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Abstract
In rice, a small increase in nighttime temperature reduces grain yield and quality. How warm nighttime temperatures (WNT) produce these detrimental effects is not well understood, especially in field conditions where the typical day-to-night temperature fluctuation exceeds the mild increase in nighttime temperature. We observed genome-wide disruption of gene expression timing during the reproductive phase in field-grown rice panicles acclimated to 2 to 3 °C WNT. Transcripts previously identified as rhythmically expressed with a 24-h period and circadian-regulated transcripts were more sensitive to WNT than were nonrhythmic transcripts. The system-wide perturbations in transcript levels suggest that WNT disrupt the tight temporal coordination between internal molecular events and the environment, resulting in reduced productivity. We identified transcriptional regulators whose predicted targets are enriched for sensitivity to WNT. The affected transcripts and candidate regulators identified through our network analysis explain molecular mechanisms driving sensitivity to WNT and identify candidates that can be targeted to enhance tolerance to WNT.
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252
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Li F, Hu Q, Chen F, Jiang JF. Transcriptome analysis reveals Vernalization is independent of cold acclimation in Arabidopsis. BMC Genomics 2021; 22:462. [PMID: 34154522 PMCID: PMC8218483 DOI: 10.1186/s12864-021-07763-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 05/31/2021] [Indexed: 01/08/2023] Open
Abstract
Background Through vernalization, plants achieve flowering competence by sensing prolonged cold exposure (constant exposure approximately 2-5 °C). During this process, plants initiate defense responses to endure cold conditions. Here, we conducted transcriptome analysis of Arabidopsis plants subjected to prolonged cold exposure (6 weeks) to explore the physiological dynamics of vernalization and uncover the relationship between vernalization and cold stress. Results Time-lag initiation of the two pathways and weighted gene co-expression network analysis (WGCNA) revealed that vernalization is independent of cold acclimation. Moreover, WGCNA revealed three major networks involving ethylene and jasmonic acid response, cold acclimation, and chromatin modification in response to prolonged cold exposure. Finally, throughout vernalization, the cold stress response is regulated via an alternative splicing-mediated mechanism. Conclusion These findings illustrate a comprehensive picture of cold stress- and vernalization-mediated global changes in Arabidopsis. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07763-3.
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Affiliation(s)
- Fei Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qian Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jia Fu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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253
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Shapiro DM, Ney M, Eghtesadi SA, Chilkoti A. Protein Phase Separation Arising from Intrinsic Disorder: First-Principles to Bespoke Applications. J Phys Chem B 2021; 125:6740-6759. [PMID: 34143622 DOI: 10.1021/acs.jpcb.1c01146] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The phase separation of biomolecules has become the focus of intense research in the past decade, with a growing body of research implicating this phenomenon in essentially all biological functions, including but not limited to homeostasis, stress responses, gene regulation, cell differentiation, and disease. Excellent reviews have been published previously on the underlying physical basis of liquid-liquid phase separation (LLPS) of biological molecules (Nat. Phys. 2015, 11, 899-904) and LLPS as it occurs natively in physiology and disease (Science 2017, 357, eaaf4382; Biochemistry 2018, 57, 2479-2487; Chem. Rev. 2014, 114, 6844-6879). Here, we review how the theoretical physical basis of LLPS has been used to better understand the behavior of biomolecules that undergo LLPS in natural systems and how this understanding has also led to the development of novel synthetic systems that exhibit biomolecular phase separation, and technologies that exploit these phenomena. In part 1 of this Review, we explore the theory behind the phase separation of biomolecules and synthetic macromolecules and introduce a few notable phase-separating biomolecules. In part 2, we cover experimental and computational methods used to study phase-separating proteins and how these techniques have uncovered the mechanisms underlying phase separation in physiology and disease. Finally, in part 3, we cover the development and applications of engineered phase-separating polypeptides, ranging from control of their self-assembly to create defined supramolecular architectures to reprogramming biological processes using engineered IDPs that exhibit LLPS.
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Affiliation(s)
- Daniel Mark Shapiro
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Max Ney
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Seyed Ali Eghtesadi
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
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254
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Emenecker RJ, Holehouse AS, Strader LC. Biological Phase Separation and Biomolecular Condensates in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:17-46. [PMID: 33684296 PMCID: PMC8221409 DOI: 10.1146/annurev-arplant-081720-015238] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A surge in research focused on understanding the physical principles governing the formation, properties, and function of membraneless compartments has occurred over the past decade. Compartments such as the nucleolus, stress granules, and nuclear speckles have been designated as biomolecular condensates to describe their shared property of spatially concentrating biomolecules. Although this research has historically been carried out in animal and fungal systems, recent work has begun to explore whether these same principles are relevant in plants. Effectively understanding and studying biomolecular condensates require interdisciplinary expertise that spans cell biology, biochemistry, and condensed matter physics and biophysics. As such, some involved concepts may be unfamiliar to any given individual. This review focuses on introducing concepts essential to the study of biomolecular condensates and phase separation for biologists seeking to carry out research in this area and further examines aspects of biomolecular condensates that are relevant to plant systems.
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Affiliation(s)
- Ryan J Emenecker
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
- Center for Science and Engineering of Living Systems, Washington University, St. Louis, Missouri 63130, USA
- Center for Engineering MechanoBiology, Washington University, St. Louis, Missouri 63130, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
- Center for Science and Engineering of Living Systems, Washington University, St. Louis, Missouri 63130, USA
| | - Lucia C Strader
- Center for Science and Engineering of Living Systems, Washington University, St. Louis, Missouri 63130, USA
- Center for Engineering MechanoBiology, Washington University, St. Louis, Missouri 63130, USA
- Department of Biology, Duke University, Durham, North Carolina 27708, USA;
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255
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Lee S, Wang W, Huq E. Spatial regulation of thermomorphogenesis by HY5 and PIF4 in Arabidopsis. Nat Commun 2021; 12:3656. [PMID: 34135347 PMCID: PMC8209091 DOI: 10.1038/s41467-021-24018-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 05/29/2021] [Indexed: 12/13/2022] Open
Abstract
Plants respond to high ambient temperature by implementing a suite of morphological changes collectively termed thermomorphogenesis. Here we show that the above and below ground tissue-response to high ambient temperature are mediated by distinct transcription factors. While the central hub transcription factor, PHYTOCHROME INTERCTING FACTOR 4 (PIF4) regulates the above ground tissue response, the below ground root elongation is primarily regulated by ELONGATED HYPOCOTYL 5 (HY5). Plants respond to high temperature by largely expressing distinct sets of genes in a tissue-specific manner. HY5 promotes root thermomorphogenesis via directly controlling the expression of many genes including the auxin and BR pathway genes. Strikingly, the above and below ground thermomorphogenesis is impaired in spaQ. Because SPA1 directly phosphorylates PIF4 and HY5, SPAs might control the stability of PIF4 and HY5 to regulate thermomorphogenesis in both tissues. These data collectively suggest that plants employ distinct combination of SPA-PIF4-HY5 module to regulate tissue-specific thermomorphogenesis. Plants undergo morphological changes collectively termed thermomorphogenesis when exposed to elevated temperature. Here the authors show that the SPA1 kinase regulates distinct thermomorphogenic responses according to tissue type by interactions with PIF4 and HY5 in shoots and roots, respectively.
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Affiliation(s)
- Sanghwa Lee
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Wenli Wang
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Enamul Huq
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.
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256
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Castroverde CDM, Dina D. Temperature regulation of plant hormone signaling during stress and development. JOURNAL OF EXPERIMENTAL BOTANY 2021:erab257. [PMID: 34081133 DOI: 10.1093/jxb/erab257] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Indexed: 05/20/2023]
Abstract
Global climate change has broad-ranging impacts on the natural environment and human civilization. Increasing average temperatures along with more frequent heat waves collectively have negative effects on cultivated crops in agricultural sectors and wild species in natural ecosystems. These aberrantly hot temperatures, together with cold stress, represent major abiotic stresses to plants. Molecular and physiological responses to high and low temperatures are intricately linked to the regulation of important plant hormones. In this review, we shall highlight our current understanding of how changing temperatures regulate plant hormone pathways during immunity, stress responses and development. This article will present an overview of known temperature-sensitive or temperature-reinforced molecular hubs in hormone biosynthesis, homeostasis, signaling and downstream responses. These include recent advances on temperature regulation at the genomic, transcriptional, post-transcriptional and post-translational levels - directly linking some plant hormone pathways to known thermosensing mechanisms. Where applicable, diverse plant species and various temperature ranges will be presented, along with emerging principles and themes. It is anticipated that a grand unifying synthesis of current and future fundamental outlooks on how fluctuating temperatures regulate important plant hormone signaling pathways can be leveraged towards forward-thinking solutions to develop climate-smart crops amidst our dynamically changing world.
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Affiliation(s)
| | - Damaris Dina
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada
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257
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Lee S, Zhu L, Huq E. An autoregulatory negative feedback loop controls thermomorphogenesis in Arabidopsis. PLoS Genet 2021; 17:e1009595. [PMID: 34061850 PMCID: PMC8195427 DOI: 10.1371/journal.pgen.1009595] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/11/2021] [Accepted: 05/11/2021] [Indexed: 12/13/2022] Open
Abstract
Plant growth and development are acutely sensitive to high ambient temperature caused in part due to climate change. However, the mechanism of high ambient temperature signaling is not well defined. Here, we show that HECATEs (HEC1 and HEC2), two helix-loop-helix transcription factors, inhibit thermomorphogenesis. While the expression of HEC1 and HEC2 is increased and HEC2 protein is stabilized at high ambient temperature, hec1hec2 double mutant showed exaggerated thermomorphogenesis. Analyses of the four PHYTOCHROME INTERACTING FACTOR (PIF1, PIF3, PIF4 and PIF5) mutants and overexpression lines showed that they all contribute to promote thermomorphogenesis. Furthermore, genetic analysis showed that pifQ is epistatic to hec1hec2. HECs and PIFs oppositely control the expression of many genes in response to high ambient temperature. PIFs activate the expression of HECs in response to high ambient temperature. HEC2 in turn interacts with PIF4 both in yeast and in vivo. In the absence of HECs, PIF4 binding to its own promoter as well as the target gene promoters was enhanced, indicating that HECs control PIF4 activity via heterodimerization. Overall, these data suggest that PIF4-HEC forms an autoregulatory composite negative feedback loop that controls growth genes to modulate thermomorphogenesis.
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Affiliation(s)
- Sanghwa Lee
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Ling Zhu
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Enamul Huq
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
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258
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van der Woude L, Piotrowski M, Klaasse G, Paulus JK, Krahn D, Ninck S, Kaschani F, Kaiser M, Novák O, Ljung K, Bulder S, van Verk M, Snoek BL, Fiers M, Martin NI, van der Hoorn RAL, Robert S, Smeekens S, van Zanten M. The chemical compound 'Heatin' stimulates hypocotyl elongation and interferes with the Arabidopsis NIT1-subfamily of nitrilases. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1523-1540. [PMID: 33768644 PMCID: PMC8360157 DOI: 10.1111/tpj.15250] [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: 01/06/2021] [Accepted: 03/22/2021] [Indexed: 05/17/2023]
Abstract
Temperature passively affects biological processes involved in plant growth. Therefore, it is challenging to study the dedicated temperature signalling pathways that orchestrate thermomorphogenesis, a suite of elongation growth-based adaptations that enhance leaf-cooling capacity. We screened a chemical library for compounds that restored hypocotyl elongation in the pif4-2-deficient mutant background at warm temperature conditions in Arabidopsis thaliana to identify modulators of thermomorphogenesis. The small aromatic compound 'Heatin', containing 1-iminomethyl-2-naphthol as a pharmacophore, was selected as an enhancer of elongation growth. We show that ARABIDOPSIS ALDEHYDE OXIDASES redundantly contribute to Heatin-mediated hypocotyl elongation. Following a chemical proteomics approach, the members of the NITRILASE1-subfamily of auxin biosynthesis enzymes were identified among the molecular targets of Heatin. Our data reveal that nitrilases are involved in promotion of hypocotyl elongation in response to high temperature and Heatin-mediated hypocotyl elongation requires the NITRILASE1-subfamily members, NIT1 and NIT2. Heatin inhibits NIT1-subfamily enzymatic activity in vitro and the application of Heatin accordingly results in the accumulation of NIT1-subfamily substrate indole-3-acetonitrile in vivo. However, levels of the NIT1-subfamily product, bioactive auxin (indole-3-acetic acid), were also significantly increased. It is likely that the stimulation of hypocotyl elongation by Heatin might be independent of its observed interaction with NITRILASE1-subfamily members. However, nitrilases may contribute to the Heatin response by stimulating indole-3-acetic acid biosynthesis in an indirect way. Heatin and its functional analogues present novel chemical entities for studying auxin biology.
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Affiliation(s)
- Lennard van der Woude
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Markus Piotrowski
- Department of Molecular Genetics and Physiology of PlantsFaculty of Biology and BiotechnologyUniversitätsstraße 150Bochum44801Germany
| | - Gruson Klaasse
- Department of Chemical Biology & Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUniversity UtrechtUniversiteitsweg 99Utrecht3584 CGthe Netherlands
| | - Judith K. Paulus
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Daniel Krahn
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Sabrina Ninck
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Farnusch Kaschani
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Markus Kaiser
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Ondřej Novák
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
- Laboratory of Growth RegulatorsThe Czech Academy of Sciences & Faculty of ScienceInstitute of Experimental BotanyPalacký UniversityŠlechtitelů 27Olomouc78371Czech Republic
| | - Karin Ljung
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
| | - Suzanne Bulder
- Bejo Zaden B.V.Trambaan 1Warmenhuizen1749 CZthe Netherlands
| | - Marcel van Verk
- Plant‐Microbe InteractionsInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
- KeygeneAgro Business Park 90Wageningen6708 PWthe Netherlands
- Theoretical Biology and BioinformaticsInstitute of Biodynamics and BiocomplexityUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Basten L. Snoek
- Theoretical Biology and BioinformaticsInstitute of Biodynamics and BiocomplexityUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Martijn Fiers
- BioscienceWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Nathaniel I. Martin
- Department of Chemical Biology & Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUniversity UtrechtUniversiteitsweg 99Utrecht3584 CGthe Netherlands
- Biological Chemistry GroupSylvius LaboratoriesInstitute of Biology LeidenLeiden UniversitySylviusweg 72Leiden2333 BEthe Netherlands
| | - Renier A. L. van der Hoorn
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Stéphanie Robert
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
| | - Sjef Smeekens
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Martijn van Zanten
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
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259
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Prusty MR, Bdolach E, Yamamoto E, Tiwari LD, Silberman R, Doron‐Faigenbaum A, Neyhart JL, Bonfil D, Kashkush K, Pillen K, Smith KP, Fridman E. Genetic loci mediating circadian clock output plasticity and crop productivity under barley domestication. THE NEW PHYTOLOGIST 2021; 230:1787-1801. [PMID: 33595846 PMCID: PMC8251863 DOI: 10.1111/nph.17284] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/06/2021] [Indexed: 05/30/2023]
Abstract
Circadian clock rhythms are shown to be intertwined with crop adaptation. To realize the adaptive value of changes in these rhythms under crop domestication and improvement, there is a need to compare the genetics of clock and yield traits. We compared circadian clock rhythmicity based on Chl leaf fluorescence and transcriptomics among wild ancestors, landraces, and breeding lines of barley under optimal and high temperatures. We conducted a genome scan to identify pleiotropic loci regulating the clock and field phenotypes. We also compared the allelic diversity in wild and cultivated barley to test for selective sweeps. We found significant loss of thermal plasticity in circadian rhythms under domestication. However, transcriptome analysis indicated that this loss was only for output genes and that temperature compensation in the core clock machinery was maintained. Drivers of the circadian clock (DOC) loci were identified via genome-wide association study. Notably, these loci also modified growth and reproductive outputs in the field. Diversity analysis indicated selective sweep in these pleiotropic DOC loci. These results indicate a selection against thermal clock plasticity under barley domestication and improvement and highlight the importance of identifying genes underlying for understanding the biochemical basis of crop adaptation to changing environments.
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Affiliation(s)
- Manas R. Prusty
- Institute of Plant SciencesAgricultural Research Organization (ARO)The Volcani CenterPO Box 6Bet Dagan5025001Israel
| | - Eyal Bdolach
- Institute of Plant SciencesAgricultural Research Organization (ARO)The Volcani CenterPO Box 6Bet Dagan5025001Israel
- Department of Life SciencesBen‐Gurion UniversityPO Box 653Beer‐ShevaIsrael
| | - Eiji Yamamoto
- Kazusa DNA Research InstitutePO Box 292‐0818ChibaJapan
| | - Lalit D. Tiwari
- Institute of Plant SciencesAgricultural Research Organization (ARO)The Volcani CenterPO Box 6Bet Dagan5025001Israel
| | - Roi Silberman
- Institute of Plant SciencesAgricultural Research Organization (ARO)The Volcani CenterPO Box 6Bet Dagan5025001Israel
| | - Adi Doron‐Faigenbaum
- Institute of Plant SciencesAgricultural Research Organization (ARO)The Volcani CenterPO Box 6Bet Dagan5025001Israel
| | - Jeffrey L. Neyhart
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt PaulMN55108USA
| | - David Bonfil
- Gilat Center, Vegetables and Field CropsAgricultural Research Organization (ARO)The Volcani CenterPO Box 6Bet Dagan5025001Israel
| | - Khalil Kashkush
- Department of Life SciencesBen‐Gurion UniversityPO Box 653Beer‐ShevaIsrael
| | - Klaus Pillen
- Institute of Agricultural and Nutritional SciencesMartin‐Luther University Halle‐WittenbergPO Box 06120Halle (Saale)Germany
| | - Kevin P. Smith
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt PaulMN55108USA
| | - Eyal Fridman
- Institute of Plant SciencesAgricultural Research Organization (ARO)The Volcani CenterPO Box 6Bet Dagan5025001Israel
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260
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Oberkofler V, Pratx L, Bäurle I. Epigenetic regulation of abiotic stress memory: maintaining the good things while they last. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:102007. [PMID: 33571730 PMCID: PMC8250047 DOI: 10.1016/j.pbi.2021.102007] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/19/2021] [Accepted: 01/19/2021] [Indexed: 05/03/2023]
Abstract
As sessile organisms, plants have evolved sophisticated ways to constantly gauge and adapt to changing environmental conditions including extremes that may be harmful to their growth and development and are thus perceived as stress. In nature, stressful events are often chronic or recurring and thus an initial stress may prime a plant to respond more efficiently to a subsequent stress event. An epigenetic basis of such stress memory was long postulated and in recent years it has been shown that this is indeed the case. High temperature stress has proven an excellent system to unpick the molecular basis of somatic stress memory, which includes histone modifications and nucleosome occupancy. This review discusses recent findings and pinpoints open questions in the field.
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Affiliation(s)
- Vicky Oberkofler
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam, Germany
| | - Loris Pratx
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam, Germany
| | - Isabel Bäurle
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam, Germany.
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261
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Huang S, Zhu S, Kumar P, MacMicking JD. A phase-separated nuclear GBPL circuit controls immunity in plants. Nature 2021; 594:424-429. [PMID: 34040255 PMCID: PMC8478157 DOI: 10.1038/s41586-021-03572-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 04/21/2021] [Indexed: 02/04/2023]
Abstract
Liquid-liquid phase separation (LLPS) has emerged as a central paradigm for understanding how membraneless organelles compartmentalize diverse cellular activities in eukaryotes1-3. Here we identify a superfamily of plant guanylate-binding protein (GBP)-like GTPases (GBPLs) that assemble LLPS-driven condensates within the nucleus to protect against infection and autoimmunity. In Arabidopsis thaliana, two members of this family-GBPL1 and GBPL3-undergo phase-transition behaviour to control transcriptional responses as part of an allosteric switch that is triggered by exposure to biotic stress. GBPL1, a pseudo-GTPase, sequesters catalytically active GBPL3 under basal conditions but is displaced by GBPL3 LLPS when it enters the nucleus following immune cues to drive the formation of unique membraneless organelles termed GBPL defence-activated condensates (GDACs) that we visualized by in situ cryo-electron tomography. Within these mesoscale GDAC structures, native GBPL3 directly bound defence-gene promoters and recruited specific transcriptional coactivators of the Mediator complex and RNA polymerase II machinery to massively reprogram host gene expression for disease resistance. Together, our study identifies a GBPL circuit that reinforces the biological importance of phase-separated condensates, in this case, as indispensable players in plant defence.
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Affiliation(s)
- Shuai Huang
- Howard Hughes Medical Institute, New Haven, CT, USA.,Yale Systems Biology Institute, West Haven, CT, USA.,Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Shiwei Zhu
- Howard Hughes Medical Institute, New Haven, CT, USA.,Yale Systems Biology Institute, West Haven, CT, USA.,Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Pradeep Kumar
- Howard Hughes Medical Institute, New Haven, CT, USA.,Yale Systems Biology Institute, West Haven, CT, USA.,Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - John D. MacMicking
- Howard Hughes Medical Institute, New Haven, CT, USA.,Yale Systems Biology Institute, West Haven, CT, USA.,Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA.,Correspondence and requests for materials should be addressed to J.D.M.,
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262
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Zhang LL, Li W, Tian YY, Davis SJ, Liu JX. The E3 ligase XBAT35 mediates thermoresponsive hypocotyl growth by targeting ELF3 for degradation in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1097-1103. [PMID: 33963671 DOI: 10.1111/jipb.13107] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 04/30/2021] [Indexed: 05/23/2023]
Abstract
Plants are capable of coordination of their growth and development with ambient temperatures. EARLY FLOWERING3 (ELF3), an essential component of the plant circadian clock, is also involved in ambient temperature sensing, as well as in inhibiting the expression and protein activity of the thermoresponsive regulator phytochrome interacting factor 4 (PIF4). The ELF3 activity is subjected to attenuation in response to warm temperature; however, how the protein level of ELF3 is regulated at warm temperature remains less understood. Here, we report that the E3 ligase XB3 ORTHOLOG 5 IN ARABIDOPSIS THALIANA, XBAT35, mediates ELF3 degradation. XBAT35 interacts with ELF3 and ubiquitinates ELF3. Loss-of-function mutation of XBAT35 increases the protein level of ELF3 and confers a short-hypocotyl phenotype under warm temperature conditions. Thus, our findings establish that XBAT35 mediates ELF3 degradation to lift the inhibition of ELF3 on PIF4 for promoting thermoresponsive hypocotyl growth in plants.
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Affiliation(s)
- Lin-Lin Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Wei Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Ying-Ying Tian
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Seth Jon Davis
- Department of Biology, University of York, Heslington, York, YO105DD, UK
- State Key Laboratory of Crop Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
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263
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Coordinative regulation of plants growth and development by light and circadian clock. ABIOTECH 2021; 2:176-189. [PMID: 36304756 PMCID: PMC9590570 DOI: 10.1007/s42994-021-00041-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/13/2021] [Indexed: 11/30/2022]
Abstract
The circadian clock, known as an endogenous timekeeping system, can integrate various cues to regulate plant physiological functions for adapting to the changing environment and thus ensure optimal plant growth. The synchronization of internal clock with external environmental information needs a process termed entrainment, and light is one of the predominant entraining signals for the plant circadian clock. Photoreceptors can detect and transmit light information to the clock core oscillator through transcriptional or post-transcriptional interactions with core-clock components to sustain circadian rhythms and regulate a myriad of downstream responses, including photomorphogenesis and photoperiodic flowering which are key links in the process of growth and development. Here we summarize the current understanding of the molecular network of the circadian clock and how light information is integrated into the circadian system, especially focus on how the circadian clock and light signals coordinately regulate the common downstream outputs. We discuss the functions of the clock and light signals in regulating photoperiodic flowering among various crop species.
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264
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Vu LD, Xu X, Zhu T, Pan L, van Zanten M, de Jong D, Wang Y, Vanremoortele T, Locke AM, van de Cotte B, De Winne N, Stes E, Russinova E, De Jaeger G, Van Damme D, Uauy C, Gevaert K, De Smet I. The membrane-localized protein kinase MAP4K4/TOT3 regulates thermomorphogenesis. Nat Commun 2021; 12:2842. [PMID: 33990595 PMCID: PMC8121802 DOI: 10.1038/s41467-021-23112-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 04/12/2021] [Indexed: 12/14/2022] Open
Abstract
Plants respond to mild warm temperature conditions by increased elongation growth of organs to enhance cooling capacity, in a process called thermomorphogenesis. To this date, the regulation of thermomorphogenesis has been exclusively shown to intersect with light signalling pathways. To identify regulators of thermomorphogenesis that are conserved in flowering plants, we map changes in protein phosphorylation in both dicots and monocots exposed to warm temperature. We identify MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE KINASE4 (MAP4K4)/TARGET OF TEMPERATURE3 (TOT3) as a regulator of thermomorphogenesis that impinges on brassinosteroid signalling in Arabidopsis thaliana. In addition, we show that TOT3 plays a role in thermal response in wheat, a monocot crop. Altogether, the conserved thermal regulation by TOT3 expands our knowledge of thermomorphogenesis beyond the well-studied pathways and can contribute to ensuring food security under a changing climate. Plants respond to warmth via growth processes termed thermomorphogenesis. Here, via a phosphoproteomics approach, the authors show that the mitogen activated protein kinase TOT3 regulates thermomorphogenesis in both wheat and Arabidopsis and modifies brassinosteroid signaling in Arabidopsis.
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Affiliation(s)
- Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, B-9000, Ghent, Belgium.,VIB Center for Medical Biotechnology, B-9000, Ghent, Belgium
| | - Xiangyu Xu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Tingting Zhu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Lixia Pan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Martijn van Zanten
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - Dorrit de Jong
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Yaowei Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Tim Vanremoortele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Anna M Locke
- Soybean & Nitrogen Fixation Research Unit, United States Department of Agriculture- Agricultural Research Service, Raleigh, NC, 27695, USA.,Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Brigitte van de Cotte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Nancy De Winne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Elisabeth Stes
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, B-9000, Ghent, Belgium.,VIB Center for Medical Biotechnology, B-9000, Ghent, Belgium.,VIB Headquarters, 9052, Gent, Belgium
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, NR4 7UH, UK
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, B-9000, Ghent, Belgium. .,VIB Center for Medical Biotechnology, B-9000, Ghent, Belgium.
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium. .,VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium.
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265
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Steed G, Ramirez DC, Hannah MA, Webb AAR. Chronoculture, harnessing the circadian clock to improve crop yield and sustainability. Science 2021; 372:372/6541/eabc9141. [PMID: 33926926 DOI: 10.1126/science.abc9141] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human health is dependent on a plentiful and nutritious supply of food, primarily derived from crop plants. Rhythmic supply of light as a result of the day and night cycle led to the evolution of circadian clocks that modulate most plant physiology, photosynthesis, metabolism, and development. To regulate crop traits and adaptation, breeders have indirectly selected for variation at circadian genes. The pervasive impact of the circadian system on crops suggests that future food production might be improved by modifying circadian rhythms, engineering the timing of transgene expression, and applying agricultural treatments at the most effective time of day. We describe the applied research required to take advantage of circadian biology in agriculture to increase production and reduce inputs.
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Affiliation(s)
- Gareth Steed
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Dora Cano Ramirez
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Matthew A Hannah
- BASF, BBCC-Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Gent, Belgium
| | - Alex A R Webb
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK.
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266
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Zanten MV, Ai H, Quint M. Plant thermotropism: an underexplored thermal engagement and avoidance strategy. JOURNAL OF EXPERIMENTAL BOTANY 2021:erab209. [PMID: 33974686 DOI: 10.1093/jxb/erab209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Indexed: 06/12/2023]
Abstract
Various strategies evolved in plants to adjust the position of organs relative to the prevailing temperature condition, which allows optimal plant growth and performance. Such responses are classically separated into nastic and tropic responses. During plant thermotropic responses, organs move towards (engage) or away (avoid) from a directional temperature cue. Despite thermotropism being a classic botanical concept, the underlying ecological function and molecular and biophysical mechanisms remain poorly understood to this day. This contrasts to the relatively well-studied thermonastic movements (hyponasty) of e.g., rosette leaves. In this review, we provide an update on the current knowledge on plant thermotropisms and propose directions for future research and application.
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Affiliation(s)
- Martijn van Zanten
- Martijn van Zanten, Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University. Padualaan 8, 3584CH Utrecht, the Netherlands
| | - Haiyue Ai
- Haiyue Ai, Marcel Quint, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty -Heimann-Str. 5 06120 Halle (Saale), Germany
| | - Marcel Quint
- Haiyue Ai, Marcel Quint, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty -Heimann-Str. 5 06120 Halle (Saale), Germany
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267
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D E Lima CFF, Kleine-Vehn J, De Smet I, Feraru E. Getting to the Root of Belowground High Temperature Responses in Plants. JOURNAL OF EXPERIMENTAL BOTANY 2021:erab202. [PMID: 33970267 DOI: 10.1093/jxb/erab202] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Indexed: 06/12/2023]
Abstract
The environment is continuously challenging plants. As a response, plants use various coping strategies, such as adaptation of their growth. Thermomorphogenesis is a specific growth adaptation that promotes organ growth in response to moderately high temperature. This would eventually enable plants to cool down by dissipating the heat. Although well understood for shoot organs, the thermomorphogenesis response in roots only recently obtained increasing research attention. Accordingly, in the last few years, the hormonal responses and underlying molecular players important for root thermomorphogenesis were revealed. Other responses triggered by high temperature in the root encompass modifications of overall root architecture and interactions with the soil environment, with consequences on the whole plant. Here, we review the scientific knowledge and highlight the current understanding on roots responding to moderately high and extreme temperature.
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Affiliation(s)
- Cassio Flavio Fonseca D E Lima
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Jürgen Kleine-Vehn
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
- Faculty of Biology, Department of Molecular Plant Physiology (MoPP), University of Freiburg, 79104 Freiburg, Germany
- Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany
| | - Ive De Smet
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Elena Feraru
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
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268
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Zhang LL, Shao YJ, Ding L, Wang MJ, Davis SJ, Liu JX. XBAT31 regulates thermoresponsive hypocotyl growth through mediating degradation of the thermosensor ELF3 in Arabidopsis. SCIENCE ADVANCES 2021; 7:7/19/eabf4427. [PMID: 33962946 PMCID: PMC8104893 DOI: 10.1126/sciadv.abf4427] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/18/2021] [Indexed: 05/23/2023]
Abstract
Elevated ambient temperature has wide effects on plant growth and development. ELF3, a proposed thermosensor, negatively regulates protein activity of the growth-promoting factor PIF4, and such an inhibitory effect is subjected to attenuation at warm temperature. However, how ELF3 stability is regulated at warm temperature remains enigmatic. Here, we report the identification of XBAT31 as the E3 ligase that mediates ELF3 degradation in response to warm temperature in Arabidopsis XBAT31 interacts with ELF3, ubiquitinates ELF3, and promotes ELF3 degradation via the 26S proteasome. Mutation of XBAT31 results in enhanced accumulation of ELF3 and reduced hypocotyl elongation at warm temperature. In contrast, overexpression of XBAT31 accelerates ELF3 degradation and promotes hypocotyl growth. Furthermore, XBAT31 interacts with the B-box protein BBX18, and the XBAT31-mediated ELF3 degradation is dependent on BBX18 Thus, our findings reveal that XBAT31-mediated destruction of ELF3 represents an additional regulatory layer of complexity in temperature signaling during plant thermomorphogenesis.
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Affiliation(s)
- Lin Lin Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Yu Jian Shao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Lan Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Mei Jing Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Seth Jon Davis
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jian Xiang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China.
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269
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Jin S, Ahn JH. Regulation of flowering time by ambient temperature: repressing the repressors and activating the activators. THE NEW PHYTOLOGIST 2021; 230:938-942. [PMID: 33474759 DOI: 10.1111/nph.17217] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/25/2020] [Indexed: 05/23/2023]
Abstract
Plants display remarkable developmental flexibility as they continuously sense and respond to changes in their environment. This flexibility allows them to select the optimal timing for critical developmental decisions such as when to flower. Ambient temperature is a major environmental factor that influences flowering; the mechanisms involved in ambient temperature-responsive flowering have attracted particular attention as a consequence of the effects of global climate change on temperature. PHYTOCHROME INTERACTING FACTOR 4 and alternative splicing of FLOWERING LOCUS M affect temperature-responsive flowering; however, the exact temperature-sensing mechanism in plants remains elusive. Further study of these molecular mechanisms will contribute to our understanding of how plants sense ambient temperature and respond via diverse biological signaling cascades.
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Affiliation(s)
- Suhyun Jin
- Department of Life Sciences, Korea University, Seoul, 02841, Korea
| | - Ji Hoon Ahn
- Department of Life Sciences, Korea University, Seoul, 02841, Korea
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270
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Kim J, Lee H, Lee HG, Seo PJ. Get closer and make hotspots: liquid-liquid phase separation in plants. EMBO Rep 2021; 22:e51656. [PMID: 33913240 DOI: 10.15252/embr.202051656] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/14/2021] [Accepted: 03/30/2021] [Indexed: 12/18/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) facilitates the formation of membraneless compartments in a cell and allows the spatiotemporal organization of biochemical reactions by concentrating macromolecules locally. In plants, LLPS defines cellular reaction hotspots, and stimulus-responsive LLPS is tightly linked to a variety of cellular and biological functions triggered by exposure to various internal and external stimuli, such as stress responses, hormone signaling, and temperature sensing. Here, we provide an overview of the current understanding of physicochemical forces and molecular factors that drive LLPS in plant cells. We illustrate how the biochemical features of cellular condensates contribute to their biological functions. Additionally, we highlight major challenges for the comprehensive understanding of biological LLPS, especially in view of the dynamic and robust organization of biochemical reactions underlying plastic responses to environmental fluctuations in plants.
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Affiliation(s)
- Jiwoo Kim
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Hongwoo Lee
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Hong Gil Lee
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
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271
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Paajanen P, Lane de Barros Dantas L, Dodd AN. Layers of crosstalk between circadian regulation and environmental signalling in plants. Curr Biol 2021; 31:R399-R413. [PMID: 33905701 DOI: 10.1016/j.cub.2021.03.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Circadian regulation has a pervasive influence upon plant development, physiology and metabolism, impacting upon components of fitness and traits of agricultural importance. Circadian regulation is inextricably connected to the responses of plants to their abiotic environments, from the cellular to whole plant scales. Here, we review the crosstalk that occurs between circadian regulation and responses to the abiotic environment from the intracellular scale through to naturally fluctuating environments. We examine the spatial crosstalk that forms part of plant circadian regulation, at the subcellular, tissue, organ and whole-plant scales. This includes a focus on chloroplast and mitochondrial signalling, alternative splicing, long-distance circadian signalling and circadian regulation within natural environments. We also consider mathematical models for plant circadian regulation, to suggest future areas for advancing understanding of roles for circadian regulation in plant responses to environmental cues.
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Affiliation(s)
- Pirita Paajanen
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Antony N Dodd
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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272
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Song P, Jia Q, Xiao X, Tang Y, Liu C, Li W, Li T, Li L, Chen H, Zhang W, Zhang Q. HSP70-3 Interacts with Phospholipase Dδ and Participates in Heat Stress Defense. PLANT PHYSIOLOGY 2021; 185:1148-1165. [PMID: 33793918 PMCID: PMC8133648 DOI: 10.1093/plphys/kiaa083] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 12/04/2020] [Indexed: 05/04/2023]
Abstract
Heat shock proteins (HSPs) function as molecular chaperones and are key components responsible for protein folding, assembly, translocation, and degradation under stress conditions. However, little is known about how HSPs stabilize proteins and membranes in response to different hormonal or environmental cues in plants. Here, we combined molecular, biochemical, and genetic approaches to elucidate the involvement of cytosolic HSP70-3 in plant stress responses and the interplay between HSP70-3 and plasma membrane (PM)-localized phospholipase Dδ (PLDδ) in Arabidopsis (Arabidopsis thaliana). Analysis using pull-down, coimmunoprecipitation, and bimolecular fluorescence complementation revealed that HSP70-3 specifically interacted with PLDδ. HSP70-3 bound to microtubules, such that it stabilized cortical microtubules upon heat stress. We also showed that heat shock induced recruitment of HSP70-3 to the PM, where HSP70-3 inhibited PLDδ activity to mediate microtubule reorganization, phospholipid metabolism, and plant thermotolerance, and this process depended on the HSP70-3-PLDδ interaction. Our results suggest a model whereby the interplay between HSP70-3 and PLDδ facilitates the re-establishment of cellular homeostasis during plant responses to external stresses and reveal a regulatory mechanism in regulating membrane lipid metabolism.
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Affiliation(s)
- Ping Song
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Qianru Jia
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Xingkai Xiao
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Yiwen Tang
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Chengjian Liu
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Wenyan Li
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Teng Li
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Li Li
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, P.R. China
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, P.R. China
| | - Huatao Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P.R. China
| | - Wenhua Zhang
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Qun Zhang
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, P.R. China
- Author for communication: (Q.Z.)
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273
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Lin J, Zhu Z. Plant responses to high temperature: a view from pre-mRNA alternative splicing. PLANT MOLECULAR BIOLOGY 2021; 105:575-583. [PMID: 33550520 DOI: 10.1007/s11103-021-01117-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/09/2021] [Indexed: 05/14/2023]
Abstract
This review focused on the recent breakthroughs in plant high temperature responses from an alternative splicing angle. With the inevitable global warming, high temperature triggers plants to change their growth and developmental programs for adapting temperature increase. In the past decades, the signaling mechanisms from plant thermo-sensing to downstream transcriptional cascades have been extensively studied. Plenty of elegant review papers have summarized these breakthroughs from signal transduction to cross-talk within plant hormones and environmental cues. Precursor messenger RNA (pre-mRNA) splicing enables plants to produce a series of functional un-related proteins and thus enhances the regulation flexibility. Plants take advantage of this strategy to modulate their proteome diversity under high ambient temperature and elicit developmental plasticity. In this review, we particularly focus on pre-mRNA splicing regulation underlying plant high temperature responses, and will shed new light on the understanding of post-transcriptional regulation on plant growth and development.
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Affiliation(s)
- Jingya Lin
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Ziqiang Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
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274
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Yang J, Cao Y, Ma L. Co-Transcriptional RNA Processing in Plants: Exploring from the Perspective of Polyadenylation. Int J Mol Sci 2021; 22:ijms22073300. [PMID: 33804866 PMCID: PMC8037041 DOI: 10.3390/ijms22073300] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/09/2021] [Accepted: 03/19/2021] [Indexed: 12/13/2022] Open
Abstract
Most protein-coding genes in eukaryotes possess at least two poly(A) sites, and alternative polyadenylation is considered a contributing factor to transcriptomic and proteomic diversity. Following transcription, a nascent RNA usually undergoes capping, splicing, cleavage, and polyadenylation, resulting in a mature messenger RNA (mRNA); however, increasing evidence suggests that transcription and RNA processing are coupled. Plants, which must produce rapid responses to environmental changes because of their limited mobility, exhibit such coupling. In this review, we summarize recent advances in our understanding of the coupling of transcription with RNA processing in plants, and we describe the possible spatial environment and important proteins involved. Moreover, we describe how liquid–liquid phase separation, mediated by the C-terminal domain of RNA polymerase II and RNA processing factors with intrinsically disordered regions, enables efficient co-transcriptional mRNA processing in plants.
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275
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Zhang X, Man Y, Zhuang X, Shen J, Zhang Y, Cui Y, Yu M, Xing J, Wang G, Lian N, Hu Z, Ma L, Shen W, Yang S, Xu H, Bian J, Jing Y, Li X, Li R, Mao T, Jiao Y, Sodmergen, Ren H, Lin J. Plant multiscale networks: charting plant connectivity by multi-level analysis and imaging techniques. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1392-1422. [PMID: 33974222 DOI: 10.1007/s11427-020-1910-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/04/2021] [Indexed: 12/21/2022]
Abstract
In multicellular and even single-celled organisms, individual components are interconnected at multiscale levels to produce enormously complex biological networks that help these systems maintain homeostasis for development and environmental adaptation. Systems biology studies initially adopted network analysis to explore how relationships between individual components give rise to complex biological processes. Network analysis has been applied to dissect the complex connectivity of mammalian brains across different scales in time and space in The Human Brain Project. In plant science, network analysis has similarly been applied to study the connectivity of plant components at the molecular, subcellular, cellular, organic, and organism levels. Analysis of these multiscale networks contributes to our understanding of how genotype determines phenotype. In this review, we summarized the theoretical framework of plant multiscale networks and introduced studies investigating plant networks by various experimental and computational modalities. We next discussed the currently available analytic methodologies and multi-level imaging techniques used to map multiscale networks in plants. Finally, we highlighted some of the technical challenges and key questions remaining to be addressed in this emerging field.
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Affiliation(s)
- Xi Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yi Man
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaohong Zhuang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Jinbo Shen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Yi Zhang
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Science, Beijing Normal University, Beijing, 100875, China
| | - Yaning Cui
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Meng Yu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Jingjing Xing
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 457004, China
| | - Guangchao Wang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Na Lian
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Zijian Hu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Lingyu Ma
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Weiwei Shen
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Shunyao Yang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Huimin Xu
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jiahui Bian
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yanping Jing
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaojuan Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Ruili Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Tonglin Mao
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing, 100101, China
| | - Sodmergen
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Haiyun Ren
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Science, Beijing Normal University, Beijing, 100875, China
| | - Jinxing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China. .,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
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276
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Xu W, Ding M, Li P. Struggle for survival: new insights into NELF condensation for adaptive transcriptional reprogramming. Mol Cell 2021; 81:896-898. [PMID: 33667379 DOI: 10.1016/j.molcel.2021.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
In this issue of Molecular Cell, Rawat et al. (2021) characterize novel stress-induced condensates of the negative elongation factor (NELF) as the nuclear counterparts of cytosolic stress granules. This provides a new perspective on transcription repression orchestrated by phase separation.
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Affiliation(s)
- Weifan Xu
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Mingrui Ding
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Pilong Li
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
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277
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Li C, Fang X. Phase Separation as a Molecular Thermosensor. Dev Cell 2021; 55:118-119. [PMID: 33108753 DOI: 10.1016/j.devcel.2020.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
How organisms sense temperature is a long-standing question. However, the identification of molecular thermosensors has been limited. Now, in a recent issue of Nature, Jung et al. demonstrate that phase separation of ELF3, a component of the circadian clock, acts as a thermosensor.
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Affiliation(s)
- Changxuan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaofeng Fang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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278
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Yan J, Kim YJ, Somers DE. Post-Translational Mechanisms of Plant Circadian Regulation. Genes (Basel) 2021; 12:325. [PMID: 33668215 PMCID: PMC7995963 DOI: 10.3390/genes12030325] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/21/2021] [Accepted: 02/22/2021] [Indexed: 12/15/2022] Open
Abstract
The molecular components of the circadian system possess the interesting feature of acting together to create a self-sustaining oscillator, while at the same time acting individually, and in complexes, to confer phase-specific circadian control over a wide range of physiological and developmental outputs. This means that many circadian oscillator proteins are simultaneously also part of the circadian output pathway. Most studies have focused on transcriptional control of circadian rhythms, but work in plants and metazoans has shown the importance of post-transcriptional and post-translational processes within the circadian system. Here we highlight recent work describing post-translational mechanisms that impact both the function of the oscillator and the clock-controlled outputs.
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Affiliation(s)
| | | | - David E. Somers
- Department of Molecular Genetics, The Ohio State University; Columbus, OH 43210, USA; (J.Y.); (Y.J.K.)
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279
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Bu T, Lu S, Wang K, Dong L, Li S, Xie Q, Xu X, Cheng Q, Chen L, Fang C, Li H, Liu B, Weller JL, Kong F. A critical role of the soybean evening complex in the control of photoperiod sensitivity and adaptation. Proc Natl Acad Sci U S A 2021; 118:e2010241118. [PMID: 33558416 PMCID: PMC7923351 DOI: 10.1073/pnas.2010241118] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Photoperiod sensitivity is a key factor in plant adaptation and crop production. In the short-day plant soybean, adaptation to low latitude environments is provided by mutations at the J locus, which confer extended flowering phase and thereby improve yield. The identity of J as an ortholog of Arabidopsis ELF3, a component of the circadian evening complex (EC), implies that orthologs of other EC components may have similar roles. Here we show that the two soybean homeologs of LUX ARRYTHMO interact with J to form a soybean EC. Characterization of mutants reveals that these genes are highly redundant in function but together are critical for flowering under short day, where the lux1 lux2 double mutant shows extremely late flowering and a massively extended flowering phase. This phenotype exceeds that of any soybean flowering mutant reported to date, and is strongly reminiscent of the "Maryland Mammoth" tobacco mutant that featured in the seminal 1920 study of plant photoperiodism by Garner and Allard [W. W. Garner, H. A. Allard, J. Agric. Res. 18, 553-606 (1920)]. We further demonstrate that the J-LUX complex suppresses transcription of the key flowering repressor E1 and its two homologs via LUX binding sites in their promoters. These results indicate that the EC-E1 interaction has a central role in soybean photoperiod sensitivity, a phenomenon also first described by Garner and Allard. EC and E1 family genes may therefore constitute key targets for customized breeding of soybean varieties with precise flowering time adaptation, either by introgression of natural variation or generation of new mutants by gene editing.
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Affiliation(s)
- Tiantian Bu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Sijia Lu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Kai Wang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Lidong Dong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Shilin Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 475004 Kaifeng, China
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 475004 Kaifeng, China
| | - Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 475004 Kaifeng, China
| | - Qun Cheng
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Liyu Chen
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Chao Fang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Haiyang Li
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Baohui Liu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081 Harbin, China
| | - James L Weller
- School of Natural Sciences, University of Tasmania, Hobart, 7001 TAS, Australia
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China;
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081 Harbin, China
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280
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Reichert P, Caudron F. Mnemons and the memorization of past signaling events. Curr Opin Cell Biol 2021; 69:127-135. [PMID: 33618243 DOI: 10.1016/j.ceb.2021.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/28/2022]
Abstract
Current advances are raising our awareness of the diverse roles that protein condensation plays in the biology of cells. Particularly, findings in organisms as diverse as yeast and Drosophila suggest that cells may utilize protein condensation to establish long-lasting changes in cellular activities and thereby encode a memory of past signaling events. Proteins that oligomerize to confer such cellular memory have been termed 'mnemons'. In the forming of super-assemblies, mnemons change their function and modulate the influence that the affected protein originally had on cellular processes. Because mnemon assemblies are self-templating, they allow cells to retain the memory of past decisions over larger timescales. Here, we review the mechanisms behind the formation of cellular memory with an emphasis on mnemon-mediated memorization of past signaling events.
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Affiliation(s)
- Polina Reichert
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Fabrice Caudron
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
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281
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Moving beyond disease to function: Physiological roles for polyglutamine-rich sequences in cell decisions. Curr Opin Cell Biol 2021; 69:120-126. [PMID: 33610098 DOI: 10.1016/j.ceb.2021.01.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/18/2020] [Accepted: 01/12/2021] [Indexed: 12/17/2022]
Abstract
Glutamine-rich tracts, also known as polyQ domains, have received a great deal of attention for their role in multiple neurodegenerative diseases, including Huntington's disease (HD), spinocerebellar ataxia (SCA), and others [22], [27]. Expansions in the normal polyQ tracts are thus commonly linked to disease, but polyQ domains themselves play multiple important functional roles in cells that are being increasingly appreciated. The biochemical nature of these domains allows them to adopt a number of different structures and form large assemblies that enable environmental responsiveness, localized signaling, and cellular memory. In many cases, these involve the formation of condensates that have varied material states. In this review, we highlight known and emerging functional roles for polyQ tracts in normal cell physiology.
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282
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Fonouni-Farde C, Ariel F, Crespi M. Plant Long Noncoding RNAs: New Players in the Field of Post-Transcriptional Regulations. Noncoding RNA 2021; 7:12. [PMID: 33671131 PMCID: PMC8005961 DOI: 10.3390/ncrna7010012] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 02/08/2023] Open
Abstract
The first reference to the "C-value paradox" reported an apparent imbalance between organismal genome size and morphological complexity. Since then, next-generation sequencing has revolutionized genomic research and revealed that eukaryotic transcriptomes contain a large fraction of non-protein-coding components. Eukaryotic genomes are pervasively transcribed and noncoding regions give rise to a plethora of noncoding RNAs with undeniable biological functions. Among them, long noncoding RNAs (lncRNAs) seem to represent a new layer of gene expression regulation, participating in a wide range of molecular mechanisms at the transcriptional and post-transcriptional levels. In addition to their role in epigenetic regulation, plant lncRNAs have been associated with the degradation of complementary RNAs, the regulation of alternative splicing, protein sub-cellular localization, the promotion of translation and protein post-translational modifications. In this review, we report and integrate numerous and complex mechanisms through which long noncoding transcripts regulate post-transcriptional gene expression in plants.
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Affiliation(s)
- Camille Fonouni-Farde
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Bat 630, 91192 Gif sur Yvette, France;
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Bat 630, 91192 Gif sur Yvette, France
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe, Argentina;
| | - Martin Crespi
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Bat 630, 91192 Gif sur Yvette, France;
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Bat 630, 91192 Gif sur Yvette, France
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283
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Pancsa R, Vranken W, Mészáros B. Computational resources for identifying and describing proteins driving liquid-liquid phase separation. Brief Bioinform 2021; 22:6124912. [PMID: 33517364 PMCID: PMC8425267 DOI: 10.1093/bib/bbaa408] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/23/2020] [Accepted: 12/12/2020] [Indexed: 01/06/2023] Open
Abstract
One of the most intriguing fields emerging in current molecular biology is the study of membraneless organelles formed via liquid–liquid phase separation (LLPS). These organelles perform crucial functions in cell regulation and signalling, and recent years have also brought about the understanding of the molecular mechanism of their formation. The LLPS field is continuously developing and optimizing dedicated in vitro and in vivo methods to identify and characterize these non-stoichiometric molecular condensates and the proteins able to drive or contribute to LLPS. Building on these observations, several computational tools and resources have emerged in parallel to serve as platforms for the collection, annotation and prediction of membraneless organelle-linked proteins. In this survey, we showcase recent advancements in LLPS bioinformatics, focusing on (i) available databases and ontologies that are necessary to describe the studied phenomena and the experimental results in an unambiguous way and (ii) prediction methods to assess the potential LLPS involvement of proteins. Through hands-on application of these resources on example proteins and representative datasets, we give a practical guide to show how they can be used in conjunction to provide in silico information on LLPS.
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Affiliation(s)
- Rita Pancsa
- Enzymology Institute of the Research Centre for Natural Sciences, Budapest, Hungary
| | - Wim Vranken
- Computer Science, chemistry and biomedical sciences at the Vrije Universiteit Brussel
| | - Bálint Mészáros
- Structural and Computational Biology Unit at the European Molecular Biology Laboratory, Heidelberg 69117, Germany
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284
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Antoniou-Kourounioti RL, Zhao Y, Dean C, Howard M. Feeling Every Bit of Winter - Distributed Temperature Sensitivity in Vernalization. FRONTIERS IN PLANT SCIENCE 2021; 12:628726. [PMID: 33584778 PMCID: PMC7873433 DOI: 10.3389/fpls.2021.628726] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/07/2021] [Indexed: 06/01/2023]
Abstract
Temperature intrinsically influences all aspects of biochemical and biophysical processes. Organisms have therefore evolved strategies to buffer themselves against thermal perturbations. Many organisms also use temperature signals as cues to align behavior and development with certain seasons. These developmentally important thermosensory mechanisms have generally been studied in constant temperature conditions. However, environmental temperature is an inherently noisy signal, and it has been unclear how organisms reliably extract specific temperature cues from fluctuating temperature profiles. In this context, we discuss plant thermosensory responses, focusing on temperature sensing throughout vernalization in Arabidopsis. We highlight many different timescales of sensing, which has led to the proposal of a distributed thermosensing paradigm. Within this paradigm, we suggest a classification system for thermosensors. Finally, we focus on the longest timescale, which is most important for sensing winter, and examine the different mechanisms in which memory of cold exposure can be achieved.
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Affiliation(s)
| | - Yusheng Zhao
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Caroline Dean
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Martin Howard
- Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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285
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Bruessow F, Bautor J, Hoffmann G, Yildiz I, Zeier J, Parker JE. Natural variation in temperature-modulated immunity uncovers transcription factor bHLH059 as a thermoresponsive regulator in Arabidopsis thaliana. PLoS Genet 2021; 17:e1009290. [PMID: 33493201 PMCID: PMC7861541 DOI: 10.1371/journal.pgen.1009290] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/04/2021] [Accepted: 11/10/2020] [Indexed: 01/31/2023] Open
Abstract
Temperature impacts plant immunity and growth but how temperature intersects with endogenous pathways to shape natural variation remains unclear. Here we uncover variation between Arabidopsis thaliana natural accessions in response to two non-stress temperatures (22°C and 16°C) affecting accumulation of the thermoresponsive stress hormone salicylic acid (SA) and plant growth. Analysis of differentially responding A. thaliana accessions shows that pre-existing SA provides a benefit in limiting infection by Pseudomonas syringae pathovar tomato DC3000 bacteria at both temperatures. Several A. thaliana genotypes display a capacity to mitigate negative effects of high SA on growth, indicating within-species plasticity in SA—growth tradeoffs. An association study of temperature x SA variation, followed by physiological and immunity phenotyping of mutant and over-expression lines, identifies the transcription factor bHLH059 as a temperature-responsive SA immunity regulator. Here we reveal previously untapped diversity in plant responses to temperature and a way forward in understanding the genetic architecture of plant adaptation to changing environments. Temperature has a profound effect on plant innate immune responses but little is known about the mechanisms underlying natural variation in transmission of temperature signals to defence pathways. Much of our understanding of temperature effects on plant immunity and tradeoffs between activated defences and growth has come from analysis of the common Arabidopsis thaliana genetic accession, Col-0. Here we examine A. thaliana genetic variation in response to temperature (within the non-stress range—22 oC and 16 oC) at the level of accumulation of the thermoresponsive biotic stress hormone salicylic acid (SA), bacterial pathogen resistance, and plant biomass. From analysis of 105 genetically diverse A. thaliana accessions we uncover plasticity in temperature-modulated SA homeostasis and in the relationship between SA levels and plant growth. We find that high SA amounts prior to infection provide a robust benefit of enhancing bacterial resistance. In some accessions this benefit comes without compromised plant growth, suggestive of altered defence–growth tradeoffs. Based on a temperature x SA association study we identify the transcription factor gene, bHLH059, and show that it has features of a temperature-sensitive immunity regulator that are unrelated to PIF4, a known thermosensitive coordinator of immunity and growth.
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Affiliation(s)
- Friederike Bruessow
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
- Cologne-Düsseldorf Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Jaqueline Bautor
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Gesa Hoffmann
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ipek Yildiz
- Institute of Plant Molecular Ecophysiology, Heinrich Heine University, Düsseldorf, Germany
| | - Jürgen Zeier
- Cologne-Düsseldorf Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
- Institute of Plant Molecular Ecophysiology, Heinrich Heine University, Düsseldorf, Germany
| | - Jane E. Parker
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
- Cologne-Düsseldorf Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
- * E-mail:
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286
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Hori K, Saisho D, Nagata K, Nonoue Y, Uehara-Yamaguchi Y, Kanatani A, Shu K, Hirayama T, Yonemaru JI, Fukuoka S, Mochida K. Genetic Elucidation for Response of Flowering Time to Ambient Temperatures in Asian Rice Cultivars. Int J Mol Sci 2021; 22:1024. [PMID: 33498523 PMCID: PMC7864171 DOI: 10.3390/ijms22031024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/16/2021] [Accepted: 01/17/2021] [Indexed: 11/27/2022] Open
Abstract
Climate resilience of crops is critical for global food security. Understanding the genetic basis of plant responses to ambient environmental changes is key to developing resilient crops. To detect genetic factors that set flowering time according to seasonal temperature conditions, we evaluated differences of flowering time over years by using chromosome segment substitution lines (CSSLs) derived from japonica rice cultivars "Koshihikari" × "Khao Nam Jen", each with different robustness of flowering time to environmental fluctuations. The difference of flowering times in 9 years' field tests was large in "Khao Nam Jen" (36.7 days) but small in "Koshihikari" (9.9 days). Part of this difference was explained by two QTLs. A CSSL with a "Khao Nam Jen" segment on chromosome 11 showed 28.0 days' difference; this QTL would encode a novel flowering-time gene. Another CSSL with a segment from "Khao Nam Jen" in the region around Hd16 on chromosome 3 showed 23.4 days" difference. A near-isogenic line (NIL) for Hd16 showed 21.6 days' difference, suggesting Hd16 as a candidate for this QTL. RNA-seq analysis showed differential expression of several flowering-time genes between early and late flowering seasons. Low-temperature treatment at panicle initiation stage significantly delayed flowering in the CSSL and NIL compared with "Koshihikari". Our results unravel the molecular control of flowering time under ambient temperature fluctuations.
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Affiliation(s)
- Kiyosumi Hori
- National Agriculture and Food Research Organization, Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan; (K.N.); (Y.N.); (K.S.); (J.-i.Y.); (S.F.)
| | - Daisuke Saisho
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan; (D.S.); (T.H.)
| | - Kazufumi Nagata
- National Agriculture and Food Research Organization, Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan; (K.N.); (Y.N.); (K.S.); (J.-i.Y.); (S.F.)
| | - Yasunori Nonoue
- National Agriculture and Food Research Organization, Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan; (K.N.); (Y.N.); (K.S.); (J.-i.Y.); (S.F.)
| | | | - Asaka Kanatani
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan; (Y.U.-Y.); (A.K.)
| | - Koka Shu
- National Agriculture and Food Research Organization, Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan; (K.N.); (Y.N.); (K.S.); (J.-i.Y.); (S.F.)
| | - Takashi Hirayama
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan; (D.S.); (T.H.)
| | - Jun-ichi Yonemaru
- National Agriculture and Food Research Organization, Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan; (K.N.); (Y.N.); (K.S.); (J.-i.Y.); (S.F.)
| | - Shuichi Fukuoka
- National Agriculture and Food Research Organization, Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan; (K.N.); (Y.N.); (K.S.); (J.-i.Y.); (S.F.)
| | - Keiichi Mochida
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan; (D.S.); (T.H.)
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan; (Y.U.-Y.); (A.K.)
- Kihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan
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287
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Favero DS, Lambolez A, Sugimoto K. Molecular pathways regulating elongation of aerial plant organs: a focus on light, the circadian clock, and temperature. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:392-420. [PMID: 32986276 DOI: 10.1111/tpj.14996] [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: 07/16/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
Organs such as hypocotyls and petioles rapidly elongate in response to shade and temperature cues, contributing to adaptive responses that improve plant fitness. Growth plasticity in these organs is achieved through a complex network of molecular signals. Besides conveying information from the environment, this signaling network also transduces internal signals, such as those associated with the circadian clock. A number of studies performed in Arabidopsis hypocotyls, and to a lesser degree in petioles, have been informative for understanding the signaling networks that regulate elongation of aerial plant organs. In particular, substantial progress has been made towards understanding the molecular mechanisms that regulate responses to light, the circadian clock, and temperature. Signals derived from these three stimuli converge on the BAP module, a set of three different types of transcription factors that interdependently promote gene transcription and growth. Additional key positive regulators of growth that are also affected by environmental cues include the CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and SUPPRESSOR OF PHYA-105 (SPA) E3 ubiquitin ligase proteins. In this review we summarize the key signaling pathways that regulate the growth of hypocotyls and petioles, focusing specifically on molecular mechanisms important for transducing signals derived from light, the circadian clock, and temperature. While it is clear that similarities abound between the signaling networks at play in these two organs, there are also important differences between the mechanisms regulating growth in hypocotyls and petioles.
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Affiliation(s)
- David S Favero
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Alice Lambolez
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Department of Biological Sciences, The University of Tokyo, Tokyo, 119-0033, Japan
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Department of Biological Sciences, The University of Tokyo, Tokyo, 119-0033, Japan
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288
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Shao YJ, Zhu QY, Yao ZW, Liu JX. Phosphoproteomic Analysis of Thermomorphogenic Responses in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:753148. [PMID: 34603364 PMCID: PMC8481946 DOI: 10.3389/fpls.2021.753148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 08/20/2021] [Indexed: 05/07/2023]
Abstract
Plants rapidly adapt to elevated ambient temperature by adjusting their growth and developmental programs. To date, a number of experiments have been carried out to understand how plants sense and respond to warm temperatures. However, how warm temperature signals are relayed from thermosensors to transcriptional regulators is largely unknown. To identify new early regulators of plant thermo-responsiveness, we performed phosphoproteomic analysis using TMT (Tandem Mass Tags) labeling and phosphopeptide enrichment with Arabidopsis etiolated seedlings treated with or without 3h of warm temperatures (29°C). In total, we identified 13,160 phosphopeptides in 5,125 proteins with 10,700 quantifiable phosphorylation sites. Among them, 200 sites (180 proteins) were upregulated, while 120 sites (87 proteins) were downregulated by elevated temperature. GO (Gene Ontology) analysis indicated that phosphorelay-related molecular function was enriched among the differentially phosphorylated proteins. We selected ATL6 (ARABIDOPSIS TOXICOS EN LEVADURA 6) from them and expressed its native and phosphorylation-site mutated (S343A S357A) forms in Arabidopsis and found that the mutated form of ATL6 was less stable than that of the native form both in vivo and in cell-free degradation assays. Taken together, our data revealed extensive protein phosphorylation during thermo-responsiveness, providing new candidate proteins/genes for studying plant thermomorphogenesis in the future.
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289
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Hwang G, Park J, Kim S, Park J, Seo D, Oh E. Overexpression of BBX18 Promotes Thermomorphogenesis Through the PRR5-PIF4 Pathway. FRONTIERS IN PLANT SCIENCE 2021; 12:782352. [PMID: 34899810 PMCID: PMC8651621 DOI: 10.3389/fpls.2021.782352] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/03/2021] [Indexed: 05/19/2023]
Abstract
Thermomorphogenesis is the morphological response of plants to an elevation in the ambient temperature, which is mediated by the bHLH transcription factor PIF4. The evening-expressed clock component, PRR5, directly represses the expression of PIF4 mRNA. Additionally, PRR5 interacts with PIF4 protein and represses its transactivation activity, which in turn suppresses the thermoresponsive growth in the evening. Here, we found that the B-box zinc finger protein, BBX18, interacts with PRR5 through the B-Box2 domain. Deletion of the B-Box2 domain abolished the functions of BBX18, including the stimulation of PIF4 mRNA expression and hypocotyl growth. Overexpression of BBX18, and not of B-Box2-deleted BBX18, restored the expression of thermoresponsive genes in the evening. We further show that BBX18 prevents PRR5 from inhibiting PIF4-mediated high temperature responses. Taken together, our results suggest that BBX18 regulates thermoresponsive growth through the PRR5-PIF4 pathway.
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290
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Plant Responses to Heat Stress: Physiology, Transcription, Noncoding RNAs, and Epigenetics. Int J Mol Sci 2020; 22:ijms22010117. [PMID: 33374376 PMCID: PMC7795586 DOI: 10.3390/ijms22010117] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/14/2020] [Accepted: 11/20/2020] [Indexed: 01/05/2023] Open
Abstract
Global warming has increased the frequency of extreme high temperature events. High temperature is a major abiotic stress that limits the growth and production of plants. Therefore, the plant response to heat stress (HS) has been a focus of research. However, the plant response to HS involves complex physiological traits and molecular or gene networks that are not fully understood. Here, we review recent progress in the physiological (photosynthesis, cell membrane thermostability, oxidative damage, and others), transcriptional, and post-transcriptional (noncoding RNAs) regulation of the plant response to HS. We also summarize advances in understanding of the epigenetic regulation (DNA methylation, histone modification, and chromatin remodeling) and epigenetic memory underlying plant–heat interactions. Finally, we discuss the challenges and opportunities of future research in the plant response to HS.
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291
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Salladini E, Jørgensen MLM, Theisen FF, Skriver K. Intrinsic Disorder in Plant Transcription Factor Systems: Functional Implications. Int J Mol Sci 2020; 21:E9755. [PMID: 33371315 PMCID: PMC7767404 DOI: 10.3390/ijms21249755] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 01/07/2023] Open
Abstract
Eukaryotic cells are complex biological systems that depend on highly connected molecular interaction networks with intrinsically disordered proteins as essential components. Through specific examples, we relate the conformational ensemble nature of intrinsic disorder (ID) in transcription factors to functions in plants. Transcription factors contain large regulatory ID-regions with numerous orphan sequence motifs, representing potential important interaction sites. ID-regions may affect DNA-binding through electrostatic interactions or allosterically as for the bZIP transcription factors, in which the DNA-binding domains also populate ensembles of dynamic transient structures. The flexibility of ID is well-suited for interaction networks requiring efficient molecular adjustments. For example, Radical Induced Cell Death1 depends on ID in transcription factors for its numerous, structurally heterogeneous interactions, and the JAZ:MYC:MED15 regulatory unit depends on protein dynamics, including binding-associated unfolding, for regulation of jasmonate-signaling. Flexibility makes ID-regions excellent targets of posttranslational modifications. For example, the extent of phosphorylation of the NAC transcription factor SOG1 regulates target gene expression and the DNA-damage response, and phosphorylation of the AP2/ERF transcription factor DREB2A acts as a switch enabling heat-regulated degradation. ID-related phase separation is emerging as being important to transcriptional regulation with condensates functioning in storage and inactivation of transcription factors. The applicative potential of ID-regions is apparent, as removal of an ID-region of the AP2/ERF transcription factor WRI1 affects its stability and consequently oil biosynthesis. The highlighted examples show that ID plays essential functional roles in plant biology and has a promising potential in engineering.
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Affiliation(s)
| | | | | | - Karen Skriver
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark; (E.S.); (M.L.M.J.); (F.F.T.)
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292
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Ouyang W, Xiong D, Li G, Li X. Unraveling the 3D Genome Architecture in Plants: Present and Future. MOLECULAR PLANT 2020; 13:1676-1693. [PMID: 33065269 DOI: 10.1016/j.molp.2020.10.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 08/09/2020] [Accepted: 10/08/2020] [Indexed: 05/02/2023]
Abstract
The eukaryotic genome has a hierarchical three-dimensional (3D) organization with functional implications for DNA replication, DNA repair, and transcriptional regulation. Over the past decade, scientists have endeavored to elucidate the spatial characteristics and functions of plant genome architecture using high-throughput chromatin conformation capturing technologies such as Hi-C, ChIA-PET, and HiChIP. Here, we systematically review current understanding of chromatin organization in plants at multiple scales. We also discuss the emerging opinions and concepts in 3D genome research, focusing on state-of-the-art 3D genome techniques, RNA-chromatin interactions, liquid-liquid phase separation, and dynamic chromatin alterations. We propose the application of single-cell/single-molecule multi-omics, multiway (DNA-DNA, DNA-RNA, and RNA-RNA interactions) chromatin conformation capturing methods, and proximity ligation-independent 3D genome-mapping technologies to explore chromatin organization structure and function in plants. Such methods could reveal the spatial interactions between trait-related SNPs and their target genes at various spatiotemporal resolutions, and elucidate the molecular mechanisms of the interactions among DNA elements, RNA molecules, and protein factors during the formation of key traits in plants.
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Affiliation(s)
- Weizhi Ouyang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Dan Xiong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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293
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Won JH, Seo PJ. Heat Makes Cellular Hotspots in Plants. MOLECULAR PLANT 2020; 13:1536-1538. [PMID: 33075507 DOI: 10.1016/j.molp.2020.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Jin Hoon Won
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea.
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294
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Emenecker RJ, Holehouse AS, Strader LC. Emerging Roles for Phase Separation in Plants. Dev Cell 2020; 55:69-83. [PMID: 33049212 PMCID: PMC7577370 DOI: 10.1016/j.devcel.2020.09.010] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/19/2020] [Accepted: 09/02/2020] [Indexed: 12/12/2022]
Abstract
The plant cell internal environment is a dynamic, intricate landscape composed of many intracellular compartments. Cells organize some cellular components through formation of biomolecular condensates-non-stoichiometric assemblies of protein and/or nucleic acids. In many cases, phase separation appears to either underly or contribute to the formation of biomolecular condensates. Many canonical membraneless compartments within animal cells form in a manner that is at least consistent with phase separation, including nucleoli, stress granules, Cajal bodies, and numerous additional bodies, regulated by developmental and environmental stimuli. In this Review, we examine the emerging roles for phase separation in plants. Further, drawing on studies carried out in other organisms, we identify cellular phenomenon in plants that might also arise via phase separation. We propose that plants make use of phase separation to a much greater extent than has been previously appreciated, implicating phase separation as an evolutionarily ancient mechanism for cellular organization.
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Affiliation(s)
- Ryan J Emenecker
- Department of Biology, Washington University, St. Louis, MO 63130, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, MO 63130, USA; Center for Engineering Mechanobiology, Washington University, St. Louis, MO 63130, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, MO 63130, USA.
| | - Lucia C Strader
- Center for Science and Engineering Living Systems (CSELS), Washington University, St. Louis, MO 63130, USA; Center for Engineering Mechanobiology, Washington University, St. Louis, MO 63130, USA; Department of Biology, Duke University, Durham, NC 27708, USA.
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295
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Gobbo D, Ballone P, Garabato BD. Coarse-Grained Model of Entropy-Driven Demixing. J Phys Chem B 2020; 124:9267-9274. [DOI: 10.1021/acs.jpcb.0c07575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- D. Gobbo
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Genova 16163, Italy
| | - P. Ballone
- School of Physics, University College, Dublin 4, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College, Dublin 4, Ireland
| | - B. D. Garabato
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Genova 16163, Italy
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296
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297
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Cacciapaglia G, Sannino F. Interplay of social distancing and border restrictions for pandemics via the epidemic renormalisation group framework. Sci Rep 2020; 10:15828. [PMID: 32985537 PMCID: PMC7522260 DOI: 10.1038/s41598-020-72175-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/21/2020] [Indexed: 01/28/2023] Open
Abstract
One of the biggest threats to humanity are pandemics. In our global society they can rage around the world with an immense toll in terms of human, economic and social impact. Forecasting the spreading of a pandemic is, therefore, paramount in helping governments to enforce a number of social and economic measures, apt at curbing the pandemic and dealing with its aftermath. We demonstrate that the epidemic renormalisation group approach to pandemics provides an effective and simple way to investigate the dynamics of disease transmission and spreading across different regions of the world. The framework also allows for reliable projections on the impact of travel limitations and social distancing measures on global epidemic spread. We test and calibrate it on reported COVID-19 cases while unveiling the mechanism that governs the delay in the relative peaks of newly infected cases among different regions of the globe. We discover that social distancing measures are more effective than travel limitations across borders in delaying the epidemic peak. We further provide the link to compartmental models such as the time-honoured SIR-like models. We also show how to generalise the framework to account for the interactions across several regions of the world, replacing or complementing large scale simulations.
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Affiliation(s)
- Giacomo Cacciapaglia
- Institut de Physique des 2 Infinis (IP2I), CNRS/IN2P3, UMR5822, 69622, Villeurbanne, France.
- Université de Lyon, Université Claude Bernard Lyon 1, 69001, Lyon, France.
| | - Francesco Sannino
- CP3-Origins & the Danish Institute for Advanced Study, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
- Dipartimento di Fisica E. Pancini, Università di Napoli Federico II & INFN sezione di Napoli, Complesso Universitario di Monte S. Angelo Edificio 6, via Cintia, 80126, Napoli, Italy
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298
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Cacciapaglia G, Cot C, Sannino F. Second wave COVID-19 pandemics in Europe: a temporal playbook. Sci Rep 2020; 10:15514. [PMID: 32968181 PMCID: PMC7511360 DOI: 10.1038/s41598-020-72611-5] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 09/04/2020] [Indexed: 02/06/2023] Open
Abstract
A second wave pandemic constitutes an imminent threat to society, with a potentially immense toll in terms of human lives and a devastating economic impact. We employ the epidemic Renormalisation Group (eRG) approach to pandemics, together with the first wave data for COVID-19, to efficiently simulate the dynamics of disease transmission and spreading across different European countries. The framework allows us to model, not only inter and extra European border control effects, but also the impact of social distancing for each country. We perform statistical analyses averaging on different level of human interaction across Europe and with the rest of the World. Our results are neatly summarised as an animation reporting the time evolution of the first and second waves of the European COVID-19 pandemic. Our temporal playbook of the second wave pandemic can be used by governments, financial markets, the industries and individual citizens, to efficiently time, prepare and implement local and global measures.
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Affiliation(s)
- Giacomo Cacciapaglia
- Institut de Physique des 2 Infinis (IP2I), CNRS/IN2P3, UMR5822, 69622, Villeurbanne, France.
- Université de Lyon, Université Claude Bernard Lyon 1, 69001, Lyon, France.
| | - Corentin Cot
- Institut de Physique des 2 Infinis (IP2I), CNRS/IN2P3, UMR5822, 69622, Villeurbanne, France
- Université de Lyon, Université Claude Bernard Lyon 1, 69001, Lyon, France
| | - Francesco Sannino
- CP3-Origins & the Danish Institute for Advanced Study, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
- Dipartimento di Fisica E. Pancini, Università di Napoli Federico II & INFN sezione di Napoli, Complesso Universitario di Monte S. Angelo Edificio 6, via Cintia, 80126, Naples, Italy
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