Proc Natl Acad Sci U S A , IF:9.412 , 2021 Mar , V118 (10) doi: 10.1073/pnas.2026330118
Predicting transcriptional responses to cold stress across plant species.
Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588.; Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588.; State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 273100, China.; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588.; Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588; schnable@unl.edu.
Although genome-sequence assemblies are available for a growing number of plant species, gene-expression responses to stimuli have been cataloged for only a subset of these species. Many genes show altered transcription patterns in response to abiotic stresses. However, orthologous genes in related species often exhibit different responses to a given stress. Accordingly, data on the regulation of gene expression in one species are not reliable predictors of orthologous gene responses in a related species. Here, we trained a supervised classification model to identify genes that transcriptionally respond to cold stress. A model trained with only features calculated directly from genome assemblies exhibited only modest decreases in performance relative to models trained by using genomic, chromatin, and evolution/diversity features. Models trained with data from one species successfully predicted which genes would respond to cold stress in other related species. Cross-species predictions remained accurate when training was performed in cold-sensitive species and predictions were performed in cold-tolerant species and vice versa. Models trained with data on gene expression in multiple species provided at least equivalent performance to models trained and tested in a single species and outperformed single-species models in cross-species prediction. These results suggest that classifiers trained on stress data from well-studied species may suffice for predicting gene-expression patterns in related, less-studied species with sequenced genomes.
PMID: 33658387
Proc Natl Acad Sci U S A , IF:9.412 , 2021 Mar , V118 (10) doi: 10.1073/pnas.2021048118
Posttranslational regulation of multiple clock-related transcription factors triggers cold-inducible gene expression in Arabidopsis.
Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan; akido@g.ecc.u-tokyo.ac.jp kazuo.shinozaki@riken.jp akys@g.ecc.u-tokyo.ac.jp.; Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan.; College of Bioscience and Biotechnology, Chubu University, Aichi 487-8501, Japan.; Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 305-0074 Tsukuba, Japan; akido@g.ecc.u-tokyo.ac.jp kazuo.shinozaki@riken.jp akys@g.ecc.u-tokyo.ac.jp.; Research Institute for Agricultural and Life Sciences, Tokyo University of Agriculture, Tokyo 156-8502, Japan.
Cold stress is an adverse environmental condition that affects plant growth, development, and crop productivity. Under cold stress conditions, the expression of numerous genes that function in the stress response and tolerance is induced in various plant species, and the dehydration-responsive element (DRE) binding protein 1/C-repeat binding factor (DREB1/CBF) transcription factors function as master switches for cold-inducible gene expression. Cold stress strongly induces these DREB1 genes. Therefore, it is important to elucidate the mechanisms of DREB1 expression in response to cold stress to clarify the perception and response of cold stress in plants. Previous studies indicated that the central oscillator components of the circadian clock, CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY), are involved in cold-inducible DREB1 expression, but the underlying mechanisms are not clear. We revealed that the clock-related MYB proteins REVEILLE4/LHY-CCA1-Like1 (RVE4/LCL1) and RVE8/LCL5 are quickly and reversibly transferred from the cytoplasm to the nucleus under cold stress conditions and function as direct transcriptional activators of DREB1 expression. We found that CCA1 and LHY suppressed the expression of DREB1s under unstressed conditions and were rapidly degraded specifically in response to cold stress, which suggests that they act as transcriptional repressors and indirectly regulate the cold-inducible expression of DREB1s We concluded that posttranslational regulation of multiple clock-related transcription factors triggers cold-inducible gene expression. Our findings clarify the complex relationship between the plant circadian clock and the regulatory mechanisms of cold-inducible gene expression.
PMID: 33649234
Environ Int , IF:7.577 , 2021 Mar , V152 : P106493 doi: 10.1016/j.envint.2021.106493
Chronic exposure to glyphosate in Florida manatee.
Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA; Aquatic Animal Health Program, College of Veterinary Medicine, University of Florida, PO Box 100136, Gainesville, FL 32610, USA. Electronic address: maitedmm@gmail.com.; Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA. Electronic address: csilvasanchez@ncasi.org.; Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA. Electronic address: krollk@ufl.edu.; Aquatic Animal Health Program, College of Veterinary Medicine, University of Florida, PO Box 100136, Gainesville, FL 32610, USA. Electronic address: walshm@ufl.edu.; Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA. Electronic address: mnouridelavar@ufl.edu.; U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL 32653, United States. Electronic address: mhunter@usgs.gov.; Clearwater Marine Aquarium, 249 Windward Passage, Clearwater, FL 33767, USA. Electronic address: mross@cmaquarium.org.; Georgia Aquarium, Atlanta, Georgia, 225 Baker Street Northwest, Atlanta, GA 30313, USA. Electronic address: tclauss@georgiaaquarium.org.; Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA; Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA. Electronic address: ndenslow@ufl.edu.
Florida manatees depend on freshwater environments as a source of drinking water and as warm-water refuges. These freshwater environments are in direct contact with human activities where glyphosate-based herbicides are being used. Glyphosate is the most used herbicide worldwide and it is intensively used in Florida as a sugarcane ripener and to control invasive aquatic plants. The objective of the present study was to determine the concentration of glyphosate and its breakdown product, aminomethylphosphonic acid (AMPA), in Florida manatee plasma and assess their exposure to manatees seeking a warm-water refuge in Crystal River (west central Florida), and in South Florida. We analyzed glyphosate's and AMPA's concentrations in Florida manatee plasma (n = 105) collected during 2009-2019 using HPLC-MS/MS. We sampled eight Florida water bodies between 2019 and 2020, three times a year: before, during and after the sugarcane harvest using grab samples and molecular imprinted passive Polar Organic Chemical Integrative Samplers (MIP-POCIS). Glyphosate was present in 55.8% of the sampled Florida manatees' plasma. The concentration of glyphosate has significantly increased in Florida manatee samples from 2009 until 2019. Glyphosate and AMPA were ubiquitous in water bodies. The concentration of glyphosate and AMPA was higher in South Florida than in Crystal River, particularly before and during the sugarcane harvest when Florida manatees depend on warm water refuges. Based on our results, Florida manatees were chronically exposed to glyphosate and AMPA, during and beyond the glyphosate applications to sugarcane, possibly associated with multiple uses of glyphosate-based herbicides for other crops or to control aquatic weeds. This chronic exposure in Florida water bodies may have consequences for Florida manatees' immune and renal systems which may further be compounded by other environmental exposures such as red tide or cold stress.
PMID: 33740675
Comp Biochem Physiol Part D Genomics Proteomics , IF:7.051 , 2021 Mar , V38 : P100823 doi: 10.1016/j.cbd.2021.100823
Metabonomics of white adipose tissue and brown adipose tissue in Tupaia belangeri during cold acclimation.
Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals-Plants in Southwest Mountain Ecosystem of Yunnan Province Higher Institutes College, School of Life Science, Yunnan Normal University, Kunming 650500, Yunnan, China; Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.; Yunnan University of Bussiness Management, Kunming 650106, Yunnan, China.; Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals-Plants in Southwest Mountain Ecosystem of Yunnan Province Higher Institutes College, School of Life Science, Yunnan Normal University, Kunming 650500, Yunnan, China.; Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals-Plants in Southwest Mountain Ecosystem of Yunnan Province Higher Institutes College, School of Life Science, Yunnan Normal University, Kunming 650500, Yunnan, China. Electronic address: zhuwanlong@ynnu.edu.cn.
In the present study, liquid chromatography-mass spectrometer (LC-MS) was used to perform untargeted metabolomics analysis of white adipose tissue (WAT) and brown adipose tissue (BAT) in Tupaia belangeri during cold acclimation. Differences in biochemical composition between WAT and BAT were compared. Clarifying how the two adipose tissues respond to the lower temperature in terms of metabolomics, which elucidate the metabolic process and energy homeostasis regulation mechanism in T. belangeri. The results showed that there were 34, 59 and 20 differential metabolites in the WAT, BAT and WAT compared with BAT, respectively. WAT and BAT had significant differences in various metabolic pathways such as sugar metabolism, amino acid metabolism, lipid metabolism, and nucleotide metabolism, which were closely related to the different biological roles of the two tissues. Increasing the concentrations of intermediate products of tricarboxylic acid (TCA) cycle, pyruvic acid, and phosphoenolpyruvic acid (PEP) in WAT and increasing the metabolites in TCA cycle, glyoxylate and dicarboxylate metabolism pathways in BAT, likely to increase the thermogenic capacity in T. belangeri in response to cold stress. There were more differential metabolic pathways in BAT during cold acclimation than that of in WAT. Moreover, compared to WAT, BAT responds to cold stress by adjusting the concentration of nucleotide metabolites.
PMID: 33721582
Plant Physiol , IF:6.902 , 2021 Mar doi: 10.1093/plphys/kiab142
GRAS-domain transcription factor PAT1 regulates jasmonic acid biosynthesis in grape cold stress response.
Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, the Chinese Academy of Science, Beijing 100093, P.R. China.; University of Chinese Academy of Sciences, Beijing 10049, P.R. China.; Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601, Australia.; China Wine Industry Technology Institute, Yinchuan, 750021, P.R. China.; Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, P.R. China.; Center of Economic botany, Core botanical gardens, Chinese academy of Sciences, Wuhan, China.
Cultivated grapevine (Vitis) is a highly valued horticultural crop, and cold stress affects its growth and productivity. Wild Amur grape (Vitis amurensis) PAT1 (Phytochrome A signal transduction 1, VaPAT1) is induced by low temperature, and ectopic expression of VaPAT1 enhances cold tolerance in Arabidopsis (Arabidopsis thaliana). However, little is known about the molecular mechanism of VaPAT1 during the cold stress response in grapevine. Here, we confirmed overexpression of VaPAT1 in transformed grape calli enhanced cold tolerance. Yeast two-hybrid and bimolecular fluorescence complementation assays highlighted an interaction between VaPAT1 with INDETERMINATE-DOMAIN 3 (VaIDD3). A role of VaIDD3 in cold tolerance was also indicated. Transcriptome analysis revealed VaPAT1 and VaIDD3 overexpression and cold treatment coordinately modulate the expression of stress-related genes including lipoxygenase 3 (LOX3), a gene encoding a key jasmonate biosynthesis enzyme. Co-expression network analysis indicated LOX3 might be a downstream target of VaPAT1. Both electrophoretic mobility shift and dual luciferase reporter assays showed the VaPAT1-IDD3 complex binds to the IDD-box (AGACAAA) in the VaLOX3 promoter to activate its expression. Overexpression of both VaPAT1 and VaIDD3 increased the transcription of VaLOX3 and JA levels in transgenic grape calli. Conversely, VaPAT1-SRDX (dominant repression) and CRISPR/Cas9-mediated mutagenesis of PAT1-ED causing the loss of the C-terminus in grape calli dramatically prohibited the accumulation of VaLOX3 and JA levels during cold treatment. Together, these findings point to a pivotal role of VaPAT1 in the cold stress response in grape by regulating JA biosynthesis.
PMID: 33752238
Food Chem , IF:6.306 , 2021 Mar , V353 : P129482 doi: 10.1016/j.foodchem.2021.129482
Effects of exogenous methyl jasmonate on quality and preservation of postharvest fruits: A review.
School of Life Sciences, Nantong University, Nantong 226019, People's Republic of China.; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 226019, People's Republic of China. Electronic address: fqliu20011@sina.com.; School of Life Sciences, Nantong University, Nantong 226019, People's Republic of China. Electronic address: pedro@ntu.edu.cn.
Methyl jasmonate (MeJA) is a volatile hormone involved in a number of plant processes, acting as a signal in response to external stresses and modulating the biosynthesis of other phytohormones. Here, we are reviewing for the first time all reports related to the effects of exogenous MeJA on postharvest fruits. Application of MeJA during preharvest and postharvest stages has been demonstrated to enhance fruit antioxidant capacity and phenolics content, which in turn extended fruit shelf-life, enhanced fruit quality and reduced chilling injury. The postharvest application of MeJA has been reported to alter volatiles pattern and to enhance the innate disease resistance of postharvest fruits against pathogenic fungi. The results obtained using different treatment conditions, such as temperature, storage time and concentration, have been highlighted and compared along the manuscript in order to provide new insights on the applicability of MeJA for enhancing postharvest fruit quality and preservation.
PMID: 33725541
Plant J , IF:6.141 , 2021 Mar doi: 10.1111/tpj.15237
Divergent DNA methylation contributes to duplicated gene evolution and chilling response in tea plants.
State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.
Tea plant is a thermophilic cash crop and contains a highly duplicated and repeat-rich genome. It is still unclear how DNA methylation regulates the evolution of duplicated genes and chilling stress in tea plants. We therefore generated a single-base resolution DNA methylation map of tea plants under chilling stress. We found that compared with other plants, the tea plant genome is highly methylated in all three sequence contexts, including CG, CHG, and CHH (H = A, T, or C), which is further proved to be correlated with its repeat content and genome size. We show that DNA methylation in the gene body negatively regulates the gene expression of tea plants, while non-CG methylation in the flanking region enables a positive regulation of gene expression. We demonstrate that transposable element-mediated methylation dynamics significantly drives the expression divergence of duplicated genes in tea plants. DNA methylation and expression divergence of tea plant duplicated genes increase with their evolutionary ages and selective pressure. Besides, we detect thousands of differentially methylated genes, some of which are functionally associated with chilling stress. We also experimentally reveal that DNA methyltransferase genes of tea plants are significantly down-regulated, while demethylase genes are up-regulated at the initial stage of chilling stress, which is in line with the significant loss of DNA methylation of three well-known cold-responsive genes at their promoter and gene body regions. Overall, our findings underscore the importance of DNA methylation regulation and offer new insights into the duplicated gene evolution and chilling tolerance in tea plants.
PMID: 33730390
Hortic Res , IF:5.404 , 2021 Mar , V8 (1) : P57 doi: 10.1038/s41438-021-00496-0
Methyl jasmonate mediates melatonin-induced cold tolerance of grafted watermelon plants.
State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, 712100, Yangling, Shaanxi, China.; College of Horticulture and Plant Protection, Henan University of Science and Technology, 471023, Luoyang, Henan, China.; State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, 712100, Yangling, Shaanxi, China. zhangxian@nwsuaf.edu.cn.; State Key Laboratory of Vegetable Germplasm Innovation, 300384, Tianjin, China. zhangxian@nwsuaf.edu.cn.
Root-shoot communication has a critical role in plant adaptation to environmental stress. Grafting is widely applied to enhance the abiotic stress tolerance of many horticultural crop species; however, the signal transduction mechanism involved in this tolerance remains unknown. Here, we show that pumpkin- or figleaf gourd rootstock-enhanced cold tolerance of watermelon shoots is accompanied by increases in the accumulation of melatonin, methyl jasmonate (MeJA), and hydrogen peroxide (H2O2). Increased melatonin levels in leaves were associated with both increased melatonin in rootstocks and MeJA-induced melatonin biosynthesis in leaves of plants under cold stress. Exogenous melatonin increased the accumulation of MeJA and H2O2 and enhanced cold tolerance, while inhibition of melatonin accumulation attenuated rootstock-induced MeJA and H2O2 accumulation and cold tolerance. MeJA application induced H2O2 accumulation and cold tolerance, but inhibition of JA biosynthesis abolished rootstock- or melatonin-induced H2O2 accumulation and cold tolerance. Additionally, inhibition of H2O2 production attenuated MeJA-induced tolerance to cold stress. Taken together, our results suggest that melatonin is involved in grafting-induced cold tolerance by inducing the accumulation of MeJA and H2O2. MeJA subsequently increases melatonin accumulation, forming a self-amplifying feedback loop that leads to increased H2O2 accumulation and cold tolerance. This study reveals a novel regulatory mechanism of rootstock-induced cold tolerance.
PMID: 33750773
Front Plant Sci , IF:4.402 , 2021 , V12 : P646910 doi: 10.3389/fpls.2021.646910
Biochar's Leacheates Affect the Abscisic Acid Pathway in Rice Seedlings Under Low Temperature.
Liaoning Biochar Engineering and Technology Research Center, Shenyang Agricultural University, Shenyang, China.; Eastern Liaoning University, Dandong, China.
Organic molecules of biochar's leacheates are known to increase the cold resistance of rice seedlings. Yet, it remains unclear whether the organic molecules of biochar leacheates can interact with the abscisic acid (ABA) signaling pathway associated with low temperature. This study used experiments and bioinformatics (molecular docking) to determine which of the organic molecules of biochar's leacheates could influence the ABA signaling pathway. Specifically, we investigated whether these molecules affected ABA, a plant hormone linked to cold resistance. The contents of endogenous ABA and its precursor carotenoids were determined under low-temperature stress (10 degrees C) and treatment with different concentrations of biochar leacheates. With increased leacheate concentrations, the endogenous ABA and carotenoid contents also increased, as did the expression of ABA- and cold-related genes. When rice seedlings were instead treated with exogenous ABA, it also affected the above-measured indexes; hence, we surmised that certain water-soluble organic molecules of biochar could exert a similar effect as ABA. We first used gas chromatography/mass spectrometry (GC/MS) to identify the organic molecules in the biochar extract, and then we used molecular docking software Autodock to show how they interact. We found that the molecule (1R, 2R, 4S)-2-(6-chloropyridin-3-yl)-7-azabicyclo(2.2.1)heptane was simplified, as Cyah could dock with the ABA receptor protein OsPYL2 in rice, which shows Cyah in biochar is probably an analog of ABA, with a similar function. Based on these results, we conclude that organic molecules of biochar's leacheates could enter into rice plants and interact with ABA-related proteins to affect the ABA signaling pathway, thereby improving the cold stress resistance of plants.
PMID: 33747027
Commun Biol , IF:4.165 , 2021 Mar , V4 (1) : P333 doi: 10.1038/s42003-021-01859-y
A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology.
US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; Applied Genomics Team, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.; Division of Biological Sciences, Genome Core, University of Montana, Missoula, MT, USA.; National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, USA.; Applied Genomics Team, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA. shawns@lanl.gov.; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. ivgrigoriev@lbl.gov.; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. ivgrigoriev@lbl.gov.; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA. ivgrigoriev@lbl.gov.
Microalgae efficiently convert sunlight into lipids and carbohydrates, offering bio-based alternatives for energy and chemical production. Improving algal productivity and robustness against abiotic stress requires a systems level characterization enabled by functional genomics. Here, we characterize a halotolerant microalga Scenedesmus sp. NREL 46B-D3 demonstrating peak growth near 25 degrees C that reaches 30 g/m(2)/day and the highest biomass accumulation capacity post cell division reported to date for a halotolerant strain. Functional genomics analysis revealed that genes involved in lipid production, ion channels and antiporters are expanded and expressed. Exposure to temperature stress shifts fatty acid metabolism and increases amino acids synthesis. Co-expression analysis shows that many fatty acid biosynthesis genes are overexpressed with specific transcription factors under cold stress. These and other genes involved in the metabolic and regulatory response to temperature stress can be further explored for strain improvement.
PMID: 33712730
Plant Cell Physiol , IF:4.062 , 2021 Mar , V62 (1) : P80-91 doi: 10.1093/pcp/pcaa139
EARLY RESPONSE TO DEHYDRATION 7 Remodels Cell Membrane Lipid Composition during Cold Stress in Arabidopsis.
Molecular Plant Biology Unit, Department of Biochemistry, University of Turku, Turku 20014, Finland.; Section Plant Cell Biology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Science Park 904, Amsterdam, XH 1098, Netherlands.; Department of Hematology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.; Department of Molecular Pharmacology and Therapeutics, Stritch School of Medicine, Loyola University Chicago, Maywod, IL 60153, USA.
Plants adjust to unfavorable conditions by altering physiological activities, such as gene expression. Although previous studies have identified multiple stress-induced genes, the function of many genes during the stress responses remains unclear. Expression of ERD7 (EARLY RESPONSE TO DEHYDRATION 7) is induced in response to dehydration. Here, we show that ERD7 plays essential roles in both plant stress responses and development. In Arabidopsis, ERD7 protein accumulated under various stress conditions, including exposure to low temperature. A triple mutant of Arabidopsis lacking ERD7 and two closely related homologs had an embryonic lethal phenotype, whereas a mutant lacking the two homologs and one ERD7 allele had relatively round leaves, indicating that the ERD7 gene family has essential roles in development. Moreover, the importance of the ERD7 family in stress responses was evidenced by the susceptibility of the mutant lines to cold stress. ERD7 protein was found to bind to several, but not all, negatively charged phospholipids and was associated with membranes. Lipid components and cold-induced reduction in PIP2 in the mutant line were altered relative to wild type. Furthermore, membranes from the mutant line had reduced fluidity. Taken together, ERD7 and its homologs are important for plant stress responses and development and associated with the modification in membrane lipid composition.
PMID: 33165601
Plant Physiol Biochem , IF:3.72 , 2021 Mar , V162 : P196-210 doi: 10.1016/j.plaphy.2021.02.041
Genome-wide identification, characterization and expression analysis of the carotenoid cleavage oxygenase (CCO) gene family in Saccharum.
Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.; College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.; New Huadu Business School, Minjiang University, Fuzhou, 350108, Fujian, China. Electronic address: 171944938@qq.com.; Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. Electronic address: queyouxiong@126.com.
Carotenoid cleavage oxygenases (CCOs) play crucial roles in plant growth and development, as well as in the response to phytohormonal, biotic and abiotic stresses. However, comprehensive and systematic research on the CCO gene family has not yet been conducted in Saccharum. In this study, 47 SsCCO and 14 ShCCO genes were identified and characterized in Saccharum spontaneum and Saccharum spp. R570 cultivar, respectively. The SsCCOs consisted of 38 SsCCDs and 9 SsNCEDs, while ShCCOs contained 11 ShCCDs and 3 ShNCEDs. The SsCCO family could be divided into 7 groups, while ShCCO family into 5 groups. The genes/proteins contained similar compositions within the same group, and the evolutionary mechanisms differed between S. spontaneum and R570. Gene Ontology annotation implied that CCOs were involved in many physiological and biochemical processes. Additionally, 41 SsCCOs were regulated by 19 miRNA families, and 8 ShCCOs by 9 miRNA families. Cis-regulatory elements analysis suggested that CCO genes functioned in the process of growth and development or under the phytohormonal, biotic and abiotic stresses. qRT-PCR analysis indicated that nine CCO genes from different groups exhibited similar expression patterns under abscisic acid treatment, while more divergent profiles were observed in response to Sporisorium scitamineum and cold stresses. Herein, comparative genomics analysis of the CCO gene family between S. spontaneum and R570 was conducted to investigate its evolution and functions. This is the first report on the CCO gene family in S. spontaneum and R570, thus providing valuable information and facilitating further investigation into its function in the future.
PMID: 33691250
Plant Physiol Biochem , IF:3.72 , 2021 Mar , V162 : P395-409 doi: 10.1016/j.plaphy.2021.03.010
Alleviating damage of photosystem and oxidative stress from chilling stress with exogenous zeaxanthin in pepper (Capsicum annuum L.) seedlings.
College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou, 730070, PR China.; College of Horticulture, Gansu Agricultural University, Yingmen Village, Anning District, Lanzhou, 730070, PR China. Electronic address: xiejianminggs@126.com.
As a typical thermophilous vegetable, the growth and yield of peppers are easily limited by chilling conditions. Zeaxanthin, a crucial carotenoid, positively regulates plant abiotic stress responses. Therefore, this study investigated the regulatory mechanisms of zeaxanthin-induced chilling tolerance in peppers. The results indicated that the pretreatment with zeaxanthin effectively alleviated chilling damage in pepper leaves and increased the plant fresh weight and photosynthetic pigment content under chilling stress. Additionally, alterations in photosynthetic chlorophyll fluorescence parameters and chlorophyll fluorescence induction curves after zeaxanthin treatment highlighted the participation of zeaxanthin in improving the photosystem response to chilling stress by heightening the quenching of excess excitation energy and protection of the photosynthetic electron transport system. In chill-stressed plants, zeaxanthin treatment also enhanced antioxidant enzyme activity and transcript expression, and reduced hydrogen peroxide (H2O2) and superoxide anion (O2(*-)) content, resulting in a decrease in biological membrane damage. Additionally, exogenous zeaxanthin upregulated the expression levels of key genes encoding beta-carotene hydroxylase (CaCA1, CaCA2), zeaxanthin epoxidase (CaZEP) and violaxanthin de-epoxidase (CaVDE), and promoted the synthesis of endogenous zeaxanthin during chilling stress. Collectively, exogenous zeaxanthin pretreatment enhances plant tolerance to chilling by improving the photosystem process, increasing oxidation resistance, and inducing alterations in endogenous zeaxanthin metabolism.
PMID: 33740679
BMC Plant Biol , IF:3.497 , 2021 Mar , V21 (1) : P156 doi: 10.1186/s12870-021-02916-8
Genome-wide identification of BAM genes in grapevine (Vitis vinifera L.) and ectopic expression of VvBAM1 modulating soluble sugar levels to improve low-temperature tolerance in tomato.
College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China.; College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China.; College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China. maojuan@gsau.edu.cn.
BACKGROUND: Low temperature (LT) is one of the main limiting factors that affect growth and development in grape. Increasing soluble sugar and scavenging reactive oxygen species (ROS) play critical roles in grapevine resistance to cold stress. However, the mechanism of beta-amylase (BAM) involved in the regulation of sugar levels and antioxidant enzyme activities in response to cold stress is unclear. RESULTS: In this study, six BAM genes were identified and clustered into four groups. Multiple sequence alignment and gene structure analysis showed that VvBAM6 lacked the Glu380 residue and contained only an exon. The transcript abundance of VvBAM1 and VvBAM3 significantly increased as temperature decreased. After LT stress, VvBAM1 was highly expressed in the leaves, petioles, stems, and roots of overexpressing tomato lines. The total amylase and BAM activities increased by 6.5- and 6.01-fold in transgenic plants compared with those in wild-type tomato plants (WT) subjected to LT, respectively. The glucose and sucrose contents in transgenic plants were significantly higher than those in WT plants, whereas the starch contents in the former decreased by 1.5-fold compared with those in the latter under LT stress. The analysis of transcriptome sequencing data revealed that 541 genes were upregulated, and 663 genes were downregulated in transgenic plants. One sugar transporter protein gene (SlSTP10), two peroxidase (POD)-related genes (SlPER7 and SlPER5), and one catalase (CAT)-related gene (SlCAT1) were upregulated by 8.6-, 3.6-, 3.0-, and 2.3-fold in transgenic plants after LT stress, respectively. CONCLUSIONS: Our results suggest that VvBAM1 overexpression promotes ROS scavenging and improves cold tolerance ability by modulating starch hydrolysis to affect soluble sugar levels in tomato plants.
PMID: 33771117
BMC Plant Biol , IF:3.497 , 2021 Mar , V21 (1) : P131 doi: 10.1186/s12870-021-02895-w
Cold stress in the harvest period: effects on tobacco leaf quality and curing characteristics.
Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, People's Republic of China.; Dali Tobacco Monopoly Bureau of Yunnan Province, Dali, Yunnan, People's Republic of China.; College of Tobacco Science, Yunnan Agricultural University, Kunming, Yunnan, People's Republic of China. fordmail@163.com.; Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, People's Republic of China. zoucongmingzcm@163.com.
BACKGROUND: Weather change in high-altitude areas subjects mature tobacco (Nicotiana tabacum L.) to cold stress, which damages tobacco leaf yield and quality. A brupt diurnal temperature differences (the daily temperature dropping more than 20 degrees C) along with rainfall in tobacco-growing areas at an altitude above 2450 m, caused cold stress to field-grown tobacco. RESULTS: After the flue-cured tobacco suffered cold stress in the field, the surface color of tobacco leaves changed and obvious large browning areas were appeared, and the curing availability was extremely poor. Further research found the quality of fresh tobacco leaves, the content of key chemical components, and the production quality were greatly reduced by cold stress. We hypothesize that cold stress in high altitude environments destroyed the antioxidant enzyme system of mature flue-cured tobacco. Therefore, the quality of fresh tobacco leaves, the content of key chemical components, and the production quality were greatly reduced by cold stress. CONCLUSION: This study confirmed that cold stress in high-altitude tobacco areas was the main reason for the browning of tobacco leaves during the tobacco curing process. This adverse environment seriously damaged the quality of tobacco leaves, but can be mitigated by pay attention to the weather forecast and pick tobacco leaves in advance.
PMID: 33685400
Planta , IF:3.39 , 2021 Mar , V253 (4) : P79 doi: 10.1007/s00425-020-03535-7
Changes in the physiological characteristics of Panax ginseng embryogenic calli and molecular mechanism of ginsenoside biosynthesis under cold stress.
Cultivation Base of State Key Laboratory for Ecological Restoration and Ecosystem Management of Jilin Province and Ministry of Science and Technology, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin, People's Republic of China.; Cultivation Base of State Key Laboratory for Ecological Restoration and Ecosystem Management of Jilin Province and Ministry of Science and Technology, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin, People's Republic of China. meih@jlau.edu.cn.; Cultivation Base of State Key Laboratory for Ecological Restoration and Ecosystem Management of Jilin Province and Ministry of Science and Technology, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin, People's Republic of China. yanglimin@jlau.edu.cn.
MAIN CONCLUSION: Short-term cold stress can induce the increased expression of key enzyme-encoding genes involved in secondary metabolite synthesis, thereby increasing secondary metabolite concentration. Cold stress is an ecologically limiting factor that strongly affects the physiological and biochemical properties of medicinal plants often resulting in changes of the secondary metabolic process. Ginsenosides are the main active ingredients in medicinal ginseng yet few studies exist on the effect of cold stress on the expression of ginsenosides or the molecular mechanism underlying its regulation. Here, we evaluated the effects of cold stress on the physiological characteristics and secondary metabolism of P. ginseng embryogenic calli. Physiological measurements and RNA-Seq analysis were used to dissect the metabolic and molecular responses of P. ginseng to cold conditions. We found that the dynamic accumulation of ginsenoside and various physiological indicators leads to homogenous adaptation to cold stress. Secondary metabolism of ginseng could be a compensation mechanism to facilitate its adaptation to cold stress. Combined with the changes in the endogenous hormone content, 9-cis-epoxycarotenoid dioxygenase (NCED), zeaxanthin epoxidase (ZEP), and short chain dehydrogenase (SDR) from the abscisic acid (ABA) synthesis pathway were identified as key mediators of this response. Thus, an appropriate degree of cold stress may promote accumulation of ginsenosides. Moreover, 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR2), squalene epoxidase (SE1), squalene synthase (SS), dammarenediol synthase (DS-II), and beta-alanine C-28 hydroxylase (CYP716A52v2) should be considered key mediators of the cold stress response and ginsenoside biosynthesis. During industrial production, short-term cold stress should be carried out on ginseng calli to improve the quality of its medicinal materials.
PMID: 33740147
Plant Mol Biol , IF:3.302 , 2021 Apr , V105 (6) : P585-599 doi: 10.1007/s11103-020-01111-x
Natural population re-sequencing detects the genetic basis of local adaptation to low temperature in a woody plant.
Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China.; University of Chinese Academy of Sciences, Beijing, 100049, China.; Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China. shshen@ibcas.ac.cn.
KEY MESSAGE: Total of 14 SNPs associated with overwintering-related traits and 75 selective regions were detected. Important candidate genes were identified and a possible network of cold-stress responses in woody plants was proposed. Local adaptation to low temperature is essential for woody plants to against changeable climate and safely survive the winter. To uncover the specific molecular mechanism of low temperature adaptation in woody plants, we sequenced 134 core individuals selected from 494 paper mulberry (Broussonetia papyrifera), which naturally distributed in different climate zones and latitudes. The population structure analysis, PCA analysis and neighbor-joining tree analysis indicated that the individuals were classified into three clusters, which showed forceful geographic distribution patterns because of the adaptation to local climate. Using two overwintering phenotypic data collected at high latitudes of 40 degrees N and one bioclimatic variable, genome-phenotype and genome-environment associations, and genome-wide scans were performed. We detected 75 selective regions which possibly undergone temperature selection and identified 14 trait-associated SNPs that corresponded to 16 candidate genes (including LRR-RLK, PP2A, BCS1, etc.). Meanwhile, low temperature adaptation was also supported by other three trait-associated SNPs which exhibiting significant differences in overwintering traits between alleles within three geographic groups. To sum up, a possible network of cold signal perception and responses in woody plants were proposed, including important genes that have been confirmed in previous studies while others could be key potential candidates of woody plants. Overall, our results highlighted the specific and complex molecular mechanism of low temperature adaptation and overwintering of woody plants.
PMID: 33651261
J Plant Physiol , IF:3.013 , 2021 Mar , V260 : P153406 doi: 10.1016/j.jplph.2021.153406
OsGRF6 interacts with SLR1 to regulate OsGA2ox1 expression for coordinating chilling tolerance and growth in rice.
Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China.; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China. Electronic address: xuyy@ibcas.ac.cn.
Low temperature is one of the abiotic stressors that affect growth and productivity of rice. The plant hormone gibberellin not only regulates growth and development but is also involved in stress defense. Our rice seedling experiments demonstrated that overexpression of SLR1, a gene that encodes the rice DELLA protein, enhanced chilling tolerance. In contrast, overexpression of the active GA synthesis gene OsGA20ox1 reduced chilling tolerance, indicating that weakening GA signaling promoted plant defense against cold stress. CoIP-MS and BiFC assays showed that SLR1 physically interacted with OsGRF6. After cold treatment and recovery, the survival rates of OsGRF6-overexpression lines and an osgrf6 mutant and its complementary lines indicated that OsGRF6 is a negative regulator of chilling tolerance in rice. The yeast one-hybrid, qRT-PCR, and transactivation assays showed that both SLR1 and OsGRF6 can bind to the promoter of the active GA catabolic gene OsGA2ox1, where SLR1 promoted and OsGRF6 suppressed OsGA2ox1 expression. At normal temperature, OsGRF6 was responsible for maintaining active GA levels by inhibiting OsGA2ox1. When rice seedlings were subjected to chilling stress, the repressive effect of OsGRF6 on OsGA2ox1 was released by cold-induced SLR1, which activated OsGA2ox1 expression to decrease the active GA levels, enhancing chilling tolerance. These results suggest that OsGRF6 is an important regulator in the balance between growth and chilling tolerance in rice.
PMID: 33756268
PeerJ , IF:2.379 , 2021 , V9 : Pe10977 doi: 10.7717/peerj.10977
Comparative transcriptomic analysis reveals the cold acclimation during chilling stress in sensitive and resistant passion fruit (Passiflora edulis) cultivars.
Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China.; Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China.
Chilling stress (CS) is an important limiting factor for the growth and development of passion fruit (Passiflora edulis) in winter in South China. However, little is known about how the passion fruit responds and adapts to CS. In this study, we performed transcriptome sequencing of cold-susceptible cultivar Huangjinguo (HJG) and cold-tolerant cultivar Tainong 1 (TN1) under normal temperature (NT) and CS conditions, and a total of 47,353 unigenes were obtained by seven databases. Using differentially expressed unigenes (DEGs) analysis, 3,248 and 4,340 DEGs were identified at two stages, respectively. The Gene Ontology (GO) enrichment analysis showed that the DEGs were mainly related to phosphorylation, membrane protein, and catalytic activity. In Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, the unigenes of plant-pathogen interaction, plant hormone signal transduction and fatty acid metabolism were enriched. Then, the 12,471 filtered unigenes were clustered into eight co-expression modules, and two modules were correlated with CS. In this two modules, 32 hub unigenes were obtained. Furthermore, the unigenes related to CS were validated using quantitative real-time PCR (RT-qPCR). This work showed that the expression levels of CS-related unigenes were very different in two passion fruit cultivars. The results provide information for the development of passion fruit with increased chilling tolerance.
PMID: 33717701
Biotechnol Lett , IF:1.977 , 2021 Mar doi: 10.1007/s10529-021-03110-4
Identification of the PP2C gene family in paper mulberry (Broussonetia papyrifera) and its roles in the regulation mechanism of the response to cold stress.
Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China.; University of Chinese Academy of Sciences, Beijing, 100049, China.; Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China. pengxianjun@ibcas.ac.cn.; Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China. shshen@ibcas.ac.cn.
OBJECTIVES: To study the possible roles of type-2C protein phosphatases (PP2Cs) which have been confirmed to play roles in the response to diverse abiotic stresses in paper mulberry, we launched a series of genomic and functional studies of BpPP2Cs. RESULTS: Sixty-three PP2C proteins in paper mulberry (Broussonetia papyrifera) were classified into 13 clades. Four BpPP2Cs with kinase domains were verified to be highly conserved in organisms ranging from algae to dicots. Seven pairs of BpPP2C genes were found to be expanding, and 18 BpPP2C genes had orthologues in Arabidopsis. BpPP2Cs showed broad expression in different tissues; the expression levels of 18 BpPP2Cs were changed and the phosphorylation levels of seven BpPP2C proteins increased at low temperature. Cold-response elements were found in the promoter region of 31 BpPP2Cs. Finally, Bp01g0320 was found to act as a hub protein and Bp01g0512 and Bp09g1278 played key roles in the ABA-signaling pathway and MAPK cascades, respectively. CONCLUSION: These results suggest that the PP2C gene family of paper mulberry is evolutionarily conserved and participates the regulation of the response to cold stress, which will play a vital role in further research on phosphatases in paper mulberry.
PMID: 33751277