1
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Kim YJ, Kim WY, Somers DE. HOS15-mediated turnover of PRR7 enhances freezing tolerance. THE NEW PHYTOLOGIST 2024; 244:798-810. [PMID: 39155726 PMCID: PMC11449641 DOI: 10.1111/nph.20062] [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: 07/03/2024] [Accepted: 07/29/2024] [Indexed: 08/20/2024]
Abstract
Arabidopsis PSEUDORESPONSE REGULATOR7 (PRR7) is a core component of the circadian oscillator which also plays a crucial role in freezing tolerance. PRR7 undergoes proteasome-dependent degradation to discretely phase maximal expression in early evening. While its repressive activity on downstream genes is integral to cold regulation, the mechanism of the conditional regulation of the PRR7 abundance is unknown. We used mutant analysis, protein interaction and ubiquitylation assays to establish that the ubiquitin ligase adaptor, HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 15 (HOS15), controls the protein accumulation pattern of PRR7 through direct protein-protein interactions at low temperatures. Freezing tolerance and electrolyte leakage assays show that PRR7 enhances cold temperature sensitivity, supported by ChIP-qPCR at C-REPEAT BINDING FACTOR1 (CBF1) and COLD-REGULATED 15A (COR15A) promoters where PRR7 levels were higher in hos15 mutants. HOS15 mediates PRR7 turnover through enhanced ubiquitylation at low temperature in the dark. Under the same conditions, increased PRR7 association with the promoters of CBFs and COR15A in hos15 correlates with decreased CBF1 and COR15A transcription and enhanced freezing sensitivity. We propose a novel mechanism whereby HOS15-mediated degradation of PRR7 provides an intersection between the circadian system and other cold acclimation pathways that lead to increased freezing tolerance.
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Affiliation(s)
- Yeon Jeong Kim
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21 Four), Plant Biological Rhythm Research Center (PBRRC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, 52828, Korea
| | - David E Somers
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
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2
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Kim YJ, Kim WY, Somers DE. HOS15-mediated turnover of PRR7 enhances freezing tolerance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599783. [PMID: 38979283 PMCID: PMC11230174 DOI: 10.1101/2024.06.20.599783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Arabidopsis PSEUDO RESPONSE REGULATOR7 (PRR7) is a core component of the circadian oscillator which also plays a crucial role in freezing tolerance. PRR7 undergoes proteasome-dependent degradation to discretely phase maximal expression in early evening. While its transcriptional repressive activity on downstream genes is integral to cold regulation, the mechanism of the conditional regulation of the PRR7 protein activity is unknown. We used double mutant analysis, protein interaction and ubiquitylation assays to establish that the ubiquitin ligase adaptor, HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 15 (HOS15), controls the protein accumulation pattern of PRR7 through direct protein-protein interactions. Freezing tolerance and electrolyte leakage assays show that PRR7 enhances cold temperature sensitivity, supported by ChIP-qPCR at C-REPEAT BINDING FACTOR (CBF) and COLD REGULATED 15A (COR15A) promoters where PRR7 levels were higher in hos15 mutants. We establish that HOS15 mediates PRR7 protein turnover through enhanced ubiquitylation at low temperature in the dark. Under the same conditions, increased PRR7 association with the promoter regions of CBFs and COR15A in hos15 correlates with decreased CBF1 and COR15A transcription and enhanced freezing sensitivity. We propose a novel mechanism whereby HOS15-mediated regulation of PRR7 provides an intersection between the circadian system and other cold acclimation pathways leading to freezing tolerance through upregulation of CBF1 and COR15A.
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Affiliation(s)
- Yeon Jeong Kim
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Woe Yeon Kim
- Division of Applied Life Science (BK21 Four), Plant Biological Rhythm Research Center (PBRRC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - David E Somers
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
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3
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Hughes CL, An Y, Maloof JN, Harmer SL. Light quality-dependent roles of REVEILLE proteins in the circadian system. PLANT DIRECT 2024; 8:e573. [PMID: 38481435 PMCID: PMC10936234 DOI: 10.1002/pld3.573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/25/2024] [Accepted: 02/10/2024] [Indexed: 03/17/2024]
Abstract
Several closely related Myb-like activator proteins are known to have partially redundant functions within the plant circadian clock, but their specific roles are not well understood. To clarify the function of the REVEILLE 4, REVEILLE 6, and REVEILLE 8 transcriptional activators, we characterized the growth and clock phenotypes of CRISPR-Cas9-generated single, double, and triple rve mutants. We found that these genes act synergistically to regulate flowering time, redundantly to regulate leaf growth, and antagonistically to regulate hypocotyl elongation. We previously reported that increasing intensities of monochromatic blue and red light have opposite effects on the period of triple rve468 mutants. Here, we further examined light quality-specific phenotypes of rve mutants and report that rve468 mutants lack the blue light-specific increase in expression of some circadian clock genes observed in wild type. To investigate the basis of these blue light-specific circadian phenotypes, we examined RVE protein abundances and degradation rates in blue and red light and found no significant differences between these conditions. We next examined genetic interactions between RVE genes and ZEITLUPE and ELONGATED HYPOCOTYL5, two factors with blue light-specific functions in the clock. We found that the RVEs interact additively with both ZEITLUPE and ELONGATED HYPOCOTYL5 to regulate circadian period, which suggests that neither of these factors are required for the blue light-specific differences that we observed. Overall, our results suggest that the RVEs have separable functions in plant growth and circadian regulation and that they are involved in blue light-specific circadian signaling via a novel mechanism.
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Affiliation(s)
- Cassandra L. Hughes
- Department of Plant BiologyUniversity of California, DavisDavisCaliforniaUSA
| | - Yuyan An
- College of Life SciencesShaanxi Normal UniversityXi'anChina
| | - Julin N. Maloof
- Department of Plant BiologyUniversity of California, DavisDavisCaliforniaUSA
| | - Stacey L. Harmer
- Department of Plant BiologyUniversity of California, DavisDavisCaliforniaUSA
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4
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Zhang H, Zhou Z, Guo J. The Function, Regulation, and Mechanism of Protein Turnover in Circadian Systems in Neurospora and Other Species. Int J Mol Sci 2024; 25:2574. [PMID: 38473819 DOI: 10.3390/ijms25052574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/18/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Circadian clocks drive a large array of physiological and behavioral activities. At the molecular level, circadian clocks are composed of positive and negative elements that form core oscillators generating the basic circadian rhythms. Over the course of the circadian period, circadian negative proteins undergo progressive hyperphosphorylation and eventually degrade, and their stability is finely controlled by complex post-translational pathways, including protein modifications, genetic codon preference, protein-protein interactions, chaperon-dependent conformation maintenance, degradation, etc. The effects of phosphorylation on the stability of circadian clock proteins are crucial for precisely determining protein function and turnover, and it has been proposed that the phosphorylation of core circadian clock proteins is tightly correlated with the circadian period. Nonetheless, recent studies have challenged this view. In this review, we summarize the research progress regarding the function, regulation, and mechanism of protein stability in the circadian clock systems of multiple model organisms, with an emphasis on Neurospora crassa, in which circadian mechanisms have been extensively investigated. Elucidation of the highly complex and dynamic regulation of protein stability in circadian clock networks would greatly benefit the integrated understanding of the function, regulation, and mechanism of protein stability in a wide spectrum of other biological processes.
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Affiliation(s)
- Haoran Zhang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zengxuan Zhou
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jinhu Guo
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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5
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Uehara TN, Takao S, Matsuo H, Saito AN, Ota E, Ono A, Itami K, Kinoshita T, Yamashino T, Yamaguchi J, Nakamichi N. A Small-Molecule Modulator Affecting the Clock-Associated PSEUDO-RESPONSE REGULATOR 7 Amount. PLANT & CELL PHYSIOLOGY 2023; 64:1397-1406. [PMID: 37705303 DOI: 10.1093/pcp/pcad107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 09/01/2023] [Accepted: 09/09/2023] [Indexed: 09/15/2023]
Abstract
Circadian clocks are biological timekeeping systems that coordinate genetic, metabolic and physiological behaviors with the external day-night cycle. The clock in plants relies on the transcriptional-translational feedback loops transcription-translation feedback loop (TTFL), consisting of transcription factors including PSUEDO-RESPONSE REGULATOR (PRR) proteins, plant lineage-specific transcriptional repressors. Here, we report that a novel synthetic small-molecule modulator, 5-(3,4-dichlorophenyl)-1-phenyl-1,7-dihydro-4H-pyrazolo[3,4-d] pyrimidine-4,6(5H)-dione (TU-892), affects the PRR7 protein amount. A clock reporter line of Arabidopsis was screened against the 10,000 small molecules in the Maybridge Hitfinder 10K chemical library. This screening identified TU-892 as a period-lengthening molecule. Gene expression analyses showed that TU-892 treatment upregulates CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) mRNA expression. TU-892 treatment reduced the amount of PRR7 protein, a transcriptional repressor of CCA1. Other PRR proteins including TIMING OF CAB EXPRESSION 1 were altered less by TU-892 treatment. TU-892-dependent CCA1 upregulation was attenuated in mutants impaired in PRR7. Collectively, TU-892 is a novel type of clock modulator that reduces the levels of PRR7 protein.
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Affiliation(s)
- Takahiro N Uehara
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
| | - Saori Takao
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
| | - Hiromi Matsuo
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Ami N Saito
- Department of Applied Chemistry, Waseda University, 513 Wasedatsurumakicho, Shinjuku, Tokyo, 162-0041 Japan
| | - Eisuke Ota
- Department of Applied Chemistry, Waseda University, 513 Wasedatsurumakicho, Shinjuku, Tokyo, 162-0041 Japan
| | - Azusa Ono
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
| | - Kenichiro Itami
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
| | - Toshinori Kinoshita
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
| | - Takafumi Yamashino
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Junichiro Yamaguchi
- Department of Applied Chemistry, Waseda University, 513 Wasedatsurumakicho, Shinjuku, Tokyo, 162-0041 Japan
| | - Norihito Nakamichi
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
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6
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Wang X, Zhang J, Liu X, Kong Y, Han L. The Roles of the PSEUDO-RESPONSE REGULATORs in Circadian Clock and Flowering Time in Medicago truncatula. Int J Mol Sci 2023; 24:16834. [PMID: 38069157 PMCID: PMC10706769 DOI: 10.3390/ijms242316834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/22/2023] [Accepted: 11/25/2023] [Indexed: 12/18/2023] Open
Abstract
PSEUDO-RESPONSE REGULATORs (PRRs) play key roles in the circadian rhythms and flowering in plants. Here, we identified the four members of the PRR family in Medicago truncatula, including MtPRR9a, MtPRR9b, MtPRR7 and MtPRR5, and isolated their Tnt1 retrotransposon-tagged mutants. They were expressed in different organs and were nuclear-localized. The four MtPRRs genes played important roles in normal clock rhythmicity maintenance by negatively regulating the expression of MtGI and MtLHY. Surprisingly, the four MtPRRs functioned redundantly in regulating flowering time under long-day conditions, and the quadruple mutant flowered earlier. Moreover, MtPRR can recruit the MtTPL/MtTPR corepressors and the other MtPRRs to form heterodimers to constitute the core mechanism of the circadian oscillator.
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Affiliation(s)
- Xiao Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (X.W.); (J.Z.); (X.L.); (Y.K.)
| | - Juanjuan Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (X.W.); (J.Z.); (X.L.); (Y.K.)
| | - Xiu Liu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (X.W.); (J.Z.); (X.L.); (Y.K.)
| | - Yiming Kong
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (X.W.); (J.Z.); (X.L.); (Y.K.)
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Lu Han
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (X.W.); (J.Z.); (X.L.); (Y.K.)
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7
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Huang T, Liu H, Tao JP, Zhang JQ, Zhao TM, Hou XL, Xiong AS, You X. Low light intensity elongates period and defers peak time of photosynthesis: a computational approach to circadian-clock-controlled photosynthesis in tomato. HORTICULTURE RESEARCH 2023; 10:uhad077. [PMID: 37323229 PMCID: PMC10261901 DOI: 10.1093/hr/uhad077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 04/09/2023] [Indexed: 06/17/2023]
Abstract
Photosynthesis is involved in the essential process of transforming light energy into chemical energy. Although the interaction between photosynthesis and the circadian clock has been confirmed, the mechanism of how light intensity affects photosynthesis through the circadian clock remains unclear. Here, we propose a first computational model for circadian-clock-controlled photosynthesis, which consists of the light-sensitive protein P, the core oscillator, photosynthetic genes, and parameters involved in the process of photosynthesis. The model parameters were determined by minimizing the cost function ( [Formula: see text]), which is defined by the errors of expression levels, periods, and phases of the clock genes (CCA1, PRR9, TOC1, ELF4, GI, and RVE8). The model recapitulates the expression pattern of the core oscillator under moderate light intensity (100 μmol m -2 s-1). Further simulation validated the dynamic behaviors of the circadian clock and photosynthetic outputs under low (62.5 μmol m-2 s-1) and normal (187.5 μmol m-2 s-1) intensities. When exposed to low light intensity, the peak times of clock and photosynthetic genes were shifted backward by 1-2 hours, the period was elongated by approximately the same length, and the photosynthetic parameters attained low values and showed delayed peak times, which confirmed our model predictions. Our study reveals a potential mechanism underlying the circadian regulation of photosynthesis by the clock under different light intensities in tomato.
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Affiliation(s)
- Ting Huang
- College of Horticulture, Nanjing Agricultural University/State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Horticultural Crop Biology and Germplasm Creation in East China of Ministry of Agriculture and Rural Affairs Nanjing 210095, Jiangsu, China
| | - Hui Liu
- College of Horticulture, Nanjing Agricultural University/State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Horticultural Crop Biology and Germplasm Creation in East China of Ministry of Agriculture and Rural Affairs Nanjing 210095, Jiangsu, China
| | - Jian-Ping Tao
- College of Horticulture, Nanjing Agricultural University/State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Horticultural Crop Biology and Germplasm Creation in East China of Ministry of Agriculture and Rural Affairs Nanjing 210095, Jiangsu, China
- The Institute of Agricultural Information, Jiangsu Province Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
| | - Jia-Qi Zhang
- College of Horticulture, Nanjing Agricultural University/State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Horticultural Crop Biology and Germplasm Creation in East China of Ministry of Agriculture and Rural Affairs Nanjing 210095, Jiangsu, China
| | - Tong-Min Zhao
- Laboratory for Genetic Improvement of High Efficiency Horticultural Crops in Jiangsu Province, Institute of Vegetable Crop, Jiangsu Province Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
| | - Xi-Lin Hou
- College of Horticulture, Nanjing Agricultural University/State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Horticultural Crop Biology and Germplasm Creation in East China of Ministry of Agriculture and Rural Affairs Nanjing 210095, Jiangsu, China
| | - Ai-Sheng Xiong
- College of Horticulture, Nanjing Agricultural University/State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Horticultural Crop Biology and Germplasm Creation in East China of Ministry of Agriculture and Rural Affairs Nanjing 210095, Jiangsu, China
| | - Xiong You
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu China
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8
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Seo D, Park J, Park J, Hwang G, Seo PJ, Oh E. ZTL regulates thermomorphogenesis through TOC1 and PRR5. PLANT, CELL & ENVIRONMENT 2023; 46:1442-1452. [PMID: 36655421 DOI: 10.1111/pce.14542] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/17/2023] [Indexed: 06/17/2023]
Abstract
Plants adapt to high temperature stresses through thermomorphogenesis, a process that includes stem elongation and hyponastic leaf growth. Thermomorphogenesis is gated by the circadian clock through two evening-expressed clock components, TIMING OF CAB EXPRESSION1 (TOC1) and PSEUDO-RESPONSE REGULATORS5 (PRR5). These proteins directly interact with and inhibit PHYTOCHROME INTERACTING FACTOR4 (PIF4), a basic helix-loop-helix transcription factor that promotes thermoresponsive growth. PIF4-mediated thermoresponsive growth is positively regulated by ZEITLUPE (ZTL), a central clock component, but the molecular mechanisms underlying this are poorly understood. Here, we show that ZTL regulates thermoresponsive growth through TOC1 and PRR5. Genetic analyses reveal that ZTL regulates PIF4 activity as well as PIF4 expression. In Arabidopsis thaliana, ztl mutants exhibit highly accumulated TOC1 and PRR5 and unresponsive expression of PIF4 target genes under exposure to high temperatures. Mutations in TOC1 and PRR5 restore thermoactivation of PIF4 target genes and thermoresponsive growth in ztl mutants. We also show that the molecular chaperone heat-shock protein 90 promotes thermoresponsive growth through the ZTL-TOC1/PRR5 signaling module. Further, we show that ZTL protein stability is increased at high temperatures. Taken together, our results demonstrate that ZTL-mediated degradation of TOC1 and PRR5 enhances the sensitivity of hypocotyl growth to high temperatures.
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Affiliation(s)
- Dain Seo
- Department of Life Sciences, Korea University, Seoul, Korea
| | | | - Jeeyoon Park
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Geonhee Hwang
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Eunkyoo Oh
- Department of Life Sciences, Korea University, Seoul, Korea
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9
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Qiang Y, He X, Li Z, Li S, Zhang J, Liu T, Tursunniyaz M, Wang X, Liu Z, Fang L. Genome-wide identification and expression analysis of the response regulator gene family in alfalfa ( Medicago sativa L.) reveals their multifarious roles in stress response. FRONTIERS IN PLANT SCIENCE 2023; 14:1149880. [PMID: 36998691 PMCID: PMC10043395 DOI: 10.3389/fpls.2023.1149880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/23/2023] [Indexed: 06/19/2023]
Abstract
As important components of the two-component regulatory system, response regulatory proteins (RRPs) play a crucial role in histidine phosphorylation-mediated signal transduction in response to environmental fluctuations. Accumulating evidence has revealed that RRPs play important roles in plant growth and stress response. However, the specific functions of RR genes (RRs) in cultivated alfalfa remain ambiguous. Therefore, in this study, we identified and characterized the RR family genes in the alfalfa genome using bioinformatics methods. Our analysis revealed 37 RRs in the alfalfa genome of Zhongmu No.1 that were unevenly distributed on the chromosomes. Cis-elements analysis revealed the involvement of RRs in responses to light, stress, and various plant hormones. Expression analysis of RRs in different tissues revealed their distinct tissue expression patterns. These findings provide preliminary insights into the roles of RRs in plant responses to abiotic stress, which can be used to improve the stress tolerance of autotetraploid-cultivated alfalfa plants via genetic engineering.
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Affiliation(s)
- Yuqin Qiang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaojuan He
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhen Li
- National Engineering Laboratory for Volatile Organic Compounds Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Siqi Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jia Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Tao Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Mamateliy Tursunniyaz
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xinyu Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhipeng Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Longfa Fang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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10
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Chuong NN, Doan PPT, Wang L, Kim JH, Kim J. Current Insights into m 6A RNA Methylation and Its Emerging Role in Plant Circadian Clock. PLANTS (BASEL, SWITZERLAND) 2023; 12:624. [PMID: 36771711 PMCID: PMC9920239 DOI: 10.3390/plants12030624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
N6-adenosine methylation (m6A) is a prevalent form of RNA modification found in the expressed transcripts of many eukaryotic organisms. Moreover, m6A methylation is a dynamic and reversible process that requires the functioning of various proteins and their complexes that are evolutionarily conserved between species and include methylases, demethylases, and m6A-binding proteins. Over the past decade, the m6A methylation process in plants has been extensively studied and the understanding thereof has drastically increased, although the regulatory function of some components relies on information derived from animal systems. Notably, m6A has been found to be involved in a variety of factors in RNA processing, such as RNA stability, alternative polyadenylation, and miRNA regulation. The circadian clock in plants is a molecular timekeeping system that regulates the daily and rhythmic activity of many cellular and physiological processes in response to environmental changes such as the day-night cycle. The circadian clock regulates the rhythmic expression of genes through post-transcriptional regulation of mRNA. Recently, m6A methylation has emerged as an additional layer of post-transcriptional regulation that is necessary for the proper functioning of the plant circadian clock. In this review, we have compiled and summarized recent insights into the molecular mechanisms behind m6A modification and its various roles in the regulation of RNA. We discuss the potential role of m6A modification in regulating the plant circadian clock and outline potential future directions for the study of mRNA methylation in plants. A deeper understanding of the mechanism of m6A RNA regulation and its role in plant circadian clocks will contribute to a greater understanding of the plant circadian clock.
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Affiliation(s)
- Nguyen Nguyen Chuong
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju 690756, Republic of Korea
| | - Phan Phuong Thao Doan
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju 690756, Republic of Korea
| | - Lanshuo Wang
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju 690756, Republic of Korea
| | - Jin Hee Kim
- Subtropical Horticulture Research Institute, Jeju National University, Jeju 690756, Republic of Korea
| | - Jeongsik Kim
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju 690756, Republic of Korea
- Subtropical Horticulture Research Institute, Jeju National University, Jeju 690756, Republic of Korea
- Faculty of Science Education, Jeju National University, Jeju 690756, Republic of Korea
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11
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Xu X. Editorial: Plant circadian rhythms. FRONTIERS IN PLANT SCIENCE 2022; 13:1109900. [PMID: 36582648 PMCID: PMC9793078 DOI: 10.3389/fpls.2022.1109900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Affiliation(s)
- Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
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12
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He Y, Yu Y, Wang X, Qin Y, Su C, Wang L. Aschoff's rule on circadian rhythms orchestrated by blue light sensor CRY2 and clock component PRR9. Nat Commun 2022; 13:5869. [PMID: 36198686 PMCID: PMC9535003 DOI: 10.1038/s41467-022-33568-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 09/22/2022] [Indexed: 11/09/2022] Open
Abstract
Circadian pace is modulated by light intensity, known as the Aschoff’s rule, with largely unrevealed mechanisms. Here we report that photoreceptor CRY2 mediates blue light input to the circadian clock by directly interacting with clock core component PRR9 in blue light dependent manner. This physical interaction dually blocks the accessibility of PRR9 protein to its co-repressor TPL/TPRs and the resulting kinase PPKs. Notably, phosphorylation of PRR9 by PPKs is critical for its DNA binding and repressive activity, hence to ensure proper circadian speed. Given the labile nature of CRY2 in strong blue light, our findings provide a mechanistic explanation for Aschoff’s rule in plants, i.e., blue light triggers CRY2 turnover in proportional to its intensity, which accordingly releasing PRR9 to fine tune circadian speed. Our findings not only reveal a network mediating light input into the circadian clock, but also unmask a mechanism by which the Arabidopsis circadian clock senses light intensity. Circadian pace is modulated by light intensity. Here the authors show that CRY2 interacts with PRR9 to mediate blue light input to the circadian clock and is degraded at higher light intensity offering a mechanistic explanation as to how intensity can modify clock place.
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Affiliation(s)
- Yuqing He
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingjun Yu
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiling Wang
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yumei Qin
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chen Su
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Wang
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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13
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Yu Y, Portolés S, Ren Y, Sun G, Wang XF, Zhang H, Guo S. The key clock component ZEITLUPE (ZTL) negatively regulates ABA signaling by degradation of CHLH in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:995907. [PMID: 36176682 PMCID: PMC9513469 DOI: 10.3389/fpls.2022.995907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
Ubiquitination-mediated protein degradation plays important roles in ABA signal transduction and delivering responses to chloroplast stress signals in plants, but additional E3 ligases of protein ubiquitination remain to be identified to understand the complex signaling network. Here we reported that ZEITLUPE (ZTL), an F-box protein, negatively regulates abscisic acid (ABA) signaling during ABA-inhibited early seedling growth and ABA-induced stomatal closure in Arabidopsis thaliana. Using molecular biology and biochemistry approaches, we demonstrated that ZTL interacts with and ubiquitinates its substrate, CHLH/ABAR (Mg-chelatase H subunit/putative ABA receptor), to modulate CHLH stability via the 26S proteasome pathway. CHLH acts genetically downstream of ZTL in ABA and drought stress signaling. Interestingly, ABA conversely induces ZTL phosphorylation, and high levels of ABA also induce CHLH proteasomal degradation, implying that phosphorylated ZTL protein may enhance the affinity to CHLH, leading to the increased degradation of CHLH after ABA treatment. Taken together, our results revealed a possible mechanism of reciprocal regulation between ABA signaling and the circadian clock, which is thought to be essential for plant fitness and survival.
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Affiliation(s)
- Yongtao Yu
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Sergi Portolés
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yi Ren
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Guangyu Sun
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Xiao-Fang Wang
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Huihui Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Shaogui Guo
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
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14
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Cha JY, Kim J, Jeong SY, Shin GI, Ji MG, Hwang JW, Khaleda L, Liao X, Ahn G, Park HJ, Kim DY, Pardo JM, Lee SY, Yun DJ, Somers DE, Kim WY. The Na +/H + antiporter SALT OVERLY SENSITIVE 1 regulates salt compensation of circadian rhythms by stabilizing GIGANTEA in Arabidopsis. Proc Natl Acad Sci U S A 2022; 119:e2207275119. [PMID: 35939685 PMCID: PMC9388102 DOI: 10.1073/pnas.2207275119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/14/2022] [Indexed: 12/27/2022] Open
Abstract
The circadian clock is a timekeeping, homeostatic system that temporally coordinates all major cellular processes. The function of the circadian clock is compensated in the face of variable environmental conditions ranging from normal to stress-inducing conditions. Salinity is a critical environmental factor affecting plant growth, and plants have evolved the SALT OVERLY SENSITIVE (SOS) pathway to acquire halotolerance. However, the regulatory systems for clock compensation under salinity are unclear. Here, we show that the plasma membrane Na+/H+ antiporter SOS1 specifically functions as a salt-specific circadian clock regulator via GIGANTEA (GI) in Arabidopsis thaliana. SOS1 directly interacts with GI in a salt-dependent manner and stabilizes this protein to sustain a proper clock period under salinity conditions. SOS1 function in circadian clock regulation requires the salt-mediated secondary messengers cytosolic free calcium and reactive oxygen species, pointing to a distinct regulatory role for SOS1 in addition to its function as a transporter to maintain Na+ homeostasis. Our results demonstrate that SOS1 maintains homeostasis of the salt response under high or daily fluctuating salt levels. These findings highlight the genetic capacity of the circadian clock to maintain timekeeping activity over a broad range of salinity levels.
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Affiliation(s)
- Joon-Yung Cha
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
- Research Institute of Life Science, Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jeongsik Kim
- Faculty of Science Education and Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju 63243, Republic of Korea
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210
| | - Song Yi Jeong
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Gyeong-Im Shin
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Myung Geun Ji
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
- Research Institute of Life Science, Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Ji-Won Hwang
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Laila Khaleda
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Xueji Liao
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Gyeongik Ahn
- Research Institute of Life Science, Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Hee-Jin Park
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Dong Young Kim
- College of Pharmacy, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Jose M. Pardo
- Institute of Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Cientificas and Universidad de Sevilla, Seville 41092, Spain
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - David E. Somers
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
- Research Institute of Life Science, Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
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15
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Nakamichi N, Yamaguchi J, Sato A, Fujimoto KJ, Ota E. Chemical biology to dissect molecular mechanisms underlying plant circadian clocks. THE NEW PHYTOLOGIST 2022; 235:1336-1343. [PMID: 35661165 DOI: 10.1111/nph.18298] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Circadian clocks regulate the diel rhythmic physiological activities of plants, enabling them to anticipate and adapt to day-night and seasonal changes. Genetic and biochemical approaches have suggested that transcription-translation feedback loops (TTFL) are crucial for Arabidopsis clock function. Recently, the study of chemical chronobiology has emerged as a discipline within the circadian clock field, with important and complementary discoveries from both plant and animal research. In this review, we introduce recent advances in chemical biology using small molecules to perturb plant circadian clock function through TTFL components. Studies using small molecule clock modulators have been instrumental for revealing the role of post-translational modification in the clock, or the metabolite-dependent clock input pathway, as well as for controlling clock-dependent flowering time.
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Affiliation(s)
- Norihito Nakamichi
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Junichiro Yamaguchi
- Department of Applied Chemistry, Waseda University, 513 Wasedatsurumakicho, Shinjuku, Tokyo, 169-8555, Japan
| | - Ayato Sato
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Kazuhiro J Fujimoto
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Chikusa, Nagoya, 464-8602, Japan
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Eisuke Ota
- Department of Applied Chemistry, Waseda University, 513 Wasedatsurumakicho, Shinjuku, Tokyo, 169-8555, Japan
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16
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Nidhi, Kumar P, Pathania D, Thakur S, Sharma M. Environment-mediated mutagenetic interference on genetic stabilization and circadian rhythm in plants. Cell Mol Life Sci 2022; 79:358. [PMID: 35687153 PMCID: PMC11072124 DOI: 10.1007/s00018-022-04368-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/21/2022] [Accepted: 05/07/2022] [Indexed: 12/29/2022]
Abstract
Many mortal organisms on this planet have developed the potential to merge all internal as well as external environmental cues to regulate various processes running inside organisms and in turn make them adaptive to the environment through the circadian clock. This moving rotator controls processes like activation of hormonal, metabolic, or defense pathways, initiation of flowering at an accurate period, and developmental processes in plants to ensure their stability in the environment. All these processes that are under the control of this rotating wheel can be changed either by external environmental factors or by an unpredictable phenomenon called mutation that can be generated by either physical mutagens, chemical mutagens, or by internal genetic interruption during metabolic processes, which alters normal functionality of organisms like innate immune responses, entrainment of the clock, biomass reduction, chlorophyll formation, and hormonal signaling, despite its fewer positive roles in plants like changing plant type, loss of vernalization treatment to make them survivable in different latitudes, and defense responses during stress. In addition, with mutation, overexpression of gene components sometimes supresses mutation effect and promote normal circadian genes abundance in the cell, while sometimes it affects circadian functionality by generating arrhythmicity and shows that not only mutation but overexpression also effects normal functional activities of plant. Therefore, this review mainly summarizes the role of each circadian clock genes in regulating rhythmicity, and shows that how circadian outputs are controlled by mutations as well as overexpression phenomenon.
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Affiliation(s)
- Nidhi
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, 173212, India
| | - Pradeep Kumar
- Central University of Himachal Pradesh, Dharmshala, India
| | - Diksha Pathania
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, 173212, India
| | - Sourbh Thakur
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, Gliwice, Poland
| | - Mamta Sharma
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, 173212, India.
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17
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Genome-Wide Identification and Characterization of PRR Gene Family and their Diurnal Rhythmic Expression Profile in Maize. Int J Genomics 2022; 2022:6941607. [PMID: 35615408 PMCID: PMC9126661 DOI: 10.1155/2022/6941607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/25/2022] [Indexed: 11/17/2022] Open
Abstract
As essential components of the circadian clock, the pseudo-response regulator (PRR) gene family plays critical roles in plant photoperiod pathway. In this study, we performed a genome-wide identification and a systematic analysis of the PRR gene family in maize. Nine ZmPRRs were identified, and the gene structure, conserved motif, evolution relationship, and expression pattern of ZmPRRs were analyzed comprehensively. Phylogenetic analysis indicated that the nine ZmPRR genes were divided into three groups, except for ZmPRR73, two of which were highly homologous to each of the AtPRR or OsPRR quintet members. Promoter cis-element analysis of ZmPRRs demonstrated that they might be involved in multiple signaling transduction pathways, such as light response, biological or abiotic stress response, and hormone response. qRT-PCR analysis revealed that the levels of ZmPRRs transcripts varied considerably and exhibited a diurnal rhythmic oscillation expression pattern in the given 24-h period under both SD and LD conditions, which indicated that the level of transcription of ZmPRRs expression is subjected to a circadian rhythm and modulated by light and the circadian clock. The present study will provide an insight into further exploring the biological function and regulatory mechanism of ZmPRR genes in circadian rhythm and response to photoperiod in maize.
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18
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Xu X, Yuan L, Yang X, Zhang X, Wang L, Xie Q. Circadian clock in plants: Linking timing to fitness. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:792-811. [PMID: 35088570 DOI: 10.1111/jipb.13230] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/25/2022] [Indexed: 05/12/2023]
Abstract
Endogenous circadian clock integrates cyclic signals of environment and daily and seasonal behaviors of organisms to achieve spatiotemporal synchronization, which greatly improves genetic diversity and fitness of species. This review addresses recent studies on the plant circadian system in the field of chronobiology, covering topics on molecular mechanisms, internal and external Zeitgebers, and hierarchical regulation of physiological outputs. The architecture of the circadian clock involves the autoregulatory transcriptional feedback loops, post-translational modifications of core oscillators, and epigenetic modifications of DNA and histones. Here, light, temperature, humidity, and internal elemental nutrients are summarized to illustrate the sensitivity of the circadian clock to timing cues. In addition, the circadian clock runs cell-autonomously, driving independent circadian rhythms in various tissues. The core oscillators responds to each other with biochemical factors including calcium ions, mineral nutrients, photosynthetic products, and hormones. We describe clock components sequentially expressed during a 24-h day that regulate rhythmic growth, aging, immune response, and resistance to biotic and abiotic stresses. Notably, more data have suggested the circadian clock links chrono-culture to key agronomic traits in crops.
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Affiliation(s)
- Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Li Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xin Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xiao Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
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19
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Xu X, Yuan L, Xie Q. The circadian clock ticks in plant stress responses. STRESS BIOLOGY 2022; 2:15. [PMID: 37676516 PMCID: PMC10441891 DOI: 10.1007/s44154-022-00040-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/15/2022] [Indexed: 09/08/2023]
Abstract
The circadian clock, a time-keeping mechanism, drives nearly 24-h self-sustaining rhythms at the physiological, cellular, and molecular levels, keeping them synchronized with the cyclic changes of environmental signals. The plant clock is sensitive to external and internal stress signals that act as timing cues to influence the circadian rhythms through input pathways of the circadian clock system. In order to cope with environmental stresses, many core oscillators are involved in defense while maintaining daily growth in various ways. Recent studies have shown that a hierarchical multi-oscillator network orchestrates the defense through rhythmic accumulation of gene transcripts, alternative splicing of mRNA precursors, modification and turnover of proteins, subcellular localization, stimuli-induced phase separation, and long-distance transport of proteins. This review summarizes the essential role of circadian core oscillators in response to stresses in Arabidopsis thaliana and crops, including daily and seasonal abiotic stresses (low or high temperature, drought, high salinity, and nutrition deficiency) and biotic stresses (pathogens and herbivorous insects). By integrating time-keeping mechanisms, circadian rhythms and stress resistance, we provide a temporal perspective for scientists to better understand plant environmental adaptation and breed high-quality crop germplasm for agricultural production.
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Affiliation(s)
- Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
| | - Li Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
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20
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Greenwood M, Tokuda IT, Locke JCW. A spatial model of the plant circadian clock reveals design principles for coordinated timing. Mol Syst Biol 2022; 18:e10140. [PMID: 35312157 PMCID: PMC8935279 DOI: 10.15252/msb.202010140] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 11/28/2022] Open
Abstract
Individual plant cells possess a genetic network, the circadian clock, that times internal processes to the day-night cycle. Mathematical models of the clock are typically either "whole-plant" that ignore tissue or cell type-specific clock behavior, or "phase-only" that do not include molecular components. To address the complex spatial coordination observed in experiments, here we implemented a clock network model on a template of a seedling. In our model, the sensitivity to light varies across the plant, and cells communicate their timing via local or long-distance sharing of clock components, causing their rhythms to couple. We found that both varied light sensitivity and long-distance coupling could generate period differences between organs, while local coupling was required to generate the spatial waves of clock gene expression observed experimentally. We then examined our model under noisy light-dark cycles and found that local coupling minimized timing errors caused by the noise while allowing each plant region to maintain a different clock phase. Thus, local sensitivity to environmental inputs combined with local coupling enables flexible yet robust circadian timing.
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Affiliation(s)
- Mark Greenwood
- Sainsbury LaboratoryUniversity of CambridgeCambridgeUK
- Department of BiochemistryUniversity of CambridgeCambridgeUK
- Present address:
Whitehead Institute for Biomedical ResearchCambridgeMAUSA
| | - Isao T Tokuda
- Department of Mechanical EngineeringRitsumeikan UniversityKusatsuJapan
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21
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Jurca M, Sjölander J, Ibáñez C, Matrosova A, Johansson M, Kozarewa I, Takata N, Bakó L, Webb AAR, Israelsson-Nordström M, Eriksson ME. ZEITLUPE Promotes ABA-Induced Stomatal Closure in Arabidopsis and Populus. FRONTIERS IN PLANT SCIENCE 2022; 13:829121. [PMID: 35310670 PMCID: PMC8924544 DOI: 10.3389/fpls.2022.829121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/26/2022] [Indexed: 05/22/2023]
Abstract
Plants balance water availability with gas exchange and photosynthesis by controlling stomatal aperture. This control is regulated in part by the circadian clock, but it remains unclear how signalling pathways of daily rhythms are integrated into stress responses. The serine/threonine protein kinase OPEN STOMATA 1 (OST1) contributes to the regulation of stomatal closure via activation of S-type anion channels. OST1 also mediates gene regulation in response to ABA/drought stress. We show that ZEITLUPE (ZTL), a blue light photoreceptor and clock component, also regulates ABA-induced stomatal closure in Arabidopsis thaliana, establishing a link between clock and ABA-signalling pathways. ZTL sustains expression of OST1 and ABA-signalling genes. Stomatal closure in response to ABA is reduced in ztl mutants, which maintain wider stomatal apertures and show higher rates of gas exchange and water loss than wild-type plants. Detached rosette leaf assays revealed a stronger water loss phenotype in ztl-3, ost1-3 double mutants, indicating that ZTL and OST1 contributed synergistically to the control of stomatal aperture. Experimental studies of Populus sp., revealed that ZTL regulated the circadian clock and stomata, indicating ZTL function was similar in these trees and Arabidopsis. PSEUDO-RESPONSE REGULATOR 5 (PRR5), a known target of ZTL, affects ABA-induced responses, including stomatal regulation. Like ZTL, PRR5 interacted physically with OST1 and contributed to the integration of ABA responses with circadian clock signalling. This suggests a novel mechanism whereby the PRR proteins-which are expressed from dawn to dusk-interact with OST1 to mediate ABA-dependent plant responses to reduce water loss in time of stress.
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Affiliation(s)
- Manuela Jurca
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Johan Sjölander
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Cristian Ibáñez
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
- Departamento de Biología Universidad de La Serena, La Serena, Chile
| | - Anastasia Matrosova
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Mikael Johansson
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
- RNA Biology and Molecular Physiology, Faculty for Biology, Bielefeld University, Bielefeld, Germany
| | - Iwanka Kozarewa
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Naoki Takata
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
- Forest Bio-Research Center, Forestry and Forest Products Research Institute, Hitachi, Japan
| | - Laszlo Bakó
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Alex A. R. Webb
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Maria Israelsson-Nordström
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Maria E. Eriksson
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Maria E. Eriksson,
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22
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Yan J, Li S, Kim YJ, Zeng Q, Radziejwoski A, Wang L, Nomura Y, Nakagami H, Somers DE. TOC1 clock protein phosphorylation controls complex formation with NF-YB/C to repress hypocotyl growth. EMBO J 2021; 40:e108684. [PMID: 34726281 DOI: 10.15252/embj.2021108684] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/09/2022] Open
Abstract
Plant photoperiodic growth is coordinated by interactions between circadian clock and light signaling networks. How post-translational modifications of clock proteins affect these interactions to mediate rhythmic growth remains unclear. Here, we identify five phosphorylation sites in the Arabidopsis core clock protein TIMING OF CAB EXPRESSION 1 (TOC1) which when mutated to alanine eliminate detectable phosphorylation. The TOC1 phospho-mutant fails to fully rescue the clock, growth, and flowering phenotypes of the toc1 mutant. Further, the TOC1 phospho-mutant shows advanced phase, a faster degradation rate, reduced interactions with PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) and HISTONE DEACETYLASE 15 (HDA15), and poor binding at pre-dawn hypocotyl growth-related genes (PHGs), leading to a net de-repression of hypocotyl growth. NUCLEAR FACTOR Y subunits B and C (NF-YB/C) stabilize TOC1 at target promoters, and this novel trimeric complex (NF-TOC1) acts as a transcriptional co-repressor with HDA15 to inhibit PIF-mediated hypocotyl elongation. Collectively, we identify a molecular mechanism suggesting how phosphorylation of TOC1 alters its phase, stability, and physical interactions with co-regulators to precisely phase PHG expression to control photoperiodic hypocotyl growth.
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Affiliation(s)
- Jiapei Yan
- Molecular Genetics, Ohio State University, Columbus, OH, USA
| | - Shibai Li
- Molecular Genetics, Ohio State University, Columbus, OH, USA.,Memorial Sloan Kettering Cancer Center, Molecular Biology Program, New York, NY, USA
| | - Yeon Jeong Kim
- Molecular Genetics, Ohio State University, Columbus, OH, USA
| | - Qingning Zeng
- Molecular Genetics, Ohio State University, Columbus, OH, USA
| | | | - Lei Wang
- Molecular Genetics, Ohio State University, Columbus, OH, USA.,The Chinese Academy of Sciences, Institute of Botany, Beijing, China
| | - Yuko Nomura
- RIKEN Center for Sustainable Resource Science (CSRS), Plant Proteomics Research Unit, Yokohama, Japan
| | - Hirofumi Nakagami
- RIKEN Center for Sustainable Resource Science (CSRS), Plant Proteomics Research Unit, Yokohama, Japan.,Max Planck Institute for Plant Breeding Research, Protein Mass Spectrometry, Cologne, Germany
| | - David E Somers
- Molecular Genetics, Ohio State University, Columbus, OH, USA.,POSTECH, Division of Integrative Biosciences and Biotechnology, Pohang, South Korea
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23
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Simple Nuclei Preparation and Co-immunoprecipitation Procedures for Studying Protein Abundance and Interactions in Plant Circadian Time Courses. Methods Mol Biol 2021. [PMID: 34674173 DOI: 10.1007/978-1-0716-1912-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The plant circadian clock regulates multiple developmental and physiological events that occur at specific times and seasons. As many of the currently known clock proteins and clock-associated regulators are transcription factors, analyzing molecular events in the nuclei is crucial. In addition, long-time course analyses of protein abundance and interactions are often required to assess the role of the circadian clock on clock-regulated phenomena. Here we introduce a simple procedure to prepare nuclear-enriched tissues, which we routinely use to study time-resolved accumulation changes in low-abundance nuclear proteins (i.e., transcription factors). In addition to measuring changes in abundance, investigating the protein-protein interaction dynamics at specific times of day or under certain environmental conditions is needed for plant chronobiology studies. Therefore, we also present our co-immunoprecipitation method for studying diurnal/circadian protein-protein interactions, tailored to nuclear-localized proteins in Arabidopsis and tobacco.
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24
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Fukayama H, Miyagawa F, Shibatani N, Koudou A, Sasayama D, Hatanaka T, Azuma T, Yamauchi Y, Matsuoka D, Morita R. CO 2 -responsive CCT protein interacts with 14-3-3 proteins and controls the expression of starch synthesis-related genes. PLANT, CELL & ENVIRONMENT 2021; 44:2480-2493. [PMID: 33989431 DOI: 10.1111/pce.14084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 04/25/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
CO2 -responsive CCT protein (CRCT) is a positive regulator of starch synthesis-related genes such as ADP-glucose pyrophosphorylase large subunit 1 and starch branching enzyme I particularly in the leaf sheath of rice (Oryza sativa L.). The promoter GUS analysis revealed that CRCT expressed exclusively in the vascular bundle, whereas starch synthesis-related genes were expressed in different sites such as mesophyll cell and starch storage parenchyma cell. However, the chromatin immunoprecipitation (ChIP) using a FLAG-CRCT overexpression line and subsequent qPCR analyses showed that the 5'-flanking regions of these starch synthesis-related genes tended to be enriched by ChIP, suggesting that CRCT can bind to the promoter regions of these genes. The monomer of CRCT is 34.2 kDa; however, CRCT was detected at 270 kDa via gel filtration chromatography, suggesting that CRCT forms a complex in vivo. Immunoprecipitation and subsequent MS analysis pulled down several 14-3-3-like proteins. A yeast two-hybrid analysis and bimolecular fluorescence complementation assays confirmed the interaction between CRCT and 14-3-3-like proteins. Although there is an inconsistency in the place of expression, this study provides important findings regarding the molecular function of CRCT to control the expression of key starch synthesis-related genes.
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Affiliation(s)
- Hiroshi Fukayama
- Laboratory of Tropical Plant Science, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Fumihiro Miyagawa
- Laboratory of Tropical Plant Science, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Naoki Shibatani
- Laboratory of Tropical Plant Science, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Aiko Koudou
- Laboratory of Tropical Plant Science, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Daisuke Sasayama
- Laboratory of Crop Science, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Tomoko Hatanaka
- Laboratory of Crop Science, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Tetsushi Azuma
- Laboratory of Tropical Plant Science, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Yasuo Yamauchi
- Laboratory of Functional Phytochemistry, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | | | - Ryutaro Morita
- Laboratory of Tropical Plant Science, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
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25
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Arefian M, Bhagya N, Prasad TSK. Phosphorylation-mediated signalling in flowering: prospects and retrospects of phosphoproteomics in crops. Biol Rev Camb Philos Soc 2021; 96:2164-2191. [PMID: 34047006 DOI: 10.1111/brv.12748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/18/2022]
Abstract
Protein phosphorylation is a major post-translational modification, regulating protein function, stability, and subcellular localization. To date, annotated phosphorylation data are available mainly for model organisms and humans, despite the economic importance of crop species and their large kinomes. Our understanding of the phospho-regulation of flowering in relation to the biology and interaction between the pollen and pistil is still significantly lagging, limiting our knowledge on kinase signalling and its potential applications to crop production. To address this gap, we bring together relevant literature that were previously disconnected to present an overview of the roles of phosphoproteomic signalling pathways in modulating molecular and cellular regulation within specific tissues at different morphological stages of flowering. This review is intended to stimulate research, with the potential to increase crop productivity by providing a platform for novel molecular tools.
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Affiliation(s)
- Mohammad Arefian
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - N Bhagya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
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26
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Tian W, Wang R, Bo C, Yu Y, Zhang Y, Shin GI, Kim WY, Wang L. SDC mediates DNA methylation-controlled clock pace by interacting with ZTL in Arabidopsis. Nucleic Acids Res 2021; 49:3764-3780. [PMID: 33675668 PMCID: PMC8053106 DOI: 10.1093/nar/gkab128] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 12/29/2022] Open
Abstract
Molecular bases of eukaryotic circadian clocks mainly rely on transcriptional-translational feedback loops (TTFLs), while epigenetic codes also play critical roles in fine-tuning circadian rhythms. However, unlike histone modification codes that play extensive and well-known roles in the regulation of circadian clocks, whether DNA methylation (5mC) can affect the circadian clock, and the associated underlying molecular mechanisms, remains largely unexplored in many organisms. Here we demonstrate that global genome DNA hypomethylation can significantly lengthen the circadian period of Arabidopsis. Transcriptomic and genetic evidence demonstrate that SUPPRESSOR OF drm1 drm2 cmt3 (SDC), encoding an F-box containing protein, is required for the DNA hypomethylation-tuned circadian clock. Moreover, SDC can physically interact with another F-box containing protein ZEITLUPE (ZTL) to diminish its accumulation. Genetic analysis further revealed that ZTL and its substrate TIMING OF CAB EXPRESSION 1 (TOC1) likely act downstream of DNA methyltransferases to control circadian rhythm. Together, our findings support the notion that DNA methylation is important to maintain proper circadian pace in Arabidopsis, and further established that SDC links DNA hypomethylation with a proteolytic cascade to assist in tuning the circadian clock.
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Affiliation(s)
- Wenwen Tian
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Ruyi Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Cunpei Bo
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yingjun Yu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yuanyuan Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Gyeong-Im Shin
- Division of Applied Life Science (BK21Plus), Research Institute of Life Sciences (RILS) and Institute of Agricultural and Life Science(IALS), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21Plus), Research Institute of Life Sciences (RILS) and Institute of Agricultural and Life Science(IALS), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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27
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Paajanen P, Lane de Barros Dantas L, Dodd AN. Layers of crosstalk between circadian regulation and environmental signalling in plants. Curr Biol 2021; 31:R399-R413. [PMID: 33905701 DOI: 10.1016/j.cub.2021.03.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Circadian regulation has a pervasive influence upon plant development, physiology and metabolism, impacting upon components of fitness and traits of agricultural importance. Circadian regulation is inextricably connected to the responses of plants to their abiotic environments, from the cellular to whole plant scales. Here, we review the crosstalk that occurs between circadian regulation and responses to the abiotic environment from the intracellular scale through to naturally fluctuating environments. We examine the spatial crosstalk that forms part of plant circadian regulation, at the subcellular, tissue, organ and whole-plant scales. This includes a focus on chloroplast and mitochondrial signalling, alternative splicing, long-distance circadian signalling and circadian regulation within natural environments. We also consider mathematical models for plant circadian regulation, to suggest future areas for advancing understanding of roles for circadian regulation in plant responses to environmental cues.
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Affiliation(s)
- Pirita Paajanen
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Antony N Dodd
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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28
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Feke A, Vanderwall M, Liu W, Gendron JM. Functional domain studies uncover novel roles for the ZTL Kelch repeat domain in clock function. PLoS One 2021; 16:e0235938. [PMID: 33730063 PMCID: PMC7968664 DOI: 10.1371/journal.pone.0235938] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 02/23/2021] [Indexed: 02/01/2023] Open
Abstract
The small LOV/F-box/Kelch family of E3 ubiquitin ligases plays an essential role in the regulation of plant circadian clocks and flowering time by sensing dusk. The family consists of three members, ZEITLUPE (ZTL), LOV KELCH PROTEIN 2 (LKP2), and FLAVIN-BINDING KELCH REPEAT F-BOX PROTEIN 1 (FKF1), which share a unique protein domain architecture allowing them to act as photoreceptors that transduce light signals via altering stability of target proteins. Despite intensive study of this protein family we still lack important knowledge about the biochemical and functional roles of the protein domains that comprise these unique photoreceptors. Here, we perform comparative analyses of transgenic lines constitutively expressing the photoreceptor LOV domain or the Kelch repeat protein-protein interaction domains of ZTL, FKF1, and LKP2. Expression of each domain alone is sufficient to disrupt circadian rhythms and flowering time, but each domain differs in the magnitude of effect. Immunoprecipitation followed by mass spectrometry with the ZTL Kelch repeat domain identified a suite of potential interacting partners. Furthermore, the ZTL Kelch repeat domain can interact with the ZTL homologs, LKP2 and FKF1, and the LOV domain of ZTL itself. This suggests a hypothesis that the Kelch repeat domain of ZTL may mediate inter- and intra-molecular interactions of the three LOV/F-box/Kelch proteins and provides added insight into the composition of the protein complexes and an additional role for the Kelch repeat domain.
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Affiliation(s)
- Ann Feke
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, United States of America
| | - Morgan Vanderwall
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, United States of America
| | - Wei Liu
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, United States of America
| | - Joshua M. Gendron
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, United States of America
- * E-mail:
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29
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McClung CR. Circadian Clock Components Offer Targets for Crop Domestication and Improvement. Genes (Basel) 2021; 12:genes12030374. [PMID: 33800720 PMCID: PMC7999361 DOI: 10.3390/genes12030374] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 12/31/2022] Open
Abstract
During plant domestication and improvement, farmers select for alleles present in wild species that improve performance in new selective environments associated with cultivation and use. The selected alleles become enriched and other alleles depleted in elite cultivars. One important aspect of crop improvement is expansion of the geographic area suitable for cultivation; this frequently includes growth at higher or lower latitudes, requiring the plant to adapt to novel photoperiodic environments. Many crops exhibit photoperiodic control of flowering and altered photoperiodic sensitivity is commonly required for optimal performance at novel latitudes. Alleles of a number of circadian clock genes have been selected for their effects on photoperiodic flowering in multiple crops. The circadian clock coordinates many additional aspects of plant growth, metabolism and physiology, including responses to abiotic and biotic stresses. Many of these clock-regulated processes contribute to plant performance. Examples of selection for altered clock function in tomato demonstrate that with domestication, the phasing of the clock is delayed with respect to the light–dark cycle and the period is lengthened; this modified clock is associated with increased chlorophyll content in long days. These and other data suggest the circadian clock is an attractive target during breeding for crop improvement.
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Affiliation(s)
- C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
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30
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Saitoh A, Takase T, Abe H, Watahiki M, Hirakawa Y, Kiyosue T. ZEITLUPE enhances expression of PIF4 and YUC8 in the upper aerial parts of Arabidopsis seedlings to positively regulate hypocotyl elongation. PLANT CELL REPORTS 2021; 40:479-489. [PMID: 33386962 DOI: 10.1007/s00299-020-02643-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Microarray and genetic analyses reveal that ZTL induces the expression of genes related to auxin synthesis, thereby promoting hypocotyl elongation. ZTL is a blue-light receptor that possesses a light-oxygen-voltage-sensing (LOV) domain, an F-box motif, and a kelch repeat domain. ZTL promotes hypocotyl elongation under high temperature (28 °C) in Arabidopsis thaliana; however, the mechanism of this regulation is unknown. Here, we divided seedlings into hypocotyls and upper aerial parts, and performed microarray analyses. In hypocotyl, 1062 genes were down-regulated in ztl mutants (ztl-3 and ztl-105) compared with wild type; some of these genes encoded enzymes involved in cell wall modification, consistent with reduced hypocotyl elongation. In upper aerial parts, 1038 genes were down-regulated in the ztl mutants compared with wild type; these included genes involved in auxin synthesis and auxin response. Furthermore, the expression of the PHYTOCHROME INTERACTING FACTOR 4 (PIF4) gene, which encodes a transcription factor known to positively regulate YUCCA genes (YUCs), was also decreased in the ztl mutants. Genetic analysis revealed that overexpression of PIF4 and YUC8 could restore the suppressed hypocotyl length in the ztl mutants. Our results suggest that ZTL induces expression of YUC8 via PIF4 in upper aerial parts and promotes hypocotyl elongation.
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Affiliation(s)
- Aya Saitoh
- Graduate Course in Life Science, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-Ku, Tokyo, 171-8588, Japan.
| | - Tomoyuki Takase
- Graduate Course in Life Science, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-Ku, Tokyo, 171-8588, Japan
| | - Hiroshi Abe
- Experimental Plant Division, Department of Biological Systems, RIKEN, BioResource Center, Tsukuba-shi, Ibaraki, 305-0074, Japan
| | - Masaaki Watahiki
- Faculty of Science, Division of Biological Sciences, Hokkaido University, Kitaku Kita 10 Nishi 8, Sapporo, 060-0810, Japan
| | - Yuki Hirakawa
- Graduate Course in Life Science, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-Ku, Tokyo, 171-8588, Japan
| | - Tomohiro Kiyosue
- Graduate Course in Life Science, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-Ku, Tokyo, 171-8588, Japan
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31
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Yan J, Kim YJ, Somers DE. Post-Translational Mechanisms of Plant Circadian Regulation. Genes (Basel) 2021; 12:325. [PMID: 33668215 PMCID: PMC7995963 DOI: 10.3390/genes12030325] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/21/2021] [Accepted: 02/22/2021] [Indexed: 12/15/2022] Open
Abstract
The molecular components of the circadian system possess the interesting feature of acting together to create a self-sustaining oscillator, while at the same time acting individually, and in complexes, to confer phase-specific circadian control over a wide range of physiological and developmental outputs. This means that many circadian oscillator proteins are simultaneously also part of the circadian output pathway. Most studies have focused on transcriptional control of circadian rhythms, but work in plants and metazoans has shown the importance of post-transcriptional and post-translational processes within the circadian system. Here we highlight recent work describing post-translational mechanisms that impact both the function of the oscillator and the clock-controlled outputs.
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Affiliation(s)
| | | | - David E. Somers
- Department of Molecular Genetics, The Ohio State University; Columbus, OH 43210, USA; (J.Y.); (Y.J.K.)
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32
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Characterization of the FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 Homolog SlFKF1 in Tomato as a Model for Plants with Fleshy Fruit. Int J Mol Sci 2021; 22:ijms22041735. [PMID: 33572254 PMCID: PMC7914597 DOI: 10.3390/ijms22041735] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/25/2021] [Accepted: 02/04/2021] [Indexed: 12/30/2022] Open
Abstract
FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1) is a blue-light receptor whose function is related to flowering promotion under long-day conditions in Arabidopsis thaliana. However, information about the physiological role of FKF1 in day-neutral plants and even the physiological role other than photoperiodic flowering is lacking. Thus, the FKF1 homolog SlFKF1 was investigated in tomato, a day-neutral plant and a useful model for plants with fleshy fruit. It was confirmed that SlFKF1 belongs to the FKF1 group by phylogenetic tree analysis. The high sequence identity with A. thaliana FKF1, the conserved amino acids essential for function, and the similarity in the diurnal change in expression suggested that SlFKF1 may have similar functions to A. thaliana FKF1. CONSTANS (CO) is a transcription factor regulated by FKF1 and is responsible for the transcription of genes downstream of CO. cis-Regulatory elements targeted by CO were found in the promoter region of SINGLE FLOWER TRUSS (SFT) and RIN, which are involved in the regulation of flowering and fruit ripening, respectively. The blue-light effects on SlFKF1 expression, flowering, and fruit lycopene concentration have been observed in this study and previous studies. It was confirmed in RNA interference lines that the low expression of SlFKF1 is associated with late flowering with increased leaflets and low lycopene concentrations. This study sheds light on the various physiological roles of FKF1 in plants.
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33
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Zhang S, Liu H, Yuan L, Li X, Wang L, Xu X, Xie Q. Recognition of CCA1 alternative protein isoforms during temperature acclimation. PLANT CELL REPORTS 2021; 40:421-432. [PMID: 33398474 DOI: 10.1007/s00299-020-02644-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/26/2020] [Indexed: 05/14/2023]
Abstract
CCA1α and CCA1β protein variants respond to environmental light and temperature cues, and higher temperature promotes CCA1β protein production and causes its retention detectable in the cytoplasm. CIRCADIAN CLOCK ASSOCIATED1 (CCA1), as the core transcription factor of circadian clock, is involved in the regulation of endogenous circadian rhythm in Arabidopsis. Previous studies have shown that CCA1 consists of two abundant splice variants, fully spliced CCA1α and intron-retaining CCA1β. CCA1β is believed to form a nonfunctional heterodimer with CCA1α and its closed-related homolog LHY. Many studies have established that CCA1β is a transcription product, while how CCA1β protein is produced and how two CCA1 isoforms respond to environmental cues have not been elucidated. In this study, we identified CCA1α and CCA1β protein variants under different photoperiods with warm or cold temperature cycles, respectively. Our results showed that CCA1 protein production is regulated by prolonged light exposure and warm temperature. The protein levels of CCA1α and CCA1β peak in the morning, but the detection of CCA1β is dependent on immunoprecipitation enrichment at 22 °C. Higher temperature of 37 °C promotes CCA1β protein production and causes its retention to be detectable in the cytoplasm. Overall, our results indicate that two splice variants of the CCA1 protein respond to environmental light and temperature signals and may, therefore, maintain the circadian rhythms and give individuals the ability to adapt to environment.
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Affiliation(s)
- Shijia Zhang
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Huili Liu
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Li Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xiaojing Li
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Lingbao Wang
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
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34
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Wei H, Wang X, He Y, Xu H, Wang L. Clock component OsPRR73 positively regulates rice salt tolerance by modulating OsHKT2;1-mediated sodium homeostasis. EMBO J 2021; 40:e105086. [PMID: 33347628 PMCID: PMC7849171 DOI: 10.15252/embj.2020105086] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 10/27/2020] [Accepted: 11/13/2020] [Indexed: 11/09/2022] Open
Abstract
The roles of clock components in salt stress tolerance remain incompletely characterized in rice. Here, we show that, among OsPRR (Oryza sativa Pseudo-Response Regulator) family members, OsPRR73 specifically confers salt tolerance in rice. Notably, the grain size and yield of osprr73 null mutants were significantly decreased in the presence of salt stress, with accumulated higher level of reactive oxygen species and sodium ions. RNA sequencing and biochemical assays identified OsHKT2;1, encoding a plasma membrane-localized Na+ transporter, as a transcriptional target of OsPRR73 in mediating salt tolerance. Correspondingly, null mutants of OsHKT2;1 displayed an increased tolerance to salt stress. Immunoprecipitation-mass spectrometry (IP-MS) assays further identified HDAC10 as nuclear interactor of OsPRR73 and co-repressor of OsHKT2;1. Consistently, H3K9ac histone marks at OsHKT2;1 promoter regions were significantly reduced in osprr73 mutant. Together, our findings reveal that salt-induced OsPRR73 expression confers salt tolerance by recruiting HDAC10 to transcriptionally repress OsHKT2;1, thus reducing cellular Na+ accumulation. This exemplifies a new molecular link between clock components and salt stress tolerance in rice.
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Affiliation(s)
- Hua Wei
- Key Laboratory of Plant Molecular PhysiologyCAS Center for Excellence in Molecular Plant SciencesInstitute of BotanyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiling Wang
- Key Laboratory of Plant Molecular PhysiologyCAS Center for Excellence in Molecular Plant SciencesInstitute of BotanyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yuqing He
- Key Laboratory of Plant Molecular PhysiologyCAS Center for Excellence in Molecular Plant SciencesInstitute of BotanyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Hang Xu
- Key Laboratory of Plant Molecular PhysiologyCAS Center for Excellence in Molecular Plant SciencesInstitute of BotanyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lei Wang
- Key Laboratory of Plant Molecular PhysiologyCAS Center for Excellence in Molecular Plant SciencesInstitute of BotanyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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35
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Wang Y, Lu Z, Wang L. Uncover the Nuclear Proteomic Landscape with Enriched Nuclei Followed by Label-Free Quantitative Mass Spectrometry. Methods Mol Biol 2021; 2297:115-124. [PMID: 33656675 DOI: 10.1007/978-1-0716-1370-2_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Treated with light pulse or under certain diurnal conditions, photoreceptors can translocate into nucleus followed by conformation change. Many critical components of light signaling pathways also majorly function in nucleus. Hence, it is beneficial to establish a combined method to uncover and compare the nuclear proteomic landscape among the mutants of light signaling components. Here we describe an optimized method to isolate nucleus with seedlings growing under light/dark cycles for further characterizing the nuclear proteome with label-free quantitation by liquid chromatography mass spectrometry (LC-MS).
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Affiliation(s)
- Yan Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Zhuang Lu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, People's Republic of China.
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36
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Valim H, Dalton H, Joo Y, McGale E, Halitschke R, Gaquerel E, Baldwin IT, Schuman MC. TOC1 in Nicotiana attenuata regulates efficient allocation of nitrogen to defense metabolites under herbivory stress. THE NEW PHYTOLOGIST 2020; 228:1227-1242. [PMID: 32608045 DOI: 10.1111/nph.16784] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
The circadian clock contextualizes plant responses to environmental signals. Plants use temporal information to respond to herbivory, but many of the functional roles of circadian clock components in these responses, and their contribution to fitness, remain unknown. We investigate the role of the central clock regulator TIMING OF CAB EXPRESSION 1 (TOC1) in Nicotiana attenuata's defense responses to the specialist herbivore Manduca sexta under both field and glasshouse conditions. We utilize 15 N pulse-labeling to quantify nitrogen incorporation into pools of three defense compounds: caffeoylputrescine (CP), dicaffeoyl spermidine (DCS) and nicotine. Nitrogen incorporation was decreased in CP and DCS and increased in nicotine pools in irTOC1 plants compared to empty vector (EV) under control conditions, but these differences were abolished after simulated herbivory. Differences between EV and irTOC1 plants in nicotine, but not phenolamide production, were abolished by treatment with the ethylene agonist 1-methylcyclopropene. Using micrografting, TOC1's effect on nicotine was isolated to the root and did not affect the fitness of heterografts under field conditions. These results suggest that the circadian clock contributes to plant fitness by balancing production of metabolically expensive nitrogen-rich defense compounds and mediating the allocation of resources between vegetative biomass and reproduction.
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Affiliation(s)
- Henrique Valim
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena, 07745, Germany
| | - Heidi Dalton
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena, 07745, Germany
| | - Youngsung Joo
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena, 07745, Germany
| | - Erica McGale
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena, 07745, Germany
| | - Rayko Halitschke
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena, 07745, Germany
| | - Emmanuel Gaquerel
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena, 07745, Germany
- Institute of Plant Molecular Biology, University of Strasbourg, 12 Rue du Général Zimmer, Strasbourg, 67084, France
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena, 07745, Germany
| | - Meredith C Schuman
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena, 07745, Germany
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37
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The Transcriptional Network in the Arabidopsis Circadian Clock System. Genes (Basel) 2020; 11:genes11111284. [PMID: 33138078 PMCID: PMC7692566 DOI: 10.3390/genes11111284] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/28/2020] [Accepted: 10/28/2020] [Indexed: 12/18/2022] Open
Abstract
The circadian clock is the biological timekeeping system that governs the approximately 24-h rhythms of genetic, metabolic, physiological and behavioral processes in most organisms. This oscillation allows organisms to anticipate and adapt to day–night changes in the environment. Molecular studies have indicated that a transcription–translation feedback loop (TTFL), consisting of transcriptional repressors and activators, is essential for clock function in Arabidopsis thaliana (Arabidopsis). Omics studies using next-generation sequencers have further revealed that transcription factors in the TTFL directly regulate key genes implicated in clock-output pathways. In this review, the target genes of the Arabidopsis clock-associated transcription factors are summarized. The Arabidopsis clock transcriptional network is partly conserved among angiosperms. In addition, the clock-dependent transcriptional network structure is discussed in the context of plant behaviors for adapting to day–night cycles.
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38
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Battle MW, Vegliani F, Jones MA. Shades of green: untying the knots of green photoperception. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5764-5770. [PMID: 32619226 PMCID: PMC7541914 DOI: 10.1093/jxb/eraa312] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/30/2020] [Indexed: 05/04/2023]
Abstract
The development of economical LED technology has enabled the application of different light qualities and quantities to control plant growth. Although we have a comprehensive understanding of plants' perception of red and blue light, the lack of a dedicated green light sensor has frustrated our utilization of intermediate wavelengths, with many contradictory reports in the literature. We discuss the contribution of red and blue photoreceptors to green light perception and highlight how green light can be used to improve crop quality. Importantly, our meta-analysis demonstrates that green light perception should instead be considered as a combination of distinct 'green' and 'yellow' light-induced responses. This distinction will enable clearer interpretation of plants' behaviour in response to green light as we seek to optimize plant growth and nutritional quality in horticultural contexts.
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Affiliation(s)
- Martin W Battle
- School of Life Sciences, University of Essex, Colchester, UK
| | - Franco Vegliani
- Institute of Molecular, Cell, and Systems Biology, University of Glasgow, Glasgow, UK
| | - Matthew A Jones
- Institute of Molecular, Cell, and Systems Biology, University of Glasgow, Glasgow, UK
- Correspondence:
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39
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Wang J, Du Z, Huo X, Zhou J, Chen Y, Zhang J, Pan A, Wang X, Wang F, Zhang J. Genome-wide analysis of PRR gene family uncovers their roles in circadian rhythmic changes and response to drought stress in Gossypium hirsutum L. PeerJ 2020; 8:e9936. [PMID: 33033660 PMCID: PMC7521341 DOI: 10.7717/peerj.9936] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/24/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The circadian clock not only participates in regulating various stages of plant growth, development and metabolism, but confers plant environmental adaptability to stress such as drought. Pseudo-Response Regulators (PRRs) are important component of the central oscillator (the core of circadian clock) and play a significant role in plant photoperiod pathway. However, no systematical study about this gene family has been performed in cotton. METHODS PRR genes were identified in diploid and tetraploid cotton using bioinformatics methods to investigate their homology, duplication and evolution relationship. Differential gene expression, KEGG enrichment analysis and qRT-PCR were conducted to analyze PRR gene expression patterns under diurnal changes and their response to drought stress. RESULTS A total of 44 PRR family members were identified in four Gossypium species, with 16 in G. hirsutum, 10 in G. raimondii, and nine in G. barbadense as well as in G. arboreum. Phylogenetic analysis indicated that PRR proteins were divided into five subfamilies and whole genome duplication or segmental duplication contributed to the expansion of Gossypium PRR gene family. Gene structure analysis revealed that members in the same clade are similar, and multiple cis-elements related to light and drought stress response were enriched in the promoters of GhPRR genes. qRT-PCR results showed that GhPRR genes transcripts presented four expression peaks (6 h, 9 h, 12 h, 15 h) during 24 h and form obvious rhythmic expression trend. Transcriptome data with PEG treatment, along with qRT-PCR verification suggested that members of clade III (GhPRR5a, b, d) and clade V (GhPRR3a and GhPRR3c) may be involved in drought response. This study provides an insight into understanding the function of PRR genes in circadian rhythm and in response to drought stress in cotton.
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Affiliation(s)
- Jingjing Wang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- College of Life Sciences, Shandong Normal University, Jinan, P. R. China
| | - Zhaohai Du
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Xuehan Huo
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- College of Life Sciences, Shandong Normal University, Jinan, P. R. China
| | - Juan Zhou
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Yu Chen
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Jingxia Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Ao Pan
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Xiaoyang Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, P. R. China
| | - Furong Wang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- College of Life Sciences, Shandong Normal University, Jinan, P. R. China
| | - Jun Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- College of Life Sciences, Shandong Normal University, Jinan, P. R. China
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40
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Joanito I, Yan CCS, Chu JW, Wu SH, Hsu CP. Basal leakage in oscillation: Coupled transcriptional and translational control using feed-forward loops. PLoS Comput Biol 2020; 16:e1007740. [PMID: 32881861 PMCID: PMC7494099 DOI: 10.1371/journal.pcbi.1007740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 09/16/2020] [Accepted: 06/26/2020] [Indexed: 11/19/2022] Open
Abstract
The circadian clock is a complex system that plays many important roles in most organisms. Previously, many mathematical models have been used to sharpen our understanding of the Arabidopsis clock, which brought to light the roles of each transcriptional and post-translational regulations. However, the presence of both regulations, instead of either transcription or post-translation, raised curiosity of whether the combination of these two regulations is important for the clock’s system. In this study, we built a series of simplified oscillators with different regulations to study the importance of post-translational regulation (specifically, 26S proteasome degradation) in the clock system. We found that a simple transcriptional-based oscillator can already generate sustained oscillation, but the oscillation can be easily destroyed in the presence of transcriptional leakage. Coupling post-translational control with transcriptional-based oscillator in a feed-forward loop will greatly improve the robustness of the oscillator in the presence of basal leakage. Using these general models, we were able to replicate the increased variability observed in the E3 ligase mutant for both plant and mammalian clocks. With this insight, we also predict a plausible regulator of several E3 ligase genes in the plant’s clock. Thus, our results provide insights into and the plausible importance in coupling transcription and post-translation controls in the clock system. For circadian clocks, several current models had successfully captured the essential dynamic behavior of the clock system mainly with transcriptional regulation. Previous studies have shown that the 26S proteasome degradation controls are important in maintaining the stability of circadian rhythms. However, how the loss-of-function or over-expression mutant of this targeted degradations lead to unstable oscillation is still unclear. In this work, we investigate the importance of coupled transcriptional and post-translational feedback loop in the circadian oscillator. With general models our study indicate that the unstable behavior of degradation mutants could be caused by the increase in the basal level of the clock genes. We found that coupling a non-linear degradation control into this transcriptional based oscillator using feed-forward loop improves the robustness of the oscillator. Using this finding, we further predict some plausible regulators of Arabidopsis’s E3 ligase protein such as COP1 and SINAT5. Hence, our results provide insights on the importance of coupling transcription and post-translation controls in the clock system.
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Affiliation(s)
- Ignasius Joanito
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan and Institute of Bioinformatics and System Biology, National Chiao Tung University, Hsinchu, Taiwan
| | | | - Jhih-Wei Chu
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan and Institute of Bioinformatics and System Biology, National Chiao Tung University, Hsinchu, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Shu-Hsing Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan
| | - Chao-Ping Hsu
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan
- * E-mail:
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41
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Shim JS, Jang G. Environmental Signal-Dependent Regulation of Flowering Time in Rice. Int J Mol Sci 2020; 21:ijms21176155. [PMID: 32858992 PMCID: PMC7504671 DOI: 10.3390/ijms21176155] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/23/2020] [Accepted: 08/24/2020] [Indexed: 01/11/2023] Open
Abstract
The transition from the vegetative to the reproductive stage of growth is a critical event in the lifecycle of a plant and is required for the plant’s reproductive success. Flowering time is tightly regulated by an internal time-keeping system and external light conditions, including photoperiod, light quality, and light quantity. Other environmental factors, such as drought and temperature, also participate in the regulation of flowering time. Thus, flexibility in flowering time in response to environmental factors is required for the successful adaptation of plants to the environment. In this review, we summarize our current understanding of the molecular mechanisms by which internal and environmental signals are integrated to regulate flowering time in Arabidopsis thaliana and rice (Oryza sativa).
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42
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Philippou K, Davis AM, Davis SJ, Sánchez-Villarreal A. Chemical Perturbation of Chloroplast-Related Processes Affects Circadian Rhythms of Gene Expression in Arabidopsis: Salicylic Acid Application Can Entrain the Clock. Front Physiol 2020; 11:429. [PMID: 32625102 PMCID: PMC7314985 DOI: 10.3389/fphys.2020.00429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 04/08/2020] [Indexed: 11/26/2022] Open
Abstract
The plant circadian system reciprocally interacts with metabolic processes. To investigate entrainment features in metabolic–circadian interactions, we used a chemical approach to perturb metabolism and monitored the pace of nuclear-driven circadian oscillations. We found that chemicals that alter chloroplast-related functions modified the circadian rhythms. Both vitamin C and paraquat altered the circadian period in a light-quality-dependent manner, whereas rifampicin lengthened the circadian period under darkness. Salicylic acid (SA) increased oscillatory robustness and shortened the period. The latter was attenuated by sucrose addition and was also gated, taking place during the first 3 h of the subjective day. Furthermore, the effect of SA on period length was dependent on light quality and genotype. Period lengthening or shortening by these chemicals was correlated to their inferred impact on photosynthetic electron transport activity and the redox state of plastoquinone (PQ). Based on these data and on previous publications on circadian effects that alter the redox state of PQ, we propose that the photosynthetic electron transport and the redox state of PQ participate in circadian periodicity. Moreover, coupling between chloroplast-derived signals and nuclear oscillations, as observed in our chemical and genetic assays, produces traits that are predicted by previous models. SA signaling or a related process forms a rhythmic input loop to drive robust nuclear oscillations in the context predicted by the zeitnehmer model, which was previously developed for Neurospora. We further discuss the possibility that electron transport chains (ETCs) are part of this mechanism.
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Affiliation(s)
- Koumis Philippou
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Amanda M Davis
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Department of Biology, University of York, York, United Kingdom
| | - Seth J Davis
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Department of Biology, University of York, York, United Kingdom.,Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Alfredo Sánchez-Villarreal
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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43
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Sanchez SE, Rugnone ML, Kay SA. Light Perception: A Matter of Time. MOLECULAR PLANT 2020; 13:363-385. [PMID: 32068156 PMCID: PMC7056494 DOI: 10.1016/j.molp.2020.02.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 05/02/2023]
Abstract
Optimizing the perception of external cues and regulating physiology accordingly help plants to cope with the constantly changing environmental conditions to which they are exposed. An array of photoreceptors and intricate signaling pathways allow plants to convey the surrounding light information and synchronize an endogenous timekeeping system known as the circadian clock. This biological clock integrates multiple cues to modulate a myriad of downstream responses, timing them to occur at the best moment of the day and the year. Notably, the mechanism underlying entrainment of the light-mediated clock is not clear. This review addresses known interactions between the light-signaling and circadian-clock networks, focusing on the role of light in clock entrainment and known molecular players in this process.
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Affiliation(s)
- Sabrina E Sanchez
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Matias L Rugnone
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Steve A Kay
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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44
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Wang Y, He Y, Su C, Zentella R, Sun TP, Wang L. Nuclear Localized O-Fucosyltransferase SPY Facilitates PRR5 Proteolysis to Fine-Tune the Pace of Arabidopsis Circadian Clock. MOLECULAR PLANT 2020; 13:446-458. [PMID: 31899321 PMCID: PMC7058189 DOI: 10.1016/j.molp.2019.12.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/25/2019] [Accepted: 12/28/2019] [Indexed: 05/07/2023]
Abstract
Post-translational modifications play essential roles in finely modulating eukaryotic circadian clock systems. In plants, the effects of O-glycosylation on the circadian clock and the underlying mechanisms remain largely unknown. The O-fucosyltransferase SPINDLY (SPY) and the O-GlcNAc transferase SECRET AGENT (SEC) are two prominent O-glycosylation enzymes in higher plants, with both overlapped and unique functions in plant growth and development. Unlike the critical role of O-GlcNAc in regulating the animal circadian clock, here we report that nuclear-localized SPY, but not SEC, specifically modulates the pace of the Arabidopsis circadian clock. By identifying the interactome of SPY, we identified PSEUDO-RESPONSE REGULATOR 5 (PRR5), one of the core circadian clock components, as a new SPY-interacting protein. PRR5 can be O-fucosylated by SPY in planta, while point mutation in the catalytic domain of SPY abolishes the O-fucosylation of PRR5. The protein abundance of PRR5 is strongly increased in spy mutants, while the degradation rate of PRR5 is much reduced, suggesting that PRR5 proteolysis is promoted by SPY-mediated O-fucosylation. Moreover, multiple lines of genetic evidence indicate that PRR5 is a major downstream target of SPY to specifically mediate its modulation of the circadian clock. Collectively, our findings provide novel insights into the specific role of the O-fucosyltransferase activity of SPY in modulating the circadian clock and implicate that O-glycosylation might play an evolutionarily conserved role in modulating the circadian clock system, via O-GlcNAcylation in mammals, but via O-fucosylation in higher plants.
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Affiliation(s)
- Yan Wang
- Key Laboratory of Plant Molecular Physiology, 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
| | - Yuqing He
- Key Laboratory of Plant Molecular Physiology, 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
| | - Chen Su
- Key Laboratory of Plant Molecular Physiology, 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
| | | | - Tai-Ping Sun
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, 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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45
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Shi Y, Zhao X, Guo S, Dong S, Wen Y, Han Z, Jin W, Chen Y. ZmCCA1a on Chromosome 10 of Maize Delays Flowering of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2020; 11:78. [PMID: 32153606 PMCID: PMC7044342 DOI: 10.3389/fpls.2020.00078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/20/2020] [Indexed: 06/01/2023]
Abstract
Maize (Zea mays) is a major cereal crop that originated at low latitudes, and thus photoperiod sensitivity is an important barrier to the use of tropical/subtropical germplasm in temperate regions. However, studies of the mechanisms underlying circadian regulation in maize are at an early stage. In this study we cloned ZmCCA1a on chromosome 10 of maize by map-based cloning. The gene is homologous to the Myb transcription factor genes AtCCA1/AtLHY in Arabidopsis thaliana; the deduced Myb domain of ZmCCA1a showed high similarity with that of AtCCA1/AtLHY and ZmCCA1b. Transiently or constitutively expressed ZmCCA1a-YFPs were localized to nuclei of Arabidopsis mesophyll protoplasts, agroinfiltrated tobacco leaves, and leaf and root cells of transgenic seedlings of Arabidopsis thaliana. Unlike AtCCA1/AtLHY, ZmCCA1a did not form homodimers nor interact with ZmCCA1b. Transcripts of ZmCCA1a showed circadian rhythm with peak expression around sunrise in maize inbred lines CML288 (photoperiod sensitive) and Huangzao 4 (HZ4; photoperiod insensitive). Under short days, transcription of ZmCCA1a in CML288 and HZ4 was repressed compared with that under long days, whereas the effect of photoperiod on ZmCCA1a expression was moderate in HZ4. In ZmCCA1a-overexpressing A. thaliana (ZmCCA1a-ox) lines, the circadian rhythm was disrupted under constant light and flowering was delayed under long days, but the hypocotyl length was not affected. In addition, expression of endogenous AtCCA1/AtLHY and the downstream genes AtGI, AtCO, and AtFt was repressed in ZmCCA1a-ox seedlings. The present results suggest that the function of ZmCCA1a is similar, at least in part, to that of AtCCA1/AtLHY and ZmCCA1b, implying that ZmCCA1a is likely to be an important component of the circadian clock pathway in maize.
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Affiliation(s)
- Yong Shi
- College of Agronomy/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Xiyong Zhao
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Sha Guo
- College of Agronomy/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Shifeng Dong
- College of Agronomy/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Yanpeng Wen
- College of Agronomy/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Zanping Han
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
| | - Weihuan Jin
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yanhui Chen
- College of Agronomy/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
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46
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Hearn TJ, Webb AAR. Recent advances in understanding regulation of the Arabidopsis circadian clock by local cellular environment. F1000Res 2020; 9. [PMID: 32047621 PMCID: PMC6993837 DOI: 10.12688/f1000research.21307.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/20/2020] [Indexed: 11/20/2022] Open
Abstract
Circadian clocks have evolved to synchronise an organism’s physiology with the environmental rhythms driven by the Earth’s rotation on its axis. Over the past two decades, many of the genetic components of the
Arabidopsis thaliana circadian oscillator have been identified. The interactions between these components have been formulized into mathematical models that describe the transcriptional translational feedback loops of the oscillator. More recently, focus has turned to the regulation and functions of the circadian clock. These studies have shown that the system dynamically responds to environmental signals and small molecules. We describe advances that have been made in discovering the cellular mechanisms by which signals regulate the circadian oscillator of Arabidopsis in the context of tissue-specific regulation.
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Affiliation(s)
- Timothy J Hearn
- Department of Plant Sciences, University of Cambridge, Downing Site, Cambridge, CB2 3EA, UK.,Research Department of Cell and Developmental Biology, Rockefeller Building, University College London, London, WC1E 6DE, UK.,Academic Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Alex A R Webb
- Department of Plant Sciences, University of Cambridge, Downing Site, Cambridge, CB2 3EA, UK
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47
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Nakamichi N, Kudo T, Makita N, Kiba T, Kinoshita T, Sakakibara H. Flowering time control in rice by introducing Arabidopsis clock-associated PSEUDO-RESPONSE REGULATOR 5. Biosci Biotechnol Biochem 2020; 84:970-979. [PMID: 31985350 DOI: 10.1080/09168451.2020.1719822] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Plants flower under appropriate day-length conditions by integrating temporal information provided by the circadian clock with light and dark information from the environment. A sub-group of plant specific circadian clock-associated PSEUDO-RESPONSE REGULATOR (PRR) genes (PRR7/PRR3 sub-group) controls flowering time both in long-day and short-day plants; however, flowering control by the other two PRR gene sub-groups has been reported only in Arabidopsis thaliana (Arabidopsis), a model long-day plant. Here, we show that an Arabidopsis PRR9/PRR5 sub-group gene can control flowering time (heading date) in rice, a short-day plant. Although PRR5 promotes flowering in Arabidopsis, transgenic rice overexpressing Arabidopsis PRR5 caused late flowering. Such transgenic rice plants produced significantly higher biomass, but not grain yield, due to the late flowering. Concomitantly, expression of Hd3a, a rice florigen gene, was reduced in the transgenic rice.Abbreviations: CCT: CONSTANS, CONSTANS-LIKE, and TOC1; HD: HEADING DATE; LHY: LATE ELONGATED HYPOCOTYL; Ppd: photoperiod; PR: pseudo-receiver; PRR: PSEUDO-RESPONSE REGULATOR; TOC1: TIMING OF CAB EXPRESSION 1; ZTL: ZEITLUPE.
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Affiliation(s)
- Norihito Nakamichi
- Institute of Transformative Bio-molecules, Nagoya University, Nagoya, Japan.,Graduate School of Sciences, Nagoya University, Nagoya, Japan
| | - Toru Kudo
- Metabologenomics, Inc., Tsuruoka, Yamagata, Japan
| | - Nobue Makita
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Takatoshi Kiba
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan.,Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Toshinori Kinoshita
- Institute of Transformative Bio-molecules, Nagoya University, Nagoya, Japan.,Graduate School of Sciences, Nagoya University, Nagoya, Japan
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan.,Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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48
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Li B, Wang Y, Zhang Y, Tian W, Chong K, Jang JC, Wang L. PRR5, 7 and 9 positively modulate TOR signaling-mediated root cell proliferation by repressing TANDEM ZINC FINGER 1 in Arabidopsis. Nucleic Acids Res 2019; 47:5001-5015. [PMID: 30892623 PMCID: PMC6547441 DOI: 10.1093/nar/gkz191] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 03/04/2019] [Accepted: 03/12/2019] [Indexed: 12/22/2022] Open
Abstract
Circadian clock coordinates numerous plant growth and developmental processes including cell elongation in the hypocotyl, whether or not it modulates cell proliferation is largely unknown. Here we have found that Pseudo Response Regulators (PRRs), essential components of circadian core oscillators, affect root meristem cell proliferation mediated by Target Of Rapamycin (TOR) signaling. The null mutants of PRRs display much reduced sensitivities to sugar-activated TOR signaling. We have subsequently identified Tandem Zinc Finger 1, encoding a processing body localized RNA-binding protein, as a direct target repressed by PRRs in mediating TOR signaling. Multiple lines of biochemical and genetic evidence have demonstrated that TZF1 acts downstream of PRRs to attenuate TOR signaling. Furthermore, TZF1 could directly bind TOR mRNA via its tandem zinc finger motif to affect TOR mRNA stability. Our findings support a notion that PRR-TZF1-TOR molecular axis modulates root meristem cell proliferation by integrating both transcriptional and post-transcriptional regulatory mechanisms.
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Affiliation(s)
- Bin Li
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, People's Republic of China
| | - Yan Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, People's Republic of China.,University of Chinese Academy of Sciences
| | - Yuanyuan Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, People's Republic of China
| | - Wenwen Tian
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, People's Republic of China.,University of Chinese Academy of Sciences
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, People's Republic of China
| | - Jyan-Chyun Jang
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH 43210, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, People's Republic of China.,University of Chinese Academy of Sciences
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49
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Hayama R, Yang P, Valverde F, Mizoguchi T, Furutani-Hayama I, Vierstra RD, Coupland G. Ubiquitin carboxyl-terminal hydrolases are required for period maintenance of the circadian clock at high temperature in Arabidopsis. Sci Rep 2019; 9:17030. [PMID: 31745110 PMCID: PMC6863813 DOI: 10.1038/s41598-019-53229-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/28/2019] [Indexed: 12/18/2022] Open
Abstract
Protein ubiquitylation participates in a number of essential cellular processes including signal transduction and transcription, often by initiating the degradation of specific substrates through the 26S proteasome. Within the ubiquitin-proteasome system, deubiquitylating enzymes (DUBs) not only help generate and maintain the supply of free ubiquitin monomers, they also directly control functions and activities of specific target proteins by modulating the pool of ubiquitylated species. Ubiquitin carboxyl-terminal hydrolases (UCHs) belong to an enzymatic subclass of DUBs, and are represented by three members in Arabidopsis, UCH1, UCH2 and UCH3. UCH1 and UCH2 influence auxin-dependent developmental pathways in Arabidopsis through their deubiquitylation activities, whereas biological and enzymatic functions of UCH3 remain unclear. Here, we demonstrate that Arabidopsis UCH3 acts to maintain the period of the circadian clock at high temperatures redundantly with UCH1 and UCH2. Whereas single uch1, uch2 and uch3 mutants have weak circadian phenotypes, the triple uch mutant displays a drastic lengthening of period at high temperatures that is more extreme than the uch1 uch2 double mutant. UCH3 also possesses a broad deubiquitylation activity against a range of substrates that link ubiquitin via peptide and isopeptide linkages. While the protein target(s) of UCH1-3 are not yet known, we propose that these DUBs act on one or more factors that control period length of the circadian clock through removal of their bound ubiquitin moieties, thus ensuring that the clock oscillates with a proper period even at elevated temperatures.
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Affiliation(s)
- Ryosuke Hayama
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, D-50829, Cologne, Germany. .,Department of Natural Sciences, International Christian University, 3-10-2 Osawa, Mitaka, 181-8585, Tokyo, Japan.
| | - Peizhen Yang
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.,, Bayer Crop Science, 800 N Lindbergh Blvd, St Louis, Missouri, 63146, USA
| | - Federico Valverde
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, D-50829, Cologne, Germany.,Plant Development Unit, Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 49th Américo Vespucio Avenue, Sevilla, 41092, Spain
| | - Tsuyoshi Mizoguchi
- Department of Natural Sciences, International Christian University, 3-10-2 Osawa, Mitaka, 181-8585, Tokyo, Japan
| | - Ikuyo Furutani-Hayama
- Department of Natural Sciences, International Christian University, 3-10-2 Osawa, Mitaka, 181-8585, Tokyo, Japan
| | - Richard D Vierstra
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.,Department of Biology, Washington University in St. Louis, Campus Box 1137, One Brookings Drive, St. Louis, Missouri, 63130, USA
| | - George Coupland
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, D-50829, Cologne, Germany.
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50
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Ono A, Sato A, Fujimoto KJ, Matsuo H, Yanai T, Kinoshita T, Nakamichi N. 3,4-Dibromo-7-Azaindole Modulates Arabidopsis Circadian Clock by Inhibiting Casein Kinase 1 Activity. PLANT & CELL PHYSIOLOGY 2019; 60:2360-2368. [PMID: 31529098 PMCID: PMC6839374 DOI: 10.1093/pcp/pcz183] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 09/10/2019] [Indexed: 05/05/2023]
Abstract
The circadian clock is a timekeeping system for regulation of numerous biological daily rhythms. One characteristic of the circadian clock is that period length remains relatively constant in spite of environmental fluctuations, such as temperature change. Here, using the curated collection of in-house small molecule chemical library (ITbM chemical library), we show that small molecule 3,4-dibromo-7-azaindole (B-AZ) lengthened the circadian period of Arabidopsis thaliana (Arabidopsis). B-AZ has not previously been reported to have any biological and biochemical activities. Target identification can elucidate the mode of action of small molecules, but we were unable to make a molecular probe of B-AZ for target identification. Instead, we performed other analysis, gene expression profiling that potentially reveals mode of action of molecules. Short-term treatment of B-AZ decreased the expression of four dawn- and morning-phased clock-associated genes, CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1), LATE ELONGATED HYPOCOTYL (LHY), PSEUDO-RESPONSE REGULATOR 9 (PRR9) and PRR7. Consistently, amounts of PRR5 and TIMING OF CAB EXPRESSION 1 (TOC1) proteins, transcriptional repressors of CCA1, LHY, PRR9 and PRR7 were increased upon B-AZ treatment. B-AZ inhibited Casein Kinase 1 family (CK1) that phosphorylates PRR5 and TOC1 for targeted degradation. A docking study and molecular dynamics simulation suggested that B-AZ interacts with the ATP-binding pocket of human CK1 delta, whose amino acid sequences are highly similar to those of Arabidopsis CK1. B-AZ-induced period-lengthening effect was attenuated in prr5 toc1 mutants. Collectively, this study provides a novel and simple structure CK1 inhibitor that modulates circadian clock via accumulation of PRR5 and TOC1.
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Affiliation(s)
- Azusa Ono
- Division of Biological Science, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, Japan
| | - Ayato Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya, Japan
| | - Kazuhiro J Fujimoto
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya, Japan
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, Japan
| | - Hiromi Matsuo
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya, Japan
| | - Takeshi Yanai
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya, Japan
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, Japan
| | - Toshinori Kinoshita
- Division of Biological Science, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya, Japan
| | - Norihito Nakamichi
- Division of Biological Science, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya, Japan
- * Corresponding author: E-mail, ; Fax, +81-789-4778
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