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de Los Reyes P, Serrano-Bueno G, Romero-Campero FJ, Gao H, Romero JM, Valverde F. CONSTANS alters the circadian clock in Arabidopsis thaliana. MOLECULAR PLANT 2024; 17:1204-1220. [PMID: 38894538 DOI: 10.1016/j.molp.2024.06.006] [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: 07/19/2023] [Revised: 04/23/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024]
Abstract
Plants are sessile organisms that have acquired highly plastic developmental strategies to adapt to the environment. Among these processes, the floral transition is essential to ensure reproductive success and is finely regulated by several internal and external genetic networks. The photoperiodic pathway, which controls plant response to day length, is one of the most important pathways controlling flowering. In Arabidopsis photoperiodic flowering, CONSTANS (CO) is the central gene activating the expression of the florigen FLOWERING LOCUS T (FT) in the leaves at the end of a long day. The circadian clock strongly regulates CO expression. However, to date, no evidence has been reported regarding a feedback loop from the photoperiod pathway back to the circadian clock. Using transcriptional networks, we have identified relevant network motifs regulating the interplay between the circadian clock and the photoperiod pathway. Gene expression, chromatin immunoprecipitation experiments, and phenotypic analysis allowed us to elucidate the role of CO over the circadian clock. Plants with altered CO expression showed a different internal clock period, measured by daily leaf rhythmic movements. We showed that CO upregulates the expression of key genes related to the circadian clock, such as CCA1, LHY, PRR5, and GI, at the end of a long day by binding to specific sites on their promoters. Moreover, a high number of PRR5-repressed target genes are upregulated by CO, and this could explain the phase transition promoted by CO. The CO-PRR5 complex interacts with the bZIP transcription factor HY5 and helps to localize the complex in the promoters of clock genes. Taken together, our results indicate that there may be a feedback loop in which CO communicates back to the circadian clock, providing seasonal information to the circadian system.
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Affiliation(s)
- Pedro de Los Reyes
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain
| | - Gloria Serrano-Bueno
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain; Department of Plant Biochemistry and Molecular Biology, Universidad de Sevilla, Seville, Spain
| | - Francisco J Romero-Campero
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain; Department of Computer Science and Artificial Intelligence, Universidad de Sevilla, Seville, Spain
| | - He Gao
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jose M Romero
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain; Department of Plant Biochemistry and Molecular Biology, Universidad de Sevilla, Seville, Spain
| | - Federico Valverde
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain.
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Liu Y, Xiao W, Wang F, Wang Y, Dong Y, Nie W, Tan C, An S, Chang E, Jiang Z, Wang J, Jia Z. Species divergence and environmental adaptation of Picea asperata complex at the whole genome level. Ecol Evol 2024; 14:e70126. [PMID: 39114168 PMCID: PMC11303459 DOI: 10.1002/ece3.70126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 07/15/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
To study the interspecific differentiation characteristics of species originating from recent radiation, the genotyping-by-sequencing (GBS) technique was used to explore the kinship, population structure, gene flow, genetic variability, genotype-environment association and selective sweeps of Picea asperata complex with similar phenotypes from a genome-wide perspective. The following results were obtained: 14 populations of P. asperata complex could be divided into 5 clades; P. wilsonii and P. neoveitchii diverged earlier and were more distantly related to the remaining 6 spruce species. Various geological events have promoted the species differentiation of P. asperata complex. There were four instances of gene flow among P. koraiensis, P. meyeri, P. asperata, P. crassifolia and P. mongolica. The population of P. mongolica had the highest level of nucleotide diversity, and P. neoveitchii may have experienced a bottleneck recently. Genotype-environment association found that a total of 20,808 genes were related to the environmental variables, which enhanced the adaptability of spruce in different environments. Genes that were selectively swept in the P. asperata complex were primarily associated with plant stress resistance. Among them were some genes involved in plant growth and development, heat stress, circadian rhythms and flowering. In addition to the commonly selected genes, different spruce species also displayed unique genes subjected to selective sweeps that improved their adaptability to different habitats. Understanding the interspecific gene flow and adaptive evolution of Picea species is beneficial to further understanding the species relationships of spruce and can provide a basis for studying spruce introgression and functional genomics.
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Affiliation(s)
- Yifu Liu
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation InstituteChinese Academy of ForestryBeijingChina
- State Key Laboratory of Tree Genetics and BreedingChinese Academy of ForestryBeijingChina
| | - Wenfa Xiao
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation InstituteChinese Academy of ForestryBeijingChina
| | - Fude Wang
- Heilongjiang Forestry Research InstituteHarbinChina
| | - Ya Wang
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of ForestryChinese Academy of ForestryBeijingChina
| | - Yao Dong
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation InstituteChinese Academy of ForestryBeijingChina
| | - Wen Nie
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation InstituteChinese Academy of ForestryBeijingChina
| | - Cancan Tan
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation InstituteChinese Academy of ForestryBeijingChina
| | - Sanping An
- Research Institute of Forestry of Xiaolong MountainGansu Provincial Key Laboratory of Secondary Forest CultivationTianshuiChina
| | - Ermei Chang
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of ForestryChinese Academy of ForestryBeijingChina
| | - Zeping Jiang
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation InstituteChinese Academy of ForestryBeijingChina
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and BreedingChinese Academy of ForestryBeijingChina
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of ForestryChinese Academy of ForestryBeijingChina
| | - Zirui Jia
- State Key Laboratory of Tree Genetics and BreedingChinese Academy of ForestryBeijingChina
- Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of ForestryChinese Academy of ForestryBeijingChina
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Vong GYW, McCarthy K, Claydon W, Davis SJ, Redmond EJ, Ezer D. AraLeTA: An Arabidopsis leaf expression atlas across diurnal and developmental scales. PLANT PHYSIOLOGY 2024; 195:1941-1953. [PMID: 38428997 PMCID: PMC11213249 DOI: 10.1093/plphys/kiae117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 03/03/2024]
Abstract
Mature plant leaves are a composite of distinct cell types, including epidermal, mesophyll, and vascular cells. Notably, the proportion of these cells and the relative transcript concentrations within different cell types may change over time. While gene expression data at a single-cell level can provide cell-type-specific expression values, it is often too expensive to obtain these data for high-resolution time series. Although bulk RNA-seq can be performed in a high-resolution time series, RNA-seq using whole leaves measures average gene expression values across all cell types in each sample. In this study, we combined single-cell RNA-seq data with time-series data from whole leaves to assemble an atlas of cell-type-specific changes in gene expression over time for Arabidopsis (Arabidopsis thaliana). We inferred how the relative transcript concentrations of different cell types vary across diurnal and developmental timescales. Importantly, this analysis revealed 3 subgroups of mesophyll cells with distinct temporal profiles of expression. Finally, we developed tissue-specific gene networks that form a community resource: an Arabidopsis Leaf Time-dependent Atlas (AraLeTa). This allows users to extract gene networks that are confirmed by transcription factor-binding data and specific to certain cell types at certain times of day and at certain developmental stages. AraLeTa is available at https://regulatorynet.shinyapps.io/araleta/.
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Affiliation(s)
- Gina Y W Vong
- Department of Biology, University of York, York YO10 5DD, UK
| | - Kayla McCarthy
- Department of Biology, University of York, York YO10 5DD, UK
| | - Will Claydon
- Department of Biology, University of York, York YO10 5DD, UK
| | - Seth J Davis
- Department of Biology, University of York, York YO10 5DD, UK
| | - Ethan J Redmond
- Department of Biology, University of York, York YO10 5DD, UK
| | - Daphne Ezer
- Department of Biology, University of York, York YO10 5DD, UK
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de Leone MJ, Yanovsky MJ. The circadian clock and thermal regulation in plants: novel insights into the role of positive circadian clock regulators in temperature responses. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2809-2818. [PMID: 38373194 DOI: 10.1093/jxb/erae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/19/2024] [Indexed: 02/21/2024]
Abstract
The impact of rising global temperatures on crop yields is a serious concern, and the development of heat-resistant crop varieties is crucial for mitigating the effects of climate change on agriculture. To achieve this, a better understanding of the molecular basis of the thermal responses of plants is necessary. The circadian clock plays a central role in modulating plant biology in synchrony with environmental changes, including temperature fluctuations. Recent studies have uncovered the role of transcriptional activators of the core circadian network in plant temperature responses. This expert view highlights key novel findings regarding the role of the RVE and LNK gene families in controlling gene expression patterns and plant growth under different temperature conditions, ranging from regular diurnal oscillations to extreme stress temperatures. These findings reinforce the essential role of the circadian clock in plant adaptation to changing temperatures and provide a basis for future studies on crop improvement.
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Affiliation(s)
- María José de Leone
- Fundación Instituto Leloir-IIBBA/CONICET, Av. Patricias Argentinas 435, Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcelo Javier Yanovsky
- Fundación Instituto Leloir-IIBBA/CONICET, Av. Patricias Argentinas 435, Ciudad Autónoma de Buenos Aires, Argentina
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Kim JS, Kidokoro S, Yamaguchi-Shinozaki K, Shinozaki K. Regulatory networks in plant responses to drought and cold stress. PLANT PHYSIOLOGY 2024; 195:170-189. [PMID: 38514098 PMCID: PMC11060690 DOI: 10.1093/plphys/kiae105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/15/2024] [Indexed: 03/23/2024]
Abstract
Drought and cold represent distinct types of abiotic stress, each initiating unique primary signaling pathways in response to dehydration and temperature changes, respectively. However, a convergence at the gene regulatory level is observed where a common set of stress-responsive genes is activated to mitigate the impacts of both stresses. In this review, we explore these intricate regulatory networks, illustrating how plants coordinate distinct stress signals into a collective transcriptional strategy. We delve into the molecular mechanisms of stress perception, stress signaling, and the activation of gene regulatory pathways, with a focus on insights gained from model species. By elucidating both the shared and distinct aspects of plant responses to drought and cold, we provide insight into the adaptive strategies of plants, paving the way for the engineering of stress-resilient crop varieties that can withstand a changing climate.
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Affiliation(s)
- June-Sik Kim
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045Japan
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046Japan
| | - Satoshi Kidokoro
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8502Japan
| | - Kazuko Yamaguchi-Shinozaki
- Research Institute for Agriculture and Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502Japan
- Graduate School of Agriculture and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032Japan
| | - Kazuo Shinozaki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045Japan
- Institute for Advanced Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601Japan
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Dwivedi SL, Quiroz LF, Spillane C, Wu R, Mattoo AK, Ortiz R. Unlocking allelic variation in circadian clock genes to develop environmentally robust and productive crops. PLANTA 2024; 259:72. [PMID: 38386103 PMCID: PMC10884192 DOI: 10.1007/s00425-023-04324-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/24/2023] [Indexed: 02/23/2024]
Abstract
MAIN CONCLUSION Molecular mechanisms of biological rhythms provide opportunities to harness functional allelic diversity in core (and trait- or stress-responsive) oscillator networks to develop more climate-resilient and productive germplasm. The circadian clock senses light and temperature in day-night cycles to drive biological rhythms. The clock integrates endogenous signals and exogenous stimuli to coordinate diverse physiological processes. Advances in high-throughput non-invasive assays, use of forward- and inverse-genetic approaches, and powerful algorithms are allowing quantitation of variation and detection of genes associated with circadian dynamics. Circadian rhythms and phytohormone pathways in response to endogenous and exogenous cues have been well documented the model plant Arabidopsis. Novel allelic variation associated with circadian rhythms facilitates adaptation and range expansion, and may provide additional opportunity to tailor climate-resilient crops. The circadian phase and period can determine adaptation to environments, while the robustness in the circadian amplitude can enhance resilience to environmental changes. Circadian rhythms in plants are tightly controlled by multiple and interlocked transcriptional-translational feedback loops involving morning (CCA1, LHY), mid-day (PRR9, PRR7, PRR5), and evening (TOC1, ELF3, ELF4, LUX) genes that maintain the plant circadian clock ticking. Significant progress has been made to unravel the functions of circadian rhythms and clock genes that regulate traits, via interaction with phytohormones and trait-responsive genes, in diverse crops. Altered circadian rhythms and clock genes may contribute to hybrid vigor as shown in Arabidopsis, maize, and rice. Modifying circadian rhythms via transgenesis or genome-editing may provide additional opportunities to develop crops with better buffering capacity to environmental stresses. Models that involve clock gene‒phytohormone‒trait interactions can provide novel insights to orchestrate circadian rhythms and modulate clock genes to facilitate breeding of all season crops.
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Affiliation(s)
| | - Luis Felipe Quiroz
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland.
| | - Rongling Wu
- Beijing Yanqi Lake Institute of Mathematical Sciences and Applications, Beijing, 101408, China
| | - Autar K Mattoo
- USDA-ARS, Sustainable Agricultural Systems Laboratory, Beltsville, MD, 20705-2350, USA
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Sundsvagen, 10, Box 190, SE 23422, Lomma, Sweden.
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Kaya S, Erdogan DE, Sancar A, Adebali O, Oztas O. Global repair is the primary nucleotide excision repair subpathway for the removal of pyrimidine-pyrimidone (6-4) damage from the Arabidopsis genome. Sci Rep 2024; 14:3308. [PMID: 38332020 PMCID: PMC10853524 DOI: 10.1038/s41598-024-53472-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/31/2024] [Indexed: 02/10/2024] Open
Abstract
Ultraviolet (UV) component of solar radiation impairs genome stability by inducing the formation of pyrimidine-pyrimidone (6-4) photoproducts [(6-4)PPs] in plant genomes. (6-4)PPs disrupt growth and development by interfering with transcription and DNA replication. To resist UV stress, plants employ both photoreactivation and nucleotide excision repair that excises oligonucleotide containing (6-4)PPs through two subpathways: global and transcription-coupled excision repair (TCR). Here, we analyzed the genome-wide excision repair-mediated repair of (6-4)PPs in Arabidopsis thaliana and found that (6-4)PPs can be repaired by TCR; however, the main subpathway to remove (6-4)PPs from the genome is global repair. Our analysis showed that open chromatin genome regions are more rapidly repaired than heterochromatin regions, and the repair level peaks at the promoter, transcription start site and transcription end site of genes. Our study revealed that the repair of (6-4)PP in plants showed a distinct genome-wide repair profile compared to the repair of other major UV-induced DNA lesion called cyclobutane pyrimidine dimers (CPDs).
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Affiliation(s)
- Sezgi Kaya
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Dugcar Ebrar Erdogan
- Department of Molecular Biology and Genetics, College of Sciences, Koc University, Istanbul, Turkey
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Ogun Adebali
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey.
| | - Onur Oztas
- Department of Molecular Biology and Genetics, College of Sciences, Koc University, Istanbul, Turkey.
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Gao M, Lu Y, Geng F, Klose C, Staudt AM, Huang H, Nguyen D, Lan H, Lu H, Mockler TC, Nusinow DA, Hiltbrunner A, Schäfer E, Wigge PA, Jaeger KE. Phytochromes transmit photoperiod information via the evening complex in Brachypodium. Genome Biol 2023; 24:256. [PMID: 37936225 PMCID: PMC10631206 DOI: 10.1186/s13059-023-03082-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 10/04/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Daylength is a key seasonal cue for animals and plants. In cereals, photoperiodic responses are a major adaptive trait, and alleles of clock genes such as PHOTOPERIOD1 (PPD1) and EARLY FLOWERING3 (ELF3) have been selected for in adapting barley and wheat to northern latitudes. How monocot plants sense photoperiod and integrate this information into growth and development is not well understood. RESULTS We find that phytochrome C (PHYC) is essential for flowering in Brachypodium distachyon. Conversely, ELF3 acts as a floral repressor and elf3 mutants display a constitutive long day phenotype and transcriptome. We find that ELF3 and PHYC occur in a common complex. ELF3 associates with the promoters of a number of conserved regulators of flowering, including PPD1 and VRN1. Consistent with observations in barley, we are able to show that PPD1 overexpression accelerates flowering in short days and is necessary for rapid flowering in response to long days. PHYC is in the active Pfr state at the end of the day, but we observe it undergoes dark reversion over the course of the night. CONCLUSIONS We propose that PHYC acts as a molecular timer and communicates information on night-length to the circadian clock via ELF3.
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Affiliation(s)
- Mingjun Gao
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge, CB2 1LR, UK
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Yunlong Lu
- Leibniz-Institut für Gemüse- und Zierpflanzenbau, Theodor-Echtermeyer-Weg 1, Großbeeren, 14979, Germany
| | - Feng Geng
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge, CB2 1LR, UK
| | - Cornelia Klose
- Institut für Biologie II, University of Freiburg, Schaenzlestr. 1, Freiburg, 79104, Germany
| | - Anne-Marie Staudt
- Institut für Biologie II, University of Freiburg, Schaenzlestr. 1, Freiburg, 79104, Germany
| | - He Huang
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Duy Nguyen
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge, CB2 1LR, UK
| | - Hui Lan
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge, CB2 1LR, UK
| | - Han Lu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | | | - Andreas Hiltbrunner
- Institut für Biologie II, University of Freiburg, Schaenzlestr. 1, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
| | - Eberhard Schäfer
- Institut für Biologie II, University of Freiburg, Schaenzlestr. 1, Freiburg, 79104, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, Freiburg, 79104, Germany
| | - Philip A Wigge
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge, CB2 1LR, UK.
- Leibniz-Institut für Gemüse- und Zierpflanzenbau, Theodor-Echtermeyer-Weg 1, Großbeeren, 14979, Germany.
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, 14476, Germany.
| | - Katja E Jaeger
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge, CB2 1LR, UK.
- Leibniz-Institut für Gemüse- und Zierpflanzenbau, Theodor-Echtermeyer-Weg 1, Großbeeren, 14979, Germany.
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Xu X, Xie Q. LNKs-RVEs complex ticks in the circadian gating of plant temperature stress responses. STRESS BIOLOGY 2023; 3:32. [PMID: 37676570 PMCID: PMC10441890 DOI: 10.1007/s44154-023-00113-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/25/2023] [Indexed: 09/08/2023]
Abstract
Recently, Kidokoro et al. found that protein complex LNK3,4-RVE4,8 and LNK1,2-RVE4,8 of the circadian clock modulates plant cold- and high-temperature tolerance, respectively. Here, we reviewed the discovery of LNKs, the dynamically formed morning-phased clock complexes, and their critical role on endogenous circadian rhythms. In addition, we summarized the research work on LNKs with the interacting proteins RVEs, CCA1 in temperature responses and discussed how the circadian clock confer increased fitness via gating the rhythmic expression of their target genes.
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Affiliation(s)
- Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
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Kidokoro S, Konoura I, Soma F, Suzuki T, Miyakawa T, Tanokura M, Shinozaki K, Yamaguchi-Shinozaki K. Clock-regulated coactivators selectively control gene expression in response to different temperature stress conditions in Arabidopsis. Proc Natl Acad Sci U S A 2023; 120:e2216183120. [PMID: 37036986 PMCID: PMC10120023 DOI: 10.1073/pnas.2216183120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/12/2023] [Indexed: 04/12/2023] Open
Abstract
Plants respond to severe temperature changes by inducing the expression of numerous genes whose products enhance stress tolerance and responses. Dehydration-responsive element (DRE)-binding protein 1/C-repeat binding factor (DREB1/CBF) transcription factors act as master switches in cold-inducible gene expression. Since DREB1 genes are rapidly and strongly induced by cold stress, the elucidation of the molecular mechanisms of DREB1 expression is vital for the recognition of the initial responses to cold stress in plants. A previous study indicated that the circadian clock-related MYB-like transcription factors REVEILLE4/LHY-CCA1-Like1 (RVE4/LCL1) and RVE8/LCL5 directly activate DREB1 expression under cold stress conditions. These RVEs function in the regulation of circadian clock-related gene expression under normal temperature conditions. They also activate the expression of HSF-independent heat-inducible genes under high-temperature conditions. Thus, there are thought to be specific regulatory mechanisms whereby the target genes of these transcription factors are switched when temperature changes are sensed. We revealed that NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED (LNK) proteins act as coactivators of RVEs in cold and heat stress responses in addition to regulating circadian-regulated genes at normal temperatures. We found that among the four Arabidopsis LNKs, LNK1 and LNK2 function under normal and high-temperature conditions, and LNK3 and LNK4 function under cold conditions. Thus, these LNK proteins play important roles in inducing specific genes under different temperature conditions. Furthermore, LNK3 and LNK4 are specifically phosphorylated under cold conditions, suggesting that phosphorylation is involved in their activation.
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Affiliation(s)
- Satoshi Kidokoro
- Laboratory of Plant Molecular Physiology, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo113-8657, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa226-8502, Japan
| | - Izumi Konoura
- Laboratory of Plant Molecular Physiology, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo113-8657, Japan
| | - Fumiyuki Soma
- Laboratory of Plant Molecular Physiology, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo113-8657, Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Matsumoto-cho, Kasugai, Aichi487-8501, Japan
| | - Takuya Miyakawa
- Laboratory of Basic Science on Healthy Longevity, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo113-8657, Japan
| | - Masaru Tanokura
- Laboratory of Basic Science on Healthy Longevity, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo113-8657, Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki305-0074, Japan
| | - Kazuko Yamaguchi-Shinozaki
- Laboratory of Plant Molecular Physiology, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo113-8657, Japan
- Research Institute for Agricultural and Life Sciences, Tokyo University of Agriculture, Setagaya-ku, Tokyo156-8502, Japan
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11
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Sorkin ML, Tzeng SC, King S, Romanowski A, Kahle N, Bindbeutel R, Hiltbrunner A, Yanovsky MJ, Evans BS, Nusinow DA. COLD REGULATED GENE 27 and 28 Antagonize the Transcriptional Activity of the RVE8/LNK1/LNK2 Circadian Complex. PLANT PHYSIOLOGY 2023:kiad210. [PMID: 37017001 DOI: 10.1093/plphys/kiad210] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 03/01/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
Many molecular and physiological processes in plants occur at a specific time of day. These daily rhythms are coordinated in part by the circadian clock, a timekeeper that uses daylength and temperature to maintain rhythms of approximately 24 hours in various clock-regulated phenotypes. The circadian MYB-like transcription factor REVEILLE 8 (RVE8) interacts with its transcriptional coactivators NIGHT LIGHT INDUCIBLE AND CLOCK REGULATED 1 (LNK1) and LNK2 to promote the expression of evening-phased clock genes and cold tolerance factors. While genetic approaches have commonly been used to discover connections within the clock and between clock elements and other pathways, here we used affinity purification coupled with mass spectrometry to identify time-of-day-specific protein interactors of the RVE8-LNK1/LNK2 complex in Arabidopsis (Arabidopsis thaliana). Among the interactors of RVE8/LNK1/LNK2 were COLD REGULATED GENE 27 (COR27) and COR28, which coprecipitated in an evening-specific manner. In addition to COR27 and COR28, we found an enrichment of temperature-related interactors that led us to establish a previously uncharacterized role for LNK1 and LNK2 in temperature entrainment of the clock. We established that RVE8, LNK1, and either COR27 or COR28 form a tripartite complex in yeast (Saccharomyces cerevisiae) and that the effect of this interaction in planta serves to antagonize transcriptional activation of RVE8 target genes, potentially through mediating RVE8 protein degradation in the evening. Together, these results illustrate how a proteomic approach can be used to identify time-of-day-specific protein interactions. Discovery of the RVE8-LNK-COR protein complex indicates a previously unknown regulatory mechanism for circadian and temperature signaling pathways.
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Affiliation(s)
- Maria L Sorkin
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Stefanie King
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA
| | - Andrés Romanowski
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Nikolai Kahle
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Andreas Hiltbrunner
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Marcelo J Yanovsky
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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12
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Cano-Ramirez DL, Panter PE, Takemura T, de Fraine TS, de Barros Dantas LL, Dekeya R, Barros-Galvão T, Paajanen P, Bellandi A, Batstone T, Manley BF, Tanaka K, Imamura S, Franklin KA, Knight H, Dodd AN. Low-temperature and circadian signals are integrated by the sigma factor SIG5. NATURE PLANTS 2023; 9:661-672. [PMID: 36997687 PMCID: PMC10119024 DOI: 10.1038/s41477-023-01377-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
Chloroplasts are a common feature of plant cells and aspects of their metabolism, including photosynthesis, are influenced by low-temperature conditions. Chloroplasts contain a small circular genome that encodes essential components of the photosynthetic apparatus and chloroplast transcription/translation machinery. Here, we show that in Arabidopsis, a nuclear-encoded sigma factor that controls chloroplast transcription (SIGMA FACTOR5) contributes to adaptation to low-temperature conditions. This process involves the regulation of SIGMA FACTOR5 expression in response to cold by the bZIP transcription factors ELONGATED HYPOCOTYL5 and ELONGATED HYPOCOTYL5 HOMOLOG. The response of this pathway to cold is gated by the circadian clock, and it enhances photosynthetic efficiency during long-term cold and freezing exposure. We identify a process that integrates low-temperature and circadian signals, and modulates the response of chloroplasts to low-temperature conditions.
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Affiliation(s)
- Dora L Cano-Ramirez
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - Tokiaki Takemura
- Laboratory for Chemistry and Life Science, Institute for Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | | | | | | | | | | | - Annalisa Bellandi
- John Innes Centre, Norwich, UK
- Laboratoire de Reproduction et Développement des Plantes, ENS de Lyon, Université de Lyon, UCBL, INRAE, CNRS, Lyon, France
| | - Tom Batstone
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Bethan F Manley
- School of Biological Sciences, University of Bristol, Bristol, UK
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute for Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Sousuke Imamura
- Laboratory for Chemistry and Life Science, Institute for Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- Space Environment and Energy Laboratories, Nippon Telegraph and Telephone Corporation, Musashino-shi, Japan
| | - Keara A Franklin
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Heather Knight
- Department of Biosciences, Durham University, Durham, UK
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13
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Wang Y, Wu F, Lin Q, Sheng P, Wu Z, Jin X, Chen W, Li S, Luo S, Duan E, Wang J, Ma W, Ren Y, Cheng Z, Zhang X, Lei C, Guo X, Wang H, Zhu S, Wan J. A regulatory loop establishes the link between the circadian clock and abscisic acid signaling in rice. PLANT PHYSIOLOGY 2023; 191:1857-1870. [PMID: 36493391 PMCID: PMC10022614 DOI: 10.1093/plphys/kiac548] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
There is a close regulatory relationship between the circadian clock and the abscisic acid (ABA) signaling pathway in regulating many developmental processes and stress responses. However, the exact feedback regulation mechanism between them is still poorly understood. Here, we identified the rice (Oryza sativa) clock component PSEUDO-RESPONSE REGULATOR 95 (OsPRR95) as a transcriptional regulator that accelerates seed germination and seedling growth by inhibiting ABA signaling. We also found that OsPRR95 binds to the ABA receptor gene REGULATORY COMPONENTS OF ABA RECEPTORS10 (OsRCAR10) DNA and inhibits its expression. Genetic analysis showed OsRCAR10 acts downstream of OsPRR95 in mediating ABA responses. In addition, the induction of OsPRR95 by ABA partly required a functional OsRCAR10, and the ABA-responsive element-binding factor ABSCISIC ACID INSENSITIVE5 (OsABI5) bound directly to the promoter of OsPRR95 and activated its expression, thus establishing a regulatory feedback loop between OsPRR95, OsRCAR10, and OsABI5. Taken together, our results demonstrated that the OsRCAR10-OsABI5-OsPRR95 feedback loop modulates ABA signaling to fine-tune seed germination and seedling growth, thus establishing the molecular link between ABA signaling and the circadian clock.
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Affiliation(s)
- Yupeng Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | | | - Peike Sheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ziming Wu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xin Jin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weiwei Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuai Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sheng Luo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Erchao Duan
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiachang Wang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiwei Ma
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yulong Ren
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhijun Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cailin Lei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuping Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiyang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | - Jianmin Wan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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14
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Global Analysis of Dark- and Heat-Regulated Alternative Splicing in Arabidopsis. Int J Mol Sci 2023; 24:ijms24065299. [PMID: 36982373 PMCID: PMC10049525 DOI: 10.3390/ijms24065299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Alternative splicing (AS) is one of the major post-transcriptional regulation mechanisms that contributes to plant responses to various environmental perturbations. Darkness and heat are two common abiotic factors affecting plant growth, yet the involvement and regulation of AS in the plant responses to these signals remain insufficiently examined. In this study, we subjected Arabidopsis seedlings to 6 h of darkness or heat stress and analyzed their transcriptome through short-read RNA sequencing. We revealed that both treatments altered the transcription and AS of a subset of genes yet with different mechanisms. Dark-regulated AS events were found enriched in photosynthesis and light signaling pathways, while heat-regulated AS events were enriched in responses to abiotic stresses but not in heat-responsive genes, which responded primarily through transcriptional regulation. The AS of splicing-related genes (SRGs) was susceptible to both treatments; while dark treatment mostly regulated the AS of these genes, heat had a strong effect on both their transcription and AS. PCR analysis showed that the AS of the Serine/Arginine-rich family gene SR30 was reversely regulated by dark and heat, and heat induced the upregulation of multiple minor SR30 isoforms with intron retention. Our results suggest that AS participates in plant responses to these two abiotic signals and reveal the regulation of splicing regulators during these processes.
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15
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Chuong NN, Doan PPT, Wang L, Kim JH, Kim J. Current Insights into m 6A RNA Methylation and Its Emerging Role in Plant Circadian Clock. PLANTS (BASEL, SWITZERLAND) 2023; 12:624. [PMID: 36771711 PMCID: PMC9920239 DOI: 10.3390/plants12030624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
N6-adenosine methylation (m6A) is a prevalent form of RNA modification found in the expressed transcripts of many eukaryotic organisms. Moreover, m6A methylation is a dynamic and reversible process that requires the functioning of various proteins and their complexes that are evolutionarily conserved between species and include methylases, demethylases, and m6A-binding proteins. Over the past decade, the m6A methylation process in plants has been extensively studied and the understanding thereof has drastically increased, although the regulatory function of some components relies on information derived from animal systems. Notably, m6A has been found to be involved in a variety of factors in RNA processing, such as RNA stability, alternative polyadenylation, and miRNA regulation. The circadian clock in plants is a molecular timekeeping system that regulates the daily and rhythmic activity of many cellular and physiological processes in response to environmental changes such as the day-night cycle. The circadian clock regulates the rhythmic expression of genes through post-transcriptional regulation of mRNA. Recently, m6A methylation has emerged as an additional layer of post-transcriptional regulation that is necessary for the proper functioning of the plant circadian clock. In this review, we have compiled and summarized recent insights into the molecular mechanisms behind m6A modification and its various roles in the regulation of RNA. We discuss the potential role of m6A modification in regulating the plant circadian clock and outline potential future directions for the study of mRNA methylation in plants. A deeper understanding of the mechanism of m6A RNA regulation and its role in plant circadian clocks will contribute to a greater understanding of the plant circadian clock.
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Affiliation(s)
- Nguyen Nguyen Chuong
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju 690756, Republic of Korea
| | - Phan Phuong Thao Doan
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju 690756, Republic of Korea
| | - Lanshuo Wang
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju 690756, Republic of Korea
| | - Jin Hee Kim
- Subtropical Horticulture Research Institute, Jeju National University, Jeju 690756, Republic of Korea
| | - Jeongsik Kim
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju 690756, Republic of Korea
- Subtropical Horticulture Research Institute, Jeju National University, Jeju 690756, Republic of Korea
- Faculty of Science Education, Jeju National University, Jeju 690756, Republic of Korea
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16
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Gulisano A, Lippolis A, van Loo EN, Paulo MJ, Trindade LM. A genome wide association study to dissect the genetic architecture of agronomic traits in Andean lupin ( Lupinus mutabilis). FRONTIERS IN PLANT SCIENCE 2023; 13:1099293. [PMID: 36684793 PMCID: PMC9846495 DOI: 10.3389/fpls.2022.1099293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Establishing Lupinus mutabilis as a protein and oil crop requires improved varieties adapted to EU climates. The genetic regulation of strategic breeding traits, including plant architecture, growing cycle length and yield, is unknown. This study aimed to identify associations between 16 669 single nucleotide polymorphisms (SNPs) and 9 agronomic traits on a panel of 223 L. mutabilis accessions, grown in four environments, by applying a genome wide association study (GWAS). Seven environment-specific QTLs linked to vegetative yield, plant height, pods number and flowering time, were identified as major effect QTLs, being able to capture 6 to 20% of the phenotypic variation observed in these traits. Furthermore, two QTLs across environments were identified for flowering time on chromosome 8. The genes FAF, GAMYB and LNK, regulating major pathways involved in flowering and growth habit, as well as GA30X1, BIM1, Dr1, HDA15, HAT3, interacting with these pathways in response to hormonal and environmental cues, were prosed as candidate genes. These results are pivotal to accelerate the development of L. mutabilis varieties adapted to European cropping conditions by using marker-assisted selection (MAS), as well as to provide a framework for further functional studies on plant development and phenology in this species.
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Affiliation(s)
- Agata Gulisano
- Wageningen University and Research Plant Breeding, Wageningen University, Wageningen, Netherlands
| | - Antonio Lippolis
- Wageningen University and Research Plant Breeding, Wageningen University, Wageningen, Netherlands
| | - Eibertus N. van Loo
- Wageningen University and Research Plant Breeding, Wageningen University, Wageningen, Netherlands
| | - Maria-João Paulo
- Wageningen University and Research Biometris, Wageningen Research, Wageningen, Netherlands
| | - Luisa M. Trindade
- Wageningen University and Research Plant Breeding, Wageningen University, Wageningen, Netherlands
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17
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Li W, Tian YY, Li JY, Yuan L, Zhang LL, Wang ZY, Xu X, Davis SJ, Liu JX. A competition-attenuation mechanism modulates thermoresponsive growth at warm temperatures in plants. THE NEW PHYTOLOGIST 2023; 237:177-191. [PMID: 36028981 DOI: 10.1111/nph.18442] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Global warming has profound impact on growth and development, and plants constantly adjust their internal circadian clock to cope with external environment. However, how clock-associated genes fine-tune thermoresponsive growth in plants is little understood. We found that loss-of-function mutation of REVEILLE5 (RVE5) reduces the expression of circadian gene EARLY FLOWERING 4 (ELF4) in Arabidopsis, and confers accelerated hypocotyl growth under warm-temperature conditions. Both RVE5 and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) accumulate at warm temperatures and bind to the same EE cis-element presented on ELF4 promoter, but the transcriptional repression activity of RVE5 is weaker than that of CCA1. The binding of CCA1 to ELF4 promoter is enhanced in the rve5-2 mutant at warm temperatures, and overexpression of ELF4 in the rve5-2 mutant background suppresses the rve5-2 mutant phenotype at warm temperatures. Therefore, the transcriptional repressor RVE5 finetunes ELF4 expression via competing at a cis-element with the stronger transcriptional repressor CCA1 at warm temperatures. Such a competition-attenuation mechanism provides a balancing system for modulating the level of ELF4 and thermoresponsive hypocotyl growth under warm-temperature conditions.
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Affiliation(s)
- Wei Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
- College of Environmental and Resource 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
| | - Jin-Yu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Li Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Lin-Lin Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Zhi-Ye Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Seth Jon Davis
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
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18
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Xu X. Editorial: Plant circadian rhythms. FRONTIERS IN PLANT SCIENCE 2022; 13:1109900. [PMID: 36582648 PMCID: PMC9793078 DOI: 10.3389/fpls.2022.1109900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
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19
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Petersen J, Rredhi A, Szyttenholm J, Mittag M. Evolution of circadian clocks along the green lineage. PLANT PHYSIOLOGY 2022; 190:924-937. [PMID: 35325228 PMCID: PMC9516769 DOI: 10.1093/plphys/kiac141] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/04/2022] [Indexed: 05/10/2023]
Abstract
Circadian clocks govern temporal programs in the green lineage (Chloroplastida) as they do in other photosynthetic pro- and eukaryotes, bacteria, fungi, animals, and humans. Their physiological properties, including entrainment, phase responses, and temperature compensation, are well conserved. The involvement of transcriptional/translational feedback loops in the oscillatory machinery and reversible phosphorylation events are also maintained. Circadian clocks control a large variety of output rhythms in green algae and terrestrial plants, adjusting their metabolism and behavior to the day-night cycle. The angiosperm Arabidopsis (Arabidopsis thaliana) represents a well-studied circadian clock model. Several molecular components of its oscillatory machinery are conserved in other Chloroplastida, but their functions may differ. Conserved clock components include at least one member of the CIRCADIAN CLOCK ASSOCIATED1/REVEILLE and one of the PSEUDO RESPONSE REGULATOR family. The Arabidopsis evening complex members EARLY FLOWERING3 (ELF3), ELF4, and LUX ARRHYTHMO are found in the moss Physcomitrium patens and in the liverwort Marchantia polymorpha. In the flagellate chlorophyte alga Chlamydomonas reinhardtii, only homologs of ELF4 and LUX (named RHYTHM OF CHLOROPLAST ROC75) are present. Temporal ROC75 expression in C. reinhardtii is opposite to that of the angiosperm LUX, suggesting different clock mechanisms. In the picoalga Ostreococcus tauri, both ELF genes are missing, suggesting that it has a progenitor circadian "green" clock. Clock-relevant photoreceptors and thermosensors vary within the green lineage, except for the CRYPTOCHROMEs, whose variety and functions may differ. More genetically tractable models of Chloroplastida are needed to draw final conclusions about the gradual evolution of circadian clocks within the green lineage.
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Affiliation(s)
- Jan Petersen
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Anxhela Rredhi
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Julie Szyttenholm
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena 07743, Germany
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20
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Maeda AE, Nakamichi N. Plant clock modifications for adapting flowering time to local environments. PLANT PHYSIOLOGY 2022; 190:952-967. [PMID: 35266545 PMCID: PMC9516756 DOI: 10.1093/plphys/kiac107] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/09/2022] [Indexed: 05/25/2023]
Abstract
During and after the domestication of crops from ancestral wild plants, humans selected cultivars that could change their flowering time in response to seasonal daylength. Continuous selection of this trait eventually allowed the introduction of crops into higher or lower latitudes and different climates from the original regions where domestication initiated. In the past two decades, numerous studies have found the causal genes or alleles that change flowering time and have assisted in adapting crop species such as barley (Hordeum vulgare), wheat (Triticum aestivum L.), rice (Oryza sativa L.), pea (Pisum sativum L.), maize (Zea mays spp. mays), and soybean (Glycine max (L.) Merr.) to new environments. This updated review summarizes the genes or alleles that contributed to crop adaptation in different climatic areas. Many of these genes are putative orthologs of Arabidopsis (Arabidopsis thaliana) core clock genes. We also discuss how knowledge of the clock's molecular functioning can facilitate molecular breeding in the future.
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Affiliation(s)
- Akari E Maeda
- Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Norihito Nakamichi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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21
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Oravec MW, Greenham K. The adaptive nature of the plant circadian clock in natural environments. PLANT PHYSIOLOGY 2022; 190:968-980. [PMID: 35894658 PMCID: PMC9516730 DOI: 10.1093/plphys/kiac337] [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: 01/05/2022] [Accepted: 06/27/2022] [Indexed: 05/10/2023]
Abstract
The plant circadian clock coordinates developmental, physiological, and metabolic processes with diel changes in light and temperature throughout the year. The balance between the persistence and plasticity of the clock in response to predictable and unpredictable environmental changes may be key to the clock's adaptive nature across temporal and spatial scales. Studies under controlled conditions have uncovered critical signaling pathways involved in light and temperature perception by the clock; however, they don't account for the natural lag of temperature behind photoperiod. Studies in natural environments provide key insights into the clock's adaptive advantage under more complex natural settings. Here, we discuss the role of the circadian clock in light and temperature perception and signaling, how the clock integrates these signals for a coordinated and adaptive response, and the adaptive advantage conferred by the clock across time and space in natural environments.
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Affiliation(s)
- Madeline W Oravec
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108, USA
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22
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Okada M, Yang Z, Mas P. Circadian autonomy and rhythmic precision of the Arabidopsis female reproductive organ. Dev Cell 2022; 57:2168-2180.e4. [PMID: 36115345 DOI: 10.1016/j.devcel.2022.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/12/2022] [Accepted: 08/26/2022] [Indexed: 11/03/2022]
Abstract
The plant circadian clock regulates essential biological processes including flowering time or petal movement. However, little is known about how the clock functions in flowers. Here, we identified the circadian components and transcriptional networks contributing to the generation of rhythms in pistils, the female reproductive organ. When detached from the rest of the flower, pistils sustain highly precise rhythms, indicating organ-specific circadian autonomy. Analyses of clock mutants and chromatin immunoprecipitation assays showed distinct expression patterns and specific regulatory functions for clock activators and repressors in pistils. Genetic interaction studies also suggested a hierarchy of the repressing activities that provide robustness and precision to the pistil clock. Globally, the circadian function in pistils primarily governs responses to environmental stimuli and photosynthesis and controls pistil growth and seed weight and production. Understanding the circadian intricacies in reproductive organs may prove useful for optimizing plant reproduction and productivity.
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Affiliation(s)
- Masaaki Okada
- Centre for Research in Agricultural Genomics (CRAG), CSIC, IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Zhiyuan Yang
- Centre for Research in Agricultural Genomics (CRAG), CSIC, IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Paloma Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC, IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain; Consejo Superior de Investigaciones Científicas (CSIC), 08028 Barcelona, Spain.
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23
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Nidhi, Kumar P, Pathania D, Thakur S, Sharma M. Environment-mediated mutagenetic interference on genetic stabilization and circadian rhythm in plants. Cell Mol Life Sci 2022; 79:358. [PMID: 35687153 PMCID: PMC11072124 DOI: 10.1007/s00018-022-04368-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/21/2022] [Accepted: 05/07/2022] [Indexed: 12/29/2022]
Abstract
Many mortal organisms on this planet have developed the potential to merge all internal as well as external environmental cues to regulate various processes running inside organisms and in turn make them adaptive to the environment through the circadian clock. This moving rotator controls processes like activation of hormonal, metabolic, or defense pathways, initiation of flowering at an accurate period, and developmental processes in plants to ensure their stability in the environment. All these processes that are under the control of this rotating wheel can be changed either by external environmental factors or by an unpredictable phenomenon called mutation that can be generated by either physical mutagens, chemical mutagens, or by internal genetic interruption during metabolic processes, which alters normal functionality of organisms like innate immune responses, entrainment of the clock, biomass reduction, chlorophyll formation, and hormonal signaling, despite its fewer positive roles in plants like changing plant type, loss of vernalization treatment to make them survivable in different latitudes, and defense responses during stress. In addition, with mutation, overexpression of gene components sometimes supresses mutation effect and promote normal circadian genes abundance in the cell, while sometimes it affects circadian functionality by generating arrhythmicity and shows that not only mutation but overexpression also effects normal functional activities of plant. Therefore, this review mainly summarizes the role of each circadian clock genes in regulating rhythmicity, and shows that how circadian outputs are controlled by mutations as well as overexpression phenomenon.
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Affiliation(s)
- Nidhi
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, 173212, India
| | - Pradeep Kumar
- Central University of Himachal Pradesh, Dharmshala, India
| | - Diksha Pathania
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, 173212, India
| | - Sourbh Thakur
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, Gliwice, Poland
| | - Mamta Sharma
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, 173212, India.
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24
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Rakpenthai A, Apodiakou A, Whitcomb SJ, Hoefgen R. In silico analysis of cis-elements and identification of transcription factors putatively involved in the regulation of the OAS cluster genes SDI1 and SDI2. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1286-1304. [PMID: 35315155 DOI: 10.1111/tpj.15735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 02/09/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Arabidopsis thaliana sulfur deficiency-induced 1 and sulfur deficiency-induced 2 (SDI1 and SDI2) are involved in partitioning sulfur among metabolite pools during sulfur deficiency, and their transcript levels strongly increase in this condition. However, little is currently known about the cis- and trans-factors that regulate SDI expression. We aimed at identifying DNA sequence elements (cis-elements) and transcription factors (TFs) involved in regulating expression of the SDI genes. We performed in silico analysis of their promoter sequences cataloging known cis-elements and identifying conserved sequence motifs. We screened by yeast-one-hybrid an arrayed library of Arabidopsis TFs for binding to the SDI1 and SDI2 promoters. In total, 14 candidate TFs were identified. Direct association between particular cis-elements in the proximal SDI promoter regions and specific TFs was established via electrophoretic mobility shift assays: sulfur limitation 1 (SLIM1) was shown to bind SURE cis-element(s), the basic domain/leucine zipper (bZIP) core cis-element was shown to be important for HY5-homolog (HYH) binding, and G-box binding factor 1 (GBF1) was shown to bind the E box. Functional analysis of GBF1 and HYH using mutant and over-expressing lines indicated that these TFs promote a higher transcript level of SDI1 in vivo. Additionally, we performed a meta-analysis of expression changes of the 14 TF candidates in a variety of conditions that alter SDI expression. The presented results expand our understanding of sulfur pool regulation by SDI genes.
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Affiliation(s)
- Apidet Rakpenthai
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Anastasia Apodiakou
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Sarah J Whitcomb
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
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25
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Xiang Y, Sapir T, Rouillard P, Ferrand M, Jiménez-Gómez JM. Interaction between photoperiod and variation in circadian rhythms in tomato. BMC PLANT BIOLOGY 2022; 22:187. [PMID: 35395725 PMCID: PMC8994279 DOI: 10.1186/s12870-022-03565-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/23/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND Many biological processes follow circadian rhythmicity and are controlled by the circadian clock. Predictable environmental changes such as seasonal variation in photoperiod can modulate circadian rhythms, allowing organisms to adjust the timing of their biological processes to the time of the year. In some crops such as rice, barley or soybean, mutations in circadian clock genes have altered photoperiod sensitivity, enhancing their cultivability in specific seasons and latitudes. However, how changes in circadian rhythms interact with the perception of photoperiod in crops remain poorly studied. In tomato, the appearance during domestication of mutations in EMPFINDLICHER IM DUNKELROTEN LICHT 1 (EID1, Solyc09g075080) and NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED GENE 2 (LNK2, Solyc01g068560) delayed both the phase and period of its circadian rhythms. The fact that variation in period and phase are separated in tomato provides an optimal tool to study how these factors affect the perception of photoperiod. RESULTS Here we develop tomato near isogenic lines carrying combinations of wild alleles of EID1 and LNK2 and show that they recreate the changes in phase and period that occurred during its domestication. We perform transcriptomic profiling of these near isogenic lines under two different photoperiods, and observe that EID1, but not LNK2, has a large effect on how the tomato transcriptome responds to photoperiod. This large effect of EID1 is likely a consequence of the global phase shift elicited by this gene in tomato's circadian rhythms. CONCLUSIONS Our study shows that changes in phase that occurred during tomato domestication determine photoperiod perception in this species, while changes in period have little effect.
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Affiliation(s)
- Yanli Xiang
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
- VIB-UGent Center for Plant Systems Biology, Technologiepark 71, 9052, Gent, Belgium
| | - Thomas Sapir
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Pauline Rouillard
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Marina Ferrand
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - José M Jiménez-Gómez
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France.
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain.
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26
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Venkat A, Muneer S. Role of Circadian Rhythms in Major Plant Metabolic and Signaling Pathways. FRONTIERS IN PLANT SCIENCE 2022; 13:836244. [PMID: 35463437 PMCID: PMC9019581 DOI: 10.3389/fpls.2022.836244] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/23/2022] [Indexed: 05/10/2023]
Abstract
Plants require an endogenous regulatory network and mechanism to cope with diurnal environmental changes and compensate for their sessile nature. Plants use the circadian clock to anticipate diurnal changes. Circadian rhythm predicts a 24-h cycle with 16 h of light and 8 h of darkness in response to abiotic and biotic factors as well as the appropriate temperature. For a plant's fitness, proper growth, and development, these rhythms synchronize the diurnal photoperiodic changes. Input pathway, central oscillator, and output pathway are the three components that make up the endogenous clock. There are also transcriptional and translational feedback loops (TTFLs) in the clock, which are dependent on the results of gene expression. Several physiological processes, such as stress acclimatization, hormone signaling, morphogenesis, carbon metabolism, and defense response, are currently being investigated for their interactions with the circadian clock using phenotypic, genomic, and metabolic studies. This review examines the role of circadian rhythms in the regulation of plant metabolic pathways, such as photosynthesis and carbon metabolism, as well as developmental and degenerative processes, such as flowering and senescence. Furthermore, we summarized signaling pathways related to circadian rhythms, such as defense response and gene regulatory pathways.
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Affiliation(s)
- Ajila Venkat
- Horticulture and Molecular Physiology Lab, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, India
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Sowbiya Muneer
- Horticulture and Molecular Physiology Lab, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, India
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27
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Xu X, Yuan L, Yang X, Zhang X, Wang L, Xie Q. Circadian clock in plants: Linking timing to fitness. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:792-811. [PMID: 35088570 DOI: 10.1111/jipb.13230] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/25/2022] [Indexed: 05/12/2023]
Abstract
Endogenous circadian clock integrates cyclic signals of environment and daily and seasonal behaviors of organisms to achieve spatiotemporal synchronization, which greatly improves genetic diversity and fitness of species. This review addresses recent studies on the plant circadian system in the field of chronobiology, covering topics on molecular mechanisms, internal and external Zeitgebers, and hierarchical regulation of physiological outputs. The architecture of the circadian clock involves the autoregulatory transcriptional feedback loops, post-translational modifications of core oscillators, and epigenetic modifications of DNA and histones. Here, light, temperature, humidity, and internal elemental nutrients are summarized to illustrate the sensitivity of the circadian clock to timing cues. In addition, the circadian clock runs cell-autonomously, driving independent circadian rhythms in various tissues. The core oscillators responds to each other with biochemical factors including calcium ions, mineral nutrients, photosynthetic products, and hormones. We describe clock components sequentially expressed during a 24-h day that regulate rhythmic growth, aging, immune response, and resistance to biotic and abiotic stresses. Notably, more data have suggested the circadian clock links chrono-culture to key agronomic traits in crops.
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Affiliation(s)
- Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Li Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xin Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xiao Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
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28
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Hasseb NM, Sallam A, Karam MA, Gao L, Wang RRC, Moursi YS. High-LD SNP markers exhibiting pleiotropic effects on salt tolerance at germination and seedlings stages in spring wheat. PLANT MOLECULAR BIOLOGY 2022; 108:585-603. [PMID: 35217965 PMCID: PMC8967789 DOI: 10.1007/s11103-022-01248-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 01/25/2022] [Indexed: 06/01/2023]
Abstract
Salt tolerance at germination and seedling growth stages was investigated. GWAS revealed nine genomic regions with pleiotropic effects on salt tolerance. Salt tolerant genotypes were identified for future breeding program. With 20% of the irrigated land worldwide affected by it, salinity is a serious threat to plant development and crop production. While wheat is the most stable food source worldwide, it has been classified as moderately tolerant to salinity. In several crop plants; such as barley, maize and rice, it has been shown that salinity tolerance at seed germination and seedling establishment is under polygenic control. As yield was the ultimate goal of breeders and geneticists, less attention has been paid to understanding the genetic architecture of salt tolerance at early stages. Thus, the genetic control of salt tolerance at these stages is poorly understood relative to the late stages. In the current study, 176 genotypes of spring wheat were tested for salinity tolerance at seed germination and seedling establishment. Genome-Wide Association Study (GWAS) has been used to identify the genomic regions/genes conferring salt tolerance at seed germination and seedling establishment. Salinity stress negatively impacted all germination and seedling development parameters. A set of 137 SNPs showed significant association with the traits of interest. Across the whole genome, 33 regions showed high linkage disequilibrium (LD). These high LD regions harbored 15 SNPs with pleiotropic effect (i.e. SNPs that control more than one trait). Nine genes belonging to different functional groups were found to be associated with the pleiotropic SNPs. Noteworthy, chromosome 2B harbored the gene TraesCS2B02G135900 that acts as a potassium transporter. Remarkably, one SNP marker, reported in an early study, associated with salt tolerance was validated in this study. Our findings represent potential targets of genetic manipulation to understand and improve salinity tolerance in wheat.
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Affiliation(s)
- Nouran M Hasseb
- Department of Botany, Faculty of Science, Fayoum University, Fayoum, 63514, Egypt
| | - Ahmed Sallam
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt.
| | - Mohamed A Karam
- Department of Botany, Faculty of Science, Fayoum University, Fayoum, 63514, Egypt
| | - Liangliang Gao
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State Univ, Manhattan, KS, 66502, USA
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Buxin Road 97, Dapeng-District, Shenzhen, 518120, Guangdong, China
| | - Richard R C Wang
- USDA-ARS Forage and Range Research Lab, Utah State University, Logan, UT, 84322-6300, USA
| | - Yasser S Moursi
- Department of Botany, Faculty of Science, Fayoum University, Fayoum, 63514, Egypt
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29
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Singh G, Singh V, Singh V. Systems scale characterization of circadian rhythm pathway in Camellia sinensis. Comput Struct Biotechnol J 2022; 20:598-607. [PMID: 35116135 PMCID: PMC8790616 DOI: 10.1016/j.csbj.2021.12.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 12/14/2021] [Accepted: 12/18/2021] [Indexed: 11/29/2022] Open
Abstract
Tea (Camellia sinensis) is among the most valuable commercial crops being a non-alcoholic beverage having antioxidant properties. Like in other plants, circadian oscillator in tea modulates several biological processes according to earth's revolution dependent variations in environmental cues like light and temperature. In the present study, we report genome wide identification and characterization of circadian oscillator (CO) proteins in tea. We first mined the genes (24, in total) involved in circadian rhythm pathway in the 56 plant species having available genomic information and then built their hidden Markov models (HMMs). Using these HMMs, 24 proteins were identified in tea and were further assessed for their functional annotation. Expression analysis of all these 24 CO proteins was then performed in 3 abiotic (A) and 3 biotic conditions (B) stress conditions and co-expressed as well as differentially expressed genes in the selected 6 stress conditions were elaborated. A methodology to identify the differentially expressed genes in specific types of stresses (A or B) is proposed and novel markers among CO proteins are presented. By mapping the identified CO proteins against the recently reported genome wide interologous protein-protein interaction network of tea (TeaGPIN), an interaction sub-network of tea CO proteins (TeaCO-PIN) is developed and analysed. Out of 24 CO proteins, structures of 4 proteins could be successfully predicted and validated using consensus of three structure prediction algorithms and their stability was further assessed using molecular dynamic simulations at 100 ns. Phylogenetic analysis of these proteins is performed to examine their molecular evolution.
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Affiliation(s)
| | | | - Vikram Singh
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Dharamshala 176206, India
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30
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Lagercrantz U, Billhardt A, Rousku SN, Leso M, Reza SH, Eklund DM. DE-ETIOLATED1 has a role in the circadian clock of the liverwort Marchantia polymorpha. THE NEW PHYTOLOGIST 2021; 232:595-609. [PMID: 34320227 DOI: 10.1111/nph.17653] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Previous studies of plant circadian clock evolution have often relied on clock models and genes defined in Arabidopsis. These studies identified homologues with seemingly conserved function, as well as frequent gene loss. In the present study, we aimed to identify candidate clock genes in the liverwort Marchantia polymorpha using a more unbiased approach. To identify genes with circadian rhythm we sequenced the transcriptomes of gemmalings in a time series in constant light conditions. Subsequently, we performed functional studies using loss-of-function mutants and gene expression reporters. Among the genes displaying circadian rhythm, a homologue to the transcriptional co-repressor Arabidopsis DE-ETIOLATED1 showed high amplitude and morning phase. Because AtDET1 is arrhythmic and associated with the morning gene function of AtCCA1/LHY, that lack a homologue in liverworts, we functionally studied DET1 in M. polymorpha. We found that the circadian rhythm of MpDET1 expression is disrupted in loss-of-function mutants of core clock genes and putative evening-complex genes. MpDET1 knock-down in turn results in altered circadian rhythm of nyctinastic thallus movement and clock gene expression. We could not detect any effect of MpDET1 knock-down on circadian response to light, suggesting that MpDET1 has a yet unknown function in the M. polymorpha circadian clock.
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Affiliation(s)
- Ulf Lagercrantz
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Anja Billhardt
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Sabine N Rousku
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Martina Leso
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Salim Hossain Reza
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - D Magnus Eklund
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
- Physiological Botany, Department of Organismal Biology, Linnean Centre for Plant Biology in Uppsala, Uppsala University, Ulls Väg 24E, SE-756 51, Uppsala, Sweden
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31
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Uncovering Transcriptional Responses to Fractional Gravity in Arabidopsis Roots. Life (Basel) 2021; 11:life11101010. [PMID: 34685382 PMCID: PMC8539686 DOI: 10.3390/life11101010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/14/2021] [Accepted: 09/17/2021] [Indexed: 11/17/2022] Open
Abstract
Although many reports characterize the transcriptional response of Arabidopsis seedlings to microgravity, few investigate the effect of partial or fractional gravity on gene expression. Understanding plant responses to fractional gravity is relevant for plant growth on lunar and Martian surfaces. The plant signaling flight experiment utilized the European Modular Cultivation System (EMCS) onboard the International Space Station (ISS). The EMCS consisted of two rotors within a controlled chamber allowing for two experimental conditions, microgravity (stationary rotor) and simulated gravity in space. Seedlings were grown for 5 days under continuous light in seed cassettes. The arrangement of the seed cassettes within each experimental container results in a gradient of fractional g (in the spinning rotor). To investigate whether gene expression patterns are sensitive to fractional g, we carried out transcriptional profiling of root samples exposed to microgravity or partial g (ranging from 0.53 to 0.88 g). Data were analyzed using DESeq2 with fractional g as a continuous variable in the design model in order to query gene expression across the gravity continuum. We identified a subset of genes whose expression correlates with changes in fractional g. Interestingly, the most responsive genes include those encoding transcription factors, defense, and cell wall-related proteins and heat shock proteins.
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32
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Abstract
Circadian clocks are important to much of life on Earth and are of inherent interest to humanity, implicated in fields ranging from agriculture and ecology to developmental biology and medicine. New techniques show that it is not simply the presence of clocks, but coordination between them that is critical for complex physiological processes across the kingdoms of life. Recent years have also seen impressive advances in synthetic biology to the point where parallels can be drawn between synthetic biological and circadian oscillators. This review will emphasize theoretical and experimental studies that have revealed a fascinating dichotomy of coupling and heterogeneity among circadian clocks. We will also consolidate the fields of chronobiology and synthetic biology, discussing key design principles of their respective oscillators.
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Affiliation(s)
- Chris N Micklem
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK.,The Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CH3 0HE, UK
| | - James C W Locke
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
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33
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Zhang T. Tick-tock: BBX19 functions as a novel regulator of the circadian clock. THE PLANT CELL 2021; 33:2511-2512. [PMID: 35233620 PMCID: PMC8408439 DOI: 10.1093/plcell/koab142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Tian Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
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34
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Yuan L, Yu Y, Liu M, Song Y, Li H, Sun J, Wang Q, Xie Q, Wang L, Xu X. BBX19 fine-tunes the circadian rhythm by interacting with PSEUDO-RESPONSE REGULATOR proteins to facilitate their repressive effect on morning-phased clock genes. THE PLANT CELL 2021; 33:2602-2617. [PMID: 34164694 PMCID: PMC8408442 DOI: 10.1093/plcell/koab133] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/11/2021] [Indexed: 05/19/2023]
Abstract
The core plant circadian oscillator is composed of multiple interlocked transcriptional-translational feedback loops, which synchronize endogenous diel physiological rhythms to the cyclic changes of environmental cues. PSEUDO-RESPONSE REGULATORS (PRRs) have been identified as negative components in the circadian clock, though their underlying molecular mechanisms remain largely unknown. Here, we found that a subfamily of zinc finger transcription factors, B-box (BBX)-containing proteins, have a critical role in fine-tuning circadian rhythm. We demonstrated that overexpressing Arabidopsis thaliana BBX19 and BBX18 significantly lengthened the circadian period, while the null mutation of BBX19 accelerated the circadian speed. Moreover, BBX19 and BBX18, which are expressed during the day, physically interacted with PRR9, PRR7, and PRR5 in the nucleus in precise temporal ordering from dawn to dusk, consistent with the respective protein accumulation pattern of PRRs. Our transcriptomic and genetic analysis indicated that BBX19 and PRR9, PRR7, and PRR5 cooperatively inhibited the expression of morning-phased clock genes. PRR proteins affected BBX19 recruitment to the CCA1, LHY, and RVE8 promoters. Collectively, our findings show that BBX19 interacts with PRRs to orchestrate circadian rhythms, and suggest the indispensable role of transcriptional regulators in fine-tuning the circadian clock.
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Affiliation(s)
- Li Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yingjun Yu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingming Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yang Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Hongmin Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Junqiu Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Qiao Wang
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Authors for correspondence: (X.X.), (L.W.), (Q.X.)
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Authors for correspondence: (X.X.), (L.W.), (Q.X.)
| | - Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Authors for correspondence: (X.X.), (L.W.), (Q.X.)
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35
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Ooi SE, Feshah I, Nuraziyan A, Sarpan N, Ata N, Lim CC, Choo CN, Wong WC, Wong FH, Wong CK, Ong-Abdullah M. Leaf transcriptomic signatures for somatic embryogenesis potential of Elaeis guineensis. PLANT CELL REPORTS 2021; 40:1141-1154. [PMID: 33929599 DOI: 10.1007/s00299-021-02698-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/13/2021] [Indexed: 06/12/2023]
Abstract
Potentially embryogenic oil palms can be identified through leaf transcriptomic signatures. Differential expression of genes involved in flowering time, and stress and light responses may associate with somatic embryogenesis potential. Clonal propagation is an attractive approach for the mass propagation of high yielding oil palms. A major issue hampering the effectiveness of oil palm tissue culture is the low somatic embryogenesis rate. Previous studies have identified numerous genes involved in oil palm somatic embryogenesis, but their association with embryogenic potential has not been determined. In this study, differential expression analysis of leaf transcriptomes from embryogenic and non-embryogenic mother palms revealed that transcriptome profiles from non- and poor embryogenic mother palms were more similar than highly embryogenic palms. A total of 171 genes exhibiting differential expression in non- and low embryogenesis groups could also discriminate high from poor embryogenesis groups of another tissue culture agency. Genes related to flowering time or transition such as FTIP, FRIGIDA-LIKE, and NF-YA were up-regulated in embryogenic ortets, suggesting that reproduction timing of the plant may associate with somatic embryogenesis potential. Several light response or photosynthesis-related genes were down-regulated in embryogenic ortets, suggesting a link between photosynthesis activity and embryogenic potential. As expression profiles of the differentially expressed genes are very similar between non- and low embryogenic groups, machine learning approaches with several candidate genes may generate a more sensitive model to better discriminate non-embryogenic from embryogenic ortets.
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Affiliation(s)
- Siew-Eng Ooi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia.
| | - Ishak Feshah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia
| | - Azimi Nuraziyan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia
| | - Norashikin Sarpan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia
| | - Nabeel Ata
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia
| | - Chin-Ching Lim
- United Plantations Bhd., Jenderata Estate, 36009, Teluk Intan, Perak, Malaysia
| | - Chin-Nee Choo
- Advanced Agriecological Research Sdn. Bhd., 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810, Petaling Jaya, Selangor, Malaysia
| | - Wei-Chee Wong
- Advanced Agriecological Research Sdn. Bhd., 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810, Petaling Jaya, Selangor, Malaysia
| | - Foo-Hin Wong
- United Plantations Bhd., Jenderata Estate, 36009, Teluk Intan, Perak, Malaysia
| | - Choo-Kien Wong
- Advanced Agriecological Research Sdn. Bhd., 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810, Petaling Jaya, Selangor, Malaysia
| | - Meilina Ong-Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia
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Balcerowicz M, Mahjoub M, Nguyen D, Lan H, Stoeckle D, Conde S, Jaeger KE, Wigge PA, Ezer D. An early-morning gene network controlled by phytochromes and cryptochromes regulates photomorphogenesis pathways in Arabidopsis. MOLECULAR PLANT 2021; 14:983-996. [PMID: 33766657 DOI: 10.1016/j.molp.2021.03.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/04/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Light perception at dawn plays a key role in coordinating multiple molecular processes and in entraining the plant circadian clock. The Arabidopsis mutant lacking the main photoreceptors, however, still shows clock entrainment, indicating that the integration of light into the morning transcriptome is not well understood. In this study, we performed a high-resolution RNA-sequencing time-series experiment, sampling every 2 min beginning at dawn. In parallel experiments, we perturbed temperature, the circadian clock, photoreceptor signaling, and chloroplast-derived light signaling. We used these data to infer a gene network that describes the gene expression dynamics after light stimulus in the morning, and then validated key edges. By sampling time points at high density, we are able to identify three light- and temperature-sensitive bursts of transcription factor activity, one of which lasts for only about 8 min. Phytochrome and cryptochrome mutants cause a delay in the transcriptional bursts at dawn, and completely remove a burst of expression in key photomorphogenesis genes (HY5 and BBX family). Our complete network is available online (http://www-users.york.ac.uk/∼de656/dawnBurst/dawnBurst.html). Taken together, our results show that phytochrome and cryptochrome signaling is required for fine-tuning the dawn transcriptional response to light, but separate pathways can robustly activate much of the program in their absence.
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Affiliation(s)
| | - Mahiar Mahjoub
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Duy Nguyen
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Hui Lan
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | | | - Susana Conde
- Department of Statistics, University of Warwick, Coventry, UK; Alan Turing Institute, London, UK
| | - Katja E Jaeger
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), 14979 Großbeeren, Germany
| | - Philip A Wigge
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), 14979 Großbeeren, Germany; Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Daphne Ezer
- Alan Turing Institute, London, UK; Department of Biology, University of York, York YO10 5DD, UK.
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37
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Zhuo X, Zheng T, Li S, Zhang Z, Zhang M, Zhang Y, Ahmad S, Sun L, Wang J, Cheng T, Zhang Q. Identification of the PmWEEP locus controlling weeping traits in Prunus mume through an integrated genome-wide association study and quantitative trait locus mapping. HORTICULTURE RESEARCH 2021; 8:131. [PMID: 34059642 PMCID: PMC8167129 DOI: 10.1038/s41438-021-00573-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 01/20/2021] [Accepted: 04/07/2021] [Indexed: 05/20/2023]
Abstract
Weeping Prunus mume (mei) has long been cultivated in East Asia for its specific ornamental value. However, little is known about the regulatory mechanism of the weeping trait in mei, which limits molecular breeding for the improvement of weeping-type cultivars. Here, we quantified the weeping trait in mei using nested phenotyping of 214 accessions and 342 F1 hybrids. Two major associated loci were identified from the genome-wide association study (GWAS), which was conducted using 3,014,409 single nucleotide polymorphisms (SNPs) derived from resequencing, and 8 QTLs and 55 epistatic loci were identified from QTL mapping using 7,545 specific lengths amplified fragment (SLAF) markers. Notably, an overlapping PmWEEP major QTL was fine mapped within a 0.29 Mb region on chromosome 7 (Pa7), and a core SNP locus closely associated with the weeping trait was screened and validated. Furthermore, a total of 22 genes in the PmWEEP QTL region were expressed in weeping or upright mei based on RNA-seq analysis. Among them, only a novel gene (Pm024213) containing a thioredoxin (Trx) domain was found to be close to the core SNP and specifically expressed in buds and branches of weeping mei. Co-expression analysis of Pm024213 showed that most of the related genes were involved in auxin and lignin biosynthesis. These findings provide insights into the regulatory mechanism of the weeping trait and effective molecular markers for molecular-assisted breeding in Prunus mume.
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Affiliation(s)
- Xiaokang Zhuo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Tangchun Zheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China.
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China.
| | - Suzhen Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Zhiyong Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Man Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Yichi Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Sagheer Ahmad
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Lidan Sun
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China
| | - Qixiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, 100083, Beijing, China.
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 100083, Beijing, China.
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38
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Cao S, Luo X, Xu D, Tian X, Song J, Xia X, Chu C, He Z. Genetic architecture underlying light and temperature mediated flowering in Arabidopsis, rice, and temperate cereals. THE NEW PHYTOLOGIST 2021; 230:1731-1745. [PMID: 33586137 DOI: 10.1111/nph.17276] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 01/20/2021] [Indexed: 05/23/2023]
Abstract
Timely flowering is essential for optimum crop reproduction and yield. To determine the best flowering-time genes (FTGs) relevant to local adaptation and breeding, it is essential to compare the interspecific genetic architecture of flowering in response to light and temperature, the two most important environmental cues in crop breeding. However, the conservation and variations of FTGs across species lack systematic dissection. This review summarizes current knowledge on the genetic architectures underlying light and temperature-mediated flowering initiation in Arabidopsis, rice, and temperate cereals. Extensive comparative analyses show that most FTGs are conserved, whereas functional variations in FTGs may be species specific and confer local adaptation in different species. To explore evolutionary dynamics underpinning the conservation and variations in FTGs, domestication and selection of some key FTGs are further dissected. Based on our analyses of genetic control of flowering time, a number of key issues are highlighted. Strategies for modulation of flowering behavior in crop breeding are also discussed. The resultant resources provide a wealth of reference information to uncover molecular mechanisms of flowering in plants and achieve genetic improvement in crops.
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Affiliation(s)
- Shuanghe Cao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xumei Luo
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dengan Xu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiuling Tian
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jie Song
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- International Maize and Wheat Improvement Center China Office, c/o Chinese Academy Agricultural Sciences, Beijing, 100081, China
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39
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Ma H, Wu J, Zhang H, Tang H, Wan Y. Identification and expression profiling of genes involved in circadian clock regulation in red dragon fruit ( Hylocereus polyrhizus) by full-length transcriptome sequencing. PLANT SIGNALING & BEHAVIOR 2021; 16:1907054. [PMID: 33825662 PMCID: PMC8143213 DOI: 10.1080/15592324.2021.1907054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
Crassulacean acid metabolism (CAM) plants fix CO2 at night, exhibiting a reversed regulatory pattern of metabolomic pathways compared with most model plants, which have C3 and C4 pathways. In this study, we used a valuable tropic fruit, red dragon fruit (Hylocereus polyrhizus), as model plant to identify and analyze the circadian regulation genes. Due to the absence of red dragon fruit's whole-genome dataset, we established a full-length transcriptome dataset using single-molecule real-time (SMRT) sequencing method. A 7.66-Gb dataset with 4,552,474 subreads was generated, with an average length of 1,683 bp and an N50 of 2,446 bp. Using this dataset, we identified center oscillator genes: CCA1 (CIRCADIAN CLOCK ASSOCIATED1), ELF3 (EARLY FLOWERING 3), GI (GIGANTEA), LHY (LATE ELONGATED HYPOCOTYL), LNK1 (NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED 1), and TOC1 (TIMING OF CAB EXPRESSION 1); a gene for the input pathway: CRY1 (CRYPTOCHROME); a gene for the output pathway: CO (CONSTANS); and genes related to the CAM pathway: MDH (MALATE DEHYDROGENASE), ME (MALIC ENZYMES), and PPDK (PYRUVATE PHOSPHATE DIKINASE). We further established the 24-h rhythmic expression pattern of these genes and classified these into three groups: HpCCA1, HpELF3, HpLHY, HpLNK1, and HpGI have expression peaks during the day; HpTOC1, HpCO, and HpCRY1 have highest expression levels at night; The genes involved in the CAM pathways, namely, HpMDH, HpME1, and HpPPDK, have double expression peaks in the day and night. Comparison of these expression patterns between red dragon fruit and model plants could provide clues in understanding the circadian clock regulation and the activity of the CAM pathways in cactus plants.
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Affiliation(s)
- Huaqing Ma
- College of Tropic Crops, Hainan University, Haikou, China
| | - Jiao Wu
- College of Tropic Crops, Hainan University, Haikou, China
| | - He Zhang
- College of Tropic Crops, Hainan University, Haikou, China
| | - Hua Tang
- College of Tropic Crops, Hainan University, Haikou, China
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Yinglang Wan
- College of Tropic Crops, Hainan University, Haikou, China
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
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40
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Li Y, Cao K, Li N, Zhu G, Fang W, Chen C, Wang X, Guo J, Wang Q, Ding T, Wang J, Guan L, Wang J, Liu K, Guo W, Arús P, Huang S, Fei Z, Wang L. Genomic analyses provide insights into peach local adaptation and responses to climate change. Genome Res 2021; 31:592-606. [PMID: 33687945 PMCID: PMC8015852 DOI: 10.1101/gr.261032.120] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 01/25/2021] [Indexed: 01/30/2023]
Abstract
The environment has constantly shaped plant genomes, but the genetic bases underlying how plants adapt to environmental influences remain largely unknown. We constructed a high-density genomic variation map of 263 geographically representative peach landraces and wild relatives. A combination of whole-genome selection scans and genome-wide environmental association studies (GWEAS) was performed to reveal the genomic bases of peach adaptation to diverse climates. A total of 2092 selective sweeps that underlie local adaptation to both mild and extreme climates were identified, including 339 sweeps conferring genomic pattern of adaptation to high altitudes. Using genome-wide environmental association studies (GWEAS), a total of 2755 genomic loci strongly associated with 51 specific environmental variables were detected. The molecular mechanism underlying adaptive evolution of high drought, strong UVB, cold hardiness, sugar content, flesh color, and bloom date were revealed. Finally, based on 30 yr of observation, a candidate gene associated with bloom date advance, representing peach responses to global warming, was identified. Collectively, our study provides insights into molecular bases of how environments have shaped peach genomes by natural selection and adds candidate genes for future studies on evolutionary genetics, adaptation to climate changes, and breeding.
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Affiliation(s)
- Yong Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.,National Horticulture Germplasm Resources Center, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.,Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430000, China
| | - Ke Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.,National Horticulture Germplasm Resources Center, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Nan Li
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Gengrui Zhu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.,National Horticulture Germplasm Resources Center, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Weichao Fang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.,National Horticulture Germplasm Resources Center, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Changwen Chen
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Xinwei Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Jian Guo
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Qi Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Tiyu Ding
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Jiao Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Liping Guan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Junxiu Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Kuozhan Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Wenwu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430000, China
| | - Pere Arús
- IRTA-Centre de Recerca en Agrigenòmica (CSIC-IRTA-UAB-UB), Barcelona 08193, Spain
| | - Sanwen Huang
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853, USA.,U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853, USA
| | - Lirong Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.,National Horticulture Germplasm Resources Center, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
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41
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McClung CR. Circadian Clock Components Offer Targets for Crop Domestication and Improvement. Genes (Basel) 2021; 12:genes12030374. [PMID: 33800720 PMCID: PMC7999361 DOI: 10.3390/genes12030374] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 12/31/2022] Open
Abstract
During plant domestication and improvement, farmers select for alleles present in wild species that improve performance in new selective environments associated with cultivation and use. The selected alleles become enriched and other alleles depleted in elite cultivars. One important aspect of crop improvement is expansion of the geographic area suitable for cultivation; this frequently includes growth at higher or lower latitudes, requiring the plant to adapt to novel photoperiodic environments. Many crops exhibit photoperiodic control of flowering and altered photoperiodic sensitivity is commonly required for optimal performance at novel latitudes. Alleles of a number of circadian clock genes have been selected for their effects on photoperiodic flowering in multiple crops. The circadian clock coordinates many additional aspects of plant growth, metabolism and physiology, including responses to abiotic and biotic stresses. Many of these clock-regulated processes contribute to plant performance. Examples of selection for altered clock function in tomato demonstrate that with domestication, the phasing of the clock is delayed with respect to the light–dark cycle and the period is lengthened; this modified clock is associated with increased chlorophyll content in long days. These and other data suggest the circadian clock is an attractive target during breeding for crop improvement.
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Affiliation(s)
- C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
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42
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Estefania M, Andres R, Javier I, Marcelo Y, Ariel C. ASpli: Integrative analysis of splicing landscapes through RNA-Seq assays. Bioinformatics 2021; 37:2609-2616. [PMID: 33677494 DOI: 10.1093/bioinformatics/btab141] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/26/2021] [Accepted: 02/27/2021] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Genome-wide analysis of alternative splicing has been a very active field of research since the early days of Next Generation Sequencing technologies. Since then, ever-growing data availability and the development of increasingly sophisticated analysis methods have uncovered the complexity of the general splicing repertoire. A large number of splicing analysis methodologies exist, each of them presenting its own strengths and weaknesses. For instance methods exclusively relying on junction information do not take advantage of the large majority of reads produced in an RNA-seq assay, isoform reconstruction methods might not detect novel intron retention events, some solutions can only handle canonical splicing events, and many existing methods can only perform pairwise comparisons. RESULTS In this contribution, we present ASpli, a computational suite implemented in R statistical language, that allows the identification of changes in both, annotated and novel alternative splicing events and can deal with simple, multi-factor or paired experimental designs. Our integrative computational workflow considers the same GLM model, applied to different sets of reads and junctions, in order to compute complementary splicing signals.Analyzing simulated and real data we found that the consolidation of these signals resulted in a robust proxy of the occurrence of splicing alterations. While the analysis of junctions allowed us to uncover annotated as well as non-annotated events, read coverage signals notably increased recall capabilities at a very competitive performance when compared against other state-of-the-art splicing analysis algorithms. ASpli is freely available from the Bioconductor project site https://www.bioconductor.org/packages/ASpli. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Rabinovich Andres
- Fundacion Instituto Leloir, Buenos Aires, Argentina.,Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Iserte Javier
- Fundacion Instituto Leloir, Buenos Aires, Argentina.,Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Yanovsky Marcelo
- Fundacion Instituto Leloir, Buenos Aires, Argentina.,Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Chernomoretz Ariel
- Fundacion Instituto Leloir, Buenos Aires, Argentina.,Departamento de Fisica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Fisica de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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43
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Roeber VM, Schmülling T, Cortleven A. The Photoperiod: Handling and Causing Stress in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:781988. [PMID: 35145532 PMCID: PMC8821921 DOI: 10.3389/fpls.2021.781988] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/13/2021] [Indexed: 05/05/2023]
Abstract
The photoperiod, which is the length of the light period in the diurnal cycle of 24 h, is an important environmental signal. Plants have evolved sensitive mechanisms to measure the length of the photoperiod. Photoperiod sensing enables plants to synchronize developmental processes, such as the onset of flowering, with a specific time of the year, and enables them to alleviate the impact of environmental stresses occurring at the same time every year. During the last years, the importance of the photoperiod for plant responses to abiotic and biotic stresses has received increasing attention. In this review, we summarize the current knowledge on the signaling pathways involved in the photoperiod-dependent regulation of responses to abiotic (freezing, drought, osmotic stress) and biotic stresses. A central role of GIGANTEA (GI), which is a key player in the regulation of photoperiod-dependent flowering, in stress responses is highlighted. Special attention is paid to the role of the photoperiod in regulating the redox state of plants. Furthermore, an update on photoperiod stress, which is caused by sudden alterations in the photoperiod, is given. Finally, we will review and discuss the possible use of photoperiod-induced stress as a sustainable resource to enhance plant resistance to biotic stress in horticulture.
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The Transcriptional Network in the Arabidopsis Circadian Clock System. Genes (Basel) 2020; 11:genes11111284. [PMID: 33138078 PMCID: PMC7692566 DOI: 10.3390/genes11111284] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/28/2020] [Accepted: 10/28/2020] [Indexed: 12/18/2022] Open
Abstract
The circadian clock is the biological timekeeping system that governs the approximately 24-h rhythms of genetic, metabolic, physiological and behavioral processes in most organisms. This oscillation allows organisms to anticipate and adapt to day–night changes in the environment. Molecular studies have indicated that a transcription–translation feedback loop (TTFL), consisting of transcriptional repressors and activators, is essential for clock function in Arabidopsis thaliana (Arabidopsis). Omics studies using next-generation sequencers have further revealed that transcription factors in the TTFL directly regulate key genes implicated in clock-output pathways. In this review, the target genes of the Arabidopsis clock-associated transcription factors are summarized. The Arabidopsis clock transcriptional network is partly conserved among angiosperms. In addition, the clock-dependent transcriptional network structure is discussed in the context of plant behaviors for adapting to day–night cycles.
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Maric A, Mas P. Chromatin Dynamics and Transcriptional Control of Circadian Rhythms in Arabidopsis. Genes (Basel) 2020; 11:E1170. [PMID: 33036236 PMCID: PMC7601625 DOI: 10.3390/genes11101170] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/01/2020] [Accepted: 10/04/2020] [Indexed: 02/06/2023] Open
Abstract
Circadian rhythms pervade nearly all aspects of plant growth, physiology, and development. Generation of the rhythms relies on an endogenous timing system or circadian clock that generates 24-hour oscillations in multiple rhythmic outputs. At its bases, the plant circadian function relies on dynamic interactive networks of clock components that regulate each other to generate rhythms at specific phases during the day and night. From the initial discovery more than 13 years ago of a parallelism between the oscillations in chromatin status and the transcriptional rhythms of an Arabidopsis clock gene, a number of studies have later expanded considerably our view on the circadian epigenome and transcriptome landscapes. Here, we describe the most recent identification of chromatin-related factors that are able to directly interact with Arabidopsis clock proteins to shape the transcriptional waveforms of circadian gene expression and clock outputs. We discuss how changes in chromatin marks associate with transcript initiation, elongation, and the rhythms of nascent RNAs, and speculate on future interesting research directions in the field.
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Affiliation(s)
- Aida Maric
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain;
| | - Paloma Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain;
- Consejo Superior de Investigaciones Científicas (CSIC), 08028 Barcelona, Spain
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de Leone MJ, Hernando CE, Mora-García S, Yanovsky MJ. It's a matter of time: the role of transcriptional regulation in the circadian clock-pathogen crosstalk in plants. Transcription 2020; 11:100-116. [PMID: 32936724 DOI: 10.1080/21541264.2020.1820300] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Most living organisms possess an internal timekeeping mechanism known as the circadian clock, which enhances fitness by synchronizing the internal timing of biological processes with diurnal and seasonal environmental changes. In plants, the pace of these biological rhythms relies on oscillations in the expression level of hundreds of genes tightly controlled by a group of core clock regulators and co-regulators that engage in transcriptional and translational feedback loops. In the last decade, the role of several core clock genes in the control of defense responses has been addressed, and a growing amount of evidence demonstrates that circadian regulation is relevant for plant immunity. A reciprocal connection between these pathways was also established following the observation that in Arabidopsis thaliana, as well as in crop species like tomato, plant-pathogen interactions trigger a reconfiguration of the circadian transcriptional network. In this review, we summarize the current knowledge regarding the interaction between the circadian clock and biotic stress responses at the transcriptional level, and discuss the relevance of this crosstalk in the plant-pathogen evolutionary arms race. A better understanding of these processes could aid in the development of genetic tools that improve traditional breeding practices, enhancing tolerance to plant diseases that threaten crop yield and food security all around the world.
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Affiliation(s)
- María José de Leone
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Buenos Aires, Argentina
| | - C Esteban Hernando
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Buenos Aires, Argentina
| | - Santiago Mora-García
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Buenos Aires, Argentina
| | - Marcelo J Yanovsky
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Buenos Aires, Argentina
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Higuchi-Takeuchi M, Kondo T, Shimizu M, Kim YW, Shinozaki K, Hanada K. Effect of small coding genes on the circadian rhythms under elevated CO 2 conditions in plants. PLANT MOLECULAR BIOLOGY 2020; 104:55-65. [PMID: 32572798 DOI: 10.1007/s11103-020-01023-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
Increase in atmospheric carbon dioxide (CO2) has a significant effect on plant growth and development. To explore the elevated-CO2 response, we generated transcriptional profiles over a time course (2 h-14 days) of exposure to elevated CO2 in Arabidopsis thaliana. Genes related to photosynthesis were down-regulated and circadian rhythm-related genes were abnormally regulated in the early to middle phase of elevated CO2 exposure. To understand the novel mechanism of elevated CO2 signaling, we focused on 42 unknown small coding genes that showed differential expression patterns under elevated CO2 conditions. Four transgenic plants overexpressing the small coding gene exhibited a growth-defective phenotype under elevated CO2 but not under current CO2. Transcriptome analysis showed that circadian rhythm-related genes were commonly regulated in four transgenic plants. These circadian rhythm-related genes were transcribed in the dark when CO2 concentrations in the leaf was high. Taken together, our identified four small coding genes are likely to participate in elevated CO2 signaling to the circadian rhythm.
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Affiliation(s)
| | - Takayuki Kondo
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka-shi, Fukuoka, 820-8502, Japan
| | - Minami Shimizu
- RIKEN Center for Sustainable Resource Science, Yokohama-shi, Kanagawa, 230-0045, Japan
| | - You-Wang Kim
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka-shi, Fukuoka, 820-8502, Japan
| | - Kazuo Shinozaki
- RIKEN Center for Sustainable Resource Science, Yokohama-shi, Kanagawa, 230-0045, Japan
| | - Kousuke Hanada
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka-shi, Fukuoka, 820-8502, Japan.
- RIKEN Center for Sustainable Resource Science, Yokohama-shi, Kanagawa, 230-0045, Japan.
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MacKinnon KJM, Cole BJ, Yu C, Coomey JH, Hartwick NT, Remigereau MS, Duffy T, Michael TP, Kay SA, Hazen SP. Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation. THE NEW PHYTOLOGIST 2020; 227:1709-1724. [PMID: 32112414 DOI: 10.1111/nph.16507] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
Plants are continuously exposed to diurnal fluctuations in light and temperature, and spontaneous changes in their physical or biotic environment. The circadian clock coordinates regulation of gene expression with a 24 h period, enabling the anticipation of these events. We used RNA sequencing to characterize the Brachypodium distachyon transcriptome under light and temperature cycles, as well as under constant conditions. Approximately 3% of the transcriptome was regulated by the circadian clock, a smaller proportion than reported in most other species. For most transcripts that were rhythmic under all conditions, including many known clock genes, the period of gene expression lengthened from 24 to 27 h in the absence of external cues. To functionally characterize the cyclic transcriptome in B. distachyon, we used Gene Ontology enrichment analysis, and found several terms significantly associated with peak expression at particular times of the day. Furthermore, we identified sequence motifs enriched in the promoters of similarly phased genes, some potentially associated with transcription factors. When considering the overlap in rhythmic gene expression and specific pathway behavior, thermocycles was the prevailing cue that controlled diurnal gene regulation. Taken together, our characterization of the rhythmic B. distachyon transcriptome represents a foundational resource with implications in other grass species.
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Affiliation(s)
- Kirk J-M MacKinnon
- Biology Department, University of Massachusetts, Amherst, MA, 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, 01003, USA
| | - Benjamin J Cole
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Chang Yu
- Biology Department, University of Massachusetts, Amherst, MA, 01003, USA
| | - Joshua H Coomey
- Biology Department, University of Massachusetts, Amherst, MA, 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, 01003, USA
| | | | - Marie-Stanislas Remigereau
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Tomás Duffy
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | | | - Steve A Kay
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Samuel P Hazen
- Biology Department, University of Massachusetts, Amherst, MA, 01003, USA
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Qiao P, Bourgault R, Mohammadi M, Gore MA, Molina I, Scanlon MJ. A maize LIPID TRANSFER PROTEIN may bridge the gap between PHYTOCHROME-mediated light signaling and cuticle biosynthesis. PLANT SIGNALING & BEHAVIOR 2020; 15:1790824. [PMID: 32631108 PMCID: PMC8550183 DOI: 10.1080/15592324.2020.1790824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/28/2020] [Accepted: 06/29/2020] [Indexed: 05/22/2023]
Abstract
Plant epidermal cuticles are composed of hydrophobic lipids that provide a barrier to non-stomatal water loss, and arose in land plants as an adaptation to the dry terrestrial environment. The expanding maize adult leaf displays a dynamic, proximodistal gradient of cuticle development, from the leaf base to the tip. Recently, our gene co-expression network analyses together with reverse genetic analyses suggested a previously undescribed function for PHYTOCHROME-mediated light signaling during cuticular wax deposition. The present work extends these findings by identifying a role for a specific LIPID TRANSFER PROTEIN (LTP) in cuticle development, and validating it via transgenic experiments in Arabidopsis. Given that LTPs and cuticles both evolved in land plants and are absent from aquatic green algae, we propose that during plant evolution, LTPs arose as one of the innovations of land plants that enabled development of the cuticle.
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Affiliation(s)
- Pengfei Qiao
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Richard Bourgault
- Department of Biology, Essar Convergence Centre, Algoma University, Sault Ste. Marie, Canada
| | - Marc Mohammadi
- Department of Biology, Essar Convergence Centre, Algoma University, Sault Ste. Marie, Canada
| | - Michael A. Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Isabel Molina
- Department of Biology, Essar Convergence Centre, Algoma University, Sault Ste. Marie, Canada
| | - Michael J. Scanlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- CONTACT Michael J. Scanlon Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY14853, USA
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Jarad M, Antoniou-Kourounioti R, Hepworth J, Qüesta JI. Unique and contrasting effects of light and temperature cues on plant transcriptional programs. Transcription 2020; 11:134-159. [PMID: 33016207 PMCID: PMC7714439 DOI: 10.1080/21541264.2020.1820299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 12/12/2022] Open
Abstract
Plants have adapted to tolerate and survive constantly changing environmental conditions by reprogramming gene expression in response to stress or to drive developmental transitions. Among the many signals that plants perceive, light and temperature are of particular interest due to their intensely fluctuating nature which is combined with a long-term seasonal trend. Whereas specific receptors are key in the light-sensing mechanism, the identity of plant thermosensors for high and low temperatures remains far from fully addressed. This review aims at discussing common as well as divergent characteristics of gene expression regulation in plants, controlled by light and temperature. Light and temperature signaling control the abundance of specific transcription factors, as well as the dynamics of co-transcriptional processes such as RNA polymerase elongation rate and alternative splicing patterns. Additionally, sensing both types of cues modulates gene expression by altering the chromatin landscape and through the induction of long non-coding RNAs (lncRNAs). However, while light sensing is channeled through dedicated receptors, temperature can broadly affect chemical reactions inside plant cells. Thus, direct thermal modifications of the transcriptional machinery add another level of complexity to plant transcriptional regulation. Besides the rapid transcriptome changes that follow perception of environmental signals, plant developmental transitions and acquisition of stress tolerance depend on long-term maintenance of transcriptional states (active or silenced genes). Thus, the rapid transcriptional response to the signal (Phase I) can be distinguished from the long-term memory of the acquired transcriptional state (Phase II - remembering the signal). In this review we discuss recent advances in light and temperature signal perception, integration and memory in Arabidopsis thaliana, focusing on transcriptional regulation and highlighting the contrasting and unique features of each type of cue in the process.
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Affiliation(s)
- Mai Jarad
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
| | | | - Jo Hepworth
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Julia I. Qüesta
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
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