1
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Xu B, Hwangbo DS, Saurabh S, Rosensweig C, Allada R, Kath WL, Braun R. Temperature-driven coordination of circadian transcriptional regulation. PLoS Comput Biol 2024; 20:e1012029. [PMID: 38648221 PMCID: PMC11108206 DOI: 10.1371/journal.pcbi.1012029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 05/21/2024] [Accepted: 03/28/2024] [Indexed: 04/25/2024] Open
Abstract
The circadian clock is an evolutionarily-conserved molecular oscillator that enables species to anticipate rhythmic changes in their environment. At a molecular level, the core clock genes induce circadian oscillations in thousands of genes in a tissue-specific manner, orchestrating myriad biological processes. While previous studies have investigated how the core clock circuit responds to environmental perturbations such as temperature, the downstream effects of such perturbations on circadian regulation remain poorly understood. By analyzing bulk-RNA sequencing of Drosophila fat bodies harvested from flies subjected to different environmental conditions, we demonstrate a highly condition-specific circadian transcriptome: genes are cycling in a temperature-specific manner, and the distributions of their phases also differ between the two conditions. Further employing a reference-based gene regulatory network (Reactome), we find evidence of increased gene-gene coordination at low temperatures and synchronization of rhythmic genes that are network neighbors. We report that the phase differences between cycling genes increase as a function of geodesic distance in the low temperature condition, suggesting increased coordination of cycling on the gene regulatory network. Our results suggest a potential mechanism whereby the circadian clock mediates the fly's response to seasonal changes in temperature.
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Affiliation(s)
- Bingxian Xu
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, United States of America
| | - Dae-Sung Hwangbo
- Department of Biology, University of Louisville, Louisville, Kentucky, United States of America
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Sumit Saurabh
- Department of Biology, Loyola University, Chicago, Illinois, United States of America
| | - Clark Rosensweig
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, United States of America
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Ravi Allada
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, United States of America
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - William L. Kath
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, United States of America
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, Illinois, United States of America
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois, United States of America
| | - Rosemary Braun
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, Illinois, United States of America
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, Illinois, United States of America
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois, United States of America
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
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2
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Zhang H, Harmer SL. A Luciferase Imaging-Based Assay for Studying Temperature Compensation of the Circadian Clock. Methods Mol Biol 2024; 2795:43-53. [PMID: 38594526 DOI: 10.1007/978-1-0716-3814-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
The pace of circadian rhythms remains relatively unchanged across a physiologically relevant range of temperatures, a phenomenon known as temperature compensation. Temperature compensation is a defining characteristic of circadian rhythms, ensuring that clock-regulated processes occur at approximately the same time of day across a wide range of conditions. Despite the identification of several genes involved in the regulation of temperature compensation, the molecular mechanisms underlying this process are still not well understood. High-throughput assays of circadian period are essential for the investigation of temperature compensation. In this chapter, we present a luciferase imaging-based method that enables robust and accurate examination of temperature compensation in the plant circadian clock.
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Affiliation(s)
- Hongtao Zhang
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA, USA
| | - Stacey L Harmer
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA, USA.
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3
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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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4
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Schmal C, Maier B, Ashwal-Fluss R, Bartok O, Finger AM, Bange T, Koutsouli S, Robles MS, Kadener S, Herzel H, Kramer A. Alternative polyadenylation factor CPSF6 regulates temperature compensation of the mammalian circadian clock. PLoS Biol 2023; 21:e3002164. [PMID: 37379316 DOI: 10.1371/journal.pbio.3002164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 05/15/2023] [Indexed: 06/30/2023] Open
Abstract
A defining property of circadian clocks is temperature compensation, characterized by the resilience of their near 24-hour free-running periods against changes in environmental temperature within the physiological range. While temperature compensation is evolutionary conserved across different taxa of life and has been studied within many model organisms, its molecular underpinnings remain elusive. Posttranscriptional regulations such as temperature-sensitive alternative splicing or phosphorylation have been described as underlying reactions. Here, we show that knockdown of cleavage and polyadenylation specificity factor subunit 6 (CPSF6), a key regulator of 3'-end cleavage and polyadenylation, significantly alters circadian temperature compensation in human U-2 OS cells. We apply a combination of 3'-end-RNA-seq and mass spectrometry-based proteomics to globally quantify changes in 3' UTR length as well as gene and protein expression between wild-type and CPSF6 knockdown cells and their dependency on temperature. Since changes in temperature compensation behavior should be reflected in alterations of temperature responses within one or all of the 3 regulatory layers, we statistically assess differential responses upon changes in ambient temperature between wild-type and CPSF6 knockdown cells. By this means, we reveal candidate genes underlying circadian temperature compensation, including eukaryotic translation initiation factor 2 subunit 1 (EIF2S1).
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Affiliation(s)
- Christoph Schmal
- Institute for Theoretical Biology, Humboldt-Universität zu Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Bert Maier
- Laboratory of Chronobiology, Institute for Medical immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Reut Ashwal-Fluss
- Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Osnat Bartok
- Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anna-Marie Finger
- Laboratory of Chronobiology, Institute for Medical immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Tanja Bange
- Institute of Medical Psychology, Faculty of Medicine, Ludwig-Maximilians-Universität München, München, Germany
| | - Stella Koutsouli
- Institute of Medical Psychology, Faculty of Medicine, Ludwig-Maximilians-Universität München, München, Germany
| | - Maria S Robles
- Institute of Medical Psychology, Faculty of Medicine, Ludwig-Maximilians-Universität München, München, Germany
| | - Sebastian Kadener
- Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Humboldt-Universität zu Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Achim Kramer
- Laboratory of Chronobiology, Institute for Medical immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
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5
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Xu H, Wang X, Wei J, Zuo Y, Wang L. The Regulatory Networks of the Circadian Clock Involved in Plant Adaptation and Crop Yield. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091897. [PMID: 37176955 PMCID: PMC10181312 DOI: 10.3390/plants12091897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
Global climatic change increasingly threatens plant adaptation and crop yields. By synchronizing internal biological processes, including photosynthesis, metabolism, and responses to biotic and abiotic stress, with external environmental cures, such as light and temperature, the circadian clock benefits plant adaptation and crop yield. In this review, we focus on the multiple levels of interaction between the plant circadian clock and environmental factors, and we summarize recent progresses on how the circadian clock affects yield. In addition, we propose potential strategies for better utilizing the current knowledge of circadian biology in crop production in the future.
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Affiliation(s)
- Hang Xu
- 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
| | - Jian Wei
- College of Life Sciences, Changchun Normal University, Changchun 130032, China
| | - Yi Zuo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, 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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6
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Wang Y, Wu F, Lin Q, Sheng P, Wu Z, Jin X, Chen W, Li S, Luo S, Duan E, Wang J, Ma W, Ren Y, Cheng Z, Zhang X, Lei C, Guo X, Wang H, Zhu S, Wan J. A regulatory loop establishes the link between the circadian clock and abscisic acid signaling in rice. PLANT PHYSIOLOGY 2023; 191:1857-1870. [PMID: 36493391 PMCID: PMC10022614 DOI: 10.1093/plphys/kiac548] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
There is a close regulatory relationship between the circadian clock and the abscisic acid (ABA) signaling pathway in regulating many developmental processes and stress responses. However, the exact feedback regulation mechanism between them is still poorly understood. Here, we identified the rice (Oryza sativa) clock component PSEUDO-RESPONSE REGULATOR 95 (OsPRR95) as a transcriptional regulator that accelerates seed germination and seedling growth by inhibiting ABA signaling. We also found that OsPRR95 binds to the ABA receptor gene REGULATORY COMPONENTS OF ABA RECEPTORS10 (OsRCAR10) DNA and inhibits its expression. Genetic analysis showed OsRCAR10 acts downstream of OsPRR95 in mediating ABA responses. In addition, the induction of OsPRR95 by ABA partly required a functional OsRCAR10, and the ABA-responsive element-binding factor ABSCISIC ACID INSENSITIVE5 (OsABI5) bound directly to the promoter of OsPRR95 and activated its expression, thus establishing a regulatory feedback loop between OsPRR95, OsRCAR10, and OsABI5. Taken together, our results demonstrated that the OsRCAR10-OsABI5-OsPRR95 feedback loop modulates ABA signaling to fine-tune seed germination and seedling growth, thus establishing the molecular link between ABA signaling and the circadian clock.
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Affiliation(s)
- Yupeng Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | | | - Peike Sheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ziming Wu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xin Jin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weiwei Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuai Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sheng Luo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Erchao Duan
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiachang Wang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiwei Ma
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yulong Ren
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhijun Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cailin Lei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuping Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiyang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | - Jianmin Wan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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7
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Global Analysis of Dark- and Heat-Regulated Alternative Splicing in Arabidopsis. Int J Mol Sci 2023; 24:ijms24065299. [PMID: 36982373 PMCID: PMC10049525 DOI: 10.3390/ijms24065299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Alternative splicing (AS) is one of the major post-transcriptional regulation mechanisms that contributes to plant responses to various environmental perturbations. Darkness and heat are two common abiotic factors affecting plant growth, yet the involvement and regulation of AS in the plant responses to these signals remain insufficiently examined. In this study, we subjected Arabidopsis seedlings to 6 h of darkness or heat stress and analyzed their transcriptome through short-read RNA sequencing. We revealed that both treatments altered the transcription and AS of a subset of genes yet with different mechanisms. Dark-regulated AS events were found enriched in photosynthesis and light signaling pathways, while heat-regulated AS events were enriched in responses to abiotic stresses but not in heat-responsive genes, which responded primarily through transcriptional regulation. The AS of splicing-related genes (SRGs) was susceptible to both treatments; while dark treatment mostly regulated the AS of these genes, heat had a strong effect on both their transcription and AS. PCR analysis showed that the AS of the Serine/Arginine-rich family gene SR30 was reversely regulated by dark and heat, and heat induced the upregulation of multiple minor SR30 isoforms with intron retention. Our results suggest that AS participates in plant responses to these two abiotic signals and reveal the regulation of splicing regulators during these processes.
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8
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Wang H, Tang X, Liu Y. SlCK2α as a novel substrate for CRL4 E3 ligase regulates fruit size through maintenance of cell division homeostasis in tomato. PLANTA 2023; 257:38. [PMID: 36645501 DOI: 10.1007/s00425-023-04070-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
This study unravels a novel regulatory module (CRL4-CK2α-CDK2) involving fruit size control by mediating cell division homeostasis (SlCK2α and SlCDK2) in tomato. Fruit size is one of the crucial agronomical traits for crop production. UV-damaged DNA binding protein 1 (DDB1), a core component of Cullin4-RING E3 ubiquitin ligase complex (CRL4), has been identified as a negative regulator of fruit size in tomato (Solanum lycopersicum). However, the underlying molecular mechanism remains largely unclear. Here, we report the identification and characterization of a SlDDB1-interacting protein putatively involving fruit size control through regulating cell proliferation in tomato. It is a tomato homolog SlCK2α, the catalytic subunit of the casein kinase 2 (CK2), identified by yeast two-hybrid (Y2H) assays. The interaction between SlDDB1 and SlCK2α was demonstrated by bimolecular fluorescence complementation (BiFC) and co-immunoprecipitation (Co-IP). RNA interference (RNAi) and CRISPR/Cas9-based mutant analyses showed that lack of SlCK2α resulted in reduction of fruit size with reduced cell number, suggesting it is a positive regulator on fruit size by promoting cell proliferation. We also showed SlDDB1 is required to ubiquitinate SlCK2α and negatively regulate its stability through 26S proteasome-mediated degradation. Furthermore, we found that a tomato homolog of cell division protein kinase 2 (SlCDK2) could interact with and specifically be phosphorylated by SlCK2α, resulting in an increase of SlCDK2 protein stability. CRISPR/Cas9-based genetic evidence showed that SlCDK2 is also a positive regulator of fruit size by influencing cell division in tomato. Taken together, our findings, thus, unravel a novel regulatory module CRL4-CK2α-CDK2 in finely modulating cell division homeostasis and the consequences on fruit size.
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Affiliation(s)
- Hongtao Wang
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Xiaofeng Tang
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China.
| | - Yongsheng Liu
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China.
- School of Horticulture and State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China.
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9
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Kelliher CM, Stevenson EL, Loros JJ, Dunlap JC. Nutritional compensation of the circadian clock is a conserved process influenced by gene expression regulation and mRNA stability. PLoS Biol 2023; 21:e3001961. [PMID: 36603054 PMCID: PMC9848017 DOI: 10.1371/journal.pbio.3001961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 01/18/2023] [Accepted: 12/15/2022] [Indexed: 01/06/2023] Open
Abstract
Compensation is a defining principle of a true circadian clock, where its approximately 24-hour period length is relatively unchanged across environmental conditions. Known compensation effectors directly regulate core clock factors to buffer the oscillator's period length from variables in the environment. Temperature Compensation mechanisms have been experimentally addressed across circadian model systems, but much less is known about the related process of Nutritional Compensation, where circadian period length is maintained across physiologically relevant nutrient levels. Using the filamentous fungus Neurospora crassa, we performed a genetic screen under glucose and amino acid starvation conditions to identify new regulators of Nutritional Compensation. Our screen uncovered 16 novel mutants, and together with 4 mutants characterized in prior work, a model emerges where Nutritional Compensation of the fungal clock is achieved at the levels of transcription, chromatin regulation, and mRNA stability. However, eukaryotic circadian Nutritional Compensation is completely unstudied outside of Neurospora. To test for conservation in cultured human cells, we selected top hits from our fungal genetic screen, performed siRNA knockdown experiments of the mammalian orthologs, and characterized the cell lines with respect to compensation. We find that the wild-type mammalian clock is also compensated across a large range of external glucose concentrations, as observed in Neurospora, and that knocking down the mammalian orthologs of the Neurospora compensation-associated genes CPSF6 or SETD2 in human cells also results in nutrient-dependent period length changes. We conclude that, like Temperature Compensation, Nutritional Compensation is a conserved circadian process in fungal and mammalian clocks and that it may share common molecular determinants.
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Affiliation(s)
- Christina M. Kelliher
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Elizabeth-Lauren Stevenson
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Jennifer J. Loros
- Department of Biochemistry & Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Jay C. Dunlap
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
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10
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Zhu J, Wang WS, Yan DW, Hong LW, Li TT, Gao X, Yang YH, Ren F, Lu YT, Yuan TT. CK2 promotes jasmonic acid signaling response by phosphorylating MYC2 in Arabidopsis. Nucleic Acids Res 2022; 51:619-630. [PMID: 36546827 PMCID: PMC9881174 DOI: 10.1093/nar/gkac1213] [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: 05/24/2022] [Revised: 10/19/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Jasmonic acid (JA) signaling plays a pivotal role in plant development and defense. MYC2 is a master transcription factor in JA signaling, and was found to be phosphorylated and negatively regulated by MAP kinase and receptor-like kinase. However, the kinases that positively regulate MYC2 through phosphorylation and promote MYC2-mediated activation of JA response have not been identified. Here, we identified CK2 as a kinase that phosphorylates MYC2 and thus regulates the JA signaling. CK2 holoenzyme can interact with MYC2 using its regulatory subunits and phosphorylate MYC2 at multiple sites with its catalytic subunits. Inhibition of CK2 activity in a dominant-negative plant line, CK2mut, repressed JA response. On the other hand, increasing CK2 activity by overexpression of CKB4, a regulatory subunit gene of CK2, enhanced JA response in a MYC2-dependent manner. Substitution of the Ser and Thr residues at phosphorylation sites of MYC2 by CK2 with Ala impaired MYC2 function in activating JA response. Further investigations evidenced that CK2 facilitated the JA-induced increase of MYC2 binding to the promoters of JA-responsive genes in vivo. Our study demonstrated that CK2 plays a positive role in JA signaling, and reveals a previously undiscovered mechanism that regulates MYC2 function.
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Affiliation(s)
| | | | - Da-Wei Yan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Li-Wei Hong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Ting-Ting Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Xiang Gao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Yun-Huang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Feng Ren
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Ying-Tang Lu
- Correspondence may also be addressed to Ying-Tang Lu. Tel: +86 27 68752619; Fax: +86 27 68753551;
| | - Ting-Ting Yuan
- To whom correspondence should be addressed. Tel: +86 27 68752619; Fax: +86 27 68753551;
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11
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Li X, Deng D, Cataltepe G, Román Á, Buckley CR, Cassano Monte‐Bello C, Skirycz A, Caldana C, Haydon MJ. A reactive oxygen species Ca 2+ signalling pathway identified from a chemical screen for modifiers of sugar-activated circadian gene expression. THE NEW PHYTOLOGIST 2022; 236:1027-1041. [PMID: 35842791 PMCID: PMC9804775 DOI: 10.1111/nph.18380] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/13/2022] [Indexed: 06/10/2023]
Abstract
Sugars are essential metabolites for energy and anabolism that can also act as signals to regulate plant physiology and development. Experimental tools to disrupt major sugar signalling pathways are limited. We performed a chemical screen for modifiers of activation of circadian gene expression by sugars to discover pharmacological tools to investigate and manipulate plant sugar signalling. Using a library of commercially available bioactive compounds, we identified 75 confident hits that modified the response of a circadian luciferase reporter to sucrose in dark-adapted Arabidopsis thaliana seedlings. We validated the transcriptional effect on a subset of the hits and measured their effects on a range of sugar-dependent phenotypes for 13 of these chemicals. Chemicals were identified that appear to influence known and unknown sugar signalling pathways. Pentamidine isethionate was identified as a modifier of a sugar-activated Ca2+ signal that acts as a calmodulin inhibitor downstream of superoxide in a metabolic signalling pathway affecting circadian rhythms, primary metabolism and plant growth. Our data provide a resource of new experimental tools to manipulate plant sugar signalling and identify novel components of these pathways.
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Affiliation(s)
- Xiang Li
- School of BioSciencesUniversity of MelbourneParkvilleVic.3010Australia
| | - Dongjing Deng
- School of BioSciencesUniversity of MelbourneParkvilleVic.3010Australia
| | - Gizem Cataltepe
- School of BioSciencesUniversity of MelbourneParkvilleVic.3010Australia
- Max Planck Institute of Molecular Plant Physiology14476PotsdamGermany
| | - Ángela Román
- School of BioSciencesUniversity of MelbourneParkvilleVic.3010Australia
| | | | | | | | - Camila Caldana
- Max Planck Institute of Molecular Plant Physiology14476PotsdamGermany
| | - Michael J. Haydon
- School of BioSciencesUniversity of MelbourneParkvilleVic.3010Australia
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12
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Singh AK, Mishra P, Kashyap SP, Karkute SG, Singh PM, Rai N, Bahadur A, Behera TK. Molecular insights into mechanisms underlying thermo-tolerance in tomato. FRONTIERS IN PLANT SCIENCE 2022; 13:1040532. [PMID: 36388532 PMCID: PMC9645296 DOI: 10.3389/fpls.2022.1040532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Plant productivity is being seriously compromised by climate-change-induced temperature extremities. Agriculture and food safety are threatened due to global warming, and in many cases the negative impacts have already begun. Heat stress leads to significant losses in yield due to changes in growth pattern, plant phonologies, sensitivity to pests, flowering, grain filling, maturity period shrinkage, and senescence. Tomato is the second most important vegetable crop. It is very sensitive to heat stress and thus, yield losses in tomato due to heat stress could affect food and nutritional security. Tomato plants respond to heat stress with a variety of cellular, physiological, and molecular responses, beginning with the early heat sensing, followed by signal transduction, antioxidant defense, osmolyte synthesis and regulated gene expression. Recent findings suggest that specific plant organs are extremely sensitive to heat compared to the entire plant, redirecting the research more towards generative tissues. This is because, during sexual reproduction, developing pollens are the most sensitive to heat. Often, just a few degrees of temperature elevation during pollen development can have a negative effect on crop production. Furthermore, recent research has discovered certain genetic and epigenetic mechanisms playing key role in thermo-tolerance and have defined new directions for tomato heat stress response (HSR). Present challenges are to increase the understanding of molecular mechanisms underlying HS, and to identify superior genotypes with more tolerance to extreme temperatures. Several metabolites, genes, heat shock factors (HSFs) and microRNAs work together to regulate the plant HSR. The present review provides an insight into molecular mechanisms of heat tolerance and current knowledge of genetic and epigenetic control of heat-tolerance in tomato for sustainable agriculture in the future. The information will significantly contribute to improve breeding programs for development of heat tolerant cultivars.
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Affiliation(s)
- Achuit K. Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Pallavi Mishra
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Sarvesh Pratap Kashyap
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Suhas G. Karkute
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Prabhakar Mohan Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Nagendra Rai
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Anant Bahadur
- Division of Crop Production, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Tusar K. Behera
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
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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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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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15
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Joshi R, Cai YD, Xia Y, Chiu JC, Emery P. PERIOD Phosphoclusters Control Temperature Compensation of the Drosophila Circadian Clock. Front Physiol 2022; 13:888262. [PMID: 35721569 PMCID: PMC9201207 DOI: 10.3389/fphys.2022.888262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Ambient temperature varies constantly. However, the period of circadian pacemakers is remarkably stable over a wide-range of ecologically- and physiologically-relevant temperatures, even though the kinetics of most biochemical reactions accelerates as temperature rises. This thermal buffering phenomenon, called temperature compensation, is a critical feature of circadian rhythms, but how it is achieved remains elusive. Here, we uncovered the important role played by the Drosophila PERIOD (PER) phosphodegron in temperature compensation. This phosphorylation hotspot is crucial for PER proteasomal degradation and is the functional homolog of mammalian PER2 S478 phosphodegron, which also impacts temperature compensation. Using CRISPR-Cas9, we introduced a series of mutations that altered three Serines of the PER phosphodegron. While all three Serine to Alanine substitutions lengthened period at all temperatures tested, temperature compensation was differentially affected. S44A and S45A substitutions caused undercompensation, while S47A resulted in overcompensation. These results thus reveal unexpected functional heterogeneity of phosphodegron residues in thermal compensation. Furthermore, mutations impairing phosphorylation of the per s phosphocluster showed undercompensation, consistent with its inhibitory role on S47 phosphorylation. We observed that S47A substitution caused increased accumulation of hyper-phosphorylated PER at warmer temperatures. This finding was corroborated by cell culture assays in which S47A slowed down phosphorylation-dependent PER degradation at high temperatures, causing PER degradation to be excessively temperature-compensated. Thus, our results point to a novel role of the PER phosphodegron in temperature compensation through temperature-dependent modulation of the abundance of hyper-phosphorylated PER. Our work reveals interesting mechanistic convergences and differences between mammalian and Drosophila temperature compensation of the circadian clock.
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Affiliation(s)
- Radhika Joshi
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Yao D. Cai
- Department of Entomology and Nematology, University of California, Davis, Davis, CA, United States
| | - Yongliang Xia
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Joanna C. Chiu
- Department of Entomology and Nematology, University of California, Davis, Davis, CA, United States
| | - Patrick Emery
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, United States
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16
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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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17
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The Ubiquitin E3 Ligase PRU2 Modulates Phosphate Uptake in Arabidopsis. Int J Mol Sci 2022; 23:ijms23042273. [PMID: 35216388 PMCID: PMC8874776 DOI: 10.3390/ijms23042273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/30/2022] [Accepted: 02/09/2022] [Indexed: 11/25/2022] Open
Abstract
Phosphorus is an essential macronutrient for plants. The phosphate (Pi) concentration in soil solutions is typically low, and plants always suffer from low-Pi stress. During Pi starvation, a number of adaptive mechanisms in plants have evolved to increase Pi uptake, whereas the mechanisms are not very clear. Here, we report that an ubiquitin E3 ligase, PRU2, modulates Pi acquisition in Arabidopsis response to the low-Pi stress. The mutant pru2 showed arsenate-resistant phenotypes and reduced Pi content and Pi uptake rate. The complementation with PRU2 restored these to wild-type plants. PRU2 functioned as an ubiquitin E3 ligase, and the protein accumulation of PRU2 was elevated during Pi starvation. PRU2 interacted with a kinase CK2α1 and a ribosomal protein RPL10 and degraded CK2α1 and RPL10 under low-Pi stress. The in vitro phosphorylation assay showed that CK2α1 phosphorylated PHT1;1 at Ser-514, and prior reports demonstrated that the phosphorylation of PHT1;1 Ser-514 resulted in PHT1;1 retention in the endoplasmic reticulum. Then, the degradation of CK2α1 by PRU2 under low-Pi stress facilitated PHT1;1 to move to the plasma membrane to increase Arabidopsis Pi uptake. Taken together, this study demonstrated that the ubiquitin E3 ligase—PRU2—was an important positive regulator in modulating Pi acquisition in Arabidopsis response to low-Pi stress.
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18
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Abstract
Circadian clocks are important to much of life on Earth and are of inherent interest to humanity, implicated in fields ranging from agriculture and ecology to developmental biology and medicine. New techniques show that it is not simply the presence of clocks, but coordination between them that is critical for complex physiological processes across the kingdoms of life. Recent years have also seen impressive advances in synthetic biology to the point where parallels can be drawn between synthetic biological and circadian oscillators. This review will emphasize theoretical and experimental studies that have revealed a fascinating dichotomy of coupling and heterogeneity among circadian clocks. We will also consolidate the fields of chronobiology and synthetic biology, discussing key design principles of their respective oscillators.
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Affiliation(s)
- Chris N Micklem
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK.,The Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CH3 0HE, UK
| | - James C W Locke
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
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19
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Viana AJC, Matiolli CC, Newman DW, Vieira JGP, Duarte GT, Martins MCM, Gilbault E, Hotta CT, Caldana C, Vincentz M. The sugar-responsive circadian clock regulator bZIP63 modulates plant growth. THE NEW PHYTOLOGIST 2021; 231:1875-1889. [PMID: 34053087 PMCID: PMC9292441 DOI: 10.1111/nph.17518] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 05/18/2021] [Indexed: 05/02/2023]
Abstract
Adjustment to energy starvation is crucial to ensure growth and survival. In Arabidopsis thaliana (Arabidopsis), this process relies in part on the phosphorylation of the circadian clock regulator bZIP63 by SUCROSE non-fermenting RELATED KINASE1 (SnRK1), a key mediator of responses to low energy. We investigated the effects of mutations in bZIP63 on plant carbon (C) metabolism and growth. Results from phenotypic, transcriptomic and metabolomic analysis of bZIP63 mutants prompted us to investigate the starch accumulation pattern and the expression of genes involved in starch degradation and in the circadian oscillator. bZIP63 mutation impairs growth under light-dark cycles, but not under constant light. The reduced growth likely results from the accentuated C depletion towards the end of the night, which is caused by the accelerated starch degradation of bZIP63 mutants. The diel expression pattern of bZIP63 is dictated by both the circadian clock and energy levels, which could determine the changes in the circadian expression of clock and starch metabolic genes observed in bZIP63 mutants. We conclude that bZIP63 composes a regulatory interface between the metabolic and circadian control of starch breakdown to optimize C usage and plant growth.
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Affiliation(s)
- Américo J. C. Viana
- Centro de Biologia Molecular e Engenharia GenéticaDepartamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de CampinasCEP 13083‐875, CP 6010CampinasSPBrazil
| | - Cleverson C. Matiolli
- Centro de Biologia Molecular e Engenharia GenéticaDepartamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de CampinasCEP 13083‐875, CP 6010CampinasSPBrazil
| | - David W. Newman
- Centro de Biologia Molecular e Engenharia GenéticaDepartamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de CampinasCEP 13083‐875, CP 6010CampinasSPBrazil
| | - João G. P. Vieira
- Centro de Biologia Molecular e Engenharia GenéticaDepartamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de CampinasCEP 13083‐875, CP 6010CampinasSPBrazil
| | - Gustavo T. Duarte
- Centro de Biologia Molecular e Engenharia GenéticaDepartamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de CampinasCEP 13083‐875, CP 6010CampinasSPBrazil
| | - Marina C. M. Martins
- Brazilian Bioethanol Science and Technology Laboratory (CTBE/CNPEM)Rua Giuseppe Máximo Scolfaro 10000CampinasSPCEP 13083‐970Brazil
- Max‐Planck Partner GroupBrazilian Bioethanol Science and Technology Laboratory (CTBE/CNPEM)Campinas, SPBrazil
- Laboratory of Plant Physiological EcologyDepartment of BotanyInstitute of BiosciencesUniversity of São PauloSão Paulo, SPCEP 05508‐090Brazil
| | - Elodie Gilbault
- Institut Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersailles78000France
| | - Carlos T. Hotta
- Departamento de BioquímicaInstituto de QuímicaUniversidade de São PauloSão Paulo, SPCEP 05508‐000Brazil
| | - Camila Caldana
- Brazilian Bioethanol Science and Technology Laboratory (CTBE/CNPEM)Rua Giuseppe Máximo Scolfaro 10000CampinasSPCEP 13083‐970Brazil
- Max‐Planck Partner GroupBrazilian Bioethanol Science and Technology Laboratory (CTBE/CNPEM)Campinas, SPBrazil
- Max Planck Institute of Molecular Plant PhysiologyAm Mühlenberg 114476 PotsdamGolmGermany
| | - Michel Vincentz
- Centro de Biologia Molecular e Engenharia GenéticaDepartamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de CampinasCEP 13083‐875, CP 6010CampinasSPBrazil
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20
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Quantitative Proteomics and Phosphoproteomics Support a Role for Mut9-Like Kinases in Multiple Metabolic and Signaling Pathways in Arabidopsis. Mol Cell Proteomics 2021; 20:100063. [PMID: 33677124 PMCID: PMC8066427 DOI: 10.1016/j.mcpro.2021.100063] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 01/14/2021] [Accepted: 02/05/2021] [Indexed: 11/27/2022] Open
Abstract
Protein phosphorylation is one of the most prevalent posttranslational modifications found in eukaryotic systems. It serves as a key molecular mechanism that regulates protein function in response to environmental stimuli. The Mut9-like kinases (MLKs) are a plant-specific family of Ser/Thr kinases linked to light, circadian, and abiotic stress signaling. Here we use quantitative phosphoproteomics in conjunction with global proteomic analysis to explore the role of the MLKs in daily protein dynamics. Proteins involved in light, circadian, and hormone signaling, as well as several chromatin-modifying enzymes and DNA damage response factors, were found to have altered phosphorylation profiles in the absence of MLK family kinases. In addition to altered phosphorylation levels, mlk mutant seedlings have an increase in glucosinolate metabolism enzymes. Subsequently, we show that a functional consequence of the changes to the proteome and phosphoproteome in mlk mutant plants is elevated glucosinolate accumulation and increased sensitivity to DNA damaging agents. Combined with previous reports, this work supports the involvement of MLKs in a diverse set of stress responses and developmental processes, suggesting that the MLKs serve as key regulators linking environmental inputs to developmental outputs. MUT9-LIKE KINASE mutant quantitative proteome and phosphoproteome measured. Changes to proteome and phosphoproteome are specific to genotype and environment. Loss of MLKs alters glucosinolate enzyme abundance and metabolism. Loss of MLKs increases plant sensitivity to UV radiation and DNA damage agents.
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21
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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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22
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Wang F, Cui P, Tian Y, Huang Y, Wang H, Liu F, Chen Y. Maize ZmPT7 regulates Pi uptake and redistribution which is modulated by phosphorylation. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2406-2419. [PMID: 32431055 PMCID: PMC7680542 DOI: 10.1111/pbi.13414] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 02/26/2020] [Accepted: 05/05/2020] [Indexed: 05/20/2023]
Abstract
Phosphorus, an essential mineral macronutrient, is a major constituent of fertilizers for maize (Zea mays L.) production. However, the molecular mechanisms of phosphate (Pi) acquisition in maize plants and its redistribution remain unclear. This study presents the functional characterization of ZmPT7 in Pi uptake and redistribution in maize. The ZmPT7 was expressed in roots and leaves, and induced during Pi starvation. The ZmPT7 complemented the Pi-uptake deficiency of yeast mutant phoΔnull and Arabidopsis mutant pht1;1Δ4Δ, indicating that ZmPT7 functioned as a Pi transporter. We generated zmpt7 mutants by CRISPR/Cas9 and ZmPT7-overexpressing lines. The zmpt7 mutants showed reduced, whereas the ZmPT7-overexpressing lines displayed increased Pi-uptake capacity and Pi redistribution from old to young leaves, demonstrating that ZmPT7 played central roles in Pi acquisition and Pi redistribution from old to young leaves. The ZmCK2 kinases phosphorylated ZmPT7 at Ser-521 in old maize leaves, which enhanced transport activity of ZmPT7. The Ser-520 of Arabidopsis AtPHT1;1, a conserved residue of ZmPT7 Ser-521, was also phosphorylated by AtCK2 kinase, and the mutation of Ser-520 to Glu (phosphorylation mimic) yielded enhanced transport activity of AtPHT1;1. Taken together, these results indicate that ZmPT7 plays important roles in Pi acquisition and redistribution, and its transport activity is modulated by phosphorylation.
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Affiliation(s)
- Fang Wang
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesCenter for Maize Functional Genomics and Molecular BreedingChina Agricultural UniversityBeijingChina
| | - Peng‐Juan Cui
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesCenter for Maize Functional Genomics and Molecular BreedingChina Agricultural UniversityBeijingChina
| | - Yan Tian
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesCenter for Maize Functional Genomics and Molecular BreedingChina Agricultural UniversityBeijingChina
| | - Yun Huang
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesCenter for Maize Functional Genomics and Molecular BreedingChina Agricultural UniversityBeijingChina
| | - Hai‐Feng Wang
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesCenter for Maize Functional Genomics and Molecular BreedingChina Agricultural UniversityBeijingChina
| | - Fang Liu
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesCenter for Maize Functional Genomics and Molecular BreedingChina Agricultural UniversityBeijingChina
| | - Yi‐Fang Chen
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesCenter for Maize Functional Genomics and Molecular BreedingChina Agricultural UniversityBeijingChina
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23
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Gliech CR, Holland AJ. Keeping track of time: The fundamentals of cellular clocks. J Cell Biol 2020; 219:e202005136. [PMID: 32902596 PMCID: PMC7594491 DOI: 10.1083/jcb.202005136] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 12/13/2022] Open
Abstract
Biological timekeeping enables the coordination and execution of complex cellular processes such as developmental programs, day/night organismal changes, intercellular signaling, and proliferative safeguards. While these systems are often considered separately owing to a wide variety of mechanisms, time frames, and outputs, all clocks are built by calibrating or delaying the rate of biochemical reactions and processes. In this review, we explore the common themes and core design principles of cellular clocks, giving special consideration to the challenges associated with building timers from biochemical components. We also outline how evolution has coopted time to increase the reliability of a diverse range of biological systems.
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Affiliation(s)
| | - Andrew J. Holland
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD
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24
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Emenecker RJ, Holehouse AS, Strader LC. Emerging Roles for Phase Separation in Plants. Dev Cell 2020; 55:69-83. [PMID: 33049212 PMCID: PMC7577370 DOI: 10.1016/j.devcel.2020.09.010] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/19/2020] [Accepted: 09/02/2020] [Indexed: 12/12/2022]
Abstract
The plant cell internal environment is a dynamic, intricate landscape composed of many intracellular compartments. Cells organize some cellular components through formation of biomolecular condensates-non-stoichiometric assemblies of protein and/or nucleic acids. In many cases, phase separation appears to either underly or contribute to the formation of biomolecular condensates. Many canonical membraneless compartments within animal cells form in a manner that is at least consistent with phase separation, including nucleoli, stress granules, Cajal bodies, and numerous additional bodies, regulated by developmental and environmental stimuli. In this Review, we examine the emerging roles for phase separation in plants. Further, drawing on studies carried out in other organisms, we identify cellular phenomenon in plants that might also arise via phase separation. We propose that plants make use of phase separation to a much greater extent than has been previously appreciated, implicating phase separation as an evolutionarily ancient mechanism for cellular organization.
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Affiliation(s)
- Ryan J Emenecker
- Department of Biology, Washington University, St. Louis, MO 63130, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, MO 63130, USA; Center for Engineering Mechanobiology, Washington University, St. Louis, MO 63130, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, MO 63130, USA.
| | - Lucia C Strader
- Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, MO 63130, USA; Center for Engineering Mechanobiology, Washington University, St. Louis, MO 63130, USA; Department of Biology, Duke University, Durham, NC 27708, USA.
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25
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Maric A, Mas P. Chromatin Dynamics and Transcriptional Control of Circadian Rhythms in Arabidopsis. Genes (Basel) 2020; 11:E1170. [PMID: 33036236 PMCID: PMC7601625 DOI: 10.3390/genes11101170] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/01/2020] [Accepted: 10/04/2020] [Indexed: 02/06/2023] Open
Abstract
Circadian rhythms pervade nearly all aspects of plant growth, physiology, and development. Generation of the rhythms relies on an endogenous timing system or circadian clock that generates 24-hour oscillations in multiple rhythmic outputs. At its bases, the plant circadian function relies on dynamic interactive networks of clock components that regulate each other to generate rhythms at specific phases during the day and night. From the initial discovery more than 13 years ago of a parallelism between the oscillations in chromatin status and the transcriptional rhythms of an Arabidopsis clock gene, a number of studies have later expanded considerably our view on the circadian epigenome and transcriptome landscapes. Here, we describe the most recent identification of chromatin-related factors that are able to directly interact with Arabidopsis clock proteins to shape the transcriptional waveforms of circadian gene expression and clock outputs. We discuss how changes in chromatin marks associate with transcript initiation, elongation, and the rhythms of nascent RNAs, and speculate on future interesting research directions in the field.
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Affiliation(s)
- Aida Maric
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain;
| | - Paloma Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain;
- Consejo Superior de Investigaciones Científicas (CSIC), 08028 Barcelona, Spain
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26
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MacKinnon KJM, Cole BJ, Yu C, Coomey JH, Hartwick NT, Remigereau MS, Duffy T, Michael TP, Kay SA, Hazen SP. Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation. THE NEW PHYTOLOGIST 2020; 227:1709-1724. [PMID: 32112414 DOI: 10.1111/nph.16507] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
Plants are continuously exposed to diurnal fluctuations in light and temperature, and spontaneous changes in their physical or biotic environment. The circadian clock coordinates regulation of gene expression with a 24 h period, enabling the anticipation of these events. We used RNA sequencing to characterize the Brachypodium distachyon transcriptome under light and temperature cycles, as well as under constant conditions. Approximately 3% of the transcriptome was regulated by the circadian clock, a smaller proportion than reported in most other species. For most transcripts that were rhythmic under all conditions, including many known clock genes, the period of gene expression lengthened from 24 to 27 h in the absence of external cues. To functionally characterize the cyclic transcriptome in B. distachyon, we used Gene Ontology enrichment analysis, and found several terms significantly associated with peak expression at particular times of the day. Furthermore, we identified sequence motifs enriched in the promoters of similarly phased genes, some potentially associated with transcription factors. When considering the overlap in rhythmic gene expression and specific pathway behavior, thermocycles was the prevailing cue that controlled diurnal gene regulation. Taken together, our characterization of the rhythmic B. distachyon transcriptome represents a foundational resource with implications in other grass species.
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Affiliation(s)
- Kirk J-M MacKinnon
- Biology Department, University of Massachusetts, Amherst, MA, 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, 01003, USA
| | - Benjamin J Cole
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Chang Yu
- Biology Department, University of Massachusetts, Amherst, MA, 01003, USA
| | - Joshua H Coomey
- Biology Department, University of Massachusetts, Amherst, MA, 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, 01003, USA
| | | | - Marie-Stanislas Remigereau
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Tomás Duffy
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | | | - Steve A Kay
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Samuel P Hazen
- Biology Department, University of Massachusetts, Amherst, MA, 01003, USA
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27
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Lagercrantz U, Billhardt A, Rousku SN, Ljung K, Eklund DM. Nyctinastic thallus movement in the liverwort Marchantia polymorpha is regulated by a circadian clock. Sci Rep 2020; 10:8658. [PMID: 32457350 PMCID: PMC7251115 DOI: 10.1038/s41598-020-65372-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/29/2020] [Indexed: 11/24/2022] Open
Abstract
The circadian clock coordinates an organism's growth, development and physiology with environmental factors. One illuminating example is the rhythmic growth of hypocotyls and cotyledons in Arabidopsis thaliana. Such daily oscillations in leaf position are often referred to as sleep movements or nyctinasty. Here, we report that plantlets of the liverwort Marchantia polymorpha show analogous rhythmic movements of thallus lobes, and that the circadian clock controls this rhythm, with auxin a likely output pathway affecting these movements. The mechanisms of this circadian clock are partly conserved as compared to angiosperms, with homologs to the core clock genes PRR, RVE and TOC1 forming a core transcriptional feedback loop also in M. polymorpha.
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Affiliation(s)
- Ulf Lagercrantz
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
- The Linnean Centre for Plant Biology in Uppsala, Uppsala, Sweden
| | - Anja Billhardt
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
- The Linnean Centre for Plant Biology in Uppsala, Uppsala, Sweden
| | - Sabine N Rousku
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
- The Linnean Centre for Plant Biology in Uppsala, Uppsala, Sweden
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - D Magnus Eklund
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden.
- The Linnean Centre for Plant Biology in Uppsala, Uppsala, Sweden.
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28
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Wang F, Deng M, Chen J, He Q, Jia X, Guo H, Xu J, Liu Y, Zhang S, Shou H, Mao C. CASEIN KINASE2-Dependent Phosphorylation of PHOSPHATE2 Fine-tunes Phosphate Homeostasis in Rice. PLANT PHYSIOLOGY 2020; 183:250-262. [PMID: 32161109 PMCID: PMC7210639 DOI: 10.1104/pp.20.00078] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 02/25/2020] [Indexed: 05/21/2023]
Abstract
Plants have evolved complex physiological and biochemical mechanisms to adapt to a heterogeneous soil phosphorus environment. PHOSPHATE2 (PHO2) is a phosphate (Pi) starvation-signaling regulator involved in maintaining Pi homeostasis in plants. Arabidopsis (Arabidopsis thaliana) PHO2 targets PHOSPHATE TRANSPORTER1 (PHT1) and PHO1 for degradation, whereas rice (Oryza sativa) PHO2 is thought to mediate PHOSPHATE TRANSPORTER TRAFFIC FACILITATOR1 degradation. However, it is unclear whether and how PHO2 is post-translationally regulated. Here, we show that in rice, the CASEIN KINASE2 (OsCK2) catalytic subunit OsCK2α3 interacts with OsPHO2 in vitro and in vivo in vascular tissues cells, and phosphorylates OsPHO2 at Ser-841. Phosphorylated OsPHO2 is degraded more rapidly than native OsPHO2 in cell-free degradation assays. OsPHO2 interacts with OsPHO1 and targets it for degradation through a multivesicular body-mediated pathway. PHO1 mutation partially rescued the pho2 mutant phenotype. Further genetic analysis showed that a nonphosphorylatable version of OsPHO2 rescued the Ospho2 phenotype of high Pi accumulation in leaves better than native OsPHO2. In addition to the previously established role of OsCK2 in negatively regulating endoplasmic reticulum exit of PHT1 phosphate transporters, this work uncovers a role for OsCK2α3 in modulating Pi homeostasis through regulating the phosphorylation status and abundance of OsPHO2 in rice.
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Affiliation(s)
- Fei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Meiju Deng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jieyu Chen
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4J8, Canada
| | - Qiuju He
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xinye Jia
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huaxing Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiming Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yidong Liu
- Division of Biochemistry, Interdisciplinary Plant Group, Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Shuqun Zhang
- Division of Biochemistry, Interdisciplinary Plant Group, Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chuanzao Mao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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Chen WW, Takahashi N, Hirata Y, Ronald J, Porco S, Davis SJ, Nusinow DA, Kay SA, Mas P. A mobile ELF4 delivers circadian temperature information from shoots to roots. NATURE PLANTS 2020; 6:416-426. [PMID: 32284549 PMCID: PMC7197390 DOI: 10.1038/s41477-020-0634-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 03/11/2020] [Indexed: 05/19/2023]
Abstract
The circadian clock is synchronized by environmental cues, mostly by light and temperature. Explaining how the plant circadian clock responds to temperature oscillations is crucial to understanding plant responsiveness to the environment. Here, we found a prevalent temperature-dependent function of the Arabidopsis clock component EARLY FLOWERING 4 (ELF4) in the root clock. Although the clocks in roots are able to run in the absence of shoots, micrografting assays and mathematical analyses show that ELF4 moves from shoots to regulate rhythms in roots. ELF4 movement does not convey photoperiodic information, but trafficking is essential for controlling the period of the root clock in a temperature-dependent manner. Low temperatures favour ELF4 mobility, resulting in a slow-paced root clock, whereas high temperatures decrease movement, leading to a faster clock. Hence, the mobile ELF4 delivers temperature information and establishes a shoot-to-root dialogue that sets the pace of the clock in roots.
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Affiliation(s)
- Wei Wei Chen
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Nozomu Takahashi
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Yoshito Hirata
- Mathematics and Informatics Center, The University of Tokyo, Tokyo, Japan
- Faculty of Engineering, Information and Systems, University of Tsukuba, Tsukuba, Japan
| | - James Ronald
- Department of Biology, University of York, York, UK
| | - Silvana Porco
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Seth J Davis
- Department of Biology, University of York, York, UK
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | | | - Steve A Kay
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - Paloma Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain.
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain.
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30
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Kim TS, Wang L, Kim YJ, Somers DE. Compensatory Mutations in GI and ZTL May Modulate Temperature Compensation in the Circadian Clock. PLANT PHYSIOLOGY 2020; 182:1130-1141. [PMID: 31740505 PMCID: PMC6997678 DOI: 10.1104/pp.19.01120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/02/2019] [Indexed: 05/04/2023]
Abstract
Circadian systems share the three properties of entrainment, free-running period, and temperature compensation (TC). TC ensures nearly the same period over a broad range of physiologically relevant temperatures; however, the mechanisms behind TC remain poorly understood. Here, we identify single point mutations in two key elements of the Arabidopsis circadian clock, GIGANTEA (GI) and ZEITLUPE (ZTL), which likely act as compensatory substitutions to establish a remarkably constant free-running period over a wide range of temperatures. Using near-isogenic lines generated from the introgression of the Cape Verde Islands (Cvi) alleles of GI and ZTL into the Landsberg erecta (Ler) background, we show how longer periods in the Cvi background at higher temperatures correlate with a difference in strength of the GI/ZTL interaction. Pairwise interaction testing of all GI/ZTL allelic combinations shows similar affinities for isogenic alleles at 22°C, but very poor interaction between GI (Cvi) and ZTL (Cvi) at higher temperature. In vivo, this would result in lower ZTL levels at high temperatures leading to longer periods in the Cvi background. Mismatched allelic combinations result in extremely strong or weak GI/ZTL interactions, indicating how the corresponding natural variants likely became fixed through epistatic selection. Additionally, molecular characterization of GI (Cvi) reveals a novel functional motif that can modulate the GI/ZTL interaction as well as nucleocytoplasmic partitioning. Taken together, these results identify a plausible temperature-dependent molecular mechanism, which contributes to the robustness of TC through natural variation in GI and ZTL alleles found on the Cape Verde Islands.
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Affiliation(s)
- Tae-Sung Kim
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Lei Wang
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Yeon Jeong Kim
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - David E Somers
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
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31
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Feng YZ, Yu Y, Zhou YF, Yang YW, Lei MQ, Lian JP, He H, Zhang YC, Huang W, Chen YQ. A Natural Variant of miR397 Mediates a Feedback Loop in Circadian Rhythm. PLANT PHYSIOLOGY 2020; 182:204-214. [PMID: 31694901 PMCID: PMC6945863 DOI: 10.1104/pp.19.00710] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/19/2019] [Indexed: 05/16/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs of ∼21 nt in length, which have regulatory roles in many biological processes. In animals, proper functioning of the circadian clock, which is closely linked to the fitness of almost all living organisms, is regulated by miRNAs. However, to date, there have been no reports of the roles of miRNA in regulation of the plant circadian rhythm. Here, we report a natural variant of miR397 that lengthens the circadian period and controls flowering time in Arabidopsis (Arabidopsis thaliana). Highly conserved among angiosperms, the miRNA miR397 has two members in Arabidopsis: miR397a and miR397b. However, only miR397b significantly delayed flowering. Our results suggest that miR397b controls flowering by targeting CASEIN KINASE II SUBUNIT BETA3 (CKB3), in turn modulating the circadian period of CIRCADIAN CLOCK ASSOCIATED1 (CCA1). We further demonstrated that CCA1 directly bound to the promoter of MIR397B and suppressed its expression, forming a miR397b-CKB3-CCA1 circadian regulation feedback circuit. Evolutionary analysis revealed that miR397b is a newly evolved genetic variant in Arabidopsis, and the miR397b targeting mode may have a role in enhancing plant fitness. Our results provide evidence for miRNA-mediated circadian regulation in plants and suggest the existence of a feedback loop to manipulate plant flowering through the regulation of circadian rhythm.
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Affiliation(s)
- Yan-Zhao Feng
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Yang Yu
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Yan-Fei Zhou
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Yu-Wei Yang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Meng-Qi Lei
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Jian-Ping Lian
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Huang He
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Yu-Chan Zhang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Wei Huang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Yue-Qin Chen
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
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32
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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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33
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Contribution of time of day and the circadian clock to the heat stress responsive transcriptome in Arabidopsis. Sci Rep 2019; 9:4814. [PMID: 30886204 PMCID: PMC6423321 DOI: 10.1038/s41598-019-41234-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/04/2019] [Indexed: 12/20/2022] Open
Abstract
In Arabidopsis, a large subset of heat responsive genes exhibits diurnal or circadian oscillations. However, to what extent the dimension of time and/or the circadian clock contribute to heat stress responses remains largely unknown. To determine the direct contribution of time of day and/or the clock to differential heat stress responses, we probed wild-type and mutants of the circadian clock genes CCA1, LHY, PRR7, and PRR9 following exposure to heat (37 °C) and moderate cold (10 °C) in the early morning (ZT1) and afternoon (ZT6). Thousands of genes were differentially expressed in response to temperature, time of day, and/or the clock mutation. Approximately 30% more genes were differentially expressed in the afternoon compared to the morning, and heat stress significantly perturbed the transcriptome. Of the DEGs (~3000) specifically responsive to heat stress, ~70% showed time of day (ZT1 or ZT6) occurrence of the transcriptional response. For the DEGs (~1400) that are shared between ZT1 and ZT6, we observed changes to the magnitude of the transcriptional response. In addition, ~2% of all DEGs showed differential responses to temperature stress in the clock mutants. The findings in this study highlight a significant role for time of day in the heat stress responsive transcriptome, and the clock through CCA1 and LHY, appears to have a more profound role than PRR7 and PRR9 in modulating heat stress responses during the day. Our results emphasize the importance of considering the dimension of time in studies on abiotic stress responses in Arabidopsis.
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34
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McClung CR. The Plant Circadian Oscillator. BIOLOGY 2019; 8:E14. [PMID: 30870980 PMCID: PMC6466001 DOI: 10.3390/biology8010014] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/17/2019] [Accepted: 03/09/2019] [Indexed: 12/20/2022]
Abstract
It has been nearly 300 years since the first scientific demonstration of a self-sustaining circadian clock in plants. It has become clear that plants are richly rhythmic, and many aspects of plant biology, including photosynthetic light harvesting and carbon assimilation, resistance to abiotic stresses, pathogens, and pests, photoperiodic flower induction, petal movement, and floral fragrance emission, exhibit circadian rhythmicity in one or more plant species. Much experimental effort, primarily, but not exclusively in Arabidopsis thaliana, has been expended to characterize and understand the plant circadian oscillator, which has been revealed to be a highly complex network of interlocked transcriptional feedback loops. In addition, the plant circadian oscillator has employed a panoply of post-transcriptional regulatory mechanisms, including alternative splicing, adjustable rates of translation, and regulated protein activity and stability. This review focuses on our present understanding of the regulatory network that comprises the plant circadian oscillator. The complexity of this oscillatory network facilitates the maintenance of robust rhythmicity in response to environmental extremes and permits nuanced control of multiple clock outputs. Consistent with this view, the clock is emerging as a target of domestication and presents multiple targets for targeted breeding to improve crop performance.
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Affiliation(s)
- C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA.
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Gil KE, Park CM. Thermal adaptation and plasticity of the plant circadian clock. THE NEW PHYTOLOGIST 2019; 221:1215-1229. [PMID: 30289568 DOI: 10.1111/nph.15518] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/11/2018] [Indexed: 05/20/2023]
Abstract
Contents Summary 1215 I. Introduction 1215 II. Molecular organization of the plant circadian clock 1216 III. Temperature compensation 1219 IV. Temperature regulation of circadian behaviors 1220 V. Thermal adaptation of the clock: evolutionary considerations 1223 VI. Light and temperature information for the clock function - synergic or individual? 1224 VII. Concluding remarks and future prospects 1225 Acknowledgements 1225 References 1225 SUMMARY: Plant growth and development is widely affected by diverse temperature conditions. Although studies have been focused mainly on the effects of stressful temperature extremes in recent decades, nonstressful ambient temperatures also influence an array of plant growth and morphogenic aspects, a process termed thermomorphogenesis. Notably, accumulating evidence indicates that both stressful and nonstressful temperatures modulate the functional process of the circadian clock, a molecular timer of biological rhythms in higher eukaryotes and photosynthetic prokaryotes. The circadian clock can sustain robust and precise timing over a range of physiological temperatures. Genes and molecular mechanisms governing the temperature compensation process have been explored in different plant species. In addition, a ZEITLUPE/HSP90-mediated protein quality control mechanism helps plants maintain the thermal stability of the clock under heat stress. The thermal adaptation capability and plasticity of the clock are of particular interest in view of the growing concern about global climate changes. Considering these circumstances in the field, we believe that it is timely to provide a provoking discussion on the current knowledge of temperature regulation of the clock function. The review also will discuss stimulating ideas on this topic along with ecosystem management and future agricultural innovation.
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Affiliation(s)
- Kyung-Eun Gil
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
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Jones MA, Morohashi K, Grotewold E, Harmer SL. Arabidopsis JMJD5/JMJ30 Acts Independently of LUX ARRHYTHMO Within the Plant Circadian Clock to Enable Temperature Compensation. FRONTIERS IN PLANT SCIENCE 2019; 10:57. [PMID: 30774641 PMCID: PMC6367231 DOI: 10.3389/fpls.2019.00057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/16/2019] [Indexed: 05/08/2023]
Abstract
The circadian system ensures that plants respond appropriately to environmental change by predicting regular transitions that occur during diel cycles. In order to be most useful, the circadian system needs to be compensated against daily and seasonal changes in temperature that would otherwise alter the pace of this biological oscillator. We demonstrate that an evening-phased protein, the putative histone demethylase JMJD5, contributes to temperature compensation. JMJD5 is co-expressed with components of the Evening Complex, an agglomeration of proteins including EARLY FLOWERING3 (ELF3), ELF4, and LUX ARRHYTHYMO (LUX), which also integrates temperature changes into the molecular clockwork. One role of the Evening Complex is to regulate expression of PSEUDORESPONSE REGULATOR9 (PRR9) and PRR7, important components of the temperature compensation mechanism. Surprisingly we find that LUX, but not other Evening Complex components, is dispensable for clock function at low temperatures. Further genetic analysis suggests JMJD5 acts in a parallel pathway to LUX within the circadian system. Although an intact JMJD5 catalytic domain is required for its function within the clock, our findings suggest JMJD5 does not directly regulate H3K36 methylation at circadian loci. Such data refine our understanding of how JMDJ5 acts within the Arabidopsis circadian system.
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Affiliation(s)
- Matthew A. Jones
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
- Department of Plant Biology, University of California, Davis, Davis, CA, United States
| | - Kengo Morohashi
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Stacey L. Harmer
- Department of Plant Biology, University of California, Davis, Davis, CA, United States
- *Correspondence: Stacey L. Harmer,
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Nagatoshi Y, Fujita M, Fujita Y. Casein kinase 2 α and β subunits inversely modulate ABA signal output in Arabidopsis protoplasts. PLANTA 2018; 248:571-578. [PMID: 29799081 PMCID: PMC6244648 DOI: 10.1007/s00425-018-2919-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/13/2018] [Indexed: 06/08/2023]
Abstract
Our transient gene expression analyses in Arabidopsis protoplasts support the view that CK2αs and CK2βs positively and negatively modulate ABRE-dependent gene expression, respectively. The phytohormone abscisic acid (ABA) regulates the expression of thousands of genes via ABA-responsive elements (ABREs), and has a crucial role in abiotic stress response. Casein kinase II (CK2), a conserved Ser/Thr protein kinase in eukaryotes, is essential for plant viability. Although the CK2 has been known as a tetrameric holoenzyme comprised of two catalytic α and two regulatory β subunits, each of the two types of subunits has been proposed to have independent functions. The Arabidopsis genome encodes four α subunits (CK2α1, CK2α2, CK2α3, CK2α4) and four β subunits (CK2β1, CK2β2, CK2β3, CK2β4). There is a growing body of evidence linking CK2 to ABA signaling and abiotic stress responses. However, the roles of each CK2 subunit in ABA signaling remain largely elusive. Using the transient expression system with the core ABA signaling components in Arabidopsis leaf mesophyll protoplasts, we show here that CK2α1 and CK2α2 (CK2α1/2) positively modulate ABRE-dependent gene expression as ABA signal output in ABA signaling, whereas all four CK2βs negatively modulate the ABRE-dependent gene expression mediated by subclass III SnRK2-AREB/ABF pathway and by CK2α1/2. These data indicate that CK2α1/2 and CK2βs positively and negatively modulate ABA signal output, respectively, suggesting that the quantitative balance of CK2 subunits determines the ABA signal output in plants. Given that CK2s act as pleiotropic enzymes involved in multiple developmental and stress-responsive processes, our findings suggest that CK2 subunits may be involved in integration and coordination of ABA-dependent and -independent signaling.
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Affiliation(s)
- Yukari Nagatoshi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
| | - Miki Fujita
- RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki, 305-0074, Japan
| | - Yasunari Fujita
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan.
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
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Frank A, Matiolli CC, Viana AJC, Hearn TJ, Kusakina J, Belbin FE, Wells Newman D, Yochikawa A, Cano-Ramirez DL, Chembath A, Cragg-Barber K, Haydon MJ, Hotta CT, Vincentz M, Webb AAR, Dodd AN. Circadian Entrainment in Arabidopsis by the Sugar-Responsive Transcription Factor bZIP63. Curr Biol 2018; 28:2597-2606.e6. [PMID: 30078562 PMCID: PMC6108399 DOI: 10.1016/j.cub.2018.05.092] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/28/2018] [Accepted: 05/31/2018] [Indexed: 02/08/2023]
Abstract
Synchronization of circadian clocks to the day-night cycle ensures the correct timing of biological events. This entrainment process is essential to ensure that the phase of the circadian oscillator is synchronized with daily events within the environment [1], to permit accurate anticipation of environmental changes [2, 3]. Entrainment in plants requires phase changes in the circadian oscillator, through unidentified pathways, which alter circadian oscillator gene expression in response to light, temperature, and sugars [4, 5, 6]. To determine how circadian clocks respond to metabolic rhythms, we investigated the mechanisms by which sugars adjust the circadian phase in Arabidopsis [5]. We focused upon metabolic regulation because interactions occur between circadian oscillators and metabolism in several experimental systems [5, 7, 8, 9], but the molecular mechanisms are unidentified. Here, we demonstrate that the transcription factor BASIC LEUCINE ZIPPER63 (bZIP63) regulates the circadian oscillator gene PSEUDO RESPONSE REGULATOR7 (PRR7) to change the circadian phase in response to sugars. We find that SnRK1, a sugar-sensing kinase that regulates bZIP63 activity and circadian period [10, 11, 12, 13, 14] is required for sucrose-induced changes in circadian phase. Furthermore, TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1), which synthesizes the signaling sugar trehalose-6-phosphate, is required for circadian phase adjustment in response to sucrose. We demonstrate that daily rhythms of energy availability can entrain the circadian oscillator through the function of bZIP63, TPS1, and the KIN10 subunit of the SnRK1 energy sensor. This identifies a molecular mechanism that adjusts the circadian phase in response to sugars. The transcription factor bZIP63 binds and regulates the circadian clock gene PRR7 bZIP63 is required for adjustment of circadian period by sugars Trehalose-6-phosphate metabolism and KIN10 signaling regulate circadian period Sugar signals establish the correct circadian phase in light and dark cycles
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Affiliation(s)
- Alexander Frank
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Cleverson C Matiolli
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, CEP 13083-875, CP 6010, Campinas, São Paulo, Brazil
| | - Américo J C Viana
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, CEP 13083-875, CP 6010, Campinas, São Paulo, Brazil
| | - Timothy J Hearn
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Jelena Kusakina
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK; Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Fiona E Belbin
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - David Wells Newman
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, CEP 13083-875, CP 6010, Campinas, São Paulo, Brazil
| | - Aline Yochikawa
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK; Universidade Estadual de Campinas, Barão Geraldo, Campinas, São Paulo, Brazil
| | | | - Anupama Chembath
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK; School of Life & Health Sciences, Aston University, Birmingham B4 7ET, UK
| | | | - Michael J Haydon
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK; School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Carlos T Hotta
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Michel Vincentz
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, CEP 13083-875, CP 6010, Campinas, São Paulo, Brazil
| | - Alex A R Webb
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK.
| | - Antony N Dodd
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK.
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Ode KL, Ueda HR. Design Principles of Phosphorylation-Dependent Timekeeping in Eukaryotic Circadian Clocks. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a028357. [PMID: 29038116 DOI: 10.1101/cshperspect.a028357] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The circadian clock in cyanobacteria employs a posttranslational oscillator composed of a sequential phosphorylation-dephosphorylation cycle of KaiC protein, in which the dynamics of protein structural changes driven by temperature-compensated KaiC's ATPase activity are critical for determining the period. On the other hand, circadian clocks in eukaryotes employ transcriptional feedback loops as a core mechanism. In this system, the dynamics of protein accumulation and degradation affect the circadian period. However, recent studies of eukaryotic circadian clocks reveal that the mechanism controlling the circadian period can be independent of the regulation of protein abundance. Instead, the circadian substrate is often phosphorylated at multiple sites at flexible protein regions to induce structural changes. The phosphorylation is catalyzed by kinases that induce sequential multisite phosphorylation such as casein kinase 1 (CK1) with temperature-compensated activity. We propose that the design principles of phosphorylation-dependent circadian-period determination in eukaryotes may share characteristics with the posttranslational oscillator in cyanobacteria.
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Affiliation(s)
- Koji L Ode
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.,Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.,Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
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Liu W, Lin Z, Liu Y, Lin Y, Xu X, Lai Z. Genome-wide identification and characterization of the CKII gene family in the cultivated banana cultivar (Musa spp. cv Tianbaojiao) and the wild banana (Musa itinerans). PLoS One 2018; 13:e0200149. [PMID: 29995937 PMCID: PMC6040749 DOI: 10.1371/journal.pone.0200149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/20/2018] [Indexed: 11/19/2022] Open
Abstract
Plant casein kinase II (CKII) plays an essential role in regulating plant growth and development, and responses to biotic and abiotic stresses. Here, we report the identification and characterization of the CKII family genes in Musa spp. cv. ‘Tianbaojiao’ (AAA group) and the wild banana (Musa itinerans). The 13 cDNA sequences of the CKII family members were identified both in ‘Tianbaojiao’ and wild banana, respectively. The differences between CKII α and CKII β members are corroborated through the subcellular localizations, phosphorylation sites and gene structures. The cloning of CKII β-like-2 gDNA sequences in wild banana and ‘Tianbaojiao’ and the analysis of gene structures showed MiCKIIβ-like-2b and MaCKIIβ-like-2 are likely alternatively spliced transcripts, which were derived from the alternative splicing events that involved exon deletion. The qPCR validation showed differential expression CKII family members in response to cold stress and also in all tested tissues (leaf, pseudostem and root) of wild banana. In particular, the normal transcript MiCKIIβ-like-2a was highly expressed in response to cold stress in wild banana; oppositely, the alternatively spliced transcript MiCKIIβ-like-2b was quite lowly expressed. The complex origin and long-term evolution of Musa lineage might explain the alternative splicing events of CKII β-like-2.
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Affiliation(s)
- Weihua Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhengchun Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yanying Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - XuHan Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- * E-mail:
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Hansen LL, van den Burg HA, van Ooijen G. Sumoylation Contributes to Timekeeping and Temperature Compensation of the Plant Circadian Clock. J Biol Rhythms 2017; 32:560-569. [PMID: 29172926 DOI: 10.1177/0748730417737633] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The transcriptional circadian clock network is tuned into a 24-h oscillator by numerous posttranslational modifications on the proteins encoded by clock genes, differentially influencing their subcellular localization or activity. Clock proteins in any circadian organism are subject to posttranslational regulation, and many of the key enzymes, notably kinases and phosphatases, are functionally conserved between the clocks of mammals, fungi, and plants. We now establish sumoylation, the posttranslational modification of target proteins by the covalent attachment of the small ubiquitin-like modifier protein SUMO, as a novel mechanism regulating key clock properties in the model plant Arabidopsis. Using 2 different approaches, we show that mutant plant lines with decreased or increased levels of global sumoylation exhibit shortened or lengthened circadian period, respectively. One known functional role of sumoylation is to protect the proteome from temperature stress. The circadian clock is characterized by temperature compensation, meaning that proper timekeeping is ensured over the full range of physiologically relevant temperatures. Interestingly, we observed that the period defects in sumoylation mutant plants are strongly differential across temperature. Increased global sumoylation leads to undercompensation of the clock against temperature and decreased sumoylation to overcompensation, implying that sumoylation buffers the plant clock system against differential ambient temperature.
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Affiliation(s)
- Louise L Hansen
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Harrold A van den Burg
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Gerben van Ooijen
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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Period2 3'-UTR and microRNA-24 regulate circadian rhythms by repressing PERIOD2 protein accumulation. Proc Natl Acad Sci U S A 2017; 114:E8855-E8864. [PMID: 28973913 DOI: 10.1073/pnas.1706611114] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We previously created two PER2::LUCIFERASE (PER2::LUC) circadian reporter knockin mice that differ only in the Per2 3'-UTR region: Per2::Luc, which retains the endogenous Per2 3'-UTR and Per2::LucSV, where the endogenous Per2 3'-UTR was replaced by an SV40 late poly(A) signal. To delineate the in vivo functions of Per2 3'-UTR, we analyzed circadian rhythms of Per2::LucSV mice. Interestingly, Per2::LucSV mice displayed more than threefold stronger amplitude in bioluminescence rhythms than Per2::Luc mice, and also exhibited lengthened free-running periods (∼24.0 h), greater phase delays following light pulse, and enhanced temperature compensation relative to Per2::Luc Analysis of the Per2 3'-UTR sequence revealed that miR-24, and to a lesser degree miR-30, suppressed PER2 protein translation, and the reversal of this inhibition in Per2::LucSV augmented PER2::LUC protein level and oscillatory amplitude. Interestingly, Bmal1 mRNA and protein oscillatory amplitude as well as CRY1 protein oscillation were increased in Per2::LucSV mice, suggesting rhythmic overexpression of PER2 enhances expression of Per2 and other core clock genes. Together, these studies provide important mechanistic insights into the regulatory roles of Per2 3'-UTR, miR-24, and PER2 in Per2 expression and core clock function.
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Kushanov FN, Buriev ZT, Shermatov SE, Turaev OS, Norov TM, Pepper AE, Saha S, Ulloa M, Yu JZ, Jenkins JN, Abdukarimov A, Abdurakhmonov IY. QTL mapping for flowering-time and photoperiod insensitivity of cotton Gossypium darwinii Watt. PLoS One 2017; 12:e0186240. [PMID: 29016665 PMCID: PMC5633191 DOI: 10.1371/journal.pone.0186240] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/27/2017] [Indexed: 02/05/2023] Open
Abstract
Most wild and semi-wild species of the genus Gossypium are exhibit photoperiod-sensitive flowering. The wild germplasm cotton is a valuable source of genes for genetic improvement of modern cotton cultivars. A bi-parental cotton population segregating for photoperiodic flowering was developed by crossing a photoperiod insensitive irradiation mutant line with its pre-mutagenesis photoperiodic wild-type G. darwinii Watt genotype. Individuals from the F2 and F3 generations were grown with their parental lines and F1 hybrid progeny in the long day and short night summer condition (natural day-length) of Uzbekistan to evaluate photoperiod sensitivity, i.e., flowering-time during the seasons 2008-2009. Through genotyping the individuals of this bi-parental population segregating for flowering-time, linkage maps were constructed using 212 simple-sequence repeat (SSR) and three cleaved amplified polymorphic sequence (CAPS) markers. Six QTLs directly associated with flowering-time and photoperiodic flowering were discovered in the F2 population, whereas eight QTLs were identified in the F3 population. Two QTLs controlling photoperiodic flowering and duration of flowering were common in both populations. In silico annotations of the flanking DNA sequences of mapped SSRs from sequenced cotton (G. hirsutum L.) genome database has identified several potential 'candidate' genes that are known to be associated with regulation of flowering characteristics of plants. The outcome of this research will expand our understanding of the genetic and molecular mechanisms of photoperiodic flowering. Identified markers should be useful for marker-assisted selection in cotton breeding to improve early flowering characteristics.
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Affiliation(s)
- Fakhriddin N. Kushanov
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Zabardast T. Buriev
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Shukhrat E. Shermatov
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Ozod S. Turaev
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Tokhir M. Norov
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Alan E. Pepper
- Department of Biology, Texas A&M University, Colleges Station, Texas, United States of America
| | - Sukumar Saha
- Crop Science Research Laboratory, United States Department of Agriculture-Agricultural Research Services, Starkville, Mississippi, United States of America
| | - Mauricio Ulloa
- Plant Stress and Germplasm Development Research, United States Department of Agriculture-Agricultural Research Services, Lubbock, Texas, United States of America
| | - John Z. Yu
- Southern Plains Agricultural Research Center, United States Department of Agriculture-Agricultural Research Services, College Station, Texas, United States of America
| | - Johnie N. Jenkins
- Crop Science Research Laboratory, United States Department of Agriculture-Agricultural Research Services, Starkville, Mississippi, United States of America
| | - Abdusattor Abdukarimov
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Ibrokhim Y. Abdurakhmonov
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- * E-mail:
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44
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Molecular mechanisms at the core of the plant circadian oscillator. Nat Struct Mol Biol 2016; 23:1061-1069. [PMID: 27922614 DOI: 10.1038/nsmb.3327] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/18/2016] [Indexed: 12/18/2022]
Abstract
Circadian clocks are endogenous timekeeping networks that allow organisms to align their physiology with their changing environment and to perform biological processes at the most relevant times of the day and year. Initial feedback-loop models of the oscillator have been enriched by emerging evidence highlighting the increasing variety of factors and mechanisms that contribute to the generation of rhythms. In this Review, we consider the two major input pathways that connect the circadian clock of the model plant Arabidopsis thaliana to its environment and discuss recent advances in understanding of how transcriptional, post-translational and post-transcriptional mechanisms contribute to clock function.
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Zhu J, Wang WS, Ma D, Zhang LY, Ren F, Yuan TT. A role for CK2 β subunit 4 in the regulation of plant growth, cadmium accumulation and H 2O 2 content under cadmium stress in Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 109:240-247. [PMID: 27750098 DOI: 10.1016/j.plaphy.2016.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/06/2016] [Accepted: 10/06/2016] [Indexed: 05/26/2023]
Abstract
Protein kinase CK2, which consists of two α and two β subunits, plays an essential role in plant development and is implicated in plant responses to abiotic stresses, including salt and heat. However, the function of CK2 in response to heavy metals such as cadmium (Cd) has not yet been established. In this study, the transgenic line CKB4ox, which overexpresses CKB4 encoding the CK2β subunit and has elevated CK2 activity, was used to investigate the potential role of CK2 in response to Cd stress in Arabidopsis thaliana. Under Cd stress, CKB4ox showed reduced root growth and biomass accumulation as well as decreased chlorophyll and proline contents compared with wild type. Furthermore, increased Cd accumulation and a higher H2O2 content were found in CKB4ox, possibly contributing to the inhibition of CKB4ox growth under Cd stress. Additionally, altered levels of Cd and H2O2 were found to be associated with decreased expression of genes involved in Cd efflux, Cd sequestration and H2O2 scavenging. Taken together, these results suggest that elevated expression of CKB4 and increased CK2 activity enhance the sensitivity of plants to Cd stress by affecting Cd and H2O2 accumulation, including the modulation of genes involved in Cd transport and H2O2 scavenging. This study provides direct evidence for the involvement of plant CK2 in the response to Cd stress.
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Affiliation(s)
- Jiang Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wen-Shu Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Dan Ma
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Lin-Yu Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Feng Ren
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Ting-Ting Yuan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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Hansen LL, van Ooijen G. Rapid Analysis of Circadian Phenotypes in Arabidopsis Protoplasts Transfected with a Luminescent Clock Reporter. J Vis Exp 2016:54586. [PMID: 27684315 PMCID: PMC5092030 DOI: 10.3791/54586] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The plant circadian clock allows the anticipation of daily changes to the environment. This anticipation aids the responses to temporally predictable biotic and abiotic stress. Conversely, disruption of circadian timekeeping severely compromises plant health and reduces agricultural crop yields. It is therefore imperative that we understand the intricate regulation of circadian rhythms in plants, including the factors that affect motion of the transcriptional clockwork itself. Testing circadian defects in the model plant Arabidopsis thaliana (Arabidopsis) traditionally involves crossing specific mutant lines to a line rhythmically expressing firefly luciferase from a circadian clock gene promoter. This approach is laborious, time-consuming, and could be fruitless if a mutant has no circadian phenotype. The methodology presented here allows a rapid initial assessment of circadian phenotypes. Protoplasts derived from mutant and wild-type Arabidopsis are isolated, transfected with a rhythmically expressed luminescent reporter, and imaged under constant light conditions for 5 days. Luminescent traces will directly reveal whether the free-running period of mutant plants is different from wild-type plants. The advantage of the method is that any Arabidopsis line can efficiently be screened, without the need for generating a stably transgenic luminescent clock marker line in that mutant background.
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Affiliation(s)
- Louise L Hansen
- Institute for Molecular Plant Sciences, University of Edinburgh
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Adams S, Manfield I, Stockley P, Carré IA. Revised Morning Loops of the Arabidopsis Circadian Clock Based on Analyses of Direct Regulatory Interactions. PLoS One 2015; 10:e0143943. [PMID: 26625126 PMCID: PMC4666590 DOI: 10.1371/journal.pone.0143943] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 11/11/2015] [Indexed: 11/24/2022] Open
Abstract
The network structure of the plant circadian clock is complex and direct regulatory interactions between individual components have proven particularly difficult to predict from genetic analyses. Here, we systematically investigate in vivo binding interactions between the morning-specific transcription factor, LATE ELONGATED HYPOCOTYL (LHY) and the promoters of other components of the network. We then demonstrate the functionality of these interactions by testing the responsiveness of the target gene to an ethanol-induced change in expression level of the LHY protein. We uncover novel, negative autoregulatory feedback loops from LHY and the closely related CIRCADIAN CLOCK ASSOCIATED-1 (CCA1) onto their own and each other’s expression. Furthermore we show that LHY acts as a repressor of all other clock components, including PSEUDO-RESPONSE REGULATORs (PRRs) 9 and 7, which were previously thought to be positive regulatory targets. These experimental results lead to a substantial revision of the morning loops of the clock.
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Affiliation(s)
- Sally Adams
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Ian Manfield
- Astbury Centre, University of Leeds, Leeds, United Kingdom
| | - Peter Stockley
- Astbury Centre, University of Leeds, Leeds, United Kingdom
| | - Isabelle A. Carré
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- * E-mail:
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48
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Temperature compensation and temperature sensation in the circadian clock. Proc Natl Acad Sci U S A 2015; 112:E6284-92. [PMID: 26578788 DOI: 10.1073/pnas.1511215112] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
All known circadian clocks have an endogenous period that is remarkably insensitive to temperature, a property known as temperature compensation, while at the same time being readily entrained by a diurnal temperature oscillation. Although temperature compensation and entrainment are defining features of circadian clocks, their mechanisms remain poorly understood. Most models presume that multiple steps in the circadian cycle are temperature-dependent, thus facilitating temperature entrainment, but then insist that the effect of changes around the cycle sums to zero to enforce temperature compensation. An alternative theory proposes that the circadian oscillator evolved from an adaptive temperature sensor: a gene circuit that responds only to temperature changes. This theory implies that temperature changes should linearly rescale the amplitudes of clock component oscillations but leave phase relationships and shapes unchanged. We show using timeless luciferase reporter measurements and Western blots against TIMELESS protein that this prediction is satisfied by the Drosophila circadian clock. We also review evidence for pathways that couple temperature to the circadian clock, and show previously unidentified evidence for coupling between the Drosophila clock and the heat-shock pathway.
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49
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A Hierarchical Multi-oscillator Network Orchestrates the Arabidopsis Circadian System. Cell 2015; 163:148-59. [DOI: 10.1016/j.cell.2015.08.062] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 07/01/2015] [Accepted: 08/06/2015] [Indexed: 11/23/2022]
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50
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Choudhary MK, Nomura Y, Wang L, Nakagami H, Somers DE. Quantitative Circadian Phosphoproteomic Analysis of Arabidopsis Reveals Extensive Clock Control of Key Components in Physiological, Metabolic, and Signaling Pathways. Mol Cell Proteomics 2015; 14:2243-60. [PMID: 26091701 DOI: 10.1074/mcp.m114.047183] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Indexed: 01/01/2023] Open
Abstract
The circadian clock provides adaptive advantages to an organism, resulting in increased fitness and survival. The phosphorylation events that regulate circadian-dependent signaling and the processes which post-translationally respond to clock-gated signals are largely unknown. To better elucidate post-translational events tied to the circadian system we carried out a survey of circadian-regulated protein phosphorylation events in Arabidopsis seedlings. A large-scale mass spectrometry-based quantitative phosphoproteomics approach employing TiO2-based phosphopeptide enrichment techniques identified and quantified 1586 phosphopeptides on 1080 protein groups. A total of 102 phosphopeptides displayed significant changes in abundance, enabling the identification of specific patterns of response to circadian rhythms. Our approach was sensitive enough to quantitate oscillations in the phosphorylation of low abundance clock proteins (early flowering4; ELF4 and pseudoresponse regulator3; PRR3) as well as other transcription factors and kinases. During constant light, extensive cyclic changes in phosphorylation status occurred in critical regulators, implicating direct or indirect regulation by the circadian system. These included proteins influencing transcriptional regulation, translation, metabolism, stress and phytohormones-mediated responses. We validated our analysis using the elf4-211 allele, in which an S45L transition removes the phosphorylation herein identified. We show that removal of this phosphorylatable site diminishes interaction with early flowering3 (ELF3), a key partner in a tripartite evening complex required for circadian cycling. elf4-211 lengthens period, which increases with increasing temperature, relative to the wild type, resulting in a more stable temperature compensation of circadian period over a wider temperature range.
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Affiliation(s)
- Mani Kant Choudhary
- From the ‡Division of Integrative Biosciences and Biotechnology, POSTECH, Hyojadong, Pohang, Kyungbuk, 790-784, Republic of Korea
| | - Yuko Nomura
- ¶Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan
| | - Lei Wang
- From the ‡Division of Integrative Biosciences and Biotechnology, POSTECH, Hyojadong, Pohang, Kyungbuk, 790-784, Republic of Korea §Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210; ‖Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hirofumi Nakagami
- ¶Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan
| | - David E Somers
- From the ‡Division of Integrative Biosciences and Biotechnology, POSTECH, Hyojadong, Pohang, Kyungbuk, 790-784, Republic of Korea §Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210;
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