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Zhu X, Wang H. Revisiting the role and mechanism of ELF3 in circadian clock modulation. Gene 2024; 913:148378. [PMID: 38490512 DOI: 10.1016/j.gene.2024.148378] [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] [Received: 12/06/2023] [Revised: 03/08/2024] [Accepted: 03/12/2024] [Indexed: 03/17/2024]
Abstract
The gene encoding EARLY FLOWERING3 (ELF3) is necessary for photoperiodic flowering and the normal regulation of circadian rhythms. It provides important information at the cellular level to uncover the biological mechanisms that improve plant growth and development. ELF3 interactions with transcription factors such as BROTHER OF LUX ARRHYTHMO (BOA), LIGHT-REGULATED WD1 (LWD1), PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), PHYTOCHROME-INTERACTING FACTOR 7 (PIF7), and LUX ARRHYTHMO (LUX) suggest a role in evening complex (EC) independent pathways, demanding further investigation to elucidate the EC-dependent versus EC-independent mechanisms. The ELF3 regulation of flowering time about photoperiod and temperature variations can also optimize crop cultivation across diverse latitudes. In this review paper, we summarize how ELF3's role in the circadian clock and light-responsive flowering control in crops offers substantial potential for scientific advancement and practical applications in biotechnology and agriculture. Despite its essential role in crop adaptation, very little is known in many important crops. Consequently, comprehensive and targeted research is essential for extrapolating ELF3-related insights from Arabidopsis to other crops, utilizing both computational and experimental methodologies. This research should prioritize investigations into ELF3's protein-protein interactions, post-translational modifications, and genomic targets to elucidate its contribution to accurate circadian clock regulation.
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Affiliation(s)
- Xingzun Zhu
- College of Landscape Architecture, Changchun University, No.1 Weixinglu Changchun, Jilin, China.
| | - Hongtao Wang
- College of Life Sciences, Tonghua Normal University, Tonghua, 950, Yucai Road, China.
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2
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Vives-Peris V, Gómez-Cadenas A, Pérez-Clemente RM. Proline accumulation and antioxidant response are crucial for citrus tolerance to UV-B light-induced stress. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:521-531. [PMID: 38568875 DOI: 10.1111/plb.13640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/03/2024] [Indexed: 04/05/2024]
Abstract
Plants face a wide range of biotic and abiotic stress conditions, which are further intensified by climate change. Among these stressors, increased irradiation in terms of intensity and wavelength range can lead to detrimental effects, such as chlorophyll degradation, destruction of the PSII reaction center, generation of ROS, alterations to plant metabolism, and even plant death. Here, we investigated the responses of two citrus genotypes, Citrus macrophylla (CM), and Troyer citrange (TC) to UV-B light-induced stress, by growing plants of both genotypes under control and UV-B stress conditions for 5 days to evaluate their tolerance mechanisms. TC seedlings had higher sensitivity to UV-B light than CM seedlings, as they showed more damage and increased levels of oxidative harm (indicated by the accumulation of MDA). In contrast, CM seedlings exhibited specific adaptive mechanisms, including accumulation of higher levels of proline under stressful conditions, and enhanced antioxidant capacity, as evidenced by increased ascorbate peroxidase activity and upregulation of the CsAPX2 gene. Phytohormone accumulation patterns were similar in both genotypes, with a decrease in ABA content in response to UV-B light. Furthermore, expression of genes involved in light perception and response was specifically affected in the tolerant CM seedlings, which exhibited higher expression of CsHYH/CsHY5 and CsRUP1-2 genes. These findings underscore the importance of the antioxidant system in citrus plants subjected to UV-B light-induced stress and suggest that CsHYH/CsHY5 and CsRUP1-2 could be considered genes associated with tolerance to such challenging conditions.
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Affiliation(s)
- V Vives-Peris
- Department of Biology, Biochemistry and Natural Sciences, Jaume I University, Castelló de la Plana, Spain
| | - A Gómez-Cadenas
- Department of Biology, Biochemistry and Natural Sciences, Jaume I University, Castelló de la Plana, Spain
| | - R M Pérez-Clemente
- Department of Biology, Biochemistry and Natural Sciences, Jaume I University, Castelló de la Plana, Spain
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3
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Yang X, Huang Y, Xia P. The property and function of proteins undergoing liquid-liquid phase separation in plants. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38808958 DOI: 10.1111/pce.14988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/16/2024] [Accepted: 05/19/2024] [Indexed: 05/30/2024]
Abstract
A wide variety of membrane-less organelles in cells play an essential role in regulating gene expression, RNA processing, plant growth and development, and helping organisms cope with changing external environments. In biology, liquid-liquid phase separation (LLPS) usually refers to a reversible process in which one or more specific molecular components are spontaneously separated from the bulk environment, producing two distinct liquid phases: concentrated and dilute. LLPS may be a powerful cellular compartmentalisation mechanism whereby biocondensates formed via LLPS when biomolecules exceed critical or saturating concentrations in the environment where they are found will be generated. It has been widely used to explain the formation of membrane-less organelles in organisms. LLPS studies in the context of plant physiology are now widespread, but most of the research is still focused on non-plant systems; the study of phase separation in plants needs to be more thorough. Proteins and nucleic acids are the main components involved in LLPS. This review summarises the specific features and properties of biomolecules undergoing LLPS in plants. We describe in detail these biomolecules' structural characteristics, the mechanism of formation of condensates, and the functions of these condensates. Finally, We summarised the phase separation mechanisms in plant growth, development, and stress adaptation.
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Affiliation(s)
- Xuejiao Yang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yang Huang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Pengguo Xia
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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4
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de Leone MJ, Yanovsky MJ. The circadian clock and thermal regulation in plants: novel insights into the role of positive circadian clock regulators in temperature responses. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2809-2818. [PMID: 38373194 DOI: 10.1093/jxb/erae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/19/2024] [Indexed: 02/21/2024]
Abstract
The impact of rising global temperatures on crop yields is a serious concern, and the development of heat-resistant crop varieties is crucial for mitigating the effects of climate change on agriculture. To achieve this, a better understanding of the molecular basis of the thermal responses of plants is necessary. The circadian clock plays a central role in modulating plant biology in synchrony with environmental changes, including temperature fluctuations. Recent studies have uncovered the role of transcriptional activators of the core circadian network in plant temperature responses. This expert view highlights key novel findings regarding the role of the RVE and LNK gene families in controlling gene expression patterns and plant growth under different temperature conditions, ranging from regular diurnal oscillations to extreme stress temperatures. These findings reinforce the essential role of the circadian clock in plant adaptation to changing temperatures and provide a basis for future studies on crop improvement.
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Affiliation(s)
- María José de Leone
- Fundación Instituto Leloir-IIBBA/CONICET, Av. Patricias Argentinas 435, Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcelo Javier Yanovsky
- Fundación Instituto Leloir-IIBBA/CONICET, Av. Patricias Argentinas 435, Ciudad Autónoma de Buenos Aires, Argentina
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5
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Sato H, Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K. Complex plant responses to drought and heat stress under climate change. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1873-1892. [PMID: 38168757 DOI: 10.1111/tpj.16612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/10/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024]
Abstract
Global climate change is predicted to result in increased yield losses of agricultural crops caused by environmental conditions. In particular, heat and drought stress are major factors that negatively affect plant development and reproduction, and previous studies have revealed how these stresses induce plant responses at physiological and molecular levels. Here, we provide a comprehensive overview of current knowledge concerning how drought, heat, and combinations of these stress conditions affect the status of plants, including crops, by affecting factors such as stomatal conductance, photosynthetic activity, cellular oxidative conditions, metabolomic profiles, and molecular signaling mechanisms. We further discuss stress-responsive regulatory factors such as transcription factors and signaling factors, which play critical roles in adaptation to both drought and heat stress conditions and potentially function as 'hubs' in drought and/or heat stress responses. Additionally, we present recent findings based on forward genetic approaches that reveal natural variations in agricultural crops that play critical roles in agricultural traits under drought and/or heat conditions. Finally, we provide an overview of the application of decades of study results to actual agricultural fields as a strategy to increase drought and/or heat stress tolerance. This review summarizes our current understanding of plant responses to drought, heat, and combinations of these stress conditions.
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Affiliation(s)
- Hikaru Sato
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Junya Mizoi
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kazuo Shinozaki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Institute for Advanced Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Kazuko Yamaguchi-Shinozaki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Research Institute for Agricultural and Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuraoka, Setagara-ku, Tokyo, 156-8502, Japan
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6
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Hughes CL, An Y, Maloof JN, Harmer SL. Light quality-dependent roles of REVEILLE proteins in the circadian system. PLANT DIRECT 2024; 8:e573. [PMID: 38481435 PMCID: PMC10936234 DOI: 10.1002/pld3.573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/25/2024] [Accepted: 02/10/2024] [Indexed: 03/17/2024]
Abstract
Several closely related Myb-like activator proteins are known to have partially redundant functions within the plant circadian clock, but their specific roles are not well understood. To clarify the function of the REVEILLE 4, REVEILLE 6, and REVEILLE 8 transcriptional activators, we characterized the growth and clock phenotypes of CRISPR-Cas9-generated single, double, and triple rve mutants. We found that these genes act synergistically to regulate flowering time, redundantly to regulate leaf growth, and antagonistically to regulate hypocotyl elongation. We previously reported that increasing intensities of monochromatic blue and red light have opposite effects on the period of triple rve468 mutants. Here, we further examined light quality-specific phenotypes of rve mutants and report that rve468 mutants lack the blue light-specific increase in expression of some circadian clock genes observed in wild type. To investigate the basis of these blue light-specific circadian phenotypes, we examined RVE protein abundances and degradation rates in blue and red light and found no significant differences between these conditions. We next examined genetic interactions between RVE genes and ZEITLUPE and ELONGATED HYPOCOTYL5, two factors with blue light-specific functions in the clock. We found that the RVEs interact additively with both ZEITLUPE and ELONGATED HYPOCOTYL5 to regulate circadian period, which suggests that neither of these factors are required for the blue light-specific differences that we observed. Overall, our results suggest that the RVEs have separable functions in plant growth and circadian regulation and that they are involved in blue light-specific circadian signaling via a novel mechanism.
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Affiliation(s)
- Cassandra L. Hughes
- Department of Plant BiologyUniversity of California, DavisDavisCaliforniaUSA
| | - Yuyan An
- College of Life SciencesShaanxi Normal UniversityXi'anChina
| | - Julin N. Maloof
- Department of Plant BiologyUniversity of California, DavisDavisCaliforniaUSA
| | - Stacey L. Harmer
- Department of Plant BiologyUniversity of California, DavisDavisCaliforniaUSA
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7
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Ji Z, Belfield EJ, Li S, Fu X, Harberd NP. Discovery of a second-site nia2 mutation in the background of multiple Arabidopsis PIF-related mutants containing the pif3-3 allele. THE NEW PHYTOLOGIST 2024; 241:17-23. [PMID: 37891447 PMCID: PMC10952432 DOI: 10.1111/nph.19344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023]
Affiliation(s)
- Zhe Ji
- Department of BiologyUniversity of OxfordOxfordOX1 3RBUK
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
| | | | - Shan Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjing210095China
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
- New Cornerstone Science LaboratoryBeijing100101China
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8
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Zhang Y, Ma Y, Zhang H, Xu J, Gao X, Zhang T, Liu X, Guo L, Zhao D. Environmental F actors coordinate circadian clock function and rhythm to regulate plant development. PLANT SIGNALING & BEHAVIOR 2023; 18:2231202. [PMID: 37481743 PMCID: PMC10364662 DOI: 10.1080/15592324.2023.2231202] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 07/25/2023]
Abstract
Changes in the external environment necessitate plant growth plasticity, with environmental signals such as light, temperature, and humidity regulating growth and development. The plant circadian clock is a biological time keeper that can be "reset" to adjust internal time to changes in the external environment. Exploring the regulatory mechanisms behind plant acclimation to environmental factors is important for understanding how plant growth and development are shaped and for boosting agricultural production. In this review, we summarize recent insights into the coordinated regulation of plant growth and development by environmental signals and the circadian clock, further discussing the potential of this knowledge.
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Affiliation(s)
- Ying Zhang
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- Institute of Biotechnology and Food Science, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Yuru Ma
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Hao Zhang
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Jiahui Xu
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Xiaokuan Gao
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
| | - Tengteng Zhang
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Xigang Liu
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Lin Guo
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Dan Zhao
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
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9
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Wu T, Wen H, Zhang X, Jia H, Xu C, Song W, Jiang B, Yuan S, Sun S, Wu C, Han T. Genome-wide association study for temperature response and photo-thermal interaction of flowering time in soybean using a panel of cultivars with diverse maturity groups. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:245. [PMID: 37962664 DOI: 10.1007/s00122-023-04496-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023]
Abstract
KEY MESSAGE A total of 101 QTNs were found to be associated with soybean flowering time responses to photo-thermal conditions; three candidate genes with non-synonymous substitutions were identified: Glyma.08G302500 (GmHY5), Glyma.08G303900 (GmPIF4c), and Glyma.16G046700 (GmVRN1). The flowering transition is a crucial component of soybean (Glycine max L. Merr.) development. The transition process is regulated by photoperiod, temperature, and their interaction. To examine the genetic architecture associated with temperature- and photo-thermal-mediated regulation of soybean flowering, we here performed a genome-wide association study using a panel of 201 soybean cultivars with maturity groups ranging from MG 000 to VIII. Each cultivar was grown in artificially controlled photoperiod and different seasons in 2017 and 2018 to assess the thermal response (TR) and the interactive photo-thermal response (IPT) of soybean flowering time. The panel contained 96,299 SNPs with minor allele frequencies > 5%; 33, 19, and 49 of these SNPs were significantly associated with only TR, only IPT, and both TR and IPT, respectively. Twenty-one SNPs were located in or near previously reported quantitative trait loci for first-flowering; 16 SNPs were located within 200 kb of the main-effect flowering genes GmFT2a, GmFT2b, GmFT3a, GmFT3b, GmFT5a, GmFT5b, GmCOL2b, GmPIF4b, and GmPIF4c, or near homologs of the known Arabidopsis thaliana flowering genes BBX19, VRN1, TFL1, FUL, AGL19, SPA1, HY5, PFT1, and EDF1. Natural non-synonymous allelic variations were identified in the candidate genes Glyma.08G302500 (GmHY5), Glyma.08G303900 (GmPIF4c), and Glyma.16G046700 (GmVRN1). Cultivars with different haplotypes showed significant variations in TR, IPT, and flowering time in multiple environments. The favorable alleles, candidate genes, and diagnostic SNP markers identified here provide valuable information for future improvement of soybean photo-thermal adaptability, enabling expansion of soybean production regions and improving plant resilience to global climate change.
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Affiliation(s)
- Tingting Wu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huiwen Wen
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinyue Zhang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongchang Jia
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe, 164300, China
| | - Cailong Xu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wenwen Song
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Bingjun Jiang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shan Yuan
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shi Sun
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Cunxiang Wu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Tianfu Han
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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10
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Gao G, Chen M, Mo R, Li N, Xu Y, Lu Y. Linking New Alleles at the Oscillator Loci to Flowering and Expansion of Asian Rice. Genes (Basel) 2023; 14:2027. [PMID: 38002970 PMCID: PMC10671530 DOI: 10.3390/genes14112027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
The central oscillator is believed to be the key mechanism by which plants adapt to new environments. However, impacts from hybridization, the natural environment, and human selection have rarely been assessed on the oscillator of a crop. Here, from clearly identified alleles at oscillator loci (OsCCA1/LHY, OsPRR95, OsPRR37, OsPRR59, and OsPRR1) in ten diverse genomes of Oryza sativa, additional accessions, and functional analysis, we show that rice's oscillator was rebuilt primarily by new alleles from recombining parental sequences and subsequent 5' or/and coding mutations. New alleles may exhibit altered transcript levels from that of a parental allele and are transcribed variably among genetic backgrounds and natural environments in RIL lines. Plants carrying more expressed OsCCA1_a and less transcribed OsPRR1_e flower early in the paddy field. 5' mutations are instrumental in varied transcription, as shown by EMSA tests on one deletion at the 5' region of highly transcribed OsPRR1_a. Compared to relatively balanced mutations at oscillator loci of Arabidopsis thaliana, 5' mutations of OsPRR37 (and OsCCA1 to a less degree) were under negative selection while those of OsPRR1 alleles were under strong positive selection. Together, range expansion of Asian rice can be elucidated by human selection on OsPRR1 alleles via local flowering time-yield relationships.
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Affiliation(s)
- Guangtong Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maoxian Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rong Mo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunzhang Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Yingqing Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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11
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Brooks CJ, Atamian HS, Harmer SL. Multiple light signaling pathways control solar tracking in sunflowers. PLoS Biol 2023; 21:e3002344. [PMID: 37906610 PMCID: PMC10617704 DOI: 10.1371/journal.pbio.3002344] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/21/2023] [Indexed: 11/02/2023] Open
Abstract
Sunflowers are famous for their ability to track the sun throughout the day and then reorient at night to face east the following morning. This occurs by differential growth patterns, with the east sides of stems growing more during the day and the west sides of stems growing more at night. This process, termed heliotropism, is generally believed to be a specialized form of phototropism; however, the underlying mechanism is unknown. To better understand heliotropism, we compared gene expression patterns in plants undergoing phototropism in a controlled environment and in plants initiating and maintaining heliotropic growth in the field. We found the expected transcriptome signatures of phototropin-mediated phototropism in sunflower stems bending towards monochromatic blue light. Surprisingly, the expression patterns of these phototropism-regulated genes are quite different in heliotropic plants. Most genes rapidly induced during phototropism display only minor differences in expression across solar tracking stems. However, some genes that are both rapidly induced during phototropism and are implicated in growth responses to foliar shade are rapidly induced on the west sides of stems at the onset of heliotropism, suggesting a possible role for red light photoreceptors in solar tracking. To test the involvement of different photoreceptor signaling pathways in heliotropism, we modulated the light environment of plants initiating solar tracking. We found that depletion of either red and far-red light or blue light did not hinder the initiation or maintenance of heliotropism in the field. Together, our results suggest that the transcriptional regulation of heliotropism is distinct from phototropin-mediated phototropism and likely involves inputs from multiple light signaling pathways.
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Affiliation(s)
- Christopher J. Brooks
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Hagop S. Atamian
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
- Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Stacey L. Harmer
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
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12
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Watanabe E, Muranaka T, Nakamura S, Isoda M, Horikawa Y, Aiso T, Ito S, Oyama T. A non-cell-autonomous circadian rhythm of bioluminescence reporter activities in individual duckweed cells. PLANT PHYSIOLOGY 2023; 193:677-688. [PMID: 37042358 DOI: 10.1093/plphys/kiad218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
The circadian clock is responsible for the temporal regulation of various physiological processes in plants. Individual cells contain a circadian oscillator consisting of a clock gene circuit that coordinates physiological rhythms within the plant body in an orderly manner. The coordination of time information has been studied from the perspective of cell-cell local coupling and long-distance communication between tissues based on the view that the behavior of circadian oscillators represents physiological rhythms. Here, we report the cellular circadian rhythm of bioluminescence reporters that are not governed by the clock gene circuit in expressing cells. We detected cellular bioluminescence rhythms with different free-running periods in the same cells using a dual-color bioluminescence monitoring system in duckweed (Lemna minor) transfected with Arabidopsis CIRCADIAN CLOCK ASSOCIATED 1::luciferace+ (AtCCA1::LUC+) and Cauliflower mosaic virus 35S::modified click-beetle red-color luciferase (CaMV35S::PtRLUC) reporters. Co-transfection experiments with the two reporters and a clock gene-overexpressing effector revealed that the AtCCA1::LUC+ rhythm, but not the CaMV35S::PtRLUC rhythm, was altered in cells with a dysfunctional clock gene circuit. This indicated that the AtCCA1::LUC+ rhythm is a direct output of the cellular circadian oscillator, whereas the CaMV35S::PtRLUC rhythm is not. After plasmolysis, the CaMV35S::PtRLUC rhythm disappeared, whereas the AtCCA1::LUC+ rhythm persisted. This suggests that the CaMV35S::PtRLUC bioluminescence has a symplast/apoplast-mediated circadian rhythm generated at the organismal level. The CaMV35S::PtRLUC-type bioluminescence rhythm was also observed when other bioluminescence reporters were expressed. These results reveal that the plant circadian system consists of both cell-autonomous and noncell-autonomous rhythms that are unaffected by cellular oscillators.
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Affiliation(s)
- Emiri Watanabe
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
- Department of Complexity Science and Engineering, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Tomoaki Muranaka
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan
| | - Shunji Nakamura
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Minako Isoda
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yu Horikawa
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tsuyoshi Aiso
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Shogo Ito
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tokitaka Oyama
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
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13
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Wu T, Lu S, Cai Y, Xu X, Zhang L, Chen F, Jiang B, Zhang H, Sun S, Zhai H, Zhao L, Xia Z, Hou W, Kong F, Han T. Molecular breeding for improvement of photothermal adaptability in soybean. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:60. [PMID: 37496825 PMCID: PMC10366068 DOI: 10.1007/s11032-023-01406-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 07/08/2023] [Indexed: 07/28/2023]
Abstract
Soybean (Glycine max (L.) Merr.) is a typical short-day and temperate crop that is sensitive to photoperiod and temperature. Responses of soybean to photothermal conditions determine plant growth and development, which affect its architecture, yield formation, and capacity for geographic adaptation. Flowering time, maturity, and other traits associated with photothermal adaptability are controlled by multiple major-effect and minor-effect genes and genotype-by-environment interactions. Genetic studies have identified at least 11 loci (E1-E4, E6-E11, and J) that participate in photoperiodic regulation of flowering time and maturity in soybean. Molecular cloning and characterization of major-effect flowering genes have clarified the photoperiod-dependent flowering pathway, in which the photoreceptor gene phytochrome A, circadian evening complex (EC) components, central flowering repressor E1, and FLOWERING LOCUS T family genes play key roles in regulation of flowering time, maturity, and adaptability to photothermal conditions. Here, we provide an overview of recent progress in genetic and molecular analysis of traits associated with photothermal adaptability, summarizing advances in molecular breeding practices and tools for improving these traits. Furthermore, we discuss methods for breeding soybean varieties with better adaptability to specific ecological regions, with emphasis on a novel strategy, the Potalaization model, which allows breeding of widely adapted soybean varieties through the use of multiple molecular tools in existing elite widely adapted varieties. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01406-z.
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Affiliation(s)
- Tingting Wu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Sijia Lu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Yupeng Cai
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xin Xu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Lixin Zhang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Fulu Chen
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Bingjun Jiang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Honglei Zhang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Shi Sun
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hong Zhai
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 China
| | - Lin Zhao
- Key Laboratory of Soybean Biology of Ministry of Education of China, Northeast Agricultural University, Harbin, 150030 China
| | - Zhengjun Xia
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 China
| | - Wensheng Hou
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Tianfu Han
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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14
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Scandola S, Mehta D, Castillo B, Boyce N, Uhrig RG. Systems-level proteomics and metabolomics reveals the diel molecular landscape of diverse kale cultivars. FRONTIERS IN PLANT SCIENCE 2023; 14:1170448. [PMID: 37575922 PMCID: PMC10421703 DOI: 10.3389/fpls.2023.1170448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/26/2023] [Indexed: 08/15/2023]
Abstract
Kale is a group of diverse Brassicaceae species that are nutritious leafy greens consumed for their abundance of vitamins and micronutrients. Typified by their curly, serrated and/or wavy leaves, kale varieties have been primarily defined based on their leaf morphology and geographic origin, despite having complex genetic backgrounds. Kale is a very promising crop for vertical farming due to its high nutritional content; however, being a non-model organism, foundational, systems-level analyses of kale are lacking. Previous studies in kale have shown that time-of-day harvesting can affect its nutritional composition. Therefore, to gain a systems-level diel understanding of kale across its wide-ranging and diverse genetic landscape, we selected nine publicly available and commercially grown kale cultivars for growth under near-sunlight LED light conditions ideal for vertical farming. We then analyzed changes in morphology, growth and nutrition using a combination of plant phenotyping, proteomics and metabolomics. As the diel molecular activities of plants drive their daily growth and development, ultimately determining their productivity as a crop, we harvested kale leaf tissue at both end-of-day (ED) and end-of-night (EN) time-points for all molecular analyses. Our results reveal that diel proteome and metabolome signatures divide the selected kale cultivars into two groups defined by their amino acid and sugar content, along with significant proteome differences involving carbon and nitrogen metabolism, mRNA splicing, protein translation and light harvesting. Together, our multi-cultivar, multi-omic analysis provides new insights into the molecular underpinnings of the diel growth and development landscape of kale, advancing our fundamental understanding of this nutritious leafy green super-food for horticulture/vertical farming applications.
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Affiliation(s)
| | | | | | | | - R. Glen Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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15
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Dalle Carbonare L, Basile A, Rindi L, Bulleri F, Hamedeh H, Iacopino S, Shukla V, Weits DA, Lombardi L, Sbrana A, Benedetti-Cecchi L, Giuntoli B, Licausi F, Maggi E. Dim artificial light at night alters gene expression rhythms and growth in a key seagrass species (Posidonia oceanica). Sci Rep 2023; 13:10620. [PMID: 37391536 PMCID: PMC10313690 DOI: 10.1038/s41598-023-37261-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 06/19/2023] [Indexed: 07/02/2023] Open
Abstract
Artificial light at night (ALAN) is a globally spreading anthropogenic stressor, affecting more than 20% of coastal habitats. The alteration of the natural light/darkness cycle is expected to impact the physiology of organisms by acting on the complex circuits termed as circadian rhythms. Our understanding of the impact of ALAN on marine organisms is lagging behind that of terrestrial ones, and effects on marine primary producers are almost unexplored. Here, we investigated the molecular and physiological response of the Mediterranean seagrass, Posidonia oceanica (L.) Delile, as model to evaluate the effect of ALAN on seagrass populations established in shallow waters, by taking advantage of a decreasing gradient of dim nocturnal light intensity (from < 0.01 to 4 lx) along the NW Mediterranean coastline. We first monitored the fluctuations of putative circadian-clock genes over a period of 24 h along the ALAN gradient. We then investigated whether key physiological processes, known to be synchronized with day length by the circadian rhythm, were also affected by ALAN. ALAN influenced the light signalling at dusk/night in P. oceanica, including that of shorter blue wavelengths, through the ELF3-LUX1-ZTL regulatory network, and suggested that the daily perturbation of internal clock orthologs in seagrass might have caused the recruitment of PoSEND33 and PoPSBS genes to mitigate the repercussions of a nocturnal stress on photosynthesis during the day. A long-lasting impairment of gene fluctuations in sites characterised by ALAN could explain the reduced growth of the seagrass leaves when these were transferred into controlled conditions and without lighting during the night. Our results highlight the potential contribution of ALAN to the global loss of seagrass meadows, posing questions about key interactions with a variety of other human-related stressors in urban areas, in order to develop more efficient strategies to globally preserve these coastal foundation species.
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Affiliation(s)
- L Dalle Carbonare
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri Della Libertà, 56127, Pisa, Italy.
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK.
| | - A Basile
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri Della Libertà, 56127, Pisa, Italy
| | - L Rindi
- Dipartimento di Biologia, Universita' di Pisa, CoNISMa, Via Luca Ghini 13, 56126, Pisa, Italy
| | - F Bulleri
- Dipartimento di Biologia, Universita' di Pisa, CoNISMa, Via Luca Ghini 13, 56126, Pisa, Italy
| | - H Hamedeh
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri Della Libertà, 56127, Pisa, Italy
| | - S Iacopino
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri Della Libertà, 56127, Pisa, Italy
| | - V Shukla
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri Della Libertà, 56127, Pisa, Italy
| | - D A Weits
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri Della Libertà, 56127, Pisa, Italy
| | - L Lombardi
- Dipartimento di Biologia, Universita' di Pisa, CoNISMa, Via Luca Ghini 13, 56126, Pisa, Italy
| | - A Sbrana
- Dipartimento di Biologia, Universita' di Pisa, CoNISMa, Via Luca Ghini 13, 56126, Pisa, Italy
| | - L Benedetti-Cecchi
- Dipartimento di Biologia, Universita' di Pisa, CoNISMa, Via Luca Ghini 13, 56126, Pisa, Italy
| | - B Giuntoli
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri Della Libertà, 56127, Pisa, Italy
- Dipartimento di Biologia, Universita' di Pisa, CoNISMa, Via Luca Ghini 13, 56126, Pisa, Italy
| | - F Licausi
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - E Maggi
- Dipartimento di Biologia, Universita' di Pisa, CoNISMa, Via Luca Ghini 13, 56126, Pisa, Italy.
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16
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Sakeef N, Scandola S, Kennedy C, Lummer C, Chang J, Uhrig RG, Lin G. Machine learning classification of plant genotypes grown under different light conditions through the integration of multi-scale time-series data. Comput Struct Biotechnol J 2023; 21:3183-3195. [PMID: 37333861 PMCID: PMC10275741 DOI: 10.1016/j.csbj.2023.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 06/20/2023] Open
Abstract
In order to mitigate the effects of a changing climate, agriculture requires more effective evaluation, selection, and production of crop cultivars in order to accelerate genotype-to-phenotype connections and the selection of beneficial traits. Critically, plant growth and development are highly dependent on sunlight, with light energy providing plants with the energy required to photosynthesize as well as a means to directly intersect with the environment in order to develop. In plant analyses, machine learning and deep learning techniques have a proven ability to learn plant growth patterns, including detection of disease, plant stress, and growth using a variety of image data. To date, however, studies have not assessed machine learning and deep learning algorithms for their ability to differentiate a large cohort of genotypes grown under several growth conditions using time-series data automatically acquired across multiple scales (daily and developmentally). Here, we extensively evaluate a wide range of machine learning and deep learning algorithms for their ability to differentiate 17 well-characterized photoreceptor deficient genotypes differing in their light detection capabilities grown under several different light conditions. Using algorithm performance measurements of precision, recall, F1-Score, and accuracy, we find that Suport Vector Machine (SVM) maintains the greatest classification accuracy, while a combined ConvLSTM2D deep learning model produces the best genotype classification results across the different growth conditions. Our successful integration of time-series growth data across multiple scales, genotypes and growth conditions sets a new foundational baseline from which more complex plant science traits can be assessed for genotype-to-phenotype connections.
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Affiliation(s)
- Nazmus Sakeef
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Sabine Scandola
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Curtis Kennedy
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Christina Lummer
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Jiameng Chang
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
| | - R. Glen Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Guohui Lin
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
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17
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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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18
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Tang J, Liu H, Quan Y, Yao Y, Li K, Tang G, Du D. Fine mapping and causal gene identification of a novel QTL for early flowering by QTL-seq, Target-seq and RNA-seq in spring oilseed rape. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:80. [PMID: 36952057 DOI: 10.1007/s00122-023-04310-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
A novel quantitative trait locus for early flowering in spring oilseed rape, BnaC08cqDTF, was mapped to an 86-kb region on chromosome C08, and its causal gene, CRY2, was uncovered. Days to flowering is a very important agronomic and adaptive trait of Brassica napus oilseed rape (AACC, 2n = 38). We previously identified BnaC08cqDTF as a novel candidate quantitative trait locus (QTL) for early flowering in spring oilseed rape. Here, we present fine mapping of the locus and a study of its causal gene. Initial mapping was performed by QTL sequencing of DNA pools of BC3F2 plants with extreme flowering times derived from crosses between the spring-type cv. No. 4512 (early flowering) and cv. No. 5246 (late flowering), along with fine mapping by target sequencing of the BC3F2 and BC4F2 populations. Fine mapping narrowed down BnaC08cqDTF to an 86-kb region on chromosome C08. The region harbored fifteen genes. After comparative analyses of the DNA sequences for mutation between A and C syntenic regions and detected by RNA-seq and qRT-PCR between the two parents, we found that BnaC08G0010400ZS harbors an A/G nonsynonymous mutation in exon 3. This single nucleotide polymorphism (SNP) haplotype was also correlated with early flowering in a 256 accession panel. BnaC08G0010400ZS is a homolog of the AT1G04400 gene (CRY2) in Arabidopsis. The analyses of transgenic Arabidopsis verified that BnaC08G0010400ZS is responsible for early flowering. Our results contribute to a better understanding of the genetic control mechanism of early flowering in spring Brassica napus and will promote the breeding for early mature varieties.
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Affiliation(s)
- Jie Tang
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai Spring Rape Engineering Research Center, Qinghai Research Branch of the National Oil Crop Genetic Improvement Center, Spring Rape Scientific Observation Experimental Station of Ministry of Agriculture and Rural Areas, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China
- Crop Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, Jiangxi, China
| | - Haidong Liu
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai Spring Rape Engineering Research Center, Qinghai Research Branch of the National Oil Crop Genetic Improvement Center, Spring Rape Scientific Observation Experimental Station of Ministry of Agriculture and Rural Areas, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China
| | - Youjuan Quan
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai Spring Rape Engineering Research Center, Qinghai Research Branch of the National Oil Crop Genetic Improvement Center, Spring Rape Scientific Observation Experimental Station of Ministry of Agriculture and Rural Areas, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China
| | - Yanmei Yao
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai Spring Rape Engineering Research Center, Qinghai Research Branch of the National Oil Crop Genetic Improvement Center, Spring Rape Scientific Observation Experimental Station of Ministry of Agriculture and Rural Areas, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China
| | - Kaixiang Li
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai Spring Rape Engineering Research Center, Qinghai Research Branch of the National Oil Crop Genetic Improvement Center, Spring Rape Scientific Observation Experimental Station of Ministry of Agriculture and Rural Areas, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China
| | - Guoyong Tang
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai Spring Rape Engineering Research Center, Qinghai Research Branch of the National Oil Crop Genetic Improvement Center, Spring Rape Scientific Observation Experimental Station of Ministry of Agriculture and Rural Areas, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China.
| | - Dezhi Du
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai Spring Rape Engineering Research Center, Qinghai Research Branch of the National Oil Crop Genetic Improvement Center, Spring Rape Scientific Observation Experimental Station of Ministry of Agriculture and Rural Areas, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China.
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19
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Breen S, McLellan H, Birch PRJ, Gilroy EM. Tuning the Wavelength: Manipulation of Light Signaling to Control Plant Defense. Int J Mol Sci 2023; 24:ijms24043803. [PMID: 36835216 PMCID: PMC9958957 DOI: 10.3390/ijms24043803] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
The growth-defense trade-off in plants is a phenomenon whereby plants must balance the allocation of their resources between developmental growth and defense against attack by pests and pathogens. Consequently, there are a series of points where growth signaling can negatively regulate defenses and where defense signaling can inhibit growth. Light perception by various photoreceptors has a major role in the control of growth and thus many points where it can influence defense. Plant pathogens secrete effector proteins to manipulate defense signaling in their hosts. Evidence is emerging that some of these effectors target light signaling pathways. Several effectors from different kingdoms of life have converged on key chloroplast processes to take advantage of regulatory crosstalk. Moreover, plant pathogens also perceive and react to light in complex ways to regulate their own growth, development, and virulence. Recent work has shown that varying light wavelengths may provide a novel way of controlling or preventing disease outbreaks in plants.
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Affiliation(s)
- Susan Breen
- Division of Plant Sciences, University of Dundee, At James Hutton Institute, Errol Road, Invergowrie, Dundee DD2 5DA, UK
| | - Hazel McLellan
- Division of Plant Sciences, University of Dundee, At James Hutton Institute, Errol Road, Invergowrie, Dundee DD2 5DA, UK
| | - Paul R. J. Birch
- Division of Plant Sciences, University of Dundee, At James Hutton Institute, Errol Road, Invergowrie, Dundee DD2 5DA, UK
- Cell and Molecular Sciences, James Hutton Institute, Errol Road, Invergowrie, Dundee DD2 5DA, UK
| | - Eleanor M. Gilroy
- Cell and Molecular Sciences, James Hutton Institute, Errol Road, Invergowrie, Dundee DD2 5DA, UK
- Correspondence: ; Tel.: +44-1382568827
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20
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Stafen CF, Kleine-Vehn J, Maraschin FDS. Signaling events for photomorphogenic root development. TRENDS IN PLANT SCIENCE 2022; 27:1266-1282. [PMID: 36057533 DOI: 10.1016/j.tplants.2022.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 07/26/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
A germinating seedling incorporates environmental signals such as light into developmental outputs. Light is not only a source of energy, but also a central coordinative signal in plants. Traditionally, most research focuses on aboveground organs' response to light; therefore, our understanding of photomorphogenesis in roots is relatively scarce. However, root development underground is highly responsive to light signals from the shoot and understanding these signaling mechanisms will give a better insight into early seedling development. Here, we review the central light signaling hubs and their role in root growth promotion of Arabidopsis thaliana seedlings.
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Affiliation(s)
- Cássia Fernanda Stafen
- PPGBM - Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Jürgen Kleine-Vehn
- Institute of Biology II, Chair of Molecular Plant Physiology (MoPP), University of Freiburg, Freiburg, Germany; Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany
| | - Felipe Dos Santos Maraschin
- PPGBM - Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil; Departamento de Botânica, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil.
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21
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Meng Y, Zhang N, Li J, Shen X, Sheen J, Xiong Y. TOR kinase, a GPS in the complex nutrient and hormonal signaling networks to guide plant growth and development. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7041-7054. [PMID: 35781569 PMCID: PMC9664236 DOI: 10.1093/jxb/erac282] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/24/2022] [Indexed: 06/01/2023]
Abstract
To survive and sustain growth, sessile plants have developed sophisticated internal signalling networks that respond to various external and internal cues. Despite the central roles of nutrient and hormone signaling in plant growth and development, how hormone-driven processes coordinate with metabolic status remains largely enigmatic. Target of rapamycin (TOR) kinase is an evolutionarily conserved master regulator that integrates energy, nutrients, growth factors, hormones, and stress signals to promote growth in all eukaryotes. Inspired by recent comprehensive systems, chemical, genetic, and genomic studies on TOR in plants, this review discusses a potential role of TOR as a 'global positioning system' that directs plant growth and developmental programs both temporally and spatially by integrating dynamic information in the complex nutrient and hormonal signaling networks. We further evaluate and depict the possible functional and mechanistic models for how a single protein kinase, TOR, is able to recognize, integrate, and even distinguish a plethora of positive and negative input signals to execute appropriate and distinct downstream biological processes via multiple partners and effectors.
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Affiliation(s)
| | | | - Jiatian Li
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Haixia Institute of Science and Technology, Plant Synthetic Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuehong Shen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Haixia Institute of Science and Technology, Plant Synthetic Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jen Sheen
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA, USA
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22
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Gururaj M, Ohmura A, Ozawa M, Yamano T, Fukuzawa H, Matsuo T. A potential EARLY FLOWERING 3 homolog in Chlamydomonas is involved in the red/violet and blue light signaling pathways for the degradation of RHYTHM OF CHLOROPLAST 15. PLoS Genet 2022; 18:e1010449. [PMID: 36251728 PMCID: PMC9612821 DOI: 10.1371/journal.pgen.1010449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 10/27/2022] [Accepted: 09/26/2022] [Indexed: 11/07/2022] Open
Abstract
Light plays a major role in resetting the circadian clock, allowing the organism to synchronize with the environmental day and night cycle. In Chlamydomonas the light-induced degradation of the circadian clock protein, RHYTHM OF CHLOROPLAST 15 (ROC15), is considered one of the key events in resetting the circadian clock. Red/violet and blue light signals have been shown to reach the clock via different molecular pathways; however, many of the participating components of these pathways are yet to be elucidated. Here, we used a forward genetics approach using a reporter strain that expresses a ROC15-luciferase fusion protein. We isolated a mutant that showed impaired ROC15 degradation in response to a wide range of visible wavelengths and impaired light-induced phosphorylation of ROC15. These results suggest that the effects of different wavelengths converge before acting on ROC15 or at ROC15 phosphorylation. Furthermore, the mutant showed a weakened phase resetting in response to light, but its circadian rhythmicity remained largely unaffected under constant light and constant dark conditions. Surprisingly, the gene disrupted in this mutant was found to encode a protein that possessed a very weak similarity to the Arabidopsis thaliana EARLY FLOWERING 3 (ELF3). Our results suggest that this protein is involved in the many different light signaling pathways to the Chlamydomonas circadian clock. However, it may not influence the transcriptional oscillator of Chlamydomonas to a great extent. This study provides an opportunity to further understand the mechanisms underlying light-induced clock resetting and explore the evolution of the circadian clock architecture in Viridiplantae. Resetting of the circadian clock is crucial for an organism, as it allows the synchronization of its internal processes with the day/night cycle. Environmental signals—such as light and temperature—contribute to this event. In plants, the molecular mechanisms underlying the light-induced resetting of the circadian clock have been well-studied in the streptophyte, Arabidopsis thaliana, and has been explored in some chlorophyte algae such as Ostreococcus tauri and Chlamydomonas reinhardtii. Here, we used a forward genetics approach to examine the light signaling pathway of a process considered critical for the light resetting of the Chlamydomonas clock—light-induced degradation of the circadian clock protein ROC15. We explored various aspects of the isolated mutant, such as the degradation of ROC15 in response to a range of visible wavelengths, the circadian rhythm, and the phase resetting of the rhythm. We show that the effects of different wavelengths of light converge before acting on ROC15 or at ROC15 phosphorylation with the aid of a potential homolog of the Arabidopsis thaliana ELF3. Our findings contradict the existing view that there is no known homolog of ELF3 in chlorophyte algae. This study, therefore, sheds light on the evolutionary aspects of the Viridiplantae circadian clocks and their light resetting.
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Affiliation(s)
- Malavika Gururaj
- Center for Gene Research, Nagoya University, Nagoya, Japan
- Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Ayumi Ohmura
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Mariko Ozawa
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Takashi Yamano
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Hideya Fukuzawa
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Takuya Matsuo
- Center for Gene Research, Nagoya University, Nagoya, Japan
- Graduate School of Science, Nagoya University, Nagoya, Japan
- * E-mail:
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23
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He Y, Yu Y, Wang X, Qin Y, Su C, Wang L. Aschoff's rule on circadian rhythms orchestrated by blue light sensor CRY2 and clock component PRR9. Nat Commun 2022; 13:5869. [PMID: 36198686 PMCID: PMC9535003 DOI: 10.1038/s41467-022-33568-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 09/22/2022] [Indexed: 11/09/2022] Open
Abstract
Circadian pace is modulated by light intensity, known as the Aschoff’s rule, with largely unrevealed mechanisms. Here we report that photoreceptor CRY2 mediates blue light input to the circadian clock by directly interacting with clock core component PRR9 in blue light dependent manner. This physical interaction dually blocks the accessibility of PRR9 protein to its co-repressor TPL/TPRs and the resulting kinase PPKs. Notably, phosphorylation of PRR9 by PPKs is critical for its DNA binding and repressive activity, hence to ensure proper circadian speed. Given the labile nature of CRY2 in strong blue light, our findings provide a mechanistic explanation for Aschoff’s rule in plants, i.e., blue light triggers CRY2 turnover in proportional to its intensity, which accordingly releasing PRR9 to fine tune circadian speed. Our findings not only reveal a network mediating light input into the circadian clock, but also unmask a mechanism by which the Arabidopsis circadian clock senses light intensity. Circadian pace is modulated by light intensity. Here the authors show that CRY2 interacts with PRR9 to mediate blue light input to the circadian clock and is degraded at higher light intensity offering a mechanistic explanation as to how intensity can modify clock place.
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Affiliation(s)
- Yuqing He
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingjun Yu
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiling Wang
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yumei Qin
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chen Su
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Wang
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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24
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Xiong L, Zhou W, Mas P. Illuminating the Arabidopsis circadian epigenome: Dynamics of histone acetylation and deacetylation. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102268. [PMID: 35921796 DOI: 10.1016/j.pbi.2022.102268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 06/21/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
The circadian clock generates rhythms in biological processes including plant development and metabolism. Light synchronizes the circadian clock with the day and night cycle and also triggers developmental transitions such as germination, or flowering. The circadian and light signaling pathways are closely interconnected and understanding their mechanisms of action and regulation requires the integration of both pathways in their complexity. Here, we provide a glimpse into how chromatin remodeling lies at the interface of the circadian and light signaling regulation. We focus on histone acetylation/deacetylation and the generation of permissive or repressive states for transcription. Several chromatin remodelers intervene in both pathways, suggesting that interaction with specific transcription factors might specify the proper timing or light-dependent responses. Deciphering the repertoire of chromatin remodelers and their interacting transcription factors will provide a view on the circadian and light-dependent epigenetic landscape amenable for mechanistic studies and timely regulation of transcription in plants.
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Affiliation(s)
- Lu Xiong
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Wenguan Zhou
- 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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25
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Petersen J, Rredhi A, Szyttenholm J, Mittag M. Evolution of circadian clocks along the green lineage. PLANT PHYSIOLOGY 2022; 190:924-937. [PMID: 35325228 PMCID: PMC9516769 DOI: 10.1093/plphys/kiac141] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/04/2022] [Indexed: 05/10/2023]
Abstract
Circadian clocks govern temporal programs in the green lineage (Chloroplastida) as they do in other photosynthetic pro- and eukaryotes, bacteria, fungi, animals, and humans. Their physiological properties, including entrainment, phase responses, and temperature compensation, are well conserved. The involvement of transcriptional/translational feedback loops in the oscillatory machinery and reversible phosphorylation events are also maintained. Circadian clocks control a large variety of output rhythms in green algae and terrestrial plants, adjusting their metabolism and behavior to the day-night cycle. The angiosperm Arabidopsis (Arabidopsis thaliana) represents a well-studied circadian clock model. Several molecular components of its oscillatory machinery are conserved in other Chloroplastida, but their functions may differ. Conserved clock components include at least one member of the CIRCADIAN CLOCK ASSOCIATED1/REVEILLE and one of the PSEUDO RESPONSE REGULATOR family. The Arabidopsis evening complex members EARLY FLOWERING3 (ELF3), ELF4, and LUX ARRHYTHMO are found in the moss Physcomitrium patens and in the liverwort Marchantia polymorpha. In the flagellate chlorophyte alga Chlamydomonas reinhardtii, only homologs of ELF4 and LUX (named RHYTHM OF CHLOROPLAST ROC75) are present. Temporal ROC75 expression in C. reinhardtii is opposite to that of the angiosperm LUX, suggesting different clock mechanisms. In the picoalga Ostreococcus tauri, both ELF genes are missing, suggesting that it has a progenitor circadian "green" clock. Clock-relevant photoreceptors and thermosensors vary within the green lineage, except for the CRYPTOCHROMEs, whose variety and functions may differ. More genetically tractable models of Chloroplastida are needed to draw final conclusions about the gradual evolution of circadian clocks within the green lineage.
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Affiliation(s)
- Jan Petersen
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Anxhela Rredhi
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Julie Szyttenholm
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena 07743, Germany
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26
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Scandola S, Mehta D, Li Q, Rodriguez Gallo MC, Castillo B, Uhrig RG. Multi-omic analysis shows REVEILLE clock genes are involved in carbohydrate metabolism and proteasome function. PLANT PHYSIOLOGY 2022; 190:1005-1023. [PMID: 35670757 PMCID: PMC9516735 DOI: 10.1093/plphys/kiac269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/12/2022] [Indexed: 06/01/2023]
Abstract
Plants are able to sense changes in their light environments, such as the onset of day and night, as well as anticipate these changes in order to adapt and survive. Central to this ability is the plant circadian clock, a molecular circuit that precisely orchestrates plant cell processes over the course of a day. REVEILLE (RVE) proteins are recently discovered members of the plant circadian circuitry that activate the evening complex and PSEUDO-RESPONSE REGULATOR genes to maintain regular circadian oscillation. The RVE8 protein and its two homologs, RVE 4 and 6 in Arabidopsis (Arabidopsis thaliana), have been shown to limit the length of the circadian period, with rve 4 6 8 triple-knockout plants possessing an elongated period along with increased leaf surface area, biomass, cell size, and delayed flowering relative to wild-type Col-0 plants. Here, using a multi-omics approach consisting of phenomics, transcriptomics, proteomics, and metabolomics we draw new connections between RVE8-like proteins and a number of core plant cell processes. In particular, we reveal that loss of RVE8-like proteins results in altered carbohydrate, organic acid, and lipid metabolism, including a starch excess phenotype at dawn. We further demonstrate that rve 4 6 8 plants have lower levels of 20S proteasome subunits and possess significantly reduced proteasome activity, potentially explaining the increase in cell-size observed in RVE8-like mutants. Overall, this robust, multi-omic dataset provides substantial insight into the far-reaching impact RVE8-like proteins have on the diel plant cell environment.
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Affiliation(s)
| | | | - Qiaomu Li
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | | | - Brigo Castillo
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
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27
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Wang S, Steed G, Webb AAR. Circadian entrainment in Arabidopsis. PLANT PHYSIOLOGY 2022; 190:981-993. [PMID: 35512209 PMCID: PMC9516740 DOI: 10.1093/plphys/kiac204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Circadian clocks coordinate physiology and development as an adaption to the oscillating day/night cycle caused by the rotation of Earth on its axis and the changing length of day and night away from the equator caused by orbiting the sun. Circadian clocks confer advantages by entraining to rhythmic environmental cycles to ensure that internal events within the plant occur at the correct time with respect to the cyclic external environment. Advances in determining the structure of circadian oscillators and the pathways that allow them to respond to light, temperature, and metabolic signals have begun to provide a mechanistic insight to the process of entrainment in Arabidopsis (Arabidopsis thaliana). We describe the concepts of entrainment and how it occurs. It is likely that a thorough mechanistic understanding of the genetic and physiological basis of circadian entrainment will provide opportunities for crop improvement.
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Affiliation(s)
- Shouming Wang
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
- School of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Gareth Steed
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
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28
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Wang Y, Su C, Yu Y, He Y, Wei H, Li N, Li H, Duan J, Li B, Li J, Davis SJ, Wang L. TIME FOR COFFEE regulates phytochrome A-mediated hypocotyl growth through dawn-phased signaling. THE PLANT CELL 2022; 34:2907-2924. [PMID: 35543486 PMCID: PMC9338810 DOI: 10.1093/plcell/koac138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/24/2022] [Indexed: 05/14/2023]
Abstract
To enhance plant fitness under natural conditions, the circadian clock is synchronized and entrained by light via photoreceptors. In turn, the circadian clock exquisitely regulates the abundance and activity of photoreceptors via largely uncharacterized mechanisms. Here we show that the clock regulator TIME FOR COFFEE (TIC) controls the activity of the far-red light photoreceptor phytochrome A (phyA) at multiple levels in Arabidopsis thaliana. Null mutants of TIC displayed dramatically increased sensitivity to light irradiation with respect to hypocotyl growth, especially to far-red light. RNA-sequencing demonstrated that TIC and phyA play largely opposing roles in controlling light-regulated gene expression at dawn. Additionally, TIC physically interacts with the transcriptional repressor TOPLESS (TPL), which was associated with the significantly increased PHYA transcript levels in the tic-2 and tpl-1 mutants. Moreover, TIC interacts with phyA in the nucleus, thereby affecting phyA protein turnover and the formation of phyA nuclear speckles following light irradiation. Genetically, phyA was found to act downstream of TIC in regulating far red light-inhibited growth. Taken together, these findings indicate that TIC acts as a major negative regulator of phyA by integrating transcriptional and post-translational mechanisms at multiple levels.
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Affiliation(s)
| | | | | | - Yuqing He
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hua Wei
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Li
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jie Duan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Bin Li
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, People’s Republic of China
| | - Jigang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Seth J Davis
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
- State Key Laboratory of Crop Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
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29
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Wen B, Gong X, Tan Q, Zhao W, Chen X, Li D, Li L, Xiao W. MdNAC4 Interacts With MdAPRR2 to Regulate Nitrogen Deficiency-Induced Leaf Senescence in Apple ( Malus domestica). FRONTIERS IN PLANT SCIENCE 2022; 13:925035. [PMID: 35845636 PMCID: PMC9280364 DOI: 10.3389/fpls.2022.925035] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/13/2022] [Indexed: 06/02/2023]
Abstract
Nitrogen (N) is one of the important macronutrients in plants, and N deficiency induces leaf senescence. However, the molecular mechanism underlying how N deficiency affects leaf senescence is unclear. Here, we report an apple NAC TF, MdNAC4, that participates in N deficiency-induced leaf senescence. The senescence phenotype of apple leaves overexpressing MdNAC4 was enhanced after N deficiency. Consistently, the chlorophyll content of transgenic leaves was significantly lower than that in the WT control leaves, the expression of chlorophyll catabolism-related genes (MdNYC1, MdPAO, and MdSGR1) was significantly higher than that in the WT controls, and the expression of chlorophyll synthesis-related genes (MdHEMA, MdCHLI, and MdCHLM) was significantly lower than that in the WT control leaves. Furthermore, MdNAC4 was found to directly activate the transcription of the chlorophyll catabolism-related genes MdNYC1 and MdPAO. Additionally, MdNAC4 was proven to interact with MdAPRR2 proteins both in vitro and in vivo, and overexpression of MdAPRR2 seemed to delay N deficiency-induced leaf senescence. Correspondingly, the chlorophyll loss of MdAPRR2-overexpressing (MdAPRR2-OE) lines was significantly lower than in WT control plants. Although downregulated, the expression of the chlorophyll synthesis-related genes MdHEMA, MdCHLI, and MdCHLM in the transgenic plants was more than twice that in the WT control plants. Taken together, our results enrich the regulatory network of leaf senescence induced by N deficiency through the interaction between MdNAC4 and MdAPRR2.
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30
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Cordeiro AM, Andrade L, Monteiro CC, Leitão G, Wigge PA, Saibo NJM. PHYTOCHROME-INTERACTING FACTORS: a promising tool to improve crop productivity. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3881-3897. [PMID: 35429385 DOI: 10.1093/jxb/erac142] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
Light is a key determinant for plant growth, development, and ultimately yield. Phytochromes, red/far-red photoreceptors, play an important role in plant architecture, stress tolerance, and productivity. In the model plant Arabidopsis, it has been shown that PHYTOCHROME-INTERACTING FACTORS (PIFs; bHLH transcription factors) act as central hubs in the integration of external stimuli to regulate plant development. Recent studies have unveiled the importance of PIFs in crops. They are involved in the modulation of plant architecture and productivity through the regulation of cell division and elongation in response to different environmental cues. These studies show that different PIFs have overlapping but also distinct functions in the regulation of plant growth. Therefore, understanding the molecular mechanisms by which PIFs regulate plant development is crucial to improve crop productivity under both optimal and adverse environmental conditions. In this review, we discuss current knowledge of PIFs acting as integrators of light and other signals in different crops, with particular focus on the role of PIFs in responding to different environmental conditions and how this can be used to improve crop productivity.
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Affiliation(s)
- André M Cordeiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Luis Andrade
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
- Leibniz-Institut für Gemüse- und Zierpflanzenbau, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Catarina C Monteiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Guilherme Leitão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Philip A Wigge
- Leibniz-Institut für Gemüse- und Zierpflanzenbau, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Nelson J M Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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31
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Isoda M, Ito S, Oyama T. Interspecific divergence of circadian properties in duckweed plants. PLANT, CELL & ENVIRONMENT 2022; 45:1942-1953. [PMID: 35201626 DOI: 10.1111/pce.14297] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
The circadian clock system is widely conserved in plants; however, divergence in circadian rhythm properties is poorly understood. We conducted a comparative analysis of the circadian properties of closely related duckweed species. Using a particle bombardment method, a circadian bioluminescent reporter was introduced into duckweed plants. We measured bioluminescence circadian rhythms of eight species of the genus Lemna and seven species of the genus Wolffiella at various temperatures (20, 25, and 30°C) and light conditions (constant light or constant dark). Wolffiella species inhabit relatively warm areas and lack some tissues/organs found in Lemna species. Lemna species tended to show robust bioluminescence circadian rhythms under all conditions, while Wolffiella species showed lower rhythm stability, especially at higher temperatures. For Lemna, two species (L. valdiviana and L. minuta) forming a clade showed relatively lower circadian stability. For Wolffiella, two species (W. hyalina and W. repanda) forming a clade showed extremely long period lengths. These analyses reveal that the circadian properties of species primarily reflect their phylogenetic positions. The relationships between geographical and morphological factors and circadian properties are also suggested.
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Affiliation(s)
- Minako Isoda
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Shogo Ito
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Tokitaka Oyama
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
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32
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Castro PH, Couto D, Santos MÂ, Freitas S, Lourenço T, Dias E, Huguet S, Marques da Silva J, Tavares RM, Bejarano ER, Azevedo H. SUMO E3 ligase SIZ1 connects sumoylation and reactive oxygen species homeostasis processes in Arabidopsis. PLANT PHYSIOLOGY 2022; 189:934-954. [PMID: 35238389 PMCID: PMC9157161 DOI: 10.1093/plphys/kiac085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
The ubiquitin-like modifying peptide SMALL UBIQUITIN-LIKE MODIFIER (SUMO) has become a known modulator of the plant response to multiple environmental stimuli. A common feature of many of these external stresses is the production of reactive oxygen species (ROS). Taking into account that SUMO conjugates rapidly accumulate in response to an external oxidative stimulus, it is likely that ROS and sumoylation converge at the molecular and regulatory levels. In this study, we explored the SUMO-ROS relationship, using as a model the Arabidopsis (Arabidopsis thaliana) null mutant of the major SUMO-conjugation enhancer, the E3 ligase SAP AND MIZ 1 (SIZ1). We showed that SIZ1 is involved in SUMO conjugate increase when primed with both exogenous and endogenous ROS. In siz1, seedlings were sensitive to oxidative stress imposition, and mutants accumulated different ROS throughout development. We demonstrated that the deregulation in hydrogen peroxide and superoxide homeostasis, but not of singlet O2 (1O2), was partially due to SA accumulation in siz1. Furthermore, transcriptomic analysis highlighted a transcriptional signature that implicated siz1 with 1O2 homeostasis. Subsequently, we observed that siz1 displayed chloroplast morphological defects and altered energy dissipation activity and established a link between the chlorophyll precursor protochlorophyllide and deregulation of PROTOCHLOROPHYLLIDE OXIDOREDUCTASE A (PORA), which is known to drive overproduction of 1O2. Ultimately, network analysis uncovered known and additional associations between transcriptional control of PORA and SIZ1-dependent sumoylation. Our study connects sumoylation, and specifically SIZ1, to the control of chloroplast functions and places sumoylation as a molecular mechanism involved in ROS homeostatic and signaling events.
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Affiliation(s)
- Pedro Humberto Castro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Braga 4710-057, Portugal
| | - Daniel Couto
- Biosystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Braga 4710-057, Portugal
| | - Miguel Ângelo Santos
- Biosystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Braga 4710-057, Portugal
| | - Sara Freitas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Braga 4710-057, Portugal
| | - Tiago Lourenço
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Braga 4710-057, Portugal
| | - Eva Dias
- Biosystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Braga 4710-057, Portugal
| | - Stéphanie Huguet
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | - Jorge Marques da Silva
- Biosystems and Integrative Sciences Institute (BioISI) and Departamento de Biologia Vegetal, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal
| | - Rui Manuel Tavares
- Biosystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Braga 4710-057, Portugal
| | - Eduardo Rodríguez Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Department of Biología Celular, Genética y Fisiología, Universidad de Málaga, Málaga 29071, Spain
| | - Herlander Azevedo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto 4099-002, Portugal
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Mo W, Zhang J, Zhang L, Yang Z, Yang L, Yao N, Xiao Y, Li T, Li Y, Zhang G, Bian M, Du X, Zuo Z. Arabidopsis cryptochrome 2 forms photobodies with TCP22 under blue light and regulates the circadian clock. Nat Commun 2022; 13:2631. [PMID: 35551190 PMCID: PMC9098493 DOI: 10.1038/s41467-022-30231-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
Cryptochromes are blue light receptors that regulate plant growth and development. They also act as the core components of the central clock oscillator in animals. Although plant cryptochromes have been reported to regulate the circadian clock in blue light, how they do so is unclear. Here we show that Arabidopsis cryptochrome 2 (CRY2) forms photobodies with the TCP22 transcription factor in response to blue light in plant cells. We provide evidence that PPK kinases influence the characteristics of these photobodies and that together these components, along with LWD transcriptional regulators, can positively regulate the expression of CCA1 encoding a central component of the circadian oscillator. Cryptochrome signaling has been reported to regulate circadian oscillations in plants. Here the authors show that CRY2 and the TCP22 transcription factors can form photobodies in a blue light dependent manner and induce expression of CCA1, a core component of the circadian oscillator.
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Affiliation(s)
- Weiliang Mo
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun, 130062, China
| | - Junchuan Zhang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun, 130062, China
| | - Li Zhang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun, 130062, China
| | - Zhenming Yang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun, 130062, China
| | - Liang Yang
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Nan Yao
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yong Xiao
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun, 130062, China
| | - Tianhong Li
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun, 130062, China
| | - Yaxing Li
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Guangmei Zhang
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mingdi Bian
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun, 130062, China
| | - Xinglin Du
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun, 130062, China
| | - Zecheng Zuo
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun, 130062, China. .,Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Xiang Y, Sapir T, Rouillard P, Ferrand M, Jiménez-Gómez JM. Interaction between photoperiod and variation in circadian rhythms in tomato. BMC PLANT BIOLOGY 2022; 22:187. [PMID: 35395725 PMCID: PMC8994279 DOI: 10.1186/s12870-022-03565-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/23/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND Many biological processes follow circadian rhythmicity and are controlled by the circadian clock. Predictable environmental changes such as seasonal variation in photoperiod can modulate circadian rhythms, allowing organisms to adjust the timing of their biological processes to the time of the year. In some crops such as rice, barley or soybean, mutations in circadian clock genes have altered photoperiod sensitivity, enhancing their cultivability in specific seasons and latitudes. However, how changes in circadian rhythms interact with the perception of photoperiod in crops remain poorly studied. In tomato, the appearance during domestication of mutations in EMPFINDLICHER IM DUNKELROTEN LICHT 1 (EID1, Solyc09g075080) and NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED GENE 2 (LNK2, Solyc01g068560) delayed both the phase and period of its circadian rhythms. The fact that variation in period and phase are separated in tomato provides an optimal tool to study how these factors affect the perception of photoperiod. RESULTS Here we develop tomato near isogenic lines carrying combinations of wild alleles of EID1 and LNK2 and show that they recreate the changes in phase and period that occurred during its domestication. We perform transcriptomic profiling of these near isogenic lines under two different photoperiods, and observe that EID1, but not LNK2, has a large effect on how the tomato transcriptome responds to photoperiod. This large effect of EID1 is likely a consequence of the global phase shift elicited by this gene in tomato's circadian rhythms. CONCLUSIONS Our study shows that changes in phase that occurred during tomato domestication determine photoperiod perception in this species, while changes in period have little effect.
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Affiliation(s)
- Yanli Xiang
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
- VIB-UGent Center for Plant Systems Biology, Technologiepark 71, 9052, Gent, Belgium
| | - Thomas Sapir
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Pauline Rouillard
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Marina Ferrand
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - José M Jiménez-Gómez
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France.
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain.
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Liu Y, Zhang XW, Liu X, Zheng PF, Su L, Wang GL, Wang XF, Li YY, You CX, An JP. Phytochrome interacting factor MdPIF7 modulates anthocyanin biosynthesis and hypocotyl growth in apple. PLANT PHYSIOLOGY 2022; 188:2342-2363. [PMID: 34983053 PMCID: PMC8968312 DOI: 10.1093/plphys/kiab605] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/26/2021] [Indexed: 06/10/2023]
Abstract
Light affects many physiological and developmental processes of plants by regulating the expression and activity of light-responsive proteins. Among them, phytochrome interacting factors (PIFs) play pivotal roles in the regulation of anthocyanin accumulation and hypocotyl growth. However, the molecular mechanism is not well understood, especially in woody plants, such as apple (Malus × domestica). In this study, we identified a light-responsive PIF protein, MdPIF7, in apple and investigated the molecular mechanism of its regulation of anthocyanin biosynthesis and hypocotyl growth. We found that overexpression of MdPIF7 decreased anthocyanin accumulation in transgenic apple materials and promoted hypocotyl elongation in ectopically expressed Arabidopsis (Arabidopsis thaliana). Further investigation showed that MdPIF7 functioned by interacting with B-box 23 (MdBBX23), a positive regulator of anthocyanin biosynthesis in apple and hypocotyl growth inhibition in ectopically expressed Arabidopsis, and attenuating the transcriptional activation of MdBBX23 on LONG HYPOCOTYL 5 (MdHY5). In addition, MdPIF7 interacted with basic region leucine zipper 44 (MdbZIP44) and ethylene response factor 38 (MdERF38), two positive regulators of anthocyanin biosynthesis, and it negatively regulated MdbZIP44- and MdERF38-promoted anthocyanin accumulation by interfering with the interaction between MdbZIP44/MdERF38 and MdMYB1. Taken together, our results reveal that MdPIF7 regulates anthocyanin biosynthesis in apple and hypocotyl growth in ectopically expressed Arabidopsis through MdPIF7-MdBBX23-MdHY5 and MdPIF7-MdbZIP44/MdERF38-MdMYB1 modules. Our findings enrich the functional studies of PIF proteins and provide insights into the molecular mechanism of PIF-mediated anthocyanin biosynthesis and hypocotyl growth.
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Affiliation(s)
| | | | - Xin Liu
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China
| | - Peng-Fei Zheng
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, Shandong, China
| | - Ling Su
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
| | - Gui-Luan Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, Shandong, China
| | - Xiao-Fei Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, Shandong, China
| | - Yuan-Yuan Li
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, Shandong, China
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Li X, Liang T, Liu H. How plants coordinate their development in response to light and temperature signals. THE PLANT CELL 2022; 34:955-966. [PMID: 34904672 PMCID: PMC8894937 DOI: 10.1093/plcell/koab302] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/06/2021] [Indexed: 05/12/2023]
Abstract
Light and temperature change constantly under natural conditions and profoundly affect plant growth and development. Light and warmer temperatures promote flowering, higher light intensity inhibits hypocotyl and petiole elongation, and warmer temperatures promote hypocotyl and petiole elongation. Moreover, exogenous light and temperature signals must be integrated with endogenous signals to fine-tune phytohormone metabolism and plant morphology. Plants perceive and respond to light and ambient temperature using common sets of factors, such as photoreceptors and multiple light signal transduction components. These highly structured signaling networks are critical for plant survival and adaptation. This review discusses how plants respond to variable light and temperature conditions using common elements to coordinate their development. Future directions for research on light and temperature signaling pathways are also discussed.
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Affiliation(s)
- Xu Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Tong Liang
- Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Hongtao Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Author for correspondence:
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37
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Xu X, Yuan L, Xie Q. The circadian clock ticks in plant stress responses. STRESS BIOLOGY 2022; 2:15. [PMID: 37676516 PMCID: PMC10441891 DOI: 10.1007/s44154-022-00040-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/15/2022] [Indexed: 09/08/2023]
Abstract
The circadian clock, a time-keeping mechanism, drives nearly 24-h self-sustaining rhythms at the physiological, cellular, and molecular levels, keeping them synchronized with the cyclic changes of environmental signals. The plant clock is sensitive to external and internal stress signals that act as timing cues to influence the circadian rhythms through input pathways of the circadian clock system. In order to cope with environmental stresses, many core oscillators are involved in defense while maintaining daily growth in various ways. Recent studies have shown that a hierarchical multi-oscillator network orchestrates the defense through rhythmic accumulation of gene transcripts, alternative splicing of mRNA precursors, modification and turnover of proteins, subcellular localization, stimuli-induced phase separation, and long-distance transport of proteins. This review summarizes the essential role of circadian core oscillators in response to stresses in Arabidopsis thaliana and crops, including daily and seasonal abiotic stresses (low or high temperature, drought, high salinity, and nutrition deficiency) and biotic stresses (pathogens and herbivorous insects). By integrating time-keeping mechanisms, circadian rhythms and stress resistance, we provide a temporal perspective for scientists to better understand plant environmental adaptation and breed high-quality crop germplasm for agricultural production.
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Affiliation(s)
- Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
| | - Li Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
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38
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Liu R, Gao Y, Fan Z, Guan C, Zhang Q. Effects of different photoperiods on flower opening, flower closing and circadian expression of clock-related genes in Iris domestica and I. dichotoma. JOURNAL OF PLANT RESEARCH 2022; 135:351-360. [PMID: 35157159 DOI: 10.1007/s10265-022-01374-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
The circadian clock can entrain to forced light-dark cycles by adjusting the phases and periods of flower opening and closing in ephemeral flowers. The responses of circadian rhythms to the same light conditions differ from species. However, the differences in internal genetic mechanisms underlying the different responses between species remain unclear. Iris domestica and I. dichotoma have ephemeral flowers and significantly divergent flower opening and closing times. The effects of different photoperiods (continuous darkness, 4L20D, 8L16D, 12L12D, 16L8D, 20L4D and continuous white light) on flower opening and closing, and expression patterns of seven genes (CRYPTOCHROME 1, PHYTOCHROME B, LATE ELONGATED HYPOCOTYL, PSEUDO RESPONSE REGULATOR 95, PHYTOCHROME INTERACTING FACTOR 4-like, SMUX AUXIN UP RNA 64-like and senescence-associated gene 39-like) involved in the circadian regulation of flower opening and closing were compared between I. domestica and I. dichotoma. Flower opening and closing in the two species exhibited circadian rhythms under continuous darkness (DD), but showed arrhythmia in continuous white light (LL). In the two species, keeping robust rhythms, strong synchronicity, rapid progressions of flower opening and closing and reaching full opening stage required a dark period longer than 4 h. In light-dark cycles with dark periods longer than 4 h, flower opening and closing times of the two species delayed with the delay of dawn, and the degree to which flower opening time varies with the time of dawn was greater in I. dichotoma than in I. domestica. The arrhythmia of flower opening and closing under 20L4D and LL would result from the arrhythmic output signals rather than arrhythmia of oscillators and photoreceptors. The different responses of the two species to the change of photoperiods would be caused by the transcriptional differences of genes in the output pathway of circadian clock system rather than in the input pathway or oscillators.
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Affiliation(s)
- Rong Liu
- Department of Landscape Architecture, Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing, China
| | - Yike Gao
- Department of Landscape Architecture, Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing, China.
| | - Zhuping Fan
- Department of Landscape Architecture, Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing, China
| | - Chunjing Guan
- Department of Landscape Architecture, Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing, China
| | - Qixiang Zhang
- Department of Landscape Architecture, Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing, China
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Zhu Z, Quint M, Anwer MU. Arabidopsis EARLY FLOWERING 3 controls temperature responsiveness of the circadian clock independently of the evening complex. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1049-1061. [PMID: 34698833 DOI: 10.1093/jxb/erab473] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Daily changes in light and temperature are major entrainment cues that enable the circadian clock to generate internal biological rhythms that are synchronized with the external environment. With the average global temperature predicted to keep increasing, the intricate light-temperature coordination that is necessary for clock functionality is expected to be seriously affected. Hence, understanding how temperature signals are perceived by the circadian clock has become an important issue. In Arabidopsis, the clock component EARLY FLOWERING 3 (ELF3) not only serves as a light Zeitnehmer, but also functions as a thermosensor participating in thermomorphogenesis. However, the role of ELF3 in temperature entrainment of the circadian clock is not fully understood. Here, we report that ELF3 is essential for delivering temperature input to the clock. We demonstrate that in the absence of ELF3, the oscillator is unable to respond to temperature changes, resulting in an impaired gating of thermoresponses. Consequently, clock-controlled physiological processes such as rhythmic growth and cotyledon movement were disturbed. Genetic analyses suggest that the evening complex is not required for ELF3-controlled thermoresponsiveness. Together, our results reveal that ELF3 is an essential Zeitnehmer for temperature sensing of the oscillator, and thereby for coordinating the rhythmic control of thermoresponsive physiological outputs.
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Affiliation(s)
- Zihao Zhu
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
| | - Muhammad Usman Anwer
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
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40
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A Point Mutation in Phytochromobilin synthase Alters the Circadian Clock and Photoperiodic Flowering of Medicago truncatula. PLANTS 2022; 11:plants11030239. [PMID: 35161220 PMCID: PMC8839385 DOI: 10.3390/plants11030239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 11/17/2022]
Abstract
Plants use seasonal cues to initiate flowering at an appropriate time of year to ensure optimal reproductive success. The circadian clock integrates these daily and seasonal cues with internal cues to initiate flowering. The molecular pathways that control the sensitivity of flowering to photoperiods (daylengths) are well described in the model plant Arabidopsis. However, much less is known for crop species, such as legumes. Here, we performed a flowering time screen of a TILLING population of Medicago truncatula and found a line with late-flowering and altered light-sensing phenotypes. Using RNA sequencing, we identified a nonsense mutation in the Phytochromobilin synthase (MtPΦBS) gene, which encodes an enzyme that carries out the final step in the biosynthesis of the chromophore required for phytochrome (phy) activity. The analysis of the circadian clock in the MtpΦbs mutant revealed a shorter circadian period, which was shared with the MtphyA mutant. The MtpΦbs and MtphyA mutants showed downregulation of the FT floral regulators MtFTa1 and MtFTb1/b2 and a change in phase for morning and night core clock genes. Our findings show that phyA is necessary to synchronize the circadian clock and integration of light signalling to precisely control the timing of flowering.
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Chen R, Deng Y, Ding Y, Guo J, Qiu J, Wang B, Wang C, Xie Y, Zhang Z, Chen J, Chen L, Chu C, He G, He Z, Huang X, Xing Y, Yang S, Xie D, Liu Y, Li J. Rice functional genomics: decades' efforts and roads ahead. SCIENCE CHINA. LIFE SCIENCES 2022. [PMID: 34881420 DOI: 10.1007/s11427-021-2024-2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.
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Affiliation(s)
- Rongzhi Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yiwen Deng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yanglin Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jingxin Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Bing Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Changsheng Wang
- National Center for Gene Research, Center of Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Yongyao Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Zhihua Zhang
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Jiaxin Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guangcun He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Daoxin Xie
- MOE Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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Rice functional genomics: decades' efforts and roads ahead. SCIENCE CHINA. LIFE SCIENCES 2021; 65:33-92. [PMID: 34881420 DOI: 10.1007/s11427-021-2024-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/01/2021] [Indexed: 12/16/2022]
Abstract
Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.
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Yousaf MJ, Hussain A, Hamayun M, Iqbal A. Exposure of Brassica to Red Light Antagonizes Low Production of IAA in Leaf Through Root Signaling Under Stress Conditions. Photochem Photobiol 2021; 98:874-885. [PMID: 34870857 DOI: 10.1111/php.13572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/26/2021] [Indexed: 11/27/2022]
Abstract
Plant leaf is highly sensitive to various growth promoting and restraining components. This sensitivity is normally caused by the alteration of different phyto-hormones (predominately by IAA), when the plants exposed to certain environmental conditions. We exposed the hydroponically grown Brassica campestris seedlings (7 days old) to red and green light in order to observe its effect on IAA secretion at leaf. The evaluated data showed that red light antagonized the low production of IAA in leaf by initiating the root signaling through flavonoids production and high redox activity. The study also explored the link between the differential phytohormonal response and biotic or abiotic stress elimination in leaf through root signaling under green or red light. The results exhibited that the biotic (P. syringae or F. alni) or abiotic stresses (100 mM AgNO3 or 100 mM tert-butyl alcohol) inhibited flavonoids at the roots and resisted the restoration of IAA at the leaf. However, under green light where IAA was not inhibited, the stresses could not produce flavonoid at the root and further passing the signals to leaf. The results concluded that the growth and photosynthetic rates of the seedlings were improved under red light exposure through flavonoid inducing stresses.
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Affiliation(s)
| | - Anwar Hussain
- Department of Botany, Garden Campus, Abdul Wali Khan University Mardan, Pakistan
| | - Muhammad Hamayun
- Department of Botany, Garden Campus, Abdul Wali Khan University Mardan, Pakistan
| | - Amjad Iqbal
- Department of Food Science & Technology, Garden Campus, Abdul Wali Khan University Mardan, Pakistan
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Xu Y, Lei Y, Su Z, Zhao M, Zhang J, Shen G, Wang L, Li J, Qi J, Wu J. A chromosome-scale Gastrodia elata genome and large-scale comparative genomic analysis indicate convergent evolution by gene loss in mycoheterotrophic and parasitic plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1609-1623. [PMID: 34647389 DOI: 10.1111/tpj.15528] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 05/27/2023]
Abstract
Mycoheterotrophic and parasitic plants are heterotrophic and parasitize on fungi and plants, respectively, to obtain nutrients. Large-scale comparative genomics analysis has not been conducted in mycoheterotrophic or parasitic plants or between these two groups of parasites. We assembled a chromosome-level genome of the fully mycoheterotrophic plant Gastrodia elata (Orchidaceae) and performed comparative genomic analyses on the genomes of G. elata and four orchids (initial mycoheterotrophs), three parasitic plants (Cuscuta australis, Striga asiatica, and Sapria himalayana), and 36 autotrophs from various angiosperm lineages. It was found that while in the hemiparasite S. asiatica and initial mycoheterotrophic orchids, approximately 4-5% of the conserved orthogroups were lost, the fully heterotrophic G. elata and C. australis both lost approximately 10% of the conserved orthogroups, indicating that increased heterotrophy is positively associated with gene loss. Importantly, many genes that are essential for autotrophs, including those involved in photosynthesis, the circadian clock, flowering time regulation, immunity, nutrient uptake, and root and leaf development, were convergently lost in both G. elata and C. australis. The high-quality genome of G. elata will facilitate future studies on the physiology, ecology, and evolution of mycoheterotrophic plants, and our findings highlight the critical role of gene loss in the evolution of plants with heterotrophic lifestyles.
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Affiliation(s)
- Yuxing Xu
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yunting Lei
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhongxiang Su
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Man Zhao
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jingxiong Zhang
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Guojing Shen
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Lei Wang
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jing Li
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jinfeng Qi
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jianqiang Wu
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
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45
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Nimmo HG, Laird J. Arabidopsis thaliana PRR7 Provides Circadian Input to the CCA1 Promoter in Shoots but not Roots. FRONTIERS IN PLANT SCIENCE 2021; 12:750367. [PMID: 34733306 PMCID: PMC8559795 DOI: 10.3389/fpls.2021.750367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/23/2021] [Indexed: 05/24/2023]
Abstract
The core of the plant circadian clock involves multiple interlocking gene expression loops and post-translational controls along with inputs from light and metabolism. The complexity of the interactions is such that few specific functions can be ascribed to single components. In previous work, we reported differences in the operation of the clocks in Arabidopsis shoots and roots, including the effects of mutations of key clock components. Here, we have used luciferase imaging to study prr7 mutants expressing CCA1::LUC and GI::LUC markers. In mature shoots expressing CCA1::LUC, loss of PRR7 radically altered behaviour in light:dark cycles and caused loss of rhythmicity in constant light but had little effect on roots. In contrast, in mature plants expressing GI::LUC, loss of PRR7 had little effect in light:dark cycles but in constant light increased the circadian period in shoots and reduced it in roots. We conclude that most or all of the circadian input to the CCA1 promoter in shoots is mediated by PRR7 and that loss of PRR7 has organ-specific effects. The results emphasise the differences in operation of the shoot and root clocks, and the importance of studying clock mutants in both light:dark cycles and constant light.
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Wang X, Jiang B, Gu L, Chen Y, Mora M, Zhu M, Noory E, Wang Q, Lin C. A photoregulatory mechanism of the circadian clock in Arabidopsis. NATURE PLANTS 2021; 7:1397-1408. [PMID: 34650267 DOI: 10.1038/s41477-021-01002-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/03/2021] [Indexed: 05/04/2023]
Abstract
Cryptochromes (CRYs) are photoreceptors that mediate light regulation of the circadian clock in plants and animals. Here we show that CRYs mediate blue-light regulation of N6-methyladenosine (m6A) modification of more than 10% of messenger RNAs in the Arabidopsis transcriptome, especially those regulated by the circadian clock. CRY2 interacts with three subunits of the METTL3/14-type N6-methyladenosine RNA methyltransferase (m6A writer): MTA, MTB and FIP37. Photo-excited CRY2 undergoes liquid-liquid phase separation (LLPS) to co-condense m6A writer proteins in vivo, without obviously altering the affinity between CRY2 and the writer proteins. mta and cry1cry2 mutants share common defects of a lengthened circadian period, reduced m6A RNA methylation and accelerated degradation of mRNA encoding the core component of the molecular oscillator circadian clock associated 1 (CCA1). These results argue for a photoregulatory mechanism by which light-induced phase separation of CRYs modulates m6A writer activity, mRNA methylation and abundance, and the circadian rhythms in plants.
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Affiliation(s)
- Xu Wang
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Bochen Jiang
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yadi Chen
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Manuel Mora
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Mulangma Zhu
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Eliace Noory
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Qin Wang
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Chentao Lin
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA.
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Watanabe E, Isoda M, Muranaka T, Ito S, Oyama T. Detection of Uncoupled Circadian Rhythms in Individual Cells of Lemna minor using a Dual-Color Bioluminescence Monitoring System. PLANT & CELL PHYSIOLOGY 2021; 62:815-826. [PMID: 33693842 DOI: 10.1093/pcp/pcab037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/01/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
The plant circadian oscillation system is based on the circadian clock of individual cells. Circadian behavior of cells has been observed by monitoring the circadian reporter activity, such as bioluminescence of AtCCA1::LUC+. To deeply analyze different circadian behaviors in individual cells, we developed the dual-color bioluminescence monitoring system that automatically measured the luminescence of two luciferase reporters simultaneously at a single-cell level. We selected a yellow-green-emitting firefly luciferase (LUC+) and a red-emitting luciferase (PtRLUC) that is a mutant form of Brazilian click beetle ELUC. We used AtCCA1::LUC+ and CaMV35S::PtRLUC. CaMV35S::LUC+ was previously reported as a circadian reporter with a low-amplitude rhythm. These bioluminescent reporters were introduced into the cells of a duckweed, Lemna minor, by particle bombardment. Time series of the bioluminescence of individual cells in a frond were obtained using a dual-color bioluminescence monitoring system with a green-pass- and red-pass filter. Luminescence intensities from the LUC+ and PtRLUC of each cell were calculated from the filtered luminescence intensities. We succeeded in reconstructing the bioluminescence behaviors of AtCCA1::LUC+ and CaMV35S::PtRLUC in the same cells. Under prolonged constant light conditions, AtCCA1::LUC+ showed a robust circadian rhythm in individual cells in an asynchronous state in the frond, as previously reported. By contrast, CaMV35S::PtRLUC stochastically showed circadian rhythms in a synchronous state. These results strongly suggested the uncoupling of cellular behavior between these circadian reporters. This dual-color bioluminescence monitoring system is a powerful tool to analyze various stochastic phenomena accompanying large cell-to-cell variation in gene expression.
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Affiliation(s)
- Emiri Watanabe
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Minako Isoda
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Tomoaki Muranaka
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
- Faculty of Agriculture, Kagoshima University, Kohrimoto 1-21-24, Kagoshima 890-0065, Japan
| | - Shogo Ito
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Tokitaka Oyama
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
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Guo Y, Ren G, Zhang K, Li Z, Miao Y, Guo H. Leaf senescence: progression, regulation, and application. MOLECULAR HORTICULTURE 2021; 1:5. [PMID: 37789484 PMCID: PMC10509828 DOI: 10.1186/s43897-021-00006-9] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/11/2021] [Indexed: 05/24/2023]
Abstract
Leaf senescence, the last stage of leaf development, is a type of postmitotic senescence and is characterized by the functional transition from nutrient assimilation to nutrient remobilization which is essential for plants' fitness. The initiation and progression of leaf senescence are regulated by a variety of internal and external factors such as age, phytohormones, and environmental stresses. Significant breakthroughs in dissecting the molecular mechanisms underpinning leaf senescence have benefited from the identification of senescence-altered mutants through forward genetic screening and functional assessment of hundreds of senescence-associated genes (SAGs) via reverse genetic research in model plant Arabidopsis thaliana as well as in crop plants. Leaf senescence involves highly complex genetic programs that are tightly tuned by multiple layers of regulation, including chromatin and transcription regulation, post-transcriptional, translational and post-translational regulation. Due to the significant impact of leaf senescence on photosynthesis, nutrient remobilization, stress responses, and productivity, much effort has been made in devising strategies based on known senescence regulatory mechanisms to manipulate the initiation and progression of leaf senescence, aiming for higher yield, better quality, or improved horticultural performance in crop plants. This review aims to provide an overview of leaf senescence and discuss recent advances in multi-dimensional regulation of leaf senescence from genetic and molecular network perspectives. We also put forward the key issues that need to be addressed, including the nature of leaf age, functional stay-green trait, coordination between different regulatory pathways, source-sink relationship and nutrient remobilization, as well as translational researches on leaf senescence.
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Affiliation(s)
- Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101 Shandong China
| | - Guodong Ren
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Kewei Zhang
- Institute of Plant Genetics and Developmental Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004 Zhejiang China
| | - Zhonghai Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083 China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Hongwei Guo
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, 518055 Guangdong China
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49
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Cao S, Luo X, Xu D, Tian X, Song J, Xia X, Chu C, He Z. Genetic architecture underlying light and temperature mediated flowering in Arabidopsis, rice, and temperate cereals. THE NEW PHYTOLOGIST 2021; 230:1731-1745. [PMID: 33586137 DOI: 10.1111/nph.17276] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 01/20/2021] [Indexed: 05/23/2023]
Abstract
Timely flowering is essential for optimum crop reproduction and yield. To determine the best flowering-time genes (FTGs) relevant to local adaptation and breeding, it is essential to compare the interspecific genetic architecture of flowering in response to light and temperature, the two most important environmental cues in crop breeding. However, the conservation and variations of FTGs across species lack systematic dissection. This review summarizes current knowledge on the genetic architectures underlying light and temperature-mediated flowering initiation in Arabidopsis, rice, and temperate cereals. Extensive comparative analyses show that most FTGs are conserved, whereas functional variations in FTGs may be species specific and confer local adaptation in different species. To explore evolutionary dynamics underpinning the conservation and variations in FTGs, domestication and selection of some key FTGs are further dissected. Based on our analyses of genetic control of flowering time, a number of key issues are highlighted. Strategies for modulation of flowering behavior in crop breeding are also discussed. The resultant resources provide a wealth of reference information to uncover molecular mechanisms of flowering in plants and achieve genetic improvement in crops.
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Affiliation(s)
- Shuanghe Cao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xumei Luo
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dengan Xu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiuling Tian
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jie Song
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- International Maize and Wheat Improvement Center China Office, c/o Chinese Academy Agricultural Sciences, Beijing, 100081, China
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50
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Rahmati Ishka M, Brown E, Rosenberg A, Romanowsky S, Davis JA, Choi WG, Harper JF. Arabidopsis Ca2+-ATPases 1, 2, and 7 in the endoplasmic reticulum contribute to growth and pollen fitness. PLANT PHYSIOLOGY 2021; 185:1966-1985. [PMID: 33575795 PMCID: PMC8133587 DOI: 10.1093/plphys/kiab021] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 11/23/2020] [Indexed: 05/18/2023]
Abstract
Generating cellular Ca2+ signals requires coordinated transport activities from both Ca2+ influx and efflux pathways. In Arabidopsis (Arabidopsis thaliana), multiple efflux pathways exist, some of which involve Ca2+-pumps belonging to the Autoinhibited Ca2+-ATPase (ACA) family. Here, we show that ACA1, 2, and 7 localize to the endoplasmic reticulum (ER) and are important for plant growth and pollen fertility. While phenotypes for plants harboring single-gene knockouts (KOs) were weak or undetected, a triple KO of aca1/2/7 displayed a 2.6-fold decrease in pollen transmission efficiency, whereas inheritance through female gametes was normal. The triple KO also resulted in smaller rosettes showing a high frequency of lesions. Both vegetative and reproductive phenotypes were rescued by transgenes encoding either ACA1, 2, or 7, suggesting that all three isoforms are biochemically redundant. Lesions were suppressed by expression of a transgene encoding NahG, an enzyme that degrades salicylic acid (SA). Triple KO mutants showed elevated mRNA expression for two SA-inducible marker genes, Pathogenesis-related1 (PR1) and PR2. The aca1/2/7 lesion phenotype was similar but less severe than SA-dependent lesions associated with a double KO of vacuolar pumps aca4 and 11. Imaging of Ca2+ dynamics triggered by blue light or the pathogen elicitor flg22 revealed that aca1/2/7 mutants display Ca2+ transients with increased magnitudes and durations. Together, these results indicate that ER-localized ACAs play important roles in regulating Ca2+ signals, and that the loss of these pumps results in male fertility and vegetative growth deficiencies.
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Affiliation(s)
- Maryam Rahmati Ishka
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Elizabeth Brown
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Alexa Rosenberg
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Shawn Romanowsky
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - James A Davis
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Won-Gyu Choi
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Jeffrey F Harper
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
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