorophyll biosynthesis and photosynthesis gene expression in etiolated seedlings. HDA15 and PIF3 cotarget to the genes involved in chlorophyll biosynthesis and photosynthesis in the dark and repress gene expression by decreasing the acetylation levels and RNA Polymerase II-associated transcription. The binding of HDA15 to the target genes depends on the presence of PIF3. In addition, PIF3 and HDA15 are dissociated from the target genes upon exposure to red light. Taken together, our results indicate that PIF3 associates with HDA15 to repress chlorophyll biosynthetic and photosynthetic genes in etiolated seedlings.
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Affiliation(s)
- Xuncheng Liu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Chia-Yang Chen
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Ko-Ching Wang
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Ming Luo
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ready Tai
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Lianyu Yuan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Minglei Zhao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Songguang Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Gang Tian
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, Ontario N5V 4T3, Canada
| | - Yuhai Cui
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, Ontario N5V 4T3, Canada
| | - Hsu-Liang Hsieh
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
- Address correspondence to
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A quartet of PIF bHLH factors provides a transcriptionally centered signaling hub that regulates seedling morphogenesis through differential expression-patterning of shared target genes in Arabidopsis. PLoS Genet 2013; 9:e1003244. [PMID: 23382695 PMCID: PMC3561105 DOI: 10.1371/journal.pgen.1003244] [Citation(s) in RCA: 301] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 11/30/2012] [Indexed: 11/19/2022] Open
Abstract
Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting bHLH Factors (PIF1, 3, 4, and 5) are critically necessary to maintaining this developmental state and that light activation of phy induces a switch to photomorphogenic development by inducing rapid degradation of the PIFs. Here, using integrated ChIP–seq and RNA–seq analyses, we have identified genes that are direct targets of PIF3 transcriptional regulation, exerted by sequence-specific binding to G-box (CACGTG) or PBE-box (CACATG) motifs in the target promoters genome-wide. In addition, expression analysis of selected genes in this set, in all triple pif-mutant combinations, provides evidence that the PIF quartet members collaborate to generate an expression pattern that is the product of a mosaic of differential transcriptional responsiveness of individual genes to the different PIFs and of differential regulatory activity of individual PIFs toward the different genes. Together with prior evidence that all four PIFs can bind to G-boxes, the data suggest that this collective activity may be exerted via shared occupancy of binding sites in target promoters. An important issue in understanding mechanisms of eukaryotic transcriptional regulation is how members of large transcription-factor families, with conserved DNA–binding domains (such as the 162-member Arabidopsis bHLH family), discriminate between target genes. However, the specific question of whether, and to what extent, closely related sub-family members, with potential overlapping functional redundancy (like the quartet of Phytochrome (phy)-Interacting bHLH transcription Factors (PIF1, 3, 4, and 5) studied here), share regulation of target genes through shared binding to promoter-localized consensus motifs does not appear to have been widely investigated. Here, using ChIP–seq analysis, we have identified genes that bind PIF3 to conserved, sequence-specific sites in their promoters; and, using RNA–seq, we have identified those genes displaying altered expression in various pif mutants. Integration of these data identifies those genes that are likely direct targets of transcriptional regulation by PIF3. Our data suggest that the PIF quartet members share directly in transcriptional activation of numerous target genes, potentially via redundant promoter occupancy, in a manner that varies quantitatively from gene to gene. This finding suggests that these PIFs function collectively as a signaling hub, selectively partitioning common upstream signals from light-activated phys at the transcriptional-network interface.
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Soy J, Leivar P, González-Schain N, Sentandreu M, Prat S, Quail PH, Monte E. Phytochrome-imposed oscillations in PIF3 protein abundance regulate hypocotyl growth under diurnal light/dark conditions in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 71:390-401. [PMID: 22409654 PMCID: PMC3465574 DOI: 10.1111/j.1365-313x.2012.04992.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Arabidopsis seedlings display rhythmic growth when grown under diurnal conditions, with maximal elongation rates occurring at the end of the night under short-day photoperiods. Current evidence indicates that this behavior involves the action of the growth-promoting bHLH factors PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) and PHYTOCHROME-INTERACTING FACTOR 5 (PIF5) at the end of the night, through a coincidence mechanism that combines their transcriptional regulation by the circadian clock with control of protein accumulation by light. To assess the possible role of PIF3 in this process, we have analyzed hypocotyl responses and marker gene expression in pif single- and higher-order mutants. The data show that PIF3 plays a prominent role as a promoter of seedling growth under diurnal light/dark conditions, in conjunction with PIF4 and PIF5. In addition, we provide evidence that PIF3 functions in this process through its intrinsic transcriptional regulatory activity, at least in part by directly targeting growth-related genes, and independently of its ability to regulate phytochrome B (phyB) levels. Furthermore, in sharp contrast to PIF4 and PIF5, our data show that the PIF3 gene is not subject to transcriptional regulation by the clock, but that PIF3 protein abundance oscillates under diurnal conditions as a result of a progressive decline in PIF3 protein degradation mediated by photoactivated phyB, and consequent accumulation of the bHLH factor during the dark period. Collectively, the data suggest that phyB-mediated, post-translational regulation allows PIF3 accumulation to peak just before dawn, at which time it accelerates hypocotyl growth, together with PIF4 and PIF5, by directly regulating the induction of growth-related genes.
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Affiliation(s)
- Judit Soy
- Departament de Genètica Molecular, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universidad Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Pablo Leivar
- Departament de Genètica Molecular, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universidad Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Nahuel González-Schain
- Departament de Genètica Molecular, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universidad Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Maria Sentandreu
- Departament de Genètica Molecular, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universidad Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Salomé Prat
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología CSIC, Campus Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Peter H. Quail
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- United States Department of Agriculture, Plant Gene Expression Center, Albany, CA 94710, USA
| | - Elena Monte
- Departament de Genètica Molecular, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universidad Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- For correspondence ()
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Sentandreu M, Leivar P, Martín G, Monte E. Branching of the PIF3 regulatory network in Arabidopsis: roles of PIF3-regulated MIDAs in seedling development in the dark and in response to light. PLANT SIGNALING & BEHAVIOR 2012; 7:510-513. [PMID: 22499182 PMCID: PMC3419041 DOI: 10.4161/psb.19339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Plants need to accurately adjust their development after germination in the underground darkness to ensure survival of the seedling, both in the dark and in the light upon reaching the soil surface. Recent studies have established that the photoreceptors phytochromes and the bHLH phytochrome interacting factors PIFs regulate seedling development to adjust it to the prevailing light environment during post-germinative growth. However, complete understanding of the downstream regulatory network implementing these developmental responses is still lacking. In a recent work, published in The Plant Cell, we report a subset of PIF3-regulated genes in dark-grown seedlings that we have named MIDAs (MISREGULATED IN DARK). Analysis of their functional relevance using mutants showed that four of them present phenotypic alterations in the dark, and that each affected a particular facet of seedling development, suggesting organ-specific branching in the signal that PIF3 relays downstream. Furthermore, our results also showed an altered response to light in seedlings with an impaired PIF3/MIDA regulatory network, indicating that these factors might also be essential to initiate and optimize the developmental adjustment of the seedling to the light environment.
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Leivar P, Tepperman JM, Cohn MM, Monte E, Al-Sady B, Erickson E, Quail PH. Dynamic antagonism between phytochromes and PIF family basic helix-loop-helix factors induces selective reciprocal responses to light and shade in a rapidly responsive transcriptional network in Arabidopsis. THE PLANT CELL 2012; 24:1398-419. [PMID: 22517317 PMCID: PMC3398554 DOI: 10.1105/tpc.112.095711] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 02/28/2012] [Accepted: 03/20/2012] [Indexed: 05/20/2023]
Abstract
Plants respond to shade-modulated light signals via phytochrome (phy)-induced adaptive changes, termed shade avoidance. To examine the roles of Phytochrome-Interacting basic helix-loop-helix Factors, PIF1, 3, 4, and 5, in relaying such signals to the transcriptional network, we compared the shade-responsive transcriptome profiles of wild-type and quadruple pif (pifq) mutants. We identify a subset of genes, enriched in transcription factor-encoding loci, that respond rapidly to shade, in a PIF-dependent manner, and contain promoter G-box motifs, known to bind PIFs. These genes are potential direct targets of phy-PIF signaling that regulate the primary downstream transcriptional circuitry. A second subset of PIF-dependent, early response genes, lacking G-box motifs, are enriched for auxin-responsive loci, and are thus potentially indirect targets of phy-PIF signaling, mediating the rapid cell expansion induced by shade. Comparing deetiolation- and shade-responsive transcriptomes identifies another subset of G-box-containing genes that reciprocally display rapid repression and induction in response to light and shade signals. These data define a core set of transcriptional and hormonal processes that appear to be dynamically poised to react rapidly to light-environment changes via perturbations in the mutually antagonistic actions of the phys and PIFs. Comparing the responsiveness of the pifq and triple pif mutants to light and shade confirms that the PIFs act with overlapping redundancy on seedling morphogenesis and transcriptional regulation but that each PIF contributes differentially to these responses.
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Affiliation(s)
- Pablo Leivar
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- U.S. Department of Agriculture, Plant Gene Expression Center, Albany, California 94710
- Department of Molecular Genetics, Center for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas–Institut de Recerca i Tecnologia Agroalimentàries–Universitat Autònoma de Barcelona–Universitat de Barcelona, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - James M. Tepperman
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- U.S. Department of Agriculture, Plant Gene Expression Center, Albany, California 94710
| | - Megan M. Cohn
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- U.S. Department of Agriculture, Plant Gene Expression Center, Albany, California 94710
| | - Elena Monte
- Department of Molecular Genetics, Center for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas–Institut de Recerca i Tecnologia Agroalimentàries–Universitat Autònoma de Barcelona–Universitat de Barcelona, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Bassem Al-Sady
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- U.S. Department of Agriculture, Plant Gene Expression Center, Albany, California 94710
| | - Erika Erickson
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- U.S. Department of Agriculture, Plant Gene Expression Center, Albany, California 94710
| | - Peter H. Quail
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- U.S. Department of Agriculture, Plant Gene Expression Center, Albany, California 94710
- Address correspondence to
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Li J, Terzaghi W, Deng XW. Genomic basis for light control of plant development. Protein Cell 2012; 3:106-16. [PMID: 22426979 PMCID: PMC4875414 DOI: 10.1007/s13238-012-2016-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 02/05/2012] [Indexed: 10/28/2022] Open
Abstract
Light is one of the key environmental signals regulating plant growth and development. Therefore, understanding the mechanisms by which light controls plant development has long been of great interest to plant biologists. Traditional genetic and molecular approaches have successfully identified key regulatory factors in light signaling, but recent genomic studies have revealed massive reprogramming of plant transcriptomes by light, identified binding sites across the entire genome of several pivotal transcription factors in light signaling, and discovered the involvement of epigenetic regulation in light-regulated gene expression. This review summarizes the key genomic work conducted in the last decade which provides new insights into light control of plant development.
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Affiliation(s)
- Jigang Li
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-biotechnology, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871 China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8104 USA
| | - William Terzaghi
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8104 USA
- Department of Biology, Wilkes University, Wilkes-Barre, PA 18766 USA
| | - Xing Wang Deng
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-biotechnology, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871 China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8104 USA
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