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Prakash V, Sharma V, Devendran R, Prajapati R, Ahmad B, Kumar R. A transition from enemies to allies: how viruses improve drought resilience in plants. STRESS BIOLOGY 2024; 4:33. [PMID: 38981936 PMCID: PMC11233480 DOI: 10.1007/s44154-024-00172-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 05/03/2024] [Indexed: 07/11/2024]
Abstract
Global crop production is severely affected by environmental factors such as drought, salinity, cold, flood etc. Among these stresses, drought is one of the major abiotic stresses reducing crop productivity. It is expected that drought conditions will further increase because of the increasing global temperature. In general, viruses are seen as a pathogen affecting the crop productivity. However, several researches are showing that viruses can induce drought tolerance in plants. This review explores the mechanisms underlying the interplay between viral infections and the drought response mechanisms in plants. We tried to address the molecular pathways and physiological changes induced by viruses that confer drought tolerance, including alterations in hormone signaling, antioxidant defenses, scavenging the reactive oxygen species, role of RNA silencing and miRNA pathway, change in the expression of several genes including heat shock proteins, cellulose synthase etc. Furthermore, we discuss various viruses implicated in providing drought tolerance and examine the range of plant species exhibiting this phenomenon. By applying current knowledge and identifying gaps in understanding, this review aims to provide valuable insights into the complex dynamics of virus-induced drought tolerance in plants, paving the way for future research directions and practical applications in sustainable agriculture.
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Affiliation(s)
- Ved Prakash
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
| | - Veerendra Sharma
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | | | - Ramgopal Prajapati
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Bilal Ahmad
- Division of Biology, Kansas State University, Manhattan, KS, USA
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2
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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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3
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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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4
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Liang T, Yu S, Pan Y, Wang J, Kay SA. The interplay between the circadian clock and abiotic stress responses mediated by ABF3 and CCA1/LHY. Proc Natl Acad Sci U S A 2024; 121:e2316825121. [PMID: 38319968 PMCID: PMC10873597 DOI: 10.1073/pnas.2316825121] [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: 10/04/2023] [Accepted: 01/09/2024] [Indexed: 02/08/2024] Open
Abstract
Climate change is a global concern for all life on our planet, including humans and plants. Plants' growth and development are significantly affected by abiotic stresses, including adverse temperature, inadequate or excess water availability, nutrient deficiency, and salinity. The circadian clock is a master regulator of numerous developmental and metabolic processes in plants. In an effort to identify new clock-related genes and outputs through bioinformatic analysis, we have revealed that CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) play a crucial role in regulating a wide range of abiotic stress responses and target ABSCISIC ACID RESPONSIVE ELEMENTS-BINDING FACTOR3 (ABF3), a key transcription factor in the plant hormone Abscisic acid (ABA)-signaling pathway. Specifically, we found that CCA1 and LHY regulate the expression of ABF3 under diel conditions, as well as seed germination under salinity. Conversely, ABF3 controls the expression of core clock genes and orchestrates the circadian period in a stress-responsive manner. ABF3 delivers the stress signal to the central oscillator by binding to the promoter of CCA1 and LHY. Overall, our study uncovers the reciprocal regulation between ABF3 and CCA1/LHY and molecular mechanisms underlying the interaction between the circadian clock and abiotic stress. This finding may aid in developing molecular and genetic solutions for plants to survive and thrive in the face of climate change.
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Affiliation(s)
- Tong Liang
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA90089
| | - Shi Yu
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA90089
| | - Yuanzhong Pan
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA90089
| | - Jiarui Wang
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA90089
| | - Steve A. Kay
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA90089
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5
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Jang J, Lee S, Kim JI, Lee S, Kim JA. The Roles of Circadian Clock Genes in Plant Temperature Stress Responses. Int J Mol Sci 2024; 25:918. [PMID: 38255990 PMCID: PMC10815334 DOI: 10.3390/ijms25020918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/17/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Plants monitor day length and memorize changes in temperature signals throughout the day, creating circadian rhythms that support the timely control of physiological and metabolic processes. The DEHYDRATION-RESPONSE ELEMENT-BINDING PROTEIN 1/C-REPEAT BINDING FACTOR (DREB1/CBF) transcription factors are known as master regulators for the acquisition of cold stress tolerance, whereas PHYTOCHROME INTERACTING FACTOR 4 (PIF4) is involved in plant adaptation to heat stress through thermomorphogenesis. Recent studies have shown that circadian clock genes control plant responses to temperature. Temperature-responsive transcriptomes show a diurnal cycle and peak expression levels at specific times of throughout the day. Circadian clock genes play essential roles in allowing plants to maintain homeostasis by accommodating temperature changes within the normal temperature range or by altering protein properties and morphogenesis at the cellular level for plant survival and growth under temperature stress conditions. Recent studies revealed that the central oscillator genes CIRCADIAN CLOCK ASSOCIATED 1/LATE ELONGATED HYPOCOTYL (CCA1/LHY) and PSEUDO-RESPONSE REGULATOR5/7/9 (PRR5/7/9), as well as the EVENING COMPLEX (EC) genes REVEILLE4/REVEILLE8 (REV4/REV8), were involved in the DREB1 pathway of the cold signaling transcription factor and regulated the thermomorphogenesis gene PIF4. Further studies showed that another central oscillator, TIMING OF CAB EXPRESSION 1 (TOC1), and the regulatory protein ZEITLUPE (ZTL) are also involved. These studies led to attempts to utilize circadian clock genes for the acquisition of temperature-stress resistance in crops. In this review, we highlight circadian rhythm regulation and the clock genes involved in plant responses to temperature changes, as well as strategies for plant survival in a rapidly changing global climate.
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Affiliation(s)
- Juna Jang
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea; (J.J.); (S.L.); (S.L.)
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea;
| | - Sora Lee
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea; (J.J.); (S.L.); (S.L.)
| | - Jeong-Il Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea;
| | - Sichul Lee
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea; (J.J.); (S.L.); (S.L.)
| | - Jin A. Kim
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju 54874, Republic of Korea; (J.J.); (S.L.); (S.L.)
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6
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Bonnot T, Somayanda I, Jagadish SVK, Nagel DH. Time of day and genotype sensitivity adjust molecular responses to temperature stress in sorghum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1081-1096. [PMID: 37715988 DOI: 10.1111/tpj.16467] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/18/2023]
Abstract
Sorghum is one of the four major C4 crops that are considered to be tolerant to environmental extremes. Sorghum shows distinct growth responses to temperature stress depending on the sensitivity of the genetic background. About half of the transcripts in sorghum exhibit diurnal rhythmic expressions emphasizing significant coordination with the environment. However, an understanding of how molecular dynamics contribute to genotype-specific stress responses in the context of the time of day is not known. We examined whether temperature stress and the time of day impact the gene expression dynamics in thermo-sensitive and thermo-tolerant sorghum genotypes. We found that time of day is highly influencing the temperature stress responses, which can be explained by the rhythmic expression of most thermo-responsive genes. This effect is more pronounced in thermo-tolerant genotypes, suggesting a stronger regulation of gene expression by the time of day and/or by the circadian clock. Genotypic differences were mostly observed on average gene expression levels, which may be responsible for contrasting sensitivities to temperature stress in tolerant versus susceptible sorghum varieties. We also identified groups of genes altered by temperature stress in a time-of-day and genotype-specific manner. These include transcriptional regulators and several members of the Ca2+ -binding EF-hand protein family. We hypothesize that expression variation of these genes between genotypes along with time-of-day independent regulation may contribute to genotype-specific fine-tuning of thermo-responsive pathways. These findings offer a new opportunity to selectively target specific genes in efforts to develop climate-resilient crops based on their time-of-day and genotype variation responses to temperature stress.
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Affiliation(s)
- Titouan Bonnot
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California, 92507, USA
| | - Impa Somayanda
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, 79409-2122, USA
| | - S V Krishna Jagadish
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, 79409-2122, USA
| | - Dawn H Nagel
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California, 92507, USA
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7
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Prasetyaningrum P, Litthauer S, Vegliani F, Battle MW, Wood MW, Liu X, Dickson C, Jones MA. Inhibition of RNA degradation integrates the metabolic signals induced by osmotic stress into the Arabidopsis circadian system. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5805-5819. [PMID: 37453132 PMCID: PMC10540740 DOI: 10.1093/jxb/erad274] [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: 02/05/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
The circadian clock system acts as an endogenous timing reference that coordinates many metabolic and physiological processes in plants. Previous studies have shown that the application of osmotic stress delays circadian rhythms via 3'-phospho-adenosine 5'-phosphate (PAP), a retrograde signalling metabolite that is produced in response to redox stress within organelles. PAP accumulation leads to the inhibition of exoribonucleases (XRNs), which are responsible for RNA degradation. Interestingly, we are now able to demonstrate that post-transcriptional processing is crucial for the circadian response to osmotic stress. Our data show that osmotic stress increases the stability of specific circadian RNAs, suggesting that RNA metabolism plays a vital role in circadian clock coordination during drought. Inactivation of XRN4 is sufficient to extend circadian rhythms as part of this response, with PRR7 and LWD1 identified as transcripts that are post-transcriptionally regulated to delay circadian progression.
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Affiliation(s)
| | | | - Franco Vegliani
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
| | | | | | - Xinmeng Liu
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Cathryn Dickson
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Matthew Alan Jones
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
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8
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Brindisi LJ, Simon JE. Preharvest and postharvest techniques that optimize the shelf life of fresh basil ( Ocimum basilicum L.): a review. FRONTIERS IN PLANT SCIENCE 2023; 14:1237577. [PMID: 37745993 PMCID: PMC10514919 DOI: 10.3389/fpls.2023.1237577] [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: 06/09/2023] [Accepted: 08/17/2023] [Indexed: 09/26/2023]
Abstract
Basil (Ocimum basilicum L.) is a popular specialty crop known for its use as a culinary herb and medicinal plant around the world. However, its profitability and availability are limited by a short postharvest shelf life due to poor handling, cold sensitivity and microbial contamination. Here, we comprehensively review the research on pre- and postharvest techniques that extend the shelf life of basil to serve as a practical tool for growers, distributors, retailers and scientists. Modifications to postharvest storage conditions, pre- and postharvest treatments, harvest time and preharvest production methods have been found to directly impact the quality of basil and its shelf life. The most effective strategies for extending the shelf life and improving the quality of basil are discussed and promising strategies that research and industry employ are identified.
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Affiliation(s)
| | - James E. Simon
- New Use Agriculture and Natural Plant Products Program, Department of Plant Biology and the Center for Agricultural Food Ecosystems (RUCAFE), Rutgers University, New Brunswick, NJ, United States
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9
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Baek D, Cho HM, Cha YJ, Jin BJ, Lee SH, Park MS, Chun HJ, Kim MC. Soybean Calmodulin-Binding Transcription Activators, GmCAMTA2 and GmCAMTA8, Coordinate the Circadian Regulation of Developmental Processes and Drought Stress Responses. Int J Mol Sci 2023; 24:11477. [PMID: 37511240 PMCID: PMC10380932 DOI: 10.3390/ijms241411477] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/03/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
The calmodulin-binding transcription activators (CAMTAs) mediate transcriptional regulation of development, growth, and responses to various environmental stresses in plants. To understand the biological roles of soybean CAMTA (GmCAMTA) family members in response to abiotic stresses, we characterized expression patterns of 15 GmCAMTA genes in response to various abiotic stresses. The GmCAMTA genes exhibited distinct circadian regulation expression patterns and were differently expressed in response to salt, drought, and cold stresses. Interestingly, the expression levels of GmCAMTA2, GmCAMTA8, and GmCAMTA12 were higher in stem tissue than in other soybean tissues. To determine the roles of GmCAMTAs in the regulation of developmental processes and stress responses, we isolated GmCAMTA2 and GmCAMTA8 cDNAs from soybean and generated Arabidopsis overexpressing transgenic plants. The GmCAMTA2-OX and GmCAMTA8-OX plants showed hypersensitivity to drought stress. The water in the leaves of GmCAMTA2-OX and GmCAMTA8-OX plants was lost faster than that in wild-type (WT) plants under drought-stress conditions. In addition, stress-responsive genes were down-regulated in the GmCAMTA2-OX and GmCAMTA8-OX plants under drought stress conditions compared to WT plants. Our results suggest that GmCAMTA2 and GmCAMTA8 genes are regulated by circadian rhythms and function as negative regulators in development and drought stress responses.
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Affiliation(s)
- Dongwon Baek
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Hyun Min Cho
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Ye Jin Cha
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Byung Jun Jin
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Su Hyeon Lee
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Mi Suk Park
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Hyun Jin Chun
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Min Chul Kim
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
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10
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Shim Y, Seong G, Choi Y, Lim C, Baek SA, Park YJ, Kim JK, An G, Kang K, Paek NC. Suppression of cuticular wax biosynthesis mediated by rice LOV KELCH REPEAT PROTEIN 2 supports a negative role in drought stress tolerance. PLANT, CELL & ENVIRONMENT 2023; 46:1504-1520. [PMID: 36683564 DOI: 10.1111/pce.14549] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 06/17/2023]
Abstract
Drought tolerance is important for grain crops, including rice (Oryza sativa); for example, rice cultivated under intermittent irrigation produces less methane gas compared to rice grown in anaerobic paddy field conditions, but these plants require greater drought tolerance. Moreover, the roles of rice circadian-clock genes in drought tolerance remain largely unknown. Here, we show that the mutation of LOV KELCH REPEAT PROTEIN 2 (OsLKP2) enhanced drought tolerance by increasing cuticular wax biosynthesis. Among ZEITLUPE family genes, OsLKP2 expression specifically increased under dehydration stress. OsLKP2 knockdown (oslkp2-1) and knockout (oslkp2-2) mutants exhibited enhanced drought tolerance. Cuticular waxes inhibit non-stomatal water loss. Under drought conditions, total wax loads on the leaf surface increased by approximately 10% in oslkp2-1 and oslkp2-2 compared to the wild type, and the transcript levels of cuticular wax biosynthesis genes were upregulated in the oslkp2 mutants. Yeast two-hybrid, bimolecular fluorescence complementation, and coimmunoprecipitation assays revealed that OsLKP2 interacts with GIGANTEA (OsGI) in the nucleus. The osgi mutants also showed enhanced tolerance to drought stress, with a high density of wax crystals on their leaf surface. These results demonstrate that the OsLKP2-OsGI interaction negatively regulates wax accumulation on leaf surfaces, thereby decreasing rice resilience to drought stress.
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Affiliation(s)
- Yejin Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Gayeong Seong
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Yumin Choi
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Chaemyeong Lim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Seung-A Baek
- Division of Life Sciences, Incheon National University, Incheon, Republic of Korea
| | - Young Jin Park
- Division of Life Sciences, Incheon National University, Incheon, Republic of Korea
| | - Jae Kwang Kim
- Division of Life Sciences, Incheon National University, Incheon, Republic of Korea
| | - Gynheung An
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea
| | - Kiyoon Kang
- Division of Life Sciences, Incheon National University, Incheon, Republic of Korea
| | - Nam-Chon Paek
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
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11
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Huang P, Ding Z, Duan M, Xiong Y, Li X, Yuan X, Huang J. OsLUX Confers Rice Cold Tolerance as a Positive Regulatory Factor. Int J Mol Sci 2023; 24:ijms24076727. [PMID: 37047700 PMCID: PMC10094877 DOI: 10.3390/ijms24076727] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 03/26/2023] [Accepted: 03/28/2023] [Indexed: 04/07/2023] Open
Abstract
During the early seedling stage, rice (Oryza sativa L.) must overcome low-temperature stress. While a few cold-tolerance genes have been characterized, further excavation of cold-resistance genes is still needed. In this study, we identified a cold-induced transcription factor—LUX ARRHYTHMO (LUX)—in rice. OsLUX was found to be specifically expressed in leaf blades and upregulated by both cold stress and circadian rhythm. The full-length OsLUX showed autoactivation activity, and the OsLUX protein localized throughout the entire onion cell. Overexpressing OsLUX resulted in increased cold tolerance and reduced ion leakage under cold-stress conditions during the seedling stage. In contrast, the knockout of OsLUX decreased seedling cold tolerance and showed higher ion leakage compared to the wild type. Furthermore, overexpressing OsLUX upregulated the expression levels of oxidative stress-responsive genes, which improved reactive oxygen species (ROS) scavenging ability and enhanced tolerance to chilling stress. Promoter analysis showed that the OsLUX promoter contains two dehydration-responsive element binding (DREB) motifs at positions −510/−505 (GTCGGa) and −162/−170 (cCACCGccc), which indicated that OsDREB1s and OsDREB2s probably regulate OsLUX expression by binding to the motif to respond to cold stress. Thus, OsLUX may act as a downstream gene of the DREB pathway. These results demonstrate that OsLUX serves as a positive regulatory factor of cold stress and that overexpressing OsLUX could be used in rice breeding programs to enhance abiotic stress tolerance.
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Affiliation(s)
- Peng Huang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Zhengquan Ding
- Jiaxing Academy of Agricultural Sciences, Jiaxing 314016, China
| | - Min Duan
- Taizhou Academy Agricultural of Sciences, Taizhou 317000, China
| | - Yi Xiong
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Xinxin Li
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Xi Yuan
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Ji Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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12
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Reinar WB, Greulich A, Stø IM, Knutsen JB, Reitan T, Tørresen OK, Jentoft S, Butenko MA, Jakobsen KS. Adaptive protein evolution through length variation of short tandem repeats in Arabidopsis. SCIENCE ADVANCES 2023; 9:eadd6960. [PMID: 36947624 PMCID: PMC10032594 DOI: 10.1126/sciadv.add6960] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Intrinsically disordered protein regions are of high importance for biotic and abiotic stress responses in plants. Tracts of identical amino acids accumulate in these regions and can vary in length over generations because of expansions and retractions of short tandem repeats at the genomic level. However, little attention has been paid to what extent length variation is shaped by natural selection. By environmental association analysis on 2514 length variable tracts in 770 whole-genome sequenced Arabidopsis thaliana, we show that length variation in glutamine and asparagine amino acid homopolymers, as well as in interaction hotspots, correlate with local bioclimatic habitat. We determined experimentally that the promoter activity of a light-stress gene depended on polyglutamine length variants in a disordered transcription factor. Our results show that length variations affect protein function and are likely adaptive. Length variants modulating protein function at a global genomic scale has implications for understanding protein evolution and eco-evolutionary biology.
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Affiliation(s)
- William B. Reinar
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Anne Greulich
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Ida M. Stø
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Jonfinn B. Knutsen
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Trond Reitan
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Melinka A. Butenko
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Kjetill S. Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316 Oslo, Norway
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13
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Identification of Key Gene Network Modules and Hub Genes Associated with Wheat Response to Biotic Stress Using Combined Microarray Meta-analysis and WGCN Analysis. Mol Biotechnol 2023; 65:453-465. [PMID: 35996047 DOI: 10.1007/s12033-022-00541-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 07/05/2022] [Indexed: 12/31/2022]
Abstract
Wheat (Triticum aestivum) is one of the major crops worldwide and a primary source of calories for human food. Biotic stresses such as fungi, bacteria, and diseases limit wheat production. Although plant breeding and genetic engineering for biotic stress resistance have been suggested as promising solutions to handle losses caused by biotic stress factors, a comprehensive understanding of molecular mechanisms and identifying key genes is a critical step to obtaining success. Here, a network-based meta-analysis approach based on two main statistical methods was used to identify key genes and molecular mechanisms of the wheat response to biotic stress. A total of 163 samples (21,792 genes) from 10 datasets were analyzed. Fisher Z test based on the p-value and REM method based on effect size resulted in 533 differentially expressed genes (p < 0.001 and FDR < 0.001). WGCNA analysis using a dynamic tree-cutting algorithm was used to construct a co-expression network and three significant modules were detected. The modules were significantly enriched by 16 BP terms and 4 KEGG pathways (Benjamini-Hochberg FDR < 0.001). A total of nine hub genes (a top 1.5% of genes with the highest degree) were identified from the constructed network. The identification of DE genes, gene-gene co-expressing network, and hub genes may contribute to uncovering the molecular mechanisms of the wheat response to biotic stress.
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14
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Liu Z, Liu W, Wang Z, Qi K, Xie Z, Zhang S, Wu J, Wang P. Diurnal transcriptome dynamics reveal the photoperiod response of Pyrus. PHYSIOLOGIA PLANTARUM 2023; 175:e13893. [PMID: 36929905 DOI: 10.1111/ppl.13893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/15/2023] [Accepted: 03/14/2023] [Indexed: 06/18/2023]
Abstract
Photoperiod provides a key environmental signal that controls plant growth. Plants have evolved an integrated mechanism for sensing photoperiods with internal clocks to orchestrate physiological events. This mechanism has been identified to enable timely plant growth and improve fitness. Although the components and pathways underlying photoperiod regulation have been described in many species, diurnal patterns of gene expression at the genome-wide level under different photoperiods are rarely reported in perennial fruit trees. To explore the global gene expression in response to photoperiod, pear plants were cultured under long-day (LD) and short-day (SD) conditions. A time-series transcriptomic study was implemented using LD and SD samples collected at 4 h intervals over 2 days. We identified 13,677 rhythmic genes, of which 7639 were identified under LD and 10,557 under SD conditions. Additionally, 4674 genes were differentially expressed in response to photoperiod change. We also characterized the candidate homologs of clock-associated genes in pear. Clock genes were involved in the regulation of many processes throughout the day, including photosynthesis, stress response, hormone dynamics, and secondary metabolism. Strikingly, genes within photosynthesis-related pathways were enriched in both the rhythmic and differential expression analyses. Several key candidate genes were identified to be associated with regulating photosynthesis and improving productivity under different photoperiods. The results suggest that temporal variation in gene expression should not be ignored in pear gene function research. Overall, our work expands the understanding of photoperiod regulation of plant growth, particularly by extending the research to non-model trees.
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Affiliation(s)
- Zhe Liu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
- Department of Pharmacy, Changzhi Medical College, Changzhi, 046000, China
| | - Weijuan Liu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhangqing Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Kaijie Qi
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhihua Xie
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Shaoling Zhang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Juyou Wu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Peng Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
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15
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Gombos M, Hapek N, Kozma-Bognár L, Grezal G, Zombori Z, Kiss E, Györgyey J. Limited water stress modulates expression of circadian clock genes in Brachypodium distachyon roots. Sci Rep 2023; 13:1241. [PMID: 36690685 PMCID: PMC9870971 DOI: 10.1038/s41598-022-27287-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 12/29/2022] [Indexed: 01/24/2023] Open
Abstract
Organisms have evolved a circadian clock for the precise timing of their biological processes. Studies primarily on model dicots have shown the complexity of the inner timekeeper responsible for maintaining circadian oscillation in plants and have highlighted that circadian regulation is more than relevant to a wide range of biological processes, especially organ development and timing of flowering. Contribution of the circadian clock to overall plant fitness and yield has also long been known. Nevertheless, the organ- and species-specific functions of the circadian clock and its relation to stress adaptation have only recently been identified. Here we report transcriptional changes of core clock genes of the model monocot Brachypodium distachyon under three different light regimes (18:6 light:dark, 24:0 light and 0:24 dark) in response to mild drought stress in roots and green plant parts. Comparative monitoring of core clock gene expression in roots and green plant parts has shown that both phase and amplitude of expression in the roots of Brachypodium plants differ markedly from those in the green plant parts, even under well-watered conditions. Moreover, circadian clock genes responded to water depletion differently in root and shoot. These results suggest an organ-specific form and functions of the circadian clock in Brachypodium roots.
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Affiliation(s)
- Magdolna Gombos
- Institute of Plant Biology, BRC-Biological Research Centre, Szeged, Hungary
| | - Nóra Hapek
- Institute of Plant Biology, BRC-Biological Research Centre, Szeged, Hungary
- Institute of Biochemistry, BRC-Biological Research Centre, Szeged, Hungary
| | - László Kozma-Bognár
- Institute of Plant Biology, BRC-Biological Research Centre, Szeged, Hungary
- Department of Genetics, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Gábor Grezal
- Institute of Biochemistry, BRC-Biological Research Centre, Szeged, Hungary
| | - Zoltán Zombori
- Institute of Plant Biology, BRC-Biological Research Centre, Szeged, Hungary
| | - Edina Kiss
- Institute of Plant Biology, BRC-Biological Research Centre, Szeged, Hungary
| | - János Györgyey
- Institute of Plant Biology, BRC-Biological Research Centre, Szeged, Hungary.
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16
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Colin L, Ruhnow F, Zhu JK, Zhao C, Zhao Y, Persson S. The cell biology of primary cell walls during salt stress. THE PLANT CELL 2023; 35:201-217. [PMID: 36149287 PMCID: PMC9806596 DOI: 10.1093/plcell/koac292] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Salt stress simultaneously causes ionic toxicity, osmotic stress, and oxidative stress, which directly impact plant growth and development. Plants have developed numerous strategies to adapt to saline environments. Whereas some of these strategies have been investigated and exploited for crop improvement, much remains to be understood, including how salt stress is perceived by plants and how plants coordinate effective responses to the stress. It is, however, clear that the plant cell wall is the first contact point between external salt and the plant. In this context, significant advances in our understanding of halotropism, cell wall synthesis, and integrity surveillance, as well as salt-related cytoskeletal rearrangements, have been achieved. Indeed, molecular mechanisms underpinning some of these processes have recently been elucidated. In this review, we aim to provide insights into how plants respond and adapt to salt stress, with a special focus on primary cell wall biology in the model plant Arabidopsis thaliana.
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Affiliation(s)
- Leia Colin
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Felix Ruhnow
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Jian-Kang Zhu
- School of Life Sciences, Institute of Advanced Biotechnology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Chunzhao Zhao
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yang Zhao
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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17
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Verslues PE, Bailey-Serres J, Brodersen C, Buckley TN, Conti L, Christmann A, Dinneny JR, Grill E, Hayes S, Heckman RW, Hsu PK, Juenger TE, Mas P, Munnik T, Nelissen H, Sack L, Schroeder JI, Testerink C, Tyerman SD, Umezawa T, Wigge PA. Burning questions for a warming and changing world: 15 unknowns in plant abiotic stress. THE PLANT CELL 2023; 35:67-108. [PMID: 36018271 PMCID: PMC9806664 DOI: 10.1093/plcell/koac263] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/21/2022] [Indexed: 05/08/2023]
Abstract
We present unresolved questions in plant abiotic stress biology as posed by 15 research groups with expertise spanning eco-physiology to cell and molecular biology. Common themes of these questions include the need to better understand how plants detect water availability, temperature, salinity, and rising carbon dioxide (CO2) levels; how environmental signals interface with endogenous signaling and development (e.g. circadian clock and flowering time); and how this integrated signaling controls downstream responses (e.g. stomatal regulation, proline metabolism, and growth versus defense balance). The plasma membrane comes up frequently as a site of key signaling and transport events (e.g. mechanosensing and lipid-derived signaling, aquaporins). Adaptation to water extremes and rising CO2 affects hydraulic architecture and transpiration, as well as root and shoot growth and morphology, in ways not fully understood. Environmental adaptation involves tradeoffs that limit ecological distribution and crop resilience in the face of changing and increasingly unpredictable environments. Exploration of plant diversity within and among species can help us know which of these tradeoffs represent fundamental limits and which ones can be circumvented by bringing new trait combinations together. Better defining what constitutes beneficial stress resistance in different contexts and making connections between genes and phenotypes, and between laboratory and field observations, are overarching challenges.
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Affiliation(s)
| | - Julia Bailey-Serres
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California 92521, USA
| | - Craig Brodersen
- School of the Environment, Yale University, New Haven, Connecticut 06511, USA
| | - Thomas N Buckley
- Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Lucio Conti
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Alexander Christmann
- School of Life Sciences, Technical University Munich, Freising-Weihenstephan 85354, Germany
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Erwin Grill
- School of Life Sciences, Technical University Munich, Freising-Weihenstephan 85354, Germany
| | - Scott Hayes
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, Wageningen 6708 PB, The Netherlands
| | - Robert W Heckman
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Po-Kai Hsu
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Paloma Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona 08193, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
| | - Teun Munnik
- Department of Plant Cell Biology, Green Life Sciences Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam NL-1098XH, The Netherlands
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Lawren Sack
- Department of Ecology and Evolutionary Biology, Institute of the Environment and Sustainability, University of California, Los Angeles, California 90095, USA
| | - Julian I Schroeder
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Christa Testerink
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, Wageningen 6708 PB, The Netherlands
| | - Stephen D Tyerman
- ARC Center Excellence, Plant Energy Biology, School of Agriculture Food and Wine, University of Adelaide, Adelaide, South Australia 5064, Australia
| | - Taishi Umezawa
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 6708 PB, Japan
| | - Philip A Wigge
- Leibniz-Institut für Gemüse- und Zierpflanzenbau, Großbeeren 14979, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam 14476, Germany
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18
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Cobo-Simón I, Gómez-Garrido J, Esteve-Codina A, Dabad M, Alioto T, Maloof JN, Méndez-Cea B, Seco JI, Linares JC, Gallego FJ. De novo transcriptome sequencing and gene co-expression reveal a genomic basis for drought sensitivity and evidence of a rapid local adaptation on Atlas cedar ( Cedrus atlantica). FRONTIERS IN PLANT SCIENCE 2023; 14:1116863. [PMID: 37152146 PMCID: PMC10155838 DOI: 10.3389/fpls.2023.1116863] [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: 12/05/2022] [Accepted: 03/30/2023] [Indexed: 05/09/2023]
Abstract
Introduction Understanding the adaptive capacity to current climate change of drought-sensitive tree species is mandatory, given their limited prospect of migration and adaptation as long-lived, sessile organisms. Knowledge about the molecular and eco-physiological mechanisms that control drought resilience is thus key, since water shortage appears as one of the main abiotic factors threatening forests ecosystems. However, our current background is scarce, especially in conifers, due to their huge and complex genomes. Methods Here we investigated the eco-physiological and transcriptomic basis of drought response of the climate change-threatened conifer Cedrus atlantica. We studied C. atlantica seedlings from two locations with contrasting drought conditions to investigate a local adaptation. Seedlings were subjected to experimental drought conditions, and were monitored at immediate (24 hours) and extended (20 days) times. In addition, post-drought recovery was investigated, depicting two contrasting responses in both locations (drought resilient and non-resilient). Single nucleotide polymorphisms (SNPs) were also studied to characterize the genomic basis of drought resilience and investigate a rapid local adaptation of C. atlantica. Results De novo transcriptome assembly was performed for the first time in this species, providing differences in gene expression between the immediate and extended treatments, as well as among the post-drought recovery phenotypes. Weighted gene co-expression network analysis showed a regulation of stomatal closing and photosynthetic activity during the immediate drought, consistent with an isohydric dynamic. During the extended drought, growth and flavonoid biosynthesis inhibition mechanisms prevailed, probably to increase root-to-shoot ratio and to limit the energy-intensive biosynthesis of secondary metabolites. Drought sensitive individuals failed in metabolism and photosynthesis regulation under drought stress, and in limiting secondary metabolite production. Moreover, genomic differences (SNPs) were found between drought resilient and sensitive seedlings, and between the two studied locations, which were mostly related to transposable elements. Discussion This work provides novel insights into the transcriptomic basis of drought response of C. atlantica, a set of candidate genes mechanistically involved in its drought sensitivity and evidence of a rapid local adaptation. Our results may help guide conservation programs for this threatened conifer, contribute to advance drought-resilience research and shed light on trees' adaptive potential to current climate change.
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Affiliation(s)
- Irene Cobo-Simón
- Department of Physical, Chemical and Natural Systems. University Pablo de Olavide, Seville, Spain
- Department of Genetics, Physiology and Microbiology, Genetics Unit. Faculty of Biological Sciences, Complutense University of Madrid, Madrid, Spain
- *Correspondence: Irene Cobo-Simón,
| | - Jèssica Gómez-Garrido
- Nacional Center for Genomic Analysis-Center for Genomic Regulation (CNAG-CRG), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Anna Esteve-Codina
- Nacional Center for Genomic Analysis-Center for Genomic Regulation (CNAG-CRG), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marc Dabad
- Nacional Center for Genomic Analysis-Center for Genomic Regulation (CNAG-CRG), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Tyler Alioto
- Nacional Center for Genomic Analysis-Center for Genomic Regulation (CNAG-CRG), Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Julin N. Maloof
- Department of Plant Biology, University of California at Davis, Davis, CA, United States
| | - Belén Méndez-Cea
- Department of Genetics, Physiology and Microbiology, Genetics Unit. Faculty of Biological Sciences, Complutense University of Madrid, Madrid, Spain
| | - José Ignacio Seco
- Department of Physical, Chemical and Natural Systems. University Pablo de Olavide, Seville, Spain
| | - Juan Carlos Linares
- Department of Physical, Chemical and Natural Systems. University Pablo de Olavide, Seville, Spain
| | - Francisco Javier Gallego
- Department of Genetics, Physiology and Microbiology, Genetics Unit. Faculty of Biological Sciences, Complutense University of Madrid, Madrid, Spain
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19
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Vuosku J, Martz F, Hallikainen V, Rautio P. Changing winter climate and snow conditions induce various transcriptional stress responses in Scots pine seedlings. FRONTIERS IN PLANT SCIENCE 2022; 13:1050903. [PMID: 36570907 PMCID: PMC9780549 DOI: 10.3389/fpls.2022.1050903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
In northern boreal forests the warming winter climate leads to more frequent snowmelt, rain-on-snow events and freeze-thaw cycles. This may be harmful or even lethal for tree seedlings that spend even a half of the year under snow. We conducted a snow cover manipulation experiment in a natural forest to find out how changing snow conditions affect young Scots pine (Pinus sylvestris L.) seedlings. The ice encasement (IE), absence of snow (NoSNOW) and snow compaction (COMP) treatments affected ground level temperature, ground frost and subnivean gas concentrations compared to the ambient snow cover (AMB) and led to the increased physical damage and mortality of seedlings. The expression responses of 28 genes related to circadian clock, aerobic and anaerobic energy metabolism, carbohydrate metabolism and stress protection revealed that seedlings were exposed to different stresses in a complex way depending on the thickness and quality of the snow cover. The IE treatment caused hypoxic stress and probably affected roots which resulted in reduced water uptake in the beginning of the growing season. Without protective snowpack in NoSNOW seedlings suffered from cold and drought stresses. The combination of hypoxic and cold stresses in COMP evoked unique transcriptional responses including oxidative stress. Snow cover manipulation induced changes in the expression of several circadian clock related genes suggested that photoreceptors and the circadian clock system play an essential role in the adaptation of Scots pine seedlings to stresses under different snow conditions. Our findings show that warming winter climate alters snow conditions and consequently causes Scots pine seedlings various abiotic stresses, whose effects extend from overwintering to the following growing season.
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Affiliation(s)
- Jaana Vuosku
- Natural Resources Unit, Natural Resources Institute Finland, Rovaniemi, Finland
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Françoise Martz
- Natural Resources Unit, Natural Resources Institute Finland, Rovaniemi, Finland
| | - Ville Hallikainen
- Natural Resources Unit, Natural Resources Institute Finland, Rovaniemi, Finland
| | - Pasi Rautio
- Natural Resources Unit, Natural Resources Institute Finland, Rovaniemi, Finland
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20
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Rodriguez Gallo MC, Li Q, Mehta D, Uhrig RG. Genome-scale analysis of Arabidopsis splicing-related protein kinase families reveals roles in abiotic stress adaptation. BMC PLANT BIOLOGY 2022; 22:496. [PMID: 36273172 PMCID: PMC9587599 DOI: 10.1186/s12870-022-03870-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/04/2022] [Indexed: 05/24/2023]
Abstract
Nearly 60 - 80 % of intron-containing plant genes undergo alternative splicing in response to either stress or plant developmental cues. RNA splicing is performed by a large ribonucleoprotein complex called the spliceosome in conjunction with associated subunits such as serine arginine (SR) proteins, all of which undergo extensive phosphorylation. In plants, there are three main protein kinase families suggested to phosphorylate core spliceosome subunits and related splicing factors based on orthology to human splicing-related kinases: the SERINE/ARGININE PROTEIN KINASES (SRPK), ARABIDOPSIS FUS3 COMPLEMENT (AFC), and Pre-mRNA PROCESSING FACTOR 4 (PRP4K) protein kinases. To better define the conservation and role(s) of these kinases in plants, we performed a genome-scale analysis of the three families across photosynthetic eukaryotes, followed by extensive transcriptomic and bioinformatic analysis of all Arabidopsis thaliana SRPK, AFC, and PRP4K protein kinases to elucidate their biological functions. Unexpectedly, this revealed the existence of SRPK and AFC phylogenetic groups with distinct promoter elements and patterns of transcriptional response to abiotic stress, while PRP4Ks possess no phylogenetic sub-divisions, suggestive of functional redundancy. We also reveal splicing-related kinase families are both diel and photoperiod regulated, implicating different orthologs as discrete time-of-day RNA splicing regulators. This foundational work establishes a number of new hypotheses regarding how reversible spliceosome phosphorylation contributes to both diel plant cell regulation and abiotic stress adaptation in plants.
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Affiliation(s)
- M C Rodriguez Gallo
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Q Li
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - D Mehta
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - R G Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
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21
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Fan T, Aslam MM, Zhou JL, Chen MX, Zhang J, Du S, Zhang KL, Chen YS. A crosstalk of circadian clock and alternative splicing under abiotic stresses in the plants. FRONTIERS IN PLANT SCIENCE 2022; 13:976807. [PMID: 36275558 PMCID: PMC9583901 DOI: 10.3389/fpls.2022.976807] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/05/2022] [Indexed: 06/16/2023]
Abstract
The circadian clock is an internal time-keeping mechanism that synchronizes the physiological adaptation of an organism to its surroundings based on day and night transition in a period of 24 h, suggesting the circadian clock provides fitness by adjusting environmental constrains. The circadian clock is driven by positive and negative elements that regulate transcriptionally and post-transcriptionally. Alternative splicing (AS) is a crucial transcriptional regulator capable of generating large numbers of mRNA transcripts from limited numbers of genes, leading to proteome diversity, which is involved in circadian to deal with abiotic stresses. Over the past decade, AS and circadian control have been suggested to coordinately regulate plant performance under fluctuating environmental conditions. However, only a few reports have reported the regulatory mechanism of this complex crosstalk. Based on the emerging evidence, this review elaborates on the existing links between circadian and AS in response to abiotic stresses, suggesting an uncovered regulatory network among circadian, AS, and abiotic stresses. Therefore, the rhythmically expressed splicing factors and core clock oscillators fill the role of temporal regulators participating in improving plant growth, development, and increasing plant tolerance against abiotic stresses.
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Affiliation(s)
- Tao Fan
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, China
- Co-Innovation Center for Sustainable Forestry in Southern China & Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Mehtab Muhammad Aslam
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Jian-Li Zhou
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, China
| | - Mo-Xian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China & Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Shenxiu Du
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kai-Lu Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China & Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yun-Sheng Chen
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, China
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22
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Bonnot T, Gillard MB, Nagel DH. CAST-R: An application to visualize circadian and heat stress-responsive genes in plants. PLANT PHYSIOLOGY 2022; 190:994-1004. [PMID: 35294034 PMCID: PMC9516734 DOI: 10.1093/plphys/kiac121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/21/2022] [Indexed: 05/08/2023]
Abstract
The circadian clock helps organisms to anticipate and coordinate gene regulatory responses to changes in environmental stimuli. Under stresses, both time of day and the circadian clock closely control the magnitude of plant responses. The identification of clock-regulated genes is, therefore, important when studying the influence of environmental factors. Here, we present CAST-R (Circadian And heat STress-Responsive), a "Shiny" application that allows users to identify and visualize circadian and heat stress-responsive genes in plants. More specifically, users can generate and export profiles and heatmaps representing transcript abundance of a single or of multiple Arabidopsis (Arabidopsis thaliana) genes over a 24-h time course, in response to heat stress and during recovery following the stress. The application also takes advantage of published Arabidopsis chromatin immunoprecipitation-sequencing datasets to visualize the connections between clock proteins and their targets in an interactive network. In addition, CAST-R offers the possibility to perform phase (i.e. timing of expression) enrichment analyses for rhythmic datasets from any species, within and beyond plants. This functionality combines statistical analyses and graphical representations to identify significantly over- and underrepresented phases within a subset of genes. Lastly, profiles of transcript abundance can be visualized from multiple circadian datasets generated in Arabidopsis, Brassica rapa, barley (Hordeum vulgare), and rice (Oryza sativa). In summary, CAST-R is a user-friendly interface that allows the rapid identification of circadian and stress-responsive genes through multiple modules of visualization. We anticipate that this tool will make it easier for users to obtain temporal and dynamic information on genes of interest that links plant responses to environmental signals.
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Perfluorobutanoic Acid (PFBA) Induces a Non-Enzymatic Oxidative Stress Response in Soybean (Glycine max L. Merr.). Int J Mol Sci 2022; 23:ijms23179934. [PMID: 36077331 PMCID: PMC9456126 DOI: 10.3390/ijms23179934] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/24/2022] [Accepted: 08/27/2022] [Indexed: 11/20/2022] Open
Abstract
Short-chain perfluoroalkyl substances (PFAS) are generally considered to be of less environmental concern than long-chain analogues due to their comparatively shorter half-lives in biological systems. Perfluorobutanoic acid (PFBA) is a short-chain PFAS with the most root–shoot transfer factor of all PFAS. We investigated the impact of extended exposure of soybean plants to irrigation water containing environmentally relevant (100 pg–100 ng/L) to high (100 µg–1 mg/L) concentrations of PFBA using phenotypical observation, biochemical characterization, and transcriptomic analysis. The results showed a non-monotonous developmental response from the plants, with maximum stimulation and inhibition at 100 ng/L and 1 mg/L, respectively. Higher reactive oxygen species and low levels of superoxide dismutase (SOD) and catalase (CAT) activity were observed in all treatment groups. However transcriptomic analysis did not demonstrate differential expression of SOD and CAT coding genes, whereas non-enzymatic response genes and pathways were enriched in both groups (100 ng/L and 1 mg/L) with glycine betaine dehydrogenase showing the highest expression. About 18% of similarly downregulated genes in both groups are involved in the ethylene signaling pathway. The circadian rhythm pathway was the only differentially regulated pathway between both groups. We conclude that, similar to long chain PFAS, PFBA induced stress in soybean plants and that the observed hormetic stimulation at 100 ng/L represents an overcompensation response, via the circadian rhythm pathway, to the induced stress.
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Ntambiyukuri A, Li X, Xiao D, Wang A, Zhan J, He L. Circadian Rhythm Regulates Reactive Oxygen Species Production and Inhibits Al-Induced Programmed Cell Death in Peanut. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081271. [PMID: 36013450 PMCID: PMC9410085 DOI: 10.3390/life12081271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/17/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022]
Abstract
Peanut is among the most important oil crops in the world. In the southern part of China, peanut is highly produced; however, the arable land is acidic. In acidic soils, aluminum (Al) inhibits plant growth and development by changing the properties of the cell wall and causing the disorder of the intracellular metabolic process. Circadian rhythm is an internal mechanism that occurs about every 24 h and enables plants to maintain internal biological processes with a daily cycle. To investigate the effect of photoperiod and Al stress on the Al-induced programmed cell death (PCD), two peanut varieties were treated with 100 μM AlCl3 under three photoperiodic conditions (8/16, SD; 12/12, ND; 16/8 h, LD). The results show that Al toxicity was higher in ZH2 than in 99-1507 and higher under LD than under SD. Root length decreased by 30, 37.5, and 50% in ZH2 and decreased by 26.08, 34.78, and 47.82% in 99-1507 under SD, ND, and LD, respectively, under Al stress. Photoperiod and Al induced cell death and ROS production. MDA content, PME activity, and LOX activity increased under SD, ND, and LD, respectively, under Al stress both in ZH2 and 99-1507. APX, SOD, CAT, and POD activities were higher under SD, ND, and LD, respectively. Al stress increased the level of AhLHY expression under SD and ND but decreased it under LD in both ZH2 and 99-1507. Contrastingly, AhSTS expression levels increased exponentially and were higher under SD, LD, and ND, respectively, under Al stress. Our results will be a useful platform to research PCD induced by Al and gain new insights into the genetic manipulation of the circadian clock for plant stress response.
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Affiliation(s)
- Aaron Ntambiyukuri
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Xia Li
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Dong Xiao
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning 530004, China
- Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Nanning 530004, China
- Correspondence: (D.X.); (L.H.)
| | - Aiqin Wang
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning 530004, China
- Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Nanning 530004, China
| | - Jie Zhan
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning 530004, China
- Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Nanning 530004, China
| | - Longfei He
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning 530004, China
- Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Nanning 530004, China
- Correspondence: (D.X.); (L.H.)
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25
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Blair EJ, Goralogia GS, Lincoln MJ, Imaizumi T, Nagel DH. Clock-Controlled and Cold-Induced CYCLING DOF FACTOR6 Alters Growth and Development in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:919676. [PMID: 35958204 PMCID: PMC9361860 DOI: 10.3389/fpls.2022.919676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
The circadian clock represents a critical regulatory network, which allows plants to anticipate environmental changes as inputs and promote plant survival by regulating various physiological outputs. Here, we examine the function of the clock-regulated transcription factor, CYCLING DOF FACTOR 6 (CDF6), during cold stress in Arabidopsis thaliana. We found that the clock gates CDF6 transcript accumulation in the vasculature during cold stress. CDF6 mis-expression results in an altered flowering phenotype during both ambient and cold stress. A genome-wide transcriptome analysis links CDF6 to genes associated with flowering and seed germination during cold and ambient temperatures, respectively. Analysis of key floral regulators indicates that CDF6 alters flowering during cold stress by repressing photoperiodic flowering components, FLOWERING LOCUS T (FT), CONSTANS (CO), and BROTHER OF FT (BFT). Gene ontology enrichment further suggests that CDF6 regulates circadian and developmental-associated genes. These results provide insights into how the clock-controlled CDF6 modulates plant development during moderate cold stress.
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Affiliation(s)
- Emily J. Blair
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Greg S. Goralogia
- Department of Biology, University of Washington, Seattle, WA, United States
| | - Matthew J. Lincoln
- Department of Biology, University of Washington, Seattle, WA, United States
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, WA, United States
| | - Dawn H. Nagel
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
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26
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Song Y, Zhang R, Gao S, Pan Z, Guo Z, Yu S, Wang Y, Jin Q, Chen X, Zhang L. Transcriptome analysis and phenotyping of walnut seedling roots under nitrogen stresses. Sci Rep 2022; 12:12066. [PMID: 35835799 PMCID: PMC9283388 DOI: 10.1038/s41598-022-14850-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 05/03/2022] [Indexed: 11/15/2022] Open
Abstract
Nitrogen is an essential core element in walnut seedling growth and development. However, nitrogen starvation and excessive nitrogen stress can cause stunted growth and development of walnut seedlings, and environmental pollution is also of concern. Therefore, it is necessary to study the mechanism of walnut seedling resistance to nitrogen stress. In this study, morphological and physiological observations and transcriptome sequencing of walnut seedlings under nitrogen starvation and excess nitrogen stress were performed. The results showed that walnut seedlings under nitrogen starvation and excess stress could adapt to the changes in the nitrogen environment by changing the coordination of their root morphology and physiological indexes. Based on an analysis of transcriptome data, 4911 differential genes (DEGs) were obtained (2180 were upregulated and 2731 were downregulated) in a comparison of nitrogen starvation and control groups. A total of 9497 DEGs (5091 upregulated and 4406 downregulated) were obtained in the comparison between the nitrogen overdose and control groups. When these DEGs were analysed, the differential genes in both groups were found to be significantly enriched in the plant’s circadian pathway. Therefore, we selected the circadian rhythm as the focus for further analysis. We made some discoveries by analysing the gene co-expression network of nitrogen metabolism, circadian rhythm, and hormone signal transduction. (a) Nitrite nitrogen (NO2−) or Glu may act as a nitrogen signal to the circadian clock. (b) Nitrogen signalling may be input into the circadian clock by regulating changes in the abundance of the CRY1 gene. (c) After the nitrogen signal enters the circadian clock, the expression of the LHY gene is upregulated, which causes a phase shift in the circadian clock. (d) The RVE protein may send information about the circadian clock’s response to nitrogen stress back to the nitrogen metabolic pathway via the hormone transduction pathway. In conclusion, various metabolic pathways in the roots of walnut seedlings coordinated with one another to resist the ill effects of nitrogen stress on the root cells, and these coordination relationships were regulated by the circadian clock. This study is expected to provide valuable information on the circadian clock regulation of plant resistance to nitrogen stress.
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Affiliation(s)
- Yan Song
- College of Plant Sciences, Tarim University, Alar, 843300, China.,National and Local Joint Engineering Laboratory for High-Efficiency and Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, Alar, 843300, China.,Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar, 843300, China
| | - Rui Zhang
- College of Plant Sciences, Tarim University, Alar, 843300, China. .,National and Local Joint Engineering Laboratory for High-Efficiency and Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, Alar, 843300, China. .,Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar, 843300, China.
| | - Shan Gao
- College of Plant Sciences, Tarim University, Alar, 843300, China.
| | - Zhiyong Pan
- College of Plant Sciences, Tarim University, Alar, 843300, China
| | - Zhongzhong Guo
- National and Local Joint Engineering Laboratory for High-Efficiency and Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, Alar, 843300, China.,Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar, 843300, China.,College of Life Sciences, Tarim University, Alar, 843300, China
| | - Shangqi Yu
- National and Local Joint Engineering Laboratory for High-Efficiency and Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, Alar, 843300, China.,Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar, 843300, China.,College of Life Sciences, Tarim University, Alar, 843300, China
| | - Yu Wang
- National and Local Joint Engineering Laboratory for High-Efficiency and Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, Alar, 843300, China.,Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar, 843300, China.,College of Life Sciences, Tarim University, Alar, 843300, China
| | - Qiang Jin
- College of Plant Sciences, Tarim University, Alar, 843300, China.,National and Local Joint Engineering Laboratory for High-Efficiency and Quality Cultivation and Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, Alar, 843300, China
| | - Xiaofei Chen
- College of Plant Sciences, Tarim University, Alar, 843300, China
| | - Lei Zhang
- College of Plant Sciences, Tarim University, Alar, 843300, China
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27
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Balogh E, Kalapos B, Ahres M, Boldizsár Á, Gierczik K, Gulyás Z, Gyugos M, Szalai G, Novák A, Kocsy G. Far-Red Light Coordinates the Diurnal Changes in the Transcripts Related to Nitrate Reduction, Glutathione Metabolism and Antioxidant Enzymes in Barley. Int J Mol Sci 2022; 23:ijms23137479. [PMID: 35806480 PMCID: PMC9267158 DOI: 10.3390/ijms23137479] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 11/16/2022] Open
Abstract
Spectral quality, intensity and period of light modify many regulatory and stress signaling pathways in plants. Both nitrate and sulfate assimilations must be synchronized with photosynthesis, which ensures energy and reductants for these pathways. However, photosynthesis is also a source of reactive oxygen species, whose levels are controlled by glutathione and other antioxidants. In this study, we investigated the effect of supplemental far-red (735 nm) and blue (450 nm) lights on the diurnal expression of the genes related to photoreceptors, the circadian clock, nitrate reduction, glutathione metabolism and various antioxidants in barley. The maximum expression of the investigated four photoreceptor and three clock-associated genes during the light period was followed by the peaking of the transcripts of the three redox-responsive transcription factors during the dark phase, while most of the nitrate and sulfate reduction, glutathione metabolism and antioxidant-enzyme-related genes exhibited high expression during light exposure in plants grown in light/dark cycles for two days. These oscillations changed or disappeared in constant white light during the subsequent two days. Supplemental far-red light induced the activation of most of the studied genes, while supplemental blue light did not affect or inhibited them during light/dark cycles. However, in constant light, several genes exhibited greater expression in blue light than in white and far-red lights. Based on a correlation analysis of the gene expression data, we propose a major role of far-red light in the coordinated transcriptional adjustment of nitrate reduction, glutathione metabolism and antioxidant enzymes to changes of the light spectrum.
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28
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Rhodes BM, Siddiqui H, Khan S, Devlin PF. Dual Role for FHY3 in Light Input to the Clock. FRONTIERS IN PLANT SCIENCE 2022; 13:862387. [PMID: 35755710 PMCID: PMC9218818 DOI: 10.3389/fpls.2022.862387] [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: 01/25/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
The red-light regulated transcription factors FHY3 and FAR1 form a key point of light input to the plant circadian clock in positively regulating expression of genes within the central clock. However, the fhy3 mutant shows an additional red light-specific disruption of rhythmicity which is inconsistent with this role. Here we demonstrate that only fhy3 and not far1 mutants show this red specific disruption of rhythmicity. We examined the differences in rhythmic transcriptome in red versus white light and reveal differences in patterns of rhythmicity among the central clock proteins suggestive of a change in emphasis within the central mechanism of the clock, changes which underlie the red specificity of the fhy3 mutant. In particular, changes in enrichment of promoter elements were consistent with a key role for the HY5 transcription factor, a known integrator of the ratio of red to blue light in regulation of the clock. Examination of differences in the rhythmic transcriptome in the fhy3 mutant in red light identified specific disruption of the CCA1-regulated ELF3 and LUX central clock genes, while the CCA1 target TBS element, TGGGCC, was enriched among genes that became arrhythmic. Coupled with the known interaction of FHY3 but not FAR1 with CCA1 we propose that the red-specific circadian phenotype of fhy3 may involve disruption of the previously demonstrated moderation of CCA1 activity by FHY3 rather than a disruption of its own transcriptional regulatory activity. Together, this evidence suggests a conditional redundancy between FHY3 and HY5 in the integration of red and blue light input to the clock in order to enable a plasticity in response to light and optimise plant adaptation. Furthermore, our evidence also suggests changes in CCA1 activity between red and white light transcriptomes. This, together with the documented interaction of HY5 with CCA1, leads us to propose a model whereby this integration of red and blue signals may at least partly occur via direct FHY3 and HY5 interaction with CCA1 leading to moderation of CCA1 activity.
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Affiliation(s)
| | | | | | - Paul F. Devlin
- Department of Biological Sciences, Royal Holloway, University of London, Egham, United Kingdom
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29
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Phan KAT, Paeng SK, Chae HB, Park JH, Lee ES, Wi SD, Bae SB, Kim MG, Yun D, Kim W, Lee SY. Universal Stress Protein (
USP
) regulates the circadian rhythm of central oscillator genes in
Arabidopsis. FEBS Lett 2022; 596:1871-1880. [DOI: 10.1002/1873-3468.14410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/18/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Kieu Anh Thi Phan
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | - Seol Ki Paeng
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | - Ho Byoung Chae
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | - Joung Hun Park
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | - Eun Seon Lee
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | - Seong Dong Wi
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | - Su Bin Bae
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | | | - Dae‐Jin Yun
- Department of Biomedical Science & Engineering Konkuk University Seoul, 05029 Korea
| | - Woe‐Yeon Kim
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
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30
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Yi F, Huo M, Li J, Yu J. Time-series transcriptomics reveals a drought-responsive temporal network and crosstalk between drought stress and the circadian clock in foxtail millet. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1213-1228. [PMID: 35262997 DOI: 10.1111/tpj.15725] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 02/23/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Drought stress is a serious factor affecting crop growth and production worldwide. The circadian clock has been identified as key to improving regional adaptability of plants. However, our understanding of the contribution of the circadian clock to drought response and the impacts of drought stress on the circadian clock in plants is still limited. To explore the interactions between the circadian clock and drought stress, foxtail millet seedlings were treated with simulated drought (20% polyethylene glycol-6000) treatment starting at the day (DD) onset zeitgeber time 0 (ZT0, lights on) and at the night (DN) onset zeitgeber time 16 (ZT16, lights off). A high temporal-resolution transcriptomic investigation was performed using DD and DN samples collected at intervals of 2 or 4 h within a 24-h drought-treatment period. Overall, we identified 13 294 drought-responsive genes (DRGs). Among these DRGs, 7931 were common between DD and DN samples, 2638 were specific to DD, and 2725 were specific to DN. Additionally, we identified 1257 circadian genes, of which 67% were DRGs. Interestingly, with drought treatment starting at the day for 8, 12 or 16 h, the circadian phase shifted to 12 h. We also found that the circadian clock led to different day and night drought-responsive pathways. The identification of DRG_Clock (DRG and circadian clock) and DRG_NonClock (DRG and not circadian clock) genes provides a reference for selecting candidate drought resistance genes. Our work reveals the temporal drought-response process and crosstalk between drought stress and the circadian clock in foxtail millet.
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Affiliation(s)
- Fei Yi
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Mingyue Huo
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jianrui Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Jingjuan Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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31
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Mishra M, Rathore RS, Joshi R, Pareek A, Singla-Pareek SL. DTH8 overexpression induces early flowering, boosts yield, and improves stress recovery in rice cv IR64. PHYSIOLOGIA PLANTARUM 2022; 174:e13691. [PMID: 35575899 DOI: 10.1111/ppl.13691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/17/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Rice yield and heading date are the two discrete traits controlled by quantitative trait loci (QTLs). Both traits are influenced by the genetic make-up of the plant as well as the environmental factors where it thrives. Drought and salinity adversely affect crop productivity in many parts of the world. Tolerance to these stresses is multigenic and complex in nature. In this study, we have characterized a QTL, DTH8 (days to heading) from Oryza sativa L. cv IR64 that encodes a putative HAP3/NF-YB/CBF subunit of CCAAT-box binding protein (HAP complex). We demonstrate DTH8 to be positively influencing the yield, heading date, and stress tolerance in IR64. DTH8 up-regulates the transcription of RFT1, Hd3a, GHD7, MOC1, and RCN1 in IR64 at the pre-flowering stage and plays a role in early flowering, increased number of tillers, enhanced panicle branching, and improved tolerance towards drought and salinity stress at the reproductive stage. The presence of DTH8 binding elements (CCAAT) in the promoter regions of all of these genes, predicted by in silico analysis of the promoter region, indicates the regulation of their expression by DTH8. In addition, DTH8 overexpressing transgenic lines showed favorable physiological parameters causing less yield penalty under stress than the WT plants. Taken together, DTH8 is a positive regulator of the network of genes related to early flowering/heading, higher yield, as well as salinity and drought stress tolerance, thus, enabling the crops to adapt to a wide range of climatic conditions.
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Affiliation(s)
- Manjari Mishra
- Plant Stress Biology, International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ray Singh Rathore
- Plant Stress Biology, International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - Rohit Joshi
- Plant Stress Biology, International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology, International Center for Genetic Engineering and Biotechnology, New Delhi, India
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32
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Dias MC, Caldeira C, Gastauer M, Ramos S, Oliveira G. Cross-species transcriptomes reveal species-specific and shared molecular adaptations for plants development on iron-rich rocky outcrops soils. BMC Genomics 2022; 23:313. [PMID: 35439930 PMCID: PMC9020022 DOI: 10.1186/s12864-022-08449-0] [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: 09/22/2021] [Accepted: 02/23/2022] [Indexed: 12/13/2022] Open
Abstract
Background Canga is the Brazilian term for the savanna-like vegetation harboring several endemic species on iron-rich rocky outcrops, usually considered for mining activities. Parkia platycephala Benth. and Stryphnodendron pulcherrimum (Willd.) Hochr. naturally occur in the cangas of Serra dos Carajás (eastern Amazonia, Brazil) and the surrounding forest, indicating high phenotypic plasticity. The morphological and physiological mechanisms of the plants’ establishment in the canga environment are well studied, but the molecular adaptative responses are still unknown. To understand these adaptative responses, we aimed to identify molecular mechanisms that allow the establishment of these plants in the canga environment. Results Plants were grown in canga and forest substrates collected in the Carajás Mineral Province. RNA was extracted from pooled leaf tissue, and RNA-seq paired-end reads were assembled into representative transcriptomes for P. platycephala and S. pulcherrimum containing 31,728 and 31,311 primary transcripts, respectively. We identified both species-specific and core molecular responses in plants grown in the canga substrate using differential expression analyses. In the species-specific analysis, we identified 1,112 and 838 differentially expressed genes for P. platycephala and S. pulcherrimum, respectively. Enrichment analyses showed that unique biological processes and metabolic pathways were affected for each species. Comparative differential expression analysis was based on shared single-copy orthologs. The overall pattern of ortholog expression was species-specific. Even so, we identified almost 300 altered genes between plants in canga and forest substrates with conserved responses in the two species. The genes were functionally associated with the response to light stimulus and the circadian rhythm pathway. Conclusions Plants possess species-specific adaptative responses to cope with the substrates. Our results also suggest that plants adapted to both canga and forest environments can adjust the circadian rhythm in a substrate-dependent manner. The circadian clock gene modulation might be a central mechanism regulating the plants’ development in the canga substrate in the studied legume species. The mechanism may be shared as a common mechanism to abiotic stress compensation in other native species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08449-0.
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Affiliation(s)
- Mariana Costa Dias
- Instituto Tecnológico Vale, Rua Boaventura da Silva 955, Belém, Pará, CEP 66055-090, Brazil.,Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, Minas Gerais, CEP 31270-901, Brazil
| | - Cecílio Caldeira
- Instituto Tecnológico Vale, Rua Boaventura da Silva 955, Belém, Pará, CEP 66055-090, Brazil
| | - Markus Gastauer
- Instituto Tecnológico Vale, Rua Boaventura da Silva 955, Belém, Pará, CEP 66055-090, Brazil
| | - Silvio Ramos
- Instituto Tecnológico Vale, Rua Boaventura da Silva 955, Belém, Pará, CEP 66055-090, Brazil
| | - Guilherme Oliveira
- Instituto Tecnológico Vale, Rua Boaventura da Silva 955, Belém, Pará, CEP 66055-090, Brazil.
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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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Regulatory Role of Circadian Clocks on ABA Production and Signaling, Stomatal Responses, and Water-Use Efficiency under Water-Deficit Conditions. Cells 2022; 11:cells11071154. [PMID: 35406719 PMCID: PMC8997731 DOI: 10.3390/cells11071154] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/15/2022] [Accepted: 03/25/2022] [Indexed: 02/04/2023] Open
Abstract
Plants deploy molecular, physiological, and anatomical adaptations to cope with long-term water-deficit exposure, and some of these processes are controlled by circadian clocks. Circadian clocks are endogenous timekeepers that autonomously modulate biological systems over the course of the day–night cycle. Plants’ responses to water deficiency vary with the time of the day. Opening and closing of stomata, which control water loss from plants, have diurnal responses based on the humidity level in the rhizosphere and the air surrounding the leaves. Abscisic acid (ABA), the main phytohormone modulating the stomatal response to water availability, is regulated by circadian clocks. The molecular mechanism of the plant’s circadian clock for regulating stress responses is composed not only of transcriptional but also posttranscriptional regulatory networks. Despite the importance of regulatory impact of circadian clock systems on ABA production and signaling, which is reflected in stomatal responses and as a consequence influences the drought tolerance response of the plants, the interrelationship between circadian clock, ABA homeostasis, and signaling and water-deficit responses has to date not been clearly described. In this review, we hypothesized that the circadian clock through ABA directs plants to modulate their responses and feedback mechanisms to ensure survival and to enhance their fitness under drought conditions. Different regulatory pathways and challenges in circadian-based rhythms and the possible adaptive advantage through them are also discussed.
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Xu X, Yuan L, Xie Q. The circadian clock ticks in plant stress responses. STRESS BIOLOGY 2022; 2:15. [PMID: 37676516 PMCID: PMC10441891 DOI: 10.1007/s44154-022-00040-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/15/2022] [Indexed: 09/08/2023]
Abstract
The circadian clock, a time-keeping mechanism, drives nearly 24-h self-sustaining rhythms at the physiological, cellular, and molecular levels, keeping them synchronized with the cyclic changes of environmental signals. The plant clock is sensitive to external and internal stress signals that act as timing cues to influence the circadian rhythms through input pathways of the circadian clock system. In order to cope with environmental stresses, many core oscillators are involved in defense while maintaining daily growth in various ways. Recent studies have shown that a hierarchical multi-oscillator network orchestrates the defense through rhythmic accumulation of gene transcripts, alternative splicing of mRNA precursors, modification and turnover of proteins, subcellular localization, stimuli-induced phase separation, and long-distance transport of proteins. This review summarizes the essential role of circadian core oscillators in response to stresses in Arabidopsis thaliana and crops, including daily and seasonal abiotic stresses (low or high temperature, drought, high salinity, and nutrition deficiency) and biotic stresses (pathogens and herbivorous insects). By integrating time-keeping mechanisms, circadian rhythms and stress resistance, we provide a temporal perspective for scientists to better understand plant environmental adaptation and breed high-quality crop germplasm for agricultural production.
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Affiliation(s)
- Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
| | - Li Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
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Osuman AS, Badu-Apraku B, Karikari B, Ifie BE, Tongoona P, Danquah EY. Genome-Wide Association Study Reveals Genetic Architecture and Candidate Genes for Yield and Related Traits under Terminal Drought, Combined Heat and Drought in Tropical Maize Germplasm. Genes (Basel) 2022; 13:genes13020349. [PMID: 35205393 PMCID: PMC8871853 DOI: 10.3390/genes13020349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 11/19/2022] Open
Abstract
Maize (Zea mays L.) production is constrained by drought and heat stresses. The combination of these two stresses is likely to be more detrimental. To breed for maize cultivars tolerant of these stresses, 162 tropical maize inbred lines were evaluated under combined heat and drought (CHD) and terminal drought (TD) conditions. The mixed linear model was employed for the genome-wide association study using 7834 SNP markers and several phenotypic data including, days to 50% anthesis (AD) and silking (SD), husk cover (HUSKC), and grain yield (GY). In total, 66, 27, and 24 SNPs were associated with the traits evaluated under CHD, TD, and their combined effects, respectively. Of these, four single nucleotide polymorphism (SNP) markers (SNP_161703060 on Chr01, SNP_196800695 on Chr02, SNP_195454836 on Chr05, and SNP_51772182 on Chr07) had pleiotropic effects on both AD and SD under CHD conditions. Four SNPs (SNP_138825271 (Chr03), SNP_244895453 (Chr04), SNP_168561609 (Chr05), and SNP_62970998 (Chr06)) were associated with AD, SD, and HUSKC under TD. Twelve candidate genes containing phytohormone cis-acting regulating elements were implicated in the regulation of plant responses to multiple stress conditions including heat and drought. The SNPs and candidate genes identified in the study will provide invaluable information for breeding climate smart maize varieties under tropical conditions following validation of the SNP markers.
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Affiliation(s)
- Alimatu Sadia Osuman
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, PMB 30 Legon, Accra 00223, Ghana; (A.S.O.); (B.E.I.); (P.T.); (E.Y.D.)
- International Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan 200001, Nigeria
- Crops Research Institute, P.O. Box 3785, Kumasi 00223, Ghana
| | - Baffour Badu-Apraku
- International Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan 200001, Nigeria
- Correspondence: ; Tel.: +234-810-848-2590
| | - Benjamin Karikari
- Department of Crop Science, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, P.O. Box TL 1882, Tamale 00223, Ghana;
| | - Beatrice Elohor Ifie
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, PMB 30 Legon, Accra 00223, Ghana; (A.S.O.); (B.E.I.); (P.T.); (E.Y.D.)
| | - Pangirayi Tongoona
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, PMB 30 Legon, Accra 00223, Ghana; (A.S.O.); (B.E.I.); (P.T.); (E.Y.D.)
| | - Eric Yirenkyi Danquah
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, PMB 30 Legon, Accra 00223, Ghana; (A.S.O.); (B.E.I.); (P.T.); (E.Y.D.)
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Samuels LJ, Setati ME, Blancquaert EH. Towards a Better Understanding of the Potential Benefits of Seaweed Based Biostimulants in Vitis vinifera L. Cultivars. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030348. [PMID: 35161328 PMCID: PMC8839555 DOI: 10.3390/plants11030348] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 05/03/2023]
Abstract
Globally, 7.4 million hectares of arable land is planted with grapevine with a farm gate value of $68.3 billion. The production of grapes faces growing pressure associated with challenges such as climate change, diminishing resources as well as the overuse of chemical fertilizers and synthetic pesticides, which have an impact on sustainability. Consequently, viticulture has over the years embraced and implemented various practices such integrated pest management, organic and biodynamic farming to curb the high chemical inputs typically used in conventional farming. Biostimulants and biofertilizers are considered environmentally friendly and cost-effective alternatives to synthetic fertilizers and plant growth regulators. Seaweed is of particular interest because of its availability globally. It was reported that brown seaweed (Ascophyllum spp.) improves plant growth and agricultural productivity, hormonal signalling, and an improved secondary plant metabolism. It also provides an alternative to soil supplementation, avoiding some of the negative effects of fertilizers through the leaching of nutrients into groundwater sources. This review aims to provide a summary of the use of seaweed extracts in grape production and their influence on grapevine physiology and stress adaptation mechanisms.
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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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Bonnot T, Blair EJ, Cordingley SJ, Nagel DH. Circadian coordination of cellular processes and abiotic stress responses. CURRENT OPINION IN PLANT BIOLOGY 2021; 64:102133. [PMID: 34773857 DOI: 10.1016/j.pbi.2021.102133] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Diel changes in the environment are perceived by the circadian clock which transmits temporal information throughout the plant cell to synchronize daily and seasonal environmental signals with internal biological processes. Dynamic modulations of diverse levels of clock gene regulation within the plant cell are impacted by stress. Recent insights into circadian control of cellular processes such as alternative splicing, polyadenylation, and noncoding RNAs are discussed. We highlight studies on the circadian regulation of reactive oxygen species, calcium signaling, and gating of temperature stress responses. Finally, we briefly summarize recent work on the translation-specific rhythmicity of cell cycle genes and the control of subcellular localization and relocalization of oscillator components. Together, this mini-review highlights these cellular events in the context of clock gene regulation and stress responses in Arabidopsis.
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Affiliation(s)
- Titouan Bonnot
- University of California, Riverside, Department of Botany and Plant Sciences, Riverside, CA 92507, USA
| | - Emily J Blair
- University of California, Riverside, Department of Botany and Plant Sciences, Riverside, CA 92507, USA
| | - Samantha J Cordingley
- University of California, Riverside, Department of Botany and Plant Sciences, Riverside, CA 92507, USA
| | - Dawn H Nagel
- University of California, Riverside, Department of Botany and Plant Sciences, Riverside, CA 92507, USA.
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Geldhof B, Pattyn J, Eyland D, Carpentier S, Van de Poel B. A digital sensor to measure real-time leaf movements and detect abiotic stress in plants. PLANT PHYSIOLOGY 2021; 187:1131-1148. [PMID: 34618089 PMCID: PMC8566216 DOI: 10.1093/plphys/kiab407] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/02/2021] [Indexed: 05/31/2023]
Abstract
Plant and plant organ movements are the result of a complex integration of endogenous growth and developmental responses, partially controlled by the circadian clock, and external environmental cues. Monitoring of plant motion is typically done by image-based phenotyping techniques with the aid of computer vision algorithms. Here we present a method to measure leaf movements using a digital inertial measurement unit (IMU) sensor. The lightweight sensor is easily attachable to a leaf or plant organ and records angular traits in real-time for two dimensions (pitch and roll) with high resolution (measured sensor oscillations of 0.36 ± 0.53° for pitch and 0.50 ± 0.65° for roll). We were able to record simple movements such as petiole bending, as well as complex lamina motions, in several crops, ranging from tomato to banana. We also assessed growth responses in terms of lettuce rosette expansion and maize seedling stem movements. The IMU sensors are capable of detecting small changes of nutations (i.e. bending movements) in leaves of different ages and in different plant species. In addition, the sensor system can also monitor stress-induced leaf movements. We observed that unfavorable environmental conditions evoke certain leaf movements, such as drastic epinastic responses, as well as subtle fading of the amplitude of nutations. In summary, the presented digital sensor system enables continuous detection of a variety of leaf motions with high precision, and is a low-cost tool in the field of plant phenotyping, with potential applications in early stress detection.
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Affiliation(s)
- Batist Geldhof
- Department of Biosystems, Division of Crop Biotechnics, Molecular Plant Hormone Physiology Lab, University of Leuven, Leuven 3001, Belgium
| | - Jolien Pattyn
- Department of Biosystems, Division of Crop Biotechnics, Molecular Plant Hormone Physiology Lab, University of Leuven, Leuven 3001, Belgium
| | - David Eyland
- Department of Biosystems, Division of Crop Biotechnics, Tropical Crop Improvement Laboratory, University of Leuven, Leuven 3001, Belgium
| | - Sebastien Carpentier
- Department of Biosystems, Division of Crop Biotechnics, Tropical Crop Improvement Laboratory, University of Leuven, Leuven 3001, Belgium
- Bioversity International, Leuven, 3001, Belgium
| | - Bram Van de Poel
- Department of Biosystems, Division of Crop Biotechnics, Molecular Plant Hormone Physiology Lab, University of Leuven, Leuven 3001, Belgium
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Hayes T, López-Martínez G. Resistance and survival to extreme heat shows circadian and sex-specific patterns in A cavity nesting bee. CURRENT RESEARCH IN INSECT SCIENCE 2021; 1:100020. [PMID: 36003599 PMCID: PMC9387514 DOI: 10.1016/j.cris.2021.100020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 06/14/2023]
Abstract
The pollination services provided by insects have been a crucial part of evolution and survival for many species, including humans. For bees to be efficient pollinators they must survive the environmental insults they face daily. Thus, looking into the short- and long-term effects of heat exposure on bee performance provides us with a foundation for investigating how stress can affect insect pollination. Solitary bees are a great model for investigating the effects of environmental stress on pollinators because the vast majority of insect pollinator species are solitary rather than social. One of the most pervasive environmental stressors to insects is temperature. Here we investigated how a one-hour heat shock affected multiple metrics of performance in the alfalfa leafcutting bee, Megachile rotundata. We found that a short heat shock (1hr at 45°C) can delay adult emergence in males but not females. Bee pupae were rather resilient to a range of high temperature exposures that larvae did not survive. Following heat shock (1hr at 50°C), adult bees were drastically less active than untreated bees, and this reduction in activity was evident over several days. Heat shock also led to a decrease in bee survival and longevity. Additionally, we found a connection between starvation survival after heat shock and time of exposure, where bees exposed in the morning survived longer than those exposed in the afternoon, when they would normally experience heat shock in the field. These data suggest that there is an unexplored daily/circadian component to the stress response in bees likely similar to that seen in flies, nematodes, and plants which is constitutive or preemptive rather than restorative. Taken together our data indicate that single heat shock events have strong potential to negatively impact multiple life history traits correlated with reproduction and fitness.
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Affiliation(s)
- Tayia Hayes
- Department of Natural Sciences and Environmental Health, Mississippi Valley State University, Itta Bena, MS 38941
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Wang X, He Y, Wei H, Wang L. A clock regulatory module is required for salt tolerance and control of heading date in rice. PLANT, CELL & ENVIRONMENT 2021; 44:3283-3301. [PMID: 34402093 DOI: 10.1111/pce.14167] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/23/2021] [Accepted: 08/10/2021] [Indexed: 05/23/2023]
Abstract
The circadian clock plays multiple roles in plant stress responses and developmental transition phases. Nevertheless, the underlying molecular mechanisms and individual clock components that coordinately regulate important agronomic traits of rice such as salt tolerance and heading date remain to be elucidated. Here, we identify a rice ternary repressive protein complex composed of OsELF4a, OsELF3-1 and OsLUX, which was designated as OsEC1 in analogy to a similar complex in Arabidopsis. OsELF4a physically interacts with OsELF3-1 and OsELF3-2 in nucleus, whilst OsELF3-1 rather than OsELF3-2 strongly interacts with OsLUX, a Myb-domain containing transcriptional factor. Phenotypic analyses show a role for this complex in heading and salt tolerance. The loss-of-function mutants of OsEC1 exhibit lower survival rate under salt stress and late heading date. Transcriptomic profiling together with biochemical assays identified the GIGANTEA homologue OsGI as a direct transcriptional target of OsEC1. Notably, the osgi-101 mutant, generated by CRISPR/Cas9, is salt tolerant and exhibits early heading date in long day conditions. Together, our findings characterized a transcriptional module in rice composed by the OsEC1 repressing OsGI, which links the circadian clock with salt tolerance and control of heading date.
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Affiliation(s)
- Xiling Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuqing He
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hua Wei
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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Yang M, Han X, Yang J, Jiang Y, Hu Y. The Arabidopsis circadian clock protein PRR5 interacts with and stimulates ABI5 to modulate abscisic acid signaling during seed germination. THE PLANT CELL 2021; 33:3022-3041. [PMID: 34152411 PMCID: PMC8462813 DOI: 10.1093/plcell/koab168] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/17/2021] [Indexed: 05/03/2023]
Abstract
Seed germination and postgerminative growth require the precise coordination of multiple intrinsic and environmental signals. The phytohormone abscisic acid (ABA) suppresses these processes in Arabidopsis thaliana and the circadian clock contributes to the regulation of ABA signaling. However, the molecular mechanism underlying circadian clock-mediated ABA signaling remains largely unknown. Here, we found that the core circadian clock proteins PSEUDO-RESPONSE REGULATOR5 (PRR5) and PRR7 physically associate with ABSCISIC ACID-INSENSITIVE5 (ABI5), a crucial transcription factor of ABA signaling. PRR5 and PRR7 positively modulate ABA signaling redundantly during seed germination. Disrupting PRR5 and PRR7 simultaneously rendered germinating seeds hyposensitive to ABA, whereas the overexpression of PRR5 enhanced ABA signaling to inhibit seed germination. Consistent with this, the expression of several ABA-responsive genes is upregulated by PRR proteins. Genetic analysis demonstrated that PRR5 promotes ABA signaling mainly dependently on ABI5. Further mechanistic investigation revealed that PRR5 stimulates the transcriptional function of ABI5 without affecting its stability. Collectively, our results indicate that these PRR proteins function synergistically with ABI5 to activate ABA responses during seed germination, thus providing a mechanistic understanding of how ABA signaling and the circadian clock are directly integrated through a transcriptional complex involving ABI5 and central circadian clock components.
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Affiliation(s)
- Milian Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao Han
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Jiajia Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanjuan Jiang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Yanru Hu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Author for correspondence:
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Ageeva-Kieferle A, Georgii E, Winkler B, Ghirardo A, Albert A, Hüther P, Mengel A, Becker C, Schnitzler JP, Durner J, Lindermayr C. Nitric oxide coordinates growth, development, and stress response via histone modification and gene expression. PLANT PHYSIOLOGY 2021; 187:336-360. [PMID: 34003928 PMCID: PMC8418403 DOI: 10.1093/plphys/kiab222] [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: 02/25/2021] [Accepted: 04/18/2021] [Indexed: 05/02/2023]
Abstract
Nitric oxide (NO) is a signaling molecule with multiple regulatory functions in plant physiology and stress response. In addition to direct effects on transcriptional machinery, NO executes its signaling function via epigenetic mechanisms. We report that light intensity-dependent changes in NO correspond to changes in global histone acetylation (H3, H3K9, and H3K9/K14) in Arabidopsis (Arabidopsis thaliana) wild-type leaves, and that this relationship depends on S-nitrosoglutathione reductase and histone deacetylase 6 (HDA6). The activity of HDA6 was sensitive to NO, demonstrating that NO participates in regulation of histone acetylation. Chromatin immunoprecipitation sequencing and RNA-seq analyses revealed that NO participates in the metabolic switch from growth and development to stress response. This coordinating function of NO might be particularly important in plant ability to adapt to a changing environment, and is therefore a promising foundation for mitigating the negative effects of climate change on plant productivity.
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Affiliation(s)
| | - Elisabeth Georgii
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Barbro Winkler
- Research Unit Environmental Simulation, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Andrea Ghirardo
- Research Unit Environmental Simulation, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Andreas Albert
- Research Unit Environmental Simulation, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Patrick Hüther
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria
| | - Alexander Mengel
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Claude Becker
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria
- Faculty of Biology, Ludwig-Maximilians-University Munich, LMU Biocenter, Martinsried 82152, Germany
| | - Jörg-Peter Schnitzler
- Research Unit Environmental Simulation, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Jörg Durner
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg 85764, Germany
- Chair of Biochemical Plant Pathology, Technische Universität München, Freising 85354, Germany
| | - Christian Lindermayr
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg 85764, Germany
- Author for communication:
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Sosa Alderete LG, Ronchi H, Monjes NM, Agostini E. Tobacco hairy root's peroxidases are rhythmically controlled by phenol exposure. Enzyme Microb Technol 2021; 149:109856. [PMID: 34311893 DOI: 10.1016/j.enzmictec.2021.109856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 11/23/2022]
Abstract
Plants like almost all living organisms, have developed a biological clock or circadian clock (CC) capable of synchronizing and adjusting various metabolic and physiological processes at certain times of the day and in a period of 24 h. This endogenous timekeeping is able to predict the environmental changes providing adaptive advantages against stressful conditions. Therefore, the aim of this work was to analyze the possible link between metabolism of xenobiotic compounds (MXC) and the CC. Synchronized Nicotiana tabacum hairy roots (HRs) were used as a validated plant model system, and peroxidases (PODs), key enzymes of the phase I in the MCX, were evaluated after phenol treatment. Two POD genes were selected and their temporal expression profiles as well as the total POD activity were analyzed in order to find circadian oscillations either under control conditions or phenol treatment. It was demonstrated that these PODs genes showed oscillatory profiles with an ultradian period (period length shorter than the circadian period), and preserving the same phases and expression peaks still under phenol treatment. The total PODs activity showed also a marked oscillatory behavior mainly in phenol-treated HRs with the highest levels at ZT23. Untreated HRs showed decrease and increase in the intensity of some basic isoforms at light and dark phase, respectively, while in phenol- treated HRs, an increase in the intensity of almost all isoforms was observed, mainly during the dark phase, being coincident with the high PODs activity detected at ZT23. The periodic analysis determined an ultradian period either in total POD activity or in the POD activity of isoform VI, being 18.7 and 15.3 h, respectively. Curiously, in phenol treated HRs, the period length of total POD activity was longer than in untreated HRs, suggesting that phenol could induce a marked oscillatory behavior in the POD activity with better performance during the dark phase, which explain the higher phenol removal efficiencies at ZT23. These findings showed novel information about the performance of PODs, which would be rhythmically controlled at biochemical level, by phenol exposure.
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Affiliation(s)
- Lucas Gastón Sosa Alderete
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Argentina; Instituto de Biotecnología Ambiental y Salud, INBIAS-CONICET, Ruta Nacional 36 Km 601 (CP 5800), Río Cuarto, Córdoba, Argentina.
| | - Hebe Ronchi
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Argentina; Instituto de Biotecnología Ambiental y Salud, INBIAS-CONICET, Ruta Nacional 36 Km 601 (CP 5800), Río Cuarto, Córdoba, Argentina
| | - Natalia M Monjes
- CIQUIBIC-CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina; Departamento de Química Biológica "Ranwel Caputto", Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Elizabeth Agostini
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Argentina; Instituto de Biotecnología Ambiental y Salud, INBIAS-CONICET, Ruta Nacional 36 Km 601 (CP 5800), Río Cuarto, Córdoba, Argentina
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Moseley RC, Motta F, Tuskan GA, Haase SB, Yang X. Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in Kalanchoë fedtschenkoi. Cells 2021; 10:2217. [PMID: 34571864 PMCID: PMC8471846 DOI: 10.3390/cells10092217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 02/01/2023] Open
Abstract
The circadian clock drives time-specific gene expression, enabling biological processes to be temporally controlled. Plants that conduct crassulacean acid metabolism (CAM) photosynthesis represent an interesting case of circadian regulation of gene expression as stomatal movement is temporally inverted relative to stomatal movement in C3 plants. The mechanisms behind how the circadian clock enabled physiological differences at the molecular level is not well understood. Recently, the rescheduling of gene expression was reported as a mechanism to explain how CAM evolved from C3. Therefore, we investigated whether core circadian clock genes in CAM plants were re-phased during evolution, or whether networks of phase-specific genes were simply re-wired to different core clock genes. We identified candidate core clock genes based on gene expression features and then applied the Local Edge Machine (LEM) algorithm to infer regulatory relationships between this new set of core candidates and known core clock genes in Kalanchoë fedtschenkoi. We further inferred stomata-related gene targets for known and candidate core clock genes and constructed a gene regulatory network for core clock and stomata-related genes. Our results provide new insight into the mechanism of circadian control of CAM-related genes in K. fedtschenkoi, facilitating the engineering of CAM machinery into non-CAM plants for sustainable crop production in water-limited environments.
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Affiliation(s)
- Robert C. Moseley
- Department of Biology, Duke University, Durham, NC 27708, USA; (R.C.M.); (S.B.H.)
| | - Francis Motta
- Department of Mathematical Sciences, Florida Atlantic University, Boca Raton, FL 33431, USA;
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA;
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Steven B. Haase
- Department of Biology, Duke University, Durham, NC 27708, USA; (R.C.M.); (S.B.H.)
- Department of Medicine, Duke University, Durham, NC 27708, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA;
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Jiménez A, Sevilla F, Martí MC. Reactive oxygen species homeostasis and circadian rhythms in plants. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5825-5840. [PMID: 34270727 DOI: 10.1093/jxb/erab318] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Elucidation of the molecular mechanisms by which plants sense and respond to environmental stimuli that influence their growth and yield is a prerequisite for understanding the adaptation of plants to climate change. Plants are sessile organisms and one important factor for their successful acclimation is the temporal coordination of the 24 h daily cycles and the stress response. The crosstalk between second messengers, such as Ca2+, reactive oxygen species (ROS), and hormones is a fundamental aspect in plant adaptation and survival under environmental stresses. In this sense, the circadian clock, in conjunction with Ca2+- and hormone-signalling pathways, appears to act as an important mechanism controlling plant adaptation to stress. The relationship between the circadian clock and ROS-generating and ROS-scavenging mechanisms is still not fully understood, especially at the post-transcriptional level and in stress situations in which ROS levels increase and changes in cell redox state occur. In this review, we summarize the information regarding the relationship between the circadian clock and the ROS homeostasis network. We pay special attention not only to the transcriptional regulation of ROS-generating and ROS-scavenging enzymes, but also to the few studies that have been performed at the biochemical level and those conducted under stress conditions.
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Affiliation(s)
- Ana Jiménez
- Abiotic Stress, Production and Quality Laboratory, Department of Stress Biology and Plant Pathology, Centre of Edaphology and Applied Biology of Segura (CEBAS-CSIC), Murcia, Spain
| | - Francisca Sevilla
- Abiotic Stress, Production and Quality Laboratory, Department of Stress Biology and Plant Pathology, Centre of Edaphology and Applied Biology of Segura (CEBAS-CSIC), Murcia, Spain
| | - María Carmen Martí
- Abiotic Stress, Production and Quality Laboratory, Department of Stress Biology and Plant Pathology, Centre of Edaphology and Applied Biology of Segura (CEBAS-CSIC), Murcia, Spain
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Interpreting machine learning models to investigate circadian regulation and facilitate exploration of clock function. Proc Natl Acad Sci U S A 2021; 118:2103070118. [PMID: 34353905 PMCID: PMC8364196 DOI: 10.1073/pnas.2103070118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The circadian clock is an internal molecular 24-h timer that is critical to life on Earth. We describe a series of artificial intelligence (AI)– and machine learning (ML)–based approaches that enable more cost-effective analysis and insight into circadian regulation and function. Throughout the manuscript, we illuminate what is inside the ML “black box” via explanation or interpretation of predictive ML models. Using this interpretation of our models, we derive biological insights into why a prediction was made, alongside accurate predictions. Most innovatively, we use only DNA sequence features for accurate circadian gene expression prediction. Using explainable AI, we define possible, responsible regulatory elements as we make these predictions; this critically requires no prior knowledge of regulatory elements. The circadian clock is an important adaptation to life on Earth. Here, we use machine learning to predict complex, temporal, and circadian gene expression patterns in Arabidopsis. Most significantly, we classify circadian genes using DNA sequence features generated de novo from public, genomic resources, facilitating downstream application of our methods with no experimental work or prior knowledge needed. We use local model explanation that is transcript specific to rank DNA sequence features, providing a detailed profile of the potential circadian regulatory mechanisms for each transcript. Furthermore, we can discriminate the temporal phase of transcript expression using the local, explanation-derived, and ranked DNA sequence features, revealing hidden subclasses within the circadian class. Model interpretation/explanation provides the backbone of our methodological advances, giving insight into biological processes and experimental design. Next, we use model interpretation to optimize sampling strategies when we predict circadian transcripts using reduced numbers of transcriptomic timepoints. Finally, we predict the circadian time from a single, transcriptomic timepoint, deriving marker transcripts that are most impactful for accurate prediction; this could facilitate the identification of altered clock function from existing datasets.
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Cna'ani A, Dener E, Ben-Zeev E, Günther J, Köllner TG, Tzin V, Seifan M. Phylogeny and abiotic conditions shape the diel floral emission patterns of desert Brassicaceae species. PLANT, CELL & ENVIRONMENT 2021; 44:2656-2671. [PMID: 33715174 DOI: 10.1111/pce.14045] [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: 12/10/2020] [Revised: 03/04/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
A key facet of floral scent is diel fluctuations in emission, often studied in the context of plant-pollinator interactions, while contributions of environment and phylogeny remain overlooked. Here, we ask if these factors are involved in shaping temporal variations in scent emission. To that end, we coupled light/dark floral emission measurements of 17 desert Brassicaceae species with environmental and phylogenetic data to explore the individual/combined impacts of these predictors on diel emission patterns. We further investigated these patterns by conducting high-resolution emission measurements in a subset of genetically distant species with contrasting temporal dynamics. While diel shifts in magnitude and richness of emission were strongly affected by genetic relatedness, they also reflect the environmental conditions under which the species grow. Specifically, light/dark emission ratios were negatively affected by an increase in winter temperatures, known to impact both plant physiology and insect locomotion, and sandy soil fractions, previously shown to exert stress that tempers with diel metabolic rhythms. Additionally, the biosynthetic origins of the compounds were associated with their corresponding production patterns, possibly to maximize emission efficacy. Using a multidisciplinary chemical/ecological approach, we uncover and differentiate the main factors shaping floral scent diel fluctuations, highlighting their consequences under changing global climate.
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Affiliation(s)
- Alon Cna'ani
- Jacob Blaustein Center for Scientific Cooperation, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer campus, Midreshet Ban-Gurion, Israel
| | - Efrat Dener
- The Albert Katz International School for Desert Studies, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer campus, Midreshet Ban-Gurion, Israel
| | - Efrat Ben-Zeev
- Nancy and Stephen Grand Israel National Center for Personalized Medicine, The Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Jan Günther
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
- Section of Plant Biochemistry, Department of Plant and Environmental Science, University of Copenhagen, Copenhagen, Denmark
| | - Tobias G Köllner
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Vered Tzin
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer campus, Midreshet Ban-Gurion, Israel
| | - Merav Seifan
- Mitrani Department of Desert Ecology, Swiss Institute for Dryland Environmental and Energy Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer campus, Midreshet Ban-Gurion, Israel
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50
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Plant virus evolution under strong drought conditions results in a transition from parasitism to mutualism. Proc Natl Acad Sci U S A 2021; 118:2020990118. [PMID: 33526695 DOI: 10.1073/pnas.2020990118] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Environmental conditions are an important factor driving pathogens' evolution. Here, we explore the effects of drought stress in plant virus evolution. We evolved turnip mosaic potyvirus in well-watered and drought conditions in Arabidopsis thaliana accessions that differ in their response to virus infection. Virus adaptation occurred in all accessions independently of watering status. Drought-evolved viruses conferred a significantly higher drought tolerance to infected plants. By contrast, nonsignificant increases in tolerance were observed in plants infected with viruses evolved under standard watering. The magnitude of this effect was dependent on the plant accessions. Differences in tolerance were correlated to alterations in the expression of host genes, some involved in regulation of the circadian clock, as well as in deep changes in the balance of phytohormones regulating defense and growth signaling pathways. Our results show that viruses can promote host survival in situations of abiotic stress, with the magnitude of such benefit being a selectable trait.
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