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Saini K, Dwivedi A, Ranjan A. High temperature restricts cell division and leaf size by coordination of PIF4 and TCP4 transcription factors. PLANT PHYSIOLOGY 2022; 190:2380-2397. [PMID: 35880840 PMCID: PMC9706436 DOI: 10.1093/plphys/kiac345] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 06/30/2022] [Indexed: 05/19/2023]
Abstract
High ambient temperature suppresses Arabidopsis (Arabidopsis thaliana) rosette leaf area and elongates the stem and petiole. While the mechanism underlying the temperature-induced elongation response has been extensively studied, the genetic basis of temperature regulation of leaf size is largely unknown. Here, we show that warm temperature inhibits cell proliferation in Arabidopsis leaves, resulting in fewer cells compared to the control condition. Cellular phenotyping and genetic and biochemical analyses established the key roles of PHYTOCHROME-INTERACTING FACTOR4 (PIF4) and TEOSINTE BRANCHED1/CYCLOIDEA/PCF4 (TCP4) transcription factors in the suppression of Arabidopsis leaf area under high temperature by a reduction in cell number. We show that temperature-mediated suppression of cell proliferation requires PIF4, which interacts with TCP4 and regulates the expression of the cell cycle inhibitor KIP-RELATED PROTEIN1 (KRP1) to control leaf size under high temperature. Warm temperature induces binding of both PIF4 and TCP4 to the KRP1 promoter. PIF4 binding to KRP1 under high temperature is TCP4 dependent as TCP4 regulates PIF4 transcript levels under high temperature. We propose a model where a warm temperature-mediated accumulation of PIF4 in leaf cells promotes its binding to the KRP1 promoter in a TCP4-dependent way to regulate cell production and leaf size. Our finding of high temperature-mediated transcriptional upregulation of KRP1 integrates a developmental signal with an environmental signal that converges on a basal cell regulatory process.
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Affiliation(s)
| | - Aditi Dwivedi
- National Institute of Plant Genome Research, New Delhi 110067, India
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2
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Jenkitkonchai J, Marriott P, Yang W, Sriden N, Jung J, Wigge PA, Charoensawan V. Exploring PIF4 's contribution to early flowering in plants under daily variable temperature and its tissue-specific flowering gene network. PLANT DIRECT 2021; 5:e339. [PMID: 34355114 PMCID: PMC8320686 DOI: 10.1002/pld3.339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 06/20/2021] [Accepted: 06/24/2021] [Indexed: 05/22/2023]
Abstract
Molecular mechanisms of how constant temperatures affect flowering time have been largely characterized in the model plant Arabidopsis thaliana; however, the effect of natural daily variable temperature outside laboratories is only partly explored. Several flowering genes have been shown to play important roles in temperature responses, including PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) and FLOWERING LOCUS C (FLC), the two genes encoding for the transcription factors (TFs) that act antagonistically to regulate flowering time by activating and repressing floral integrator FLOWERING LOCUS T (FT), respectively. In this study, we have taken a multidisciplinary approach to explore the contribution of PIF4 to the early flowering observed in the daily variable temperature (VAR) and to broaden its transcriptional network using publicly available transcriptomic data. We observed early flowering in the natural accessions Col-0, C24 and their late flowering hybrid C24xCol grown under VAR, as compared with a constant temperature (CON). The loss-of-function mutation of PIF4 exhibits later flowering in VAR in both the Col-0 parent and the C24xCol hybrid, suggesting that PIF4, at least in part, contributes to acceleration of flowering in the VAR condition. To investigate the interplay between PIF4 and its flowering regulator counterparts, FLC and FT, we performed transcriptional analyses and found that VAR increased PIF4 transcription at the end of the day when temperature peaked at 32°C, when FT transcription was also elevated. On the other hand, we observed a decrease in FLC transcription in the 4-week-old plants grown in VAR, as well as in the plants with PIF4 overexpression grown in CON. These results raise a possibility that PIF4 might also regulate FT indirectly through the repression of FLC, in addition to the well-characterized direct control of PIF4 over FT. To further expand our view on the PIF4-orientated flowering gene network in response to temperature changes, we have constructed a coexpression-transcriptional regulatory network by combining publicly available transcriptomic data and gene regulatory interactions of PIF4 and its closely related flowering genes, PIF5, FLC, and ELF3. The network model reveals conserved and tissue-specific regulatory functions, which are useful for confirming as well as predicting the functions and regulatory interactions between these key flowering genes.
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Affiliation(s)
| | - Poppy Marriott
- The Sainsbury LaboratoryUniversity of CambridgeCambridgeUK
| | - Weibing Yang
- The Sainsbury LaboratoryUniversity of CambridgeCambridgeUK
| | - Napaporn Sriden
- Department of Biochemistry, Faculty of ScienceMahidol UniversityBangkokThailand
| | - Jae‐Hoon Jung
- The Sainsbury LaboratoryUniversity of CambridgeCambridgeUK
- Department of Biological SciencesSungkyunkwan UniversitySuwonSouth Korea
| | - Philip A. Wigge
- The Sainsbury LaboratoryUniversity of CambridgeCambridgeUK
- Leibniz‐Institut für Gemüse‐ und ZierpflanzenbauGroßbeerenGermany
- Institute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| | - Varodom Charoensawan
- Department of Biochemistry, Faculty of ScienceMahidol UniversityBangkokThailand
- The Sainsbury LaboratoryUniversity of CambridgeCambridgeUK
- Integrative Computational BioScience (ICBS) CenterMahidol UniversityNakhon PathomThailand
- Systems Biology of Diseases Research Unit, Faculty of ScienceMahidol UniversityBangkokThailand
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3
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Dent CI, Singh S, Mukherjee S, Mishra S, Sarwade RD, Shamaya N, Loo KP, Harrison P, Sureshkumar S, Powell D, Balasubramanian S. Quantifying splice-site usage: a simple yet powerful approach to analyze splicing. NAR Genom Bioinform 2021; 3:lqab041. [PMID: 34017946 PMCID: PMC8121094 DOI: 10.1093/nargab/lqab041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/24/2021] [Accepted: 04/28/2021] [Indexed: 02/07/2023] Open
Abstract
RNA splicing, and variations in this process referred to as alternative splicing, are critical aspects of gene regulation in eukaryotes. From environmental responses in plants to being a primary link between genetic variation and disease in humans, splicing differences confer extensive phenotypic changes across diverse organisms (1–3). Regulation of splicing occurs through differential selection of splice sites in a splicing reaction, which results in variation in the abundance of isoforms and/or splicing events. However, genomic determinants that influence splice-site selection remain largely unknown. While traditional approaches for analyzing splicing rely on quantifying variant transcripts (i.e. isoforms) or splicing events (i.e. intron retention, exon skipping etc.) (4), recent approaches focus on analyzing complex/mutually exclusive splicing patterns (5–8). However, none of these approaches explicitly measure individual splice-site usage, which can provide valuable information about splice-site choice and its regulation. Here, we present a simple approach to quantify the empirical usage of individual splice sites reflecting their strength, which determines their selection in a splicing reaction. Splice-site strength/usage, as a quantitative phenotype, allows us to directly link genetic variation with usage of individual splice-sites. We demonstrate the power of this approach in defining the genomic determinants of splice-site choice through GWAS. Our pilot analysis with more than a thousand splice sites hints that sequence divergence in cis rather than trans is associated with variations in splicing among accessions of Arabidopsis thaliana. This approach allows deciphering principles of splicing and has broad implications from agriculture to medicine.
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Affiliation(s)
- Craig I Dent
- School of Biological Sciences, Monash University, VIC 3800, Australia
| | - Shilpi Singh
- School of Biological Sciences, Monash University, VIC 3800, Australia
| | | | - Shikhar Mishra
- School of Biological Sciences, Monash University, VIC 3800, Australia
| | - Rucha D Sarwade
- School of Biological Sciences, Monash University, VIC 3800, Australia
| | - Nawar Shamaya
- School of Biological Sciences, Monash University, VIC 3800, Australia
| | - Kok Ping Loo
- School of Biological Sciences, Monash University, VIC 3800, Australia
| | - Paul Harrison
- Monash Bioinformatics Platform, Monash University, VIC 3800, Australia
| | | | - David Powell
- Monash Bioinformatics Platform, Monash University, VIC 3800, Australia
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4
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Wang Z, Yang L, Wu D, Zhang N, Hua J. Polymorphisms in cis-elements confer SAUR26 gene expression difference for thermo-response natural variation in Arabidopsis. THE NEW PHYTOLOGIST 2021; 229:2751-2764. [PMID: 33185314 DOI: 10.1111/nph.17078] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/04/2020] [Indexed: 05/22/2023]
Abstract
The SAUR26 subfamily genes play an important role in conferring variations of thermo-responsiveness of growth architecture among natural accessions of Arabidopsis thaliana. The expression variations are critical for their activity variations, but how expression variations are generated is unknown. We identified genetic loci for gene expression variations through expression genome-wide association study (eGWAS) and investigated their mechanisms through molecular analyses. We found that cis elements are the major determinants for expression variations of SAUR26, SAUR27, and SAUR28. Polymorphisms in the promoter region likely impact PIF4 regulation while those at the 3'UTR affect mRNA stability to generate variations in SAUR26 expression levels. These polymorphisms also differentially affect the mRNA stability of SAUR26 at two temperatures. This study reveals two mechanisms involving cis elements in generating gene expression diversity, which is likely important for local adaptations in Arabidopsis natural accessions.
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Affiliation(s)
- Zhixue Wang
- State Key Laboratory of Rice Biology, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, China
- School of Integrative Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
| | - Leiyun Yang
- School of Integrative Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
| | - Dianxing Wu
- State Key Laboratory of Rice Biology, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Ning Zhang
- State Key Laboratory of Rice Biology, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Jian Hua
- School of Integrative Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
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5
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Zarnack K, Balasubramanian S, Gantier MP, Kunetsky V, Kracht M, Schmitz ML, Sträßer K. Dynamic mRNP Remodeling in Response to Internal and External Stimuli. Biomolecules 2020; 10:biom10091310. [PMID: 32932892 PMCID: PMC7565591 DOI: 10.3390/biom10091310] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/02/2020] [Accepted: 09/08/2020] [Indexed: 02/06/2023] Open
Abstract
Signal transduction and the regulation of gene expression are fundamental processes in every cell. RNA-binding proteins (RBPs) play a key role in the post-transcriptional modulation of gene expression in response to both internal and external stimuli. However, how signaling pathways regulate the assembly of RBPs with mRNAs remains largely unknown. Here, we summarize observations showing that the formation and composition of messenger ribonucleoprotein particles (mRNPs) is dynamically remodeled in space and time by specific signaling cascades and the resulting post-translational modifications. The integration of signaling events with gene expression is key to the rapid adaptation of cells to environmental changes and stress. Only a combined approach analyzing the signal transduction pathways and the changes in post-transcriptional gene expression they cause will unravel the mechanisms coordinating these important cellular processes.
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Affiliation(s)
- Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt a.M., Germany;
| | | | - Michael P. Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia;
- Department of Molecular and Translational Science, Monash University, Clayton, VIC 3800, Australia
| | - Vladislav Kunetsky
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany;
| | - Michael Kracht
- Rudolf Buchheim Institute of Pharmacology, FB11, Justus Liebig University, 35392 Giessen, Germany;
| | - M. Lienhard Schmitz
- Institute of Biochemistry, FB11, Justus Liebig University, 35392 Giessen, Germany;
| | - Katja Sträßer
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany;
- Correspondence:
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6
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Wang Z, Yang L, Liu Z, Lu M, Wang M, Sun Q, Lan Y, Shi T, Wu D, Hua J. Natural variations of growth thermo-responsiveness determined by SAUR26/27/28 proteins in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2019; 224:291-305. [PMID: 31127632 DOI: 10.1111/nph.15956] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/17/2019] [Indexed: 05/22/2023]
Abstract
How diversity in growth thermo-responsiveness is generated for local adaptation is a long-standing biological question. We investigated molecular genetic basis of natural variations in thermo-responsiveness of plant architecture in Arabidopsis thaliana. We measured the extent of rosette architecture at 22°C and 28°C in a set of 69 natural accessions and determined their thermo-responsiveness of plant architecture. A genome-wide association study was performed to identify major loci for variations in thermo-responsiveness. The SAUR26 subfamily, a new subfamily of SAUR genes, was identified as a major locus for the thermo-responsive architecture variations. The expression of SAUR26/27/28 is modulated by temperature and PIF4. Extensive natural polymorphisms in these genes affect their RNA expression levels and protein activities and influence the thermo-responsiveness of plant architecture. In addition, the SAUR26 subfamily genes exhibit a high variation frequency and their variations are associated with the local temperature climate. This study reveals that the SAUR26 subfamily is a key variation for thermo-responsive architecture and suggests a preference for generating diversity for local adaptation through signaling connectors.
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Affiliation(s)
- Zhixue Wang
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
- State Key Laboratory of Rice Biology, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
| | - Leiyun Yang
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
| | - Zhenhua Liu
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
| | - Minghui Lu
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
- College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Minghui Wang
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Qi Sun
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Yiheng Lan
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Science, East China Normal University, Shanghai, 200241, China
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Science, East China Normal University, Shanghai, 200241, China
| | - Dianxing Wu
- State Key Laboratory of Rice Biology, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
| | - Jian Hua
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
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7
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Chen K, Guo T, Li XM, Zhang YM, Yang YB, Ye WW, Dong NQ, Shi CL, Kan Y, Xiang YH, Zhang H, Li YC, Gao JP, Huang X, Zhao Q, Han B, Shan JX, Lin HX. Translational Regulation of Plant Response to High Temperature by a Dual-Function tRNA His Guanylyltransferase in Rice. MOLECULAR PLANT 2019; 12:1123-1142. [PMID: 31075443 DOI: 10.1016/j.molp.2019.04.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 04/11/2019] [Accepted: 04/29/2019] [Indexed: 05/23/2023]
Abstract
As sessile organisms, plants have evolved numerous strategies to acclimate to changes in environmental temperature. However, the molecular basis of this acclimation remains largely unclear. In this study we identified a tRNAHis guanylyltransferase, AET1, which contributes to the modification of pre-tRNAHis and is required for normal growth under high-temperature conditions in rice. Interestingly, AET1 possibly interacts with both RACK1A and eIF3h in the endoplasmic reticulum. Notably, AET1 can directly bind to OsARF mRNAs including the uORFs of OsARF19 and OsARF23, indicating that AET1 is associated with translation regulation. Furthermore, polysome profiling assays suggest that the translational status remains unaffected in the aet1 mutant, but that the translational efficiency of OsARF19 and OsARF23 is reduced; moreover, OsARF23 protein levels are obviously decreased in the aet1 mutant under high temperature, implying that AET1 regulates auxin signaling in response to high temperature. Our findings provide new insights into the molecular mechanisms whereby AET1 regulates the environmental temperature response in rice by playing a dual role in tRNA modification and translational control.
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Affiliation(s)
- Ke Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
| | - Xin-Min Li
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
| | - Yi-Min Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Bing Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wang-Wei Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
| | - Nai-Qian Dong
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
| | - Chuan-Lin Shi
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Kan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - You-Huang Xiang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hai Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ya-Chao Li
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ji-Ping Gao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China
| | - Xuehui Huang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Qiang Zhao
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Bin Han
- University of the Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Jun-Xiang Shan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China.
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences and Collaborative Innovation Center of Genetics & Development, Shanghai Institute of Plant Physiology & Ecology, Shanghai Institute for Biological Sciences, Chinese Academic of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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8
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Méndez-Vigo B, Ausín I, Zhu W, Mollá-Morales A, Balasubramanian S, Alonso-Blanco C. Genetic Interactions and Molecular Evolution of the Duplicated Genes ICARUS2 and ICARUS1 Help Arabidopsis Plants Adapt to Different Ambient Temperatures. THE PLANT CELL 2019; 31:1222-1237. [PMID: 30992321 PMCID: PMC6588312 DOI: 10.1105/tpc.18.00938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/29/2019] [Accepted: 04/12/2019] [Indexed: 05/30/2023]
Abstract
Understanding how plants adapt to ambient temperatures has become a major challenge prompted by global climate change. This has led to the identification of several genes regulating the thermal plasticity of plant growth and flowering time. However, the mechanisms accounting for the natural variation and evolution of such developmental plasticity remain mostly unknown. In this study, we determined that natural variation at ICARUS2 (ICA2), which interacts genetically with its homolog ICA1, alters growth and flowering time plasticity in relation to temperature in Arabidopsis (Arabidopsis thaliana). Transgenic analyses demonstrated multiple functional effects for ICA2 and supported the notion that structural polymorphisms in ICA2 likely underlie its natural variation. Two major ICA2 haplogroups carrying distinct functionally active alleles showed high frequency, strong geographic structure, and significant associations with climatic variables related to annual and daily fluctuations in temperature. Genome analyses across the plant phylogeny indicated that the prevalent plant ICA genes encoding two tRNAHis guanylyl transferase 1 units evolved ∼120 million years ago during the early divergence of mono- and dicotyledonous clades. In addition, ICA1/ICA2 duplication occurred specifically in the Camelineae tribe (Brassicaceae). Thus, ICA2 appears to be ubiquitous across plant evolution and likely contributes to climate adaptation through modifications of thermal developmental plasticity in Arabidopsis.
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Affiliation(s)
- Belén Méndez-Vigo
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
| | - Israel Ausín
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
| | - Wangsheng Zhu
- School of Biological Sciences, Monash University, Victoria 3800, Australia
| | - Almudena Mollá-Morales
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
| | | | - Carlos Alonso-Blanco
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
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9
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Salomé PA. Too Close to the Flame: Duplicated ICARUS Genes and Growth at Higher Temperatures. THE PLANT CELL 2019; 31:1216-1217. [PMID: 31048337 PMCID: PMC6588320 DOI: 10.1105/tpc.19.00323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Patrice A Salomé
- Department of Chemistry and Biochemistry, University of California, Los Angeles California 90095
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10
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Abstract
When exposed to warmer, nonstressful average temperatures, some plant organs grow and develop at a faster rate without affecting their final dimensions. Other plant organs show specific changes in morphology or development in a response termed thermomorphogenesis. Selected coding and noncoding RNA, chromatin features, alternative splicing variants, and signaling proteins change their abundance, localization, and/or intrinsic activity to mediate thermomorphogenesis. Temperature, light, and circadian clock cues are integrated to impinge on the level or signaling of hormones such as auxin, brassinosteroids, and gibberellins. The light receptor phytochrome B (phyB) is a temperature sensor, and the phyB-PHYTOCHROME-INTERACTING FACTOR 4 (PIF4)-auxin module is only one thread in a complex network that governs temperature sensitivity. Thermomorphogenesis offers an avenue to search for climate-smart plants to sustain crop and pasture productivity in the context of global climate change.
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Affiliation(s)
- Jorge J Casal
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Facultad de Agronomía, Universidad de Buenos Aires, C1417DSE Buenos Aires, Argentina;
- Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Fundación Instituto Leloir, C1405BWE Buenos Aires, Argentina
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11
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Monroe JG, Powell T, Price N, Mullen JL, Howard A, Evans K, Lovell JT, McKay JK. Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function. eLife 2018; 7:41038. [PMID: 30520727 PMCID: PMC6326724 DOI: 10.7554/elife.41038] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 12/06/2018] [Indexed: 11/26/2022] Open
Abstract
Interdisciplinary syntheses are needed to scale up discovery of the environmental drivers and molecular basis of adaptation in nature. Here we integrated novel approaches using whole genome sequences, satellite remote sensing, and transgenic experiments to study natural loss-of-function alleles associated with drought histories in wild Arabidopsis thaliana. The genes we identified exhibit population genetic signatures of parallel molecular evolution, selection for loss-of-function, and shared associations with flowering time phenotypes in directions consistent with longstanding adaptive hypotheses seven times more often than expected by chance. We then confirmed predicted phenotypes experimentally in transgenic knockout lines. These findings reveal the importance of drought timing to explain the evolution of alternative drought tolerance strategies and further challenge popular assumptions about the adaptive value of genetic loss-of-function in nature. These results also motivate improved species-wide sequencing efforts to better identify loss-of-function variants and inspire new opportunities for engineering climate resilience in crops. Water shortages caused by droughts lead to crop losses that affect billions of people around the world each year. By discovering how wild plants adapt to drought, it may be possible to identify traits and genes that help to improve the growth of crop plants when water is scarce. It has been suggested that plants have adapted to droughts by flowering at times of the year when droughts are less likely to occur. For example, if droughts are more likely to happen in spring, the plants may delay flowering until the summer. Arabidopsis thaliana is a small plant that is found across Eurasia, Africa and North America, including in areas that are prone to drought at different times of the year. Individual plants of the same species may carry different versions of the same gene (known as alleles). Some of these alleles may not work properly and are referred to as loss-of-function alleles. Monroe et al. investigated whether A. thaliana plants carry any loss-of-function alleles that are associated with droughts happening in the spring or summer, and whether they are linked to when those plants will flower. Monroe et al. analyzed satellite images collected over the last 30 years to measure when droughts have occurred. Next, they searched genome sequences of Arabidopsis thaliana for alleles that might help the plants to adapt to droughts in the spring or summer. Combining the two approaches revealed that loss-of-function alleles associated with spring droughts were strongly predicted to be associated with the plants flowering later in the year. Similarly, loss-of-function alleles associated with summer droughts were predicted to be associated with the plants flowering earlier in the year. These findings support the idea that plants can adapt to drought by changing when they produce flowers, and suggest that loss-of-function alleles play a major role in this process. New techniques for editing genes mean it is easier than ever to generate new loss-of-function alleles in specific genes. Therefore, the results presented by Monroe et al. may help researchers to develop new varieties of crop plants that are better adapted to droughts.
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Affiliation(s)
- J Grey Monroe
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, United States.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, United States
| | - Tyler Powell
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, United States.,Department of Biology, Colorado State University, Fort Collins, United States
| | - Nicholas Price
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, United States
| | - Jack L Mullen
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, United States
| | - Anne Howard
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, United States
| | - Kyle Evans
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, United States
| | - John T Lovell
- HudsonAlpha Institute for Biotechnology, Huntsville, United States
| | - John K McKay
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, United States.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, United States
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12
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Nakamura A, Wang D, Komatsu Y. Molecular mechanism of substrate recognition and specificity of tRNA His guanylyltransferase during nucleotide addition in the 3'-5' direction. RNA (NEW YORK, N.Y.) 2018; 24:1583-1593. [PMID: 30111535 PMCID: PMC6191723 DOI: 10.1261/rna.067330.118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/09/2018] [Indexed: 05/06/2023]
Abstract
The tRNAHis guanylyltransferase (Thg1) transfers a guanosine triphosphate (GTP) in the 3'-5' direction onto the 5'-terminal of tRNAHis, opposite adenosine at position 73 (A73). The guanosine at the -1 position (G-1) serves as an identity element for histidyl-tRNA synthetase. To investigate the mechanism of recognition for the insertion of GTP opposite A73, first we constructed a two-stranded tRNAHis molecule composed of a primer and a template strand through division at the D-loop. Next, we evaluated the structural requirements of the incoming GTP from the incorporation efficiencies of GTP analogs into the two-piece tRNAHis Nitrogen at position 7 and the 6-keto oxygen of the guanine base were important for G-1 addition; however, interestingly, the 2-amino group was found not to be essential from the highest incorporation efficiency of inosine triphosphate. Furthermore, substitution of the conserved A73 in tRNAHis revealed that the G-1 addition reaction was more efficient onto the template containing the opposite A73 than onto the template with cytidine (C73) or other bases forming canonical Watson-Crick base-pairing. Some interaction might occur between incoming GTP and A73, which plays a role in the prevention of continuous templated 3'-5' polymerization. This study provides important insights into the mechanism of accurate tRNAHis maturation.
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Affiliation(s)
- Akiyoshi Nakamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan
| | - Daole Wang
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yasuo Komatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
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13
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Tasset C, Singh Yadav A, Sureshkumar S, Singh R, van der Woude L, Nekrasov M, Tremethick D, van Zanten M, Balasubramanian S. POWERDRESS-mediated histone deacetylation is essential for thermomorphogenesis in Arabidopsis thaliana. PLoS Genet 2018; 14:e1007280. [PMID: 29547672 PMCID: PMC5874081 DOI: 10.1371/journal.pgen.1007280] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 03/28/2018] [Accepted: 02/27/2018] [Indexed: 11/19/2022] Open
Abstract
Ambient temperature affects plant growth and even minor changes can substantially impact crop yields. The underlying mechanisms of temperature perception and response are just beginning to emerge. Chromatin remodeling, via the eviction of the histone variant H2A.Z containing nucleosomes, is a critical component of thermal response in plants. However, the role of histone modifications remains unknown. Here, through a forward genetic screen, we identify POWERDRESS (PWR), a SANT-domain containing protein known to interact with HISTONE DEACETYLASE 9 (HDA9), as a novel factor required for thermomorphogenesis in Arabidopsis thaliana. We show that mutations in PWR impede thermomorphogenesis, exemplified by attenuated warm temperature-induced hypocotyl/petiole elongation and early flowering. We show that inhibitors of histone deacetylases diminish temperature-induced hypocotyl elongation, which demonstrates a requirement for histone deacetylation in thermomorphogenesis. We also show that elevated temperature is associated with deacetylation of H3K9 at the +1 nucleosomes of PHYTOCHROME INTERACTING FACTOR4 (PIF4) and YUCCA8 (YUC8), and that PWR is required for this response. There is global misregulation of genes in pwr mutants at elevated temperatures. Meta-analysis revealed that genes that are misregulated in pwr mutants display a significant overlap with genes that are H2A.Z-enriched in their gene bodies, and with genes that are differentially expressed in mutants of the components of the SWR1 complex that deposits H2A.Z. Our findings thus uncover a role for PWR in facilitating thermomorphogenesis and suggest a potential link between histone deacetylation and H2A.Z nucleosome dynamics in plants. Plant growth and development is influenced by a variety of external environmental cues. Ambient temperature affects almost all stages of plant development but the underlying molecular mechanisms remain largely unknown. In this paper, the authors show that histone deacetylation, an important chromatin remodeling processes, is essential for eliciting warm temperature-induced growth responses in plants; a process called thermomorphogenesis. The authors identify POWERDRESS, a protein known to interact with HISTONE DEACETYLASE 9, as a novel player essential for thermomorphogenesis in Arabidopsis. Another chromatin remodeling mechanism that is known to play a role in thermal response is the eviction of histone variant H2A.Z containing nucleosomes. Through transcriptome studies and meta-analysis, the authors demonstrate statistical associations between gene regulations conferred through PWR-mediated histone H3 deacetylation and those conferred by histone H2A.Z eviction/incorporation dynamics. This study identifies a novel gene that is essential for thermomorphogenesis and points to a possible link between two seemingly distinct chromatin-remodeling processes in regulating gene expression in plants.
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Affiliation(s)
- Celine Tasset
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | | | | | - Rupali Singh
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Lennard van der Woude
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Maxim Nekrasov
- The John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - David Tremethick
- The John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Martijn van Zanten
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
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14
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Optimization of Photosynthetic Productivity in Contrasting Environments by Regulons Controlling Plant Form and Function. Int J Mol Sci 2018; 19:ijms19030872. [PMID: 29543762 PMCID: PMC5877733 DOI: 10.3390/ijms19030872] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/13/2018] [Accepted: 03/13/2018] [Indexed: 01/06/2023] Open
Abstract
We review the role of a family of transcription factors and their regulons in maintaining high photosynthetic performance across a range of challenging environments with a focus on extreme temperatures and water availability. Specifically, these transcription factors include CBFs (C-repeat binding factors) and DREBs (dehydration-responsive element-binding), with CBF/DREB1 primarily orchestrating cold adaptation and other DREBs serving in heat, drought, and salinity adaptation. The central role of these modulators in plant performance under challenging environments is based on (i) interweaving of these regulators with other key signaling networks (plant hormones and redox signals) as well as (ii) their function in integrating responses across the whole plant, from light-harvesting and sugar-production in the leaf to foliar sugar export and water import and on to the plant's sugar-consuming sinks (growth, storage, and reproduction). The example of Arabidopsisthaliana ecotypes from geographic origins with contrasting climates is used to describe the links between natural genetic variation in CBF transcription factors and the differential acclimation of plant anatomical and functional features needed to support superior photosynthetic performance in contrasting environments. Emphasis is placed on considering different temperature environments (hot versus cold) and light environments (limiting versus high light), on trade-offs between adaptations to contrasting environments, and on plant lines minimizing such trade-offs.
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15
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Zhu W, Hu B, Becker C, Doğan ES, Berendzen KW, Weigel D, Liu C. Altered chromatin compaction and histone methylation drive non-additive gene expression in an interspecific Arabidopsis hybrid. Genome Biol 2017; 18:157. [PMID: 28830561 PMCID: PMC5568265 DOI: 10.1186/s13059-017-1281-4] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 07/18/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The merging of two diverged genomes can result in hybrid offspring that phenotypically differ greatly from both parents. In plants, interspecific hybridization plays important roles in evolution and speciation. In addition, many agricultural and horticultural species are derived from interspecific hybridization. However, the detailed mechanisms responsible for non-additive phenotypic novelty in hybrids remain elusive. RESULTS In an interspecific hybrid between Arabidopsis thaliana and A. lyrata, the vast majority of genes that become upregulated or downregulated relative to the parents originate from A. thaliana. Among all differentially expressed A. thaliana genes, the majority is downregulated in the hybrid. To understand why parental origin affects gene expression in this system, we compare chromatin packing patterns and epigenomic landscapes in the hybrid and parents. We find that the chromatin of A. thaliana, but not that of A. lyrata, becomes more compact in the hybrid. Parental patterns of DNA methylation and H3K27me3 deposition are mostly unaltered in the hybrid, with the exception of higher CHH DNA methylation in transposon-rich regions. However, A. thaliana genes enriched for the H3K27me3 mark are particularly likely to differ in expression between the hybrid and parent. CONCLUSIONS It has long been suspected that genome-scale properties cause the differential responses of genes from one or the other parent to hybridization. Our work links global chromatin compactness and H3K27me3 histone modification to global differences in gene expression in an interspecific Arabidopsis hybrid.
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Affiliation(s)
- Wangsheng Zhu
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Bo Hu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, 72076, Germany
| | - Claude Becker
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany.,Present Address: Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, A-1030, Vienna, Austria
| | - Ezgi Süheyla Doğan
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, 72076, Germany
| | - Kenneth Wayne Berendzen
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, 72076, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany.
| | - Chang Liu
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany. .,Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, 72076, Germany.
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16
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Ibañez C, Poeschl Y, Peterson T, Bellstädt J, Denk K, Gogol-Döring A, Quint M, Delker C. Ambient temperature and genotype differentially affect developmental and phenotypic plasticity in Arabidopsis thaliana. BMC PLANT BIOLOGY 2017; 17:114. [PMID: 28683779 PMCID: PMC5501000 DOI: 10.1186/s12870-017-1068-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/25/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Global increase in ambient temperatures constitute a significant challenge to wild and cultivated plant species. Forward genetic analyses of individual temperature-responsive traits have resulted in the identification of several signaling and response components. However, a comprehensive knowledge about temperature sensitivity of different developmental stages and the contribution of natural variation is still scarce and fragmented at best. RESULTS Here, we systematically analyze thermomorphogenesis throughout a complete life cycle in ten natural Arabidopsis thaliana accessions grown under long day conditions in four different temperatures ranging from 16 to 28 °C. We used Q10, GxE, phenotypic divergence and correlation analyses to assess temperature sensitivity and genotype effects of more than 30 morphometric and developmental traits representing five phenotype classes. We found that genotype and temperature differentially affected plant growth and development with variing strengths. Furthermore, overall correlations among phenotypic temperature responses was relatively low which seems to be caused by differential capacities for temperature adaptations of individual accessions. CONCLUSION Genotype-specific temperature responses may be attractive targets for future forward genetic approaches and accession-specific thermomorphogenesis maps may aid the assessment of functional relevance of known and novel regulatory components.
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Affiliation(s)
- Carla Ibañez
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, 06120 Halle (Saale), Germany
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Yvonne Poeschl
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06099 Halle (Saale), Germany
| | - Tom Peterson
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Julia Bellstädt
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, 06120 Halle (Saale), Germany
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Kathrin Denk
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, 06120 Halle (Saale), Germany
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Andreas Gogol-Döring
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06099 Halle (Saale), Germany
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, 06120 Halle (Saale), Germany
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Carolin Delker
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, 06120 Halle (Saale), Germany
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
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17
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Gutierrez C. 25 Years of Cell Cycle Research: What's Ahead? TRENDS IN PLANT SCIENCE 2016; 21:823-833. [PMID: 27401252 DOI: 10.1016/j.tplants.2016.06.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/13/2016] [Accepted: 06/21/2016] [Indexed: 05/27/2023]
Abstract
We have reached 25 years since the first molecular approaches to plant cell cycle. Fortunately, we have witnessed an enormous advance in this field that has benefited from using complementary approaches including molecular, cellular, genetic and genomic resources. These studies have also branched and demonstrated the functional relevance of cell cycle regulators for virtually every aspect of plant life. The question is - where are we heading? I review here the latest developments in the field and briefly elaborate on how new technological advances should contribute to novel approaches that will benefit the plant cell cycle field. Understanding how the cell division cycle is integrated at the organismal level is perhaps one of the major challenges.
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Affiliation(s)
- Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Nicolas Cabrera 1, 28049 Madrid, Spain.
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18
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Sanchez-Bermejo E, Balasubramanian S. Natural variation involving deletion alleles of FRIGIDA modulate temperature-sensitive flowering responses in Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 2016; 39:1353-65. [PMID: 26662639 DOI: 10.1111/pce.12690] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 11/28/2015] [Accepted: 11/29/2015] [Indexed: 05/12/2023]
Abstract
Ambient temperature is one of the major environmental factors that modulate plant growth and development. There is extensive natural genetic variation in thermal responses of plants exemplified by the variation exhibited by the accessions of Arabidopsis thaliana. In this work we have studied the enhanced temperature response in hypocotyl elongation and flowering shown by the Tsu-0 accession in long days. Genetic mapping in the Col-0 × Tsu-0 recombinant inbred line (RIL) population identified several QTLs for thermal response including three major effect loci encompassing candidate genes FRIGIDA (FRI), FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT). We confirm and validate these QTLs. We show that the Tsu-0 FRI allele, which is the same as FRI-Ler is associated with late flowering but only at lower temperatures in long days. Using transgenic lines and accessions, we show that the FRI-Ler allele confers temperature-sensitive late flowering confirming a role for FRI in photoperiod-dependent thermal response. Through quantitative complementation with heterogeneous inbred families, we further show that cis-regulatory variation at FT contributes to the observed hypersensitivity of Tsu-0 to ambient temperature. Overall our results suggest that multiple loci that interact epistatically govern photoperiod-dependent thermal responses of A. thaliana.
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19
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Sureshkumar S, Dent C, Seleznev A, Tasset C, Balasubramanian S. Nonsense-mediated mRNA decay modulates FLM-dependent thermosensory flowering response in Arabidopsis. NATURE PLANTS 2016; 2:16055. [PMID: 27243649 DOI: 10.1038/nplants.2016.55] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 03/18/2016] [Indexed: 05/19/2023]
Abstract
Increasing global temperatures have an impact on flowering, and the underlying mechanisms are just beginning to be unravelled(1,2). Elevated temperatures can induce flowering, and different mechanisms that involve either activation or de-repression of FLOWERING LOCUS T (FT) by transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4) or the FLOWERING LOCUS M (FLM)-SHORT VEGETATIVE PHASE (SVP) complex, respectively, have been suggested to be involved(3-6). Thermosensitivity in flowering has been mapped to FLM(5), which encodes a floral repressor(7,8). FLM undergoes alternative splicing(8) and it has been suggested that temperature-dependent alternative splicing leads to differential accumulation of the FLM-β and FLM-δ transcripts, encoding proteins with antagonistic effects, and that their ratio determines floral transition(4). Here we show that high temperatures downregulate FLM expression by alternative splicing coupled with nonsense-mediated mRNA decay (AS-NMD). We identify thermosensitive splice sites in FLM and show that the primary effect of temperature is explained by an increase in NMD target transcripts. We also show that flm is epistatic to pif4, which suggests that most of the PIF4 effects are FLM dependent. Our findings suggest a model in which the loss of the floral repressor FLM occurs through mRNA degradation in response to elevated temperatures, signifying a role for AS-NMD in conferring environmental responses in plants.
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Affiliation(s)
- Sridevi Sureshkumar
- School of Biological Sciences, Monash University, Clayton Campus, Victoria 3800, Australia
| | - Craig Dent
- School of Biological Sciences, Monash University, Clayton Campus, Victoria 3800, Australia
| | - Andrei Seleznev
- School of Biological Sciences, Monash University, Clayton Campus, Victoria 3800, Australia
| | - Celine Tasset
- School of Biological Sciences, Monash University, Clayton Campus, Victoria 3800, Australia
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20
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Casaretto JA, El-Kereamy A, Zeng B, Stiegelmeyer SM, Chen X, Bi YM, Rothstein SJ. Expression of OsMYB55 in maize activates stress-responsive genes and enhances heat and drought tolerance. BMC Genomics 2016; 17:312. [PMID: 27129581 PMCID: PMC4850646 DOI: 10.1186/s12864-016-2659-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/25/2016] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Plant response mechanisms to heat and drought stresses have been considered in strategies for generating stress tolerant genotypes, but with limited success. Here, we analyzed the transcriptome and improved tolerance to heat stress and drought of maize plants over-expressing the OsMYB55 gene. RESULTS Over-expression of OsMYB55 in maize decreased the negative effects of high temperature and drought resulting in improved plant growth and performance under these conditions. This was evidenced by the higher plant biomass and reduced leaf damage exhibited by the transgenic lines compared to wild type when plants were subjected to individual or combined stresses and during or after recovery from stress. A global transcriptomic analysis using RNA sequencing revealed that several genes induced by heat stress in wild type plants are constitutively up-regulated in OsMYB55 transgenic maize. In addition, a significant number of genes up-regulated in OsMYB55 transgenic maize under control or heat treatments have been associated with responses to abiotic stresses including high temperature, dehydration and oxidative stress. The latter is a common and major consequence of imposed heat and drought conditions, suggesting that this altered gene expression may be associated with the improved stress tolerance in these transgenic lines. Functional annotation and enrichment analysis of the transcriptome also pinpoint the relevance of specific biological processes for stress responses. CONCLUSIONS Our results show that expression of OsMYB55 can improve tolerance to heat stress and drought in maize plants. Enhanced expression of stress-associated genes may be involved in OsMYB55-mediated stress tolerance. Possible implications for the improved tolerance to heat stress and drought of OsMYB55 transgenic maize are discussed.
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Affiliation(s)
- José A Casaretto
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada.
| | - Ashraf El-Kereamy
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
- University of California, Agriculture and Natural Resources, Cooperative Extension - Kern County, Bakersfield, CA, 93307, USA
| | - Bin Zeng
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Suzy M Stiegelmeyer
- Syngenta Biotechnology Inc., Research Triangle Park, NC, 27709, USA
- Expression Analysis, Inc., Durham, NC, 27713, USA
| | - Xi Chen
- Syngenta Biotechnology Inc., Research Triangle Park, NC, 27709, USA
| | - Yong-Mei Bi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Steven J Rothstein
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
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21
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Kimura S, Suzuki T, Chen M, Kato K, Yu J, Nakamura A, Tanaka I, Yao M. Template-dependent nucleotide addition in the reverse (3'-5') direction by Thg1-like protein. SCIENCE ADVANCES 2016; 2:e1501397. [PMID: 27051866 PMCID: PMC4820378 DOI: 10.1126/sciadv.1501397] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/04/2016] [Indexed: 05/23/2023]
Abstract
Thg1-like protein (TLP) catalyzes the addition of a nucleotide to the 5'-end of truncated transfer RNA (tRNA) species in a Watson-Crick template-dependent manner. The reaction proceeds in two steps: the activation of the 5'-end by adenosine 5'-triphosphate (ATP)/guanosine 5'-triphosphate (GTP), followed by nucleotide addition. Structural analyses of the TLP and its reaction intermediates have revealed the atomic detail of the template-dependent elongation reaction in the 3'-5' direction. The enzyme creates two substrate binding sites for the first- and second-step reactions in the vicinity of one reaction center consisting of two Mg(2+) ions, and the two reactions are executed at the same reaction center in a stepwise fashion. When the incoming nucleotide is bound to the second binding site with Watson-Crick hydrogen bonds, the 3'-OH of the incoming nucleotide and the 5'-triphosphate of the tRNA are moved to the reaction center where the first reaction has occurred. That the 3'-5' elongation enzyme performs this elaborate two-step reaction in one catalytic center suggests that these two reactions have been inseparable throughout the process of protein evolution. Although TLP and Thg1 have similar tetrameric organization, the tRNA binding mode of TLP is different from that of Thg1, a tRNA(His)-specific G-1 addition enzyme. Each tRNA(His) binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin. Furthermore, mutational analyses show that tRNA(His) is bound to TLP in a similar manner as Thg1, thus indicating that TLP has a dual binding mode.
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Affiliation(s)
- Shoko Kimura
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Tateki Suzuki
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Meirong Chen
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Koji Kato
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Jian Yu
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Akiyoshi Nakamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan
| | - Isao Tanaka
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Min Yao
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
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23
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Méndez-Vigo B, Savic M, Ausín I, Ramiro M, Martín B, Picó FX, Alonso-Blanco C. Environmental and genetic interactions reveal FLOWERING LOCUS C as a modulator of the natural variation for the plasticity of flowering in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:282-94. [PMID: 26173848 DOI: 10.1111/pce.12608] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 06/30/2015] [Accepted: 07/02/2015] [Indexed: 05/12/2023]
Abstract
The timing of flowering initiation depends strongly on the environment, a property termed as the plasticity of flowering. Such plasticity determines the adaptive potential of plants because it provides phenotypic buffer against environmental changes, and its natural variation contributes to evolutionary adaptation. We addressed the genetic mechanisms of the natural variation for this plasticity in Arabidopsis thaliana by analysing a population of recombinant inbred lines derived from Don-0 and Ler accessions collected from distinct climates. Quantitative trait locus (QTL) mapping in four environmental conditions differing in photoperiod, vernalization treatment and ambient temperature detected the folllowing: (i) FLOWERING LOCUS C (FLC) as a large effect QTL affecting flowering time differentially in all environments; (ii) numerous QTL displaying smaller effects specifically in some conditions; and (iii) significant genetic interactions between FLC and other loci. Hence, the variation for the plasticity of flowering is determined by a combination of environmentally sensitive and specific QTL, and epistasis. Analysis of FLC from Don identified a new and more active allele likely caused by a cis-regulatory deletion covering the non-coding RNA COLDAIR. Further characterization of four FLC natural alleles showed different environmental and genetic interactions. Thus, FLC appears as a major modulator of the natural variation for the plasticity of flowering to multiple environmental factors.
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Affiliation(s)
- Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Marija Savic
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Israel Ausín
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Mercedes Ramiro
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - Beatriz Martín
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Sevilla, 41092, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
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24
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Quint M, Delker C, Franklin KA, Wigge PA, Halliday KJ, van Zanten M. Molecular and genetic control of plant thermomorphogenesis. NATURE PLANTS 2016; 2:15190. [PMID: 27250752 DOI: 10.1038/nplants.2015.190] [Citation(s) in RCA: 321] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/03/2015] [Indexed: 05/19/2023]
Abstract
Temperature is a major factor governing the distribution and seasonal behaviour of plants. Being sessile, plants are highly responsive to small differences in temperature and adjust their growth and development accordingly. The suite of morphological and architectural changes induced by high ambient temperatures, below the heat-stress range, is collectively called thermomorphogenesis. Understanding the molecular genetic circuitries underlying thermomorphogenesis is particularly relevant in the context of climate change, as this knowledge will be key to rational breeding for thermo-tolerant crop varieties. Until recently, the fundamental mechanisms of temperature perception and signalling remained unknown. Our understanding of temperature signalling is now progressing, mainly by exploiting the model plant Arabidopsis thaliana. The transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4) has emerged as a critical player in regulating phytohormone levels and their activity. To control thermomorphogenesis, multiple regulatory circuits are in place to modulate PIF4 levels, activity and downstream mechanisms. Thermomorphogenesis is integrally governed by various light signalling pathways, the circadian clock, epigenetic mechanisms and chromatin-level regulation. In this Review, we summarize recent progress in the field and discuss how the emerging knowledge in Arabidopsis may be transferred to relevant crop systems.
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Affiliation(s)
- Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann Strasse 5, 06120 Halle (Saale), Germany
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Carolin Delker
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann Strasse 5, 06120 Halle (Saale), Germany
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Keara A Franklin
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, United Kingdom
| | - Philip A Wigge
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Karen J Halliday
- Synthetic and Systems Biology (SynthSys), University of Edinburgh, CH Waddington Building, Mayfield Road, Edinburgh EH9 3JD, United Kingdom
| | - Martijn van Zanten
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
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25
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Tabib A, Vishwanathan S, Seleznev A, McKeown PC, Downing T, Dent C, Sanchez-Bermejo E, Colling L, Spillane C, Balasubramanian S. A Polynucleotide Repeat Expansion Causing Temperature-Sensitivity Persists in Wild Irish Accessions of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2016; 7:1311. [PMID: 27630650 PMCID: PMC5006647 DOI: 10.3389/fpls.2016.01311] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 08/16/2016] [Indexed: 05/15/2023]
Abstract
Triplet repeat expansions underlie several human genetic diseases such as Huntington's disease and Friedreich's ataxia. Although such mutations are primarily known from humans, a triplet expansion associated genetic defect has also been reported at the IIL1 locus in the Bur-0 accession of the model plant Arabidopsis thaliana. The IIL1 triplet expansion is an example of cryptic genetic variation as its phenotypic effects are seen only under genetic or environmental perturbation, with high temperatures resulting in a growth defect. Here we demonstrate that the IIL1 triplet expansion associated growth defect is not a general stress response and is specific to particular environmental perturbations. We also confirm and map genetic modifiers that suppress the effect of IIL1 triplet repeat expansion. By collecting and analyzing accessions from the island of Ireland, we recover the repeat expansion in wild populations suggesting that the repeat expansion has persisted at least 60 years in Ireland. Through genome-wide genotyping, we show that the repeat expansion is present in diverse Irish populations. Our findings indicate that even deleterious alleles can persist in populations if their effect is conditional. Our study demonstrates that analysis of groups of wild populations is a powerful tool for understanding the dynamics of cryptic genetic variation.
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Affiliation(s)
- Amanda Tabib
- School of Biological Sciences, Monash UniversityMelbourne, VIC, Australia
| | | | - Andrei Seleznev
- School of Biological Sciences, Monash UniversityMelbourne, VIC, Australia
| | - Peter C. McKeown
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, National University of IrelandGalway, Ireland
| | - Tim Downing
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, National University of IrelandGalway, Ireland
- School of Biotechnology, Dublin City UniversityDublin, Ireland
| | - Craig Dent
- School of Biological Sciences, Monash UniversityMelbourne, VIC, Australia
| | | | - Luana Colling
- School of Biological Sciences, Monash UniversityMelbourne, VIC, Australia
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, National University of IrelandGalway, Ireland
| | - Sureshkumar Balasubramanian
- School of Biological Sciences, Monash UniversityMelbourne, VIC, Australia
- *Correspondence: Sureshkumar Balasubramanian
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Sanchez-Bermejo E, Zhu W, Tasset C, Eimer H, Sureshkumar S, Singh R, Sundaramoorthi V, Colling L, Balasubramanian S. Genetic Architecture of Natural Variation in Thermal Responses of Arabidopsis. PLANT PHYSIOLOGY 2015; 169. [PMID: 26195568 PMCID: PMC4577429 DOI: 10.1104/pp.15.00942] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Wild strains of Arabidopsis (Arabidopsis thaliana) exhibit extensive natural variation in a wide variety of traits, including response to environmental changes. Ambient temperature is one of the major external factors that modulates plant growth and development. Here, we analyze the genetic architecture of natural variation in thermal responses of Arabidopsis. Exploiting wild accessions and recombinant inbred lines, we reveal extensive phenotypic variation in response to ambient temperature in distinct developmental traits such as hypocotyl elongation, root elongation, and flowering time. We show that variation in thermal response differs between traits, suggesting that the individual phenotypes do not capture all the variation associated with thermal response. Genome-wide association studies and quantitative trait locus analyses reveal that multiple rare alleles contribute to the genetic architecture of variation in thermal response. We identify at least 20 genomic regions that are associated with variation in thermal response. Further characterizations of temperature sensitivity quantitative trait loci that are shared between traits reveal a role for the blue-light receptor CRYPTOCHROME2 (CRY2) in thermosensory growth responses. We show the accession Cape Verde Islands is less sensitive to changes in ambient temperature, and through transgenic analysis, we demonstrate that allelic variation at CRY2 underlies this temperature insensitivity across several traits. Transgenic analyses suggest that the allelic effects of CRY2 on thermal response are dependent on genetic background suggestive of the presence of modifiers. In addition, our results indicate that complex light and temperature interactions, in a background-dependent manner, govern growth responses in Arabidopsis.
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Affiliation(s)
| | - Wangsheng Zhu
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Celine Tasset
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Hannes Eimer
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Sridevi Sureshkumar
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Rupali Singh
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | | | - Luana Colling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
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