Plant Cell , IF:11.277 , 2024 May , V36 (5) : P1985-1999 doi: 10.1093/plcell/koae050
Molecular dissection of an intronic enhancer governing cold-induced expression of the vacuolar invertase gene in potato.
Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, Anhui Province, China.; Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA.; Vegetable Crops Research Unit, United States Department of Agriculture-Agricultural Research Service, Madison, WI 53706, USA.; Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu 610101, Sichuan Province, China.; Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu 610101, Sichuan Province, China.; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA.; Department of Postharvest Science, The Volcani Institute, ARO, Rishon LeZion 50250, Israel.; Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA.; Michigan State University AgBioResearch, East Lansing, MI 48824, USA.; Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.
Potato (Solanum tuberosum) is the third most important food crop in the world. Potato tubers must be stored at cold temperatures to minimize sprouting and losses due to disease. However, cold temperatures strongly induce the expression of the potato vacuolar invertase gene (VInv) and cause reducing sugar accumulation. This process, referred to as "cold-induced sweetening," is a major postharvest problem for the potato industry. We discovered that the cold-induced expression of VInv is controlled by a 200 bp enhancer, VInvIn2En, located in its second intron. We identified several DNA motifs in VInvIn2En that bind transcription factors involved in the plant cold stress response. Mutation of these DNA motifs abolished VInvIn2En function as a transcriptional enhancer. We developed VInvIn2En deletion lines in both diploid and tetraploid potato using clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9)-mediated gene editing. VInv transcription in cold-stored tubers was significantly reduced in the deletion lines. Interestingly, the VInvIn2En sequence is highly conserved among distantly related Solanum species, including tomato (Solanum lycopersicum) and other non-tuber-bearing species. We conclude that the VInv gene and the VInvIn2En enhancer have adopted distinct roles in the cold stress response in tubers of tuber-bearing Solanum species.
PMID: 38374801
Plant Cell , IF:11.277 , 2024 May , V36 (6) : P2117-2139 doi: 10.1093/plcell/koae039
Pan-transcriptomic analysis reveals alternative splicing control of cold tolerance in rice.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China.; Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China.
Plants have evolved complex mechanisms to adapt to harsh environmental conditions. Rice (Oryza sativa) is a staple food crop that is sensitive to low temperatures. However, its cold stress responses remain poorly understood, thus limiting possibilities for crop engineering to achieve greater cold tolerance. In this study, we constructed a rice pan-transcriptome and characterized its transcriptional regulatory landscape in response to cold stress. We performed Iso-Seq and RNA-Seq of 11 rice cultivars subjected to a time-course cold treatment. Our analyses revealed that alternative splicing-regulated gene expression plays a significant role in the cold stress response. Moreover, we identified CATALASE C (OsCATC) and Os03g0701200 as candidate genes for engineering enhanced cold tolerance. Importantly, we uncovered central roles for the 2 serine-arginine-rich proteins OsRS33 and OsRS2Z38 in cold tolerance. Our analysis of cold tolerance and resequencing data from a diverse collection of 165 rice cultivars suggested that OsRS2Z38 may be a key selection gene in japonica domestication for cold adaptation, associated with the adaptive evolution of rice. This study systematically investigated the distribution, dynamic changes, and regulatory mechanisms of alternative splicing in rice under cold stress. Overall, our work generates a rich resource with broad implications for understanding the genetic basis of cold response mechanisms in plants.
PMID: 38345423
Plant Cell , IF:11.277 , 2024 May , V36 (5) : P1592-1593 doi: 10.1093/plcell/koae025
Histone deacetylase OsHDA716 chilling out with OsbZIP46: antagonistically regulating cold stress tolerance in rice.
Assistant Features Editor, The Plant Cell, American Society of Plant Biologists.; Biochemistry and Metabolism Department, John Innes Centre, Norwich Research Park, NR4 7UH, Norwich, UK.
PMID: 38267564
Plant Cell , IF:11.277 , 2024 May doi: 10.1093/plcell/koae160
Antisense transcription from stress-responsive transcription factors fine-tunes the cold response in Arabidopsis.
Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90187 Umea, Sweden.; National Institute of Plant Genome research, Aruna Asaf Ali Marg, New Delhi, 110067, India.; Umea Plant Science Centre, Department of Plant Physiology, Umea University, 90187 Umea, Sweden.
Transcription of antisense long noncoding RNAs (lncRNAs) occurs pervasively across eukaryotic genomes. Only a few antisense lncRNAs have been characterized and shown to control biological processes, albeit with idiosyncratic regulatory mechanisms. Thus, we largely lack knowledge about the general role of antisense transcription in eukaryotic organisms. Here, we characterized genes with antisense transcription initiating close to the Poly(A) signal (PAS genes) in Arabidopsis (Arabidopsis thaliana). We compared plant native elongation transcript sequencing (plaNET-seq) with RNA sequencing (RNA-seq) during short-term cold exposure and detected massive differences between the response in active transcription and steady-state levels of PAS gene-derived mRNAs. The cold-induced expression of transcription factors B-BOX DOMAIN PROTEIN28 (BBX28) and C2H2-TYPE ZINC FINGER FAMILY PROTEIN5 (ZAT5) was detected by plaNET-seq, while their steady-state level was only slightly altered due to high mRNA turnover. Knockdown of BBX28 and ZAT5 or of their respective antisense transcripts severely compromised plant freezing tolerance. Decreased antisense transcript expression levels resulted in a reduced cold response of BBX28 and ZAT5, revealing a positive regulatory role of both antisense transcripts. This study expands the known repertoire of noncoding transcripts. It highlights that native transcription approaches can complement steady state RNA techniques to identify biologically relevant players in stress responses.
PMID: 38801743
New Phytol , IF:10.151 , 2024 May , V242 (3) : P1377-1393 doi: 10.1111/nph.19656
Convergent and/or parallel evolution of RNA-binding proteins in angiosperms after polyploidization.
State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China.; Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.; Department of Plant Biotechnology and Bioinformatics, VIB - UGent Center for Plant Systems Biology, Ghent University, B-9052, Ghent, Belgium.; College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China.; Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa.
Increasing studies suggest that the biased retention of stress-related transcription factors (TFs) after whole-genome duplications (WGDs) could rewire gene transcriptional networks, facilitating plant adaptation to challenging environments. However, the role of posttranscriptional factors (e.g. RNA-binding proteins, RBPs) following WGDs has been largely ignored. Uncovering thousands of RBPs in 21 representative angiosperm species, we integrate genomic, transcriptomic, regulatomic, and paleotemperature datasets to unravel their evolutionary trajectories and roles in adapting to challenging environments. We reveal functional enrichments of RBP genes in stress responses and identify their convergent retention across diverse angiosperms from independent WGDs, coinciding with global cooling periods. Numerous RBP duplicates derived from WGDs are then identified as cold-induced. A significant overlap of 29 orthogroups between WGD-derived and cold-induced RBP genes across diverse angiosperms highlights a correlation between WGD and cold stress. Notably, we unveil an orthogroup (Glycine-rich RNA-binding Proteins 7/8, GRP7/8) and relevant TF duplicates (CCA1/LHY, RVE4/8, CBF2/4, etc.), co-retained in different angiosperms post-WGDs. Finally, we illustrate their roles in rewiring circadian and cold-regulatory networks at both transcriptional and posttranscriptional levels during global cooling. Altogether, we underline the adaptive evolution of RBPs in angiosperms after WGDs during global cooling, improving our understanding of plants surviving periods of environmental turmoil.
PMID: 38436132
New Phytol , IF:10.151 , 2024 Jun , V242 (5) : P2077-2092 doi: 10.1111/nph.19696
A major gene for chilling tolerance variation in Indica rice codes for a kinase OsCTK1 that phosphorylates multiple substrates under cold.
State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.; State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China.; China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China.; Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.; Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
Rice is susceptible to chilling stress. Identifying chilling tolerance genes and their mechanisms are key to improve rice performance. Here, we performed a genome-wide association study to identify regulatory genes for chilling tolerance in rice. One major gene for chilling tolerance variation in Indica rice was identified as a casein kinase gene OsCTK1. Its function and natural variation are investigated at the physiological and molecular level by its mutants and transgenic plants. Potential substrates of OsCTK1 were identified by phosphoproteomic analysis, protein-protein interaction assay, in vitro kinase assay, and mutant characterization. OsCTK1 positively regulates rice chilling tolerance. Three of its putative substrates, acidic ribosomal protein OsP3B, cyclic nucleotide-gated ion channel OsCNGC9, and dual-specific mitogen-activated protein kinase phosphatase OsMKP1, are each involved in chilling tolerance. In addition, a natural OsCTK1 chilling-tolerant (CT) variant exhibited a higher kinase activity and conferred greater chilling tolerance compared with a chilling-sensitive (CS) variant. The CT variant is more prevalent in CT accessions and is distributed more frequently in higher latitude compared with the CS variant. This study thus enables a better understanding of chilling tolerance mechanisms and provides gene variants for genetic improvement of chilling tolerance in rice.
PMID: 38494697
Plant Physiol , IF:8.34 , 2024 Apr , V195 (1) : P170-189 doi: 10.1093/plphys/kiae105
Regulatory networks in plant responses to drought and cold stress.
RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045Japan.; Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046Japan.; School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8502Japan.; Research Institute for Agriculture and Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502Japan.; Graduate School of Agriculture and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032Japan.; Institute for Advanced Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601Japan.
Drought and cold represent distinct types of abiotic stress, each initiating unique primary signaling pathways in response to dehydration and temperature changes, respectively. However, a convergence at the gene regulatory level is observed where a common set of stress-responsive genes is activated to mitigate the impacts of both stresses. In this review, we explore these intricate regulatory networks, illustrating how plants coordinate distinct stress signals into a collective transcriptional strategy. We delve into the molecular mechanisms of stress perception, stress signaling, and the activation of gene regulatory pathways, with a focus on insights gained from model species. By elucidating both the shared and distinct aspects of plant responses to drought and cold, we provide insight into the adaptive strategies of plants, paving the way for the engineering of stress-resilient crop varieties that can withstand a changing climate.
PMID: 38514098
mBio , IF:7.867 , 2024 May , V15 (5) : Pe0321123 doi: 10.1128/mbio.03211-23
Reduced cold tolerance of viral-infected leafhoppers attenuates viral persistent epidemics.
Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, China.
Most arthropod-borne viruses produce intermittent epidemics in infected plants. However, the underlying mechanisms of these epidemics are unclear. Here, we demonstrated that rice stripe mosaic virus (RSMV), a viral pathogen, significantly increases the mortality of its overwintering vector, the leafhopper species Recilia dorsalis. Cold-stress assays indicated that RSMV reduces the cold tolerance of leafhoppers, a process associated with the downregulation of leafhopper cuticular protein genes. An RSMV-derived small RNA (vsiR-t00355379) was found to facilitate the downregulation of a leafhopper endocuticle gene that is mainly expressed in the abdomen (named RdABD-5) and is conserved across dipteran species. The downregulation of RdABD-5 expression in R. dorsalis resulted in fewer and thinner endocuticle lamellae, leading to decreased cold tolerance. This effect was correlated with a reduced incidence rate of RSMV in early-planted rice plants. These findings contribute to our understanding of the mechanism by which viral pathogens reduce cold tolerance in arthropod vectors and suggest an approach to managing the fluctuating prevalence of arboviruses. IMPORTANCE: Increasing arthropod vector dispersal rates have increased the susceptibility of crop to epidemic viral diseases. However, the incidence of some viral diseases fluctuates annually. In this study, we demonstrated that a rice virus reduces the cold tolerance of its leafhopper vector, Recilia dorsalis. This effect is linked to the virus-derived small RNA-mediated downregulation of a gene encoding a leafhopper abdominal endocuticle protein. Consequently, the altered structural composition of the abdominal endocuticle reduces the overwinter survival of leafhoppers, resulting in a lower incidence of RSMV infection in early-planted rice plants. Our findings illustrate the important roles of RNA interference in virus-vector insect-environment interactions and help explain the annual fluctuations of viral disease epidemics in rice fields.
PMID: 38564693
Plant Cell Environ , IF:7.228 , 2024 May doi: 10.1111/pce.14933
SlNAC3 suppresses cold tolerance in tomatoes by enhancing ethylene biosynthesis.
Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China.; Umea Plant Science Centre, UMEA, Sweden.
Low temperature stress poses a significant challenge to the productivity of horticultural crops. The dynamic expression of cold-responsive genes plays a crucial role in plant cold tolerance. While NAC transcription factors have been extensively studied in plant growth and development, their involvement in regulating plant cold tolerance remains poorly understood. In this study, we focused on the identification and characterisation of SlNAC3 as the most rapid and robust responsive gene in tomato under low temperature conditions. Manipulating SlNAC3 through overexpression or silencing resulted in reduced or enhanced cold tolerance, respectively. Surprisingly, we discovered a negative correlation between the expression of CBF and cold tolerance in the SlNAC3 transgenic lines. These findings suggest that SlNAC3 regulates tomato cold tolerance likely through a CBF-independent pathway. Furthermore, we conducted additional investigations to identify the molecular mechanisms underlying SINAC3-mediated cold tolerance in tomatoes. Our results revealed that SlNAC3 controls the transcription of ethylene biosynthetic genes, thereby bursting ethylene release in response to cold stress. Indeed, the silencing of these genes led to an augmentation in cold tolerance. This discovery provides valuable insights into the regulatory pathways involved in ethylene-mediated cold tolerance in tomatoes, offering potential strategies for developing innovative approaches to enhance cold stress resilience in this economically important crop species.
PMID: 38693781
Plant Cell Environ , IF:7.228 , 2024 May , V47 (5) : P1834-1851 doi: 10.1111/pce.14845
MrERF039 transcription factor plays an active role in the cold response of Medicago ruthenica as a sugar molecular switch.
Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, College of Life Sciences, Inner Mongolia University, Hohhot, China.; Inner Mongolia Academy of Science and Technology, Hohhot, China.
Cold stress severely restricts plant development, causing significant agricultural losses. We found a critical transcription factor network in Medicago ruthenica was involved in plant adaptation to low-temperature. APETALA2/ethylene responsive factor (AP2/ERF) transcription factor MrERF039 was transcriptionally induced by cold stress in M. ruthenica. Overexpression of MrERF039 significantly increased the glucose and maltose content, thereby improving the tolerance of M. ruthenica. MrERF039 could bind to the DRE cis-acting element in the MrCAS15A promoter. Additionally, the methyl group of the 14th amino acid in MrERF039 was required for binding. Transcriptome analysis showed that MrERF039 acted as a sugar molecular switch, regulating numerous sugar transporters and sugar metabolism-related genes. In addition, we found that MrERF039 could directly regulate beta-amylase gene, UDP glycosyltransferase gene, and C2H2 zinc finger protein gene expression. In conclusion, these findings suggest that high expression of MrERF039 can significantly improve the cold tolerance of M. ruthenica root tissues during cold acclimation. Our results provide a new theoretical basis and candidate genes for breeding new legume forage varieties with high resistance.
PMID: 38318779
J Exp Bot , IF:6.992 , 2024 May , V75 (10) : P2965-2981 doi: 10.1093/jxb/erae099
The transcription factor RhMYB17 regulates the homeotic transformation of floral organs in rose (Rosa hybrida) under cold stress.
Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China.; School of Food and Drug, Shenzhen Polytechnic University, Shenzhen, China.
Low temperatures affect flower development in rose (Rosa hybrida), increasing petaloid stamen number and reducing normal stamen number. We identified the low-temperature-responsive R2R3-MYB transcription factor RhMYB17, which is homologous to Arabidopsis MYB17 by similarity of protein sequences. RhMYB17 was up-regulated at low temperatures, and RhMYB17 transcripts accumulated in floral buds. Transient silencing of RhMYB17 by virus-induced gene silencing decreased petaloid stamen number and increased normal stamen number. According to the ABCDE model of floral organ identity, class A genes APETALA 1 (AP1) and AP2 contribute to sepal and petal formation. Transcription factor binding analysis identified RhMYB17 binding sites in the promoters of rose APETALA 2 (RhAP2) and APETALA 2-LIKE (RhAP2L). Yeast one-hybrid assays, dual-luciferase reporter assays, and electrophoretic mobility shift assays confirmed that RhMYB17 directly binds to the promoters of RhAP2 and RhAP2L, thereby activating their expression. RNA sequencing further demonstrated that RhMYB17 plays a pivotal role in regulating the expression of class A genes, and indirectly influences the expression of the class C gene. This study reveals a novel mechanism for the homeotic transformation of floral organs in response to low temperatures.
PMID: 38452221
J Exp Bot , IF:6.992 , 2024 May , V75 (10) : P2809-2818 doi: 10.1093/jxb/erae045
The circadian clock and thermal regulation in plants: novel insights into the role of positive circadian clock regulators in temperature responses.
Fundacion Instituto Leloir-IIBBA/CONICET, Av. Patricias Argentinas 435, Ciudad Autonoma de Buenos Aires, Argentina.
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.
PMID: 38373194
Int J Biol Macromol , IF:6.953 , 2024 May , V270 (Pt 1) : P132314 doi: 10.1016/j.ijbiomac.2024.132314
Enhancing rutin accumulation in Tartary buckwheat through a novel flavonoid transporter protein FtABCC2.
College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China.; College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an 625014, China. Electronic address: wuqi@sicau.edu.cn.
Tartary buckwheat (Fagopyrum tataricum) is an annual coarse cereal from the Polygonaceae family, known for its high content of flavonoid compounds, particularly rutin. But so far, the mechanisms of the flavonoid transport and storage in Tartary buckwheat (TB) remain largely unexplored. This study focuses on ATP-binding cassette transporters subfamily C (ABCC) members, which are crucial for the biosynthesis and transport of flavonoids in plants. The evolutionary and expression pattern analyses of the ABCC genes in TB identified an ABCC protein gene, FtABCC2, that is highly correlated with rutin synthesis. Subcellular localization analysis revealed that FtABCC2 protein is specifically localized to the vacuole membrane. Heterologous expression of FtABCC2 in Saccharomyces cerevisiae confirmed that its transport ability of flavonoid glycosides such as rutin and isoquercetin, but not the aglycones such as quercetin and dihydroquercetin. Overexpression of FtABCC2 in TB hairy root lines resulted in a significant increase in total flavonoid and rutin content (P < 0.01). Analysis of the FtABCC2 promoter revealed potential cis-acting elements responsive to hormones, cold stress, mechanical injury and light stress. Overall, this study demonstrates that FtABCC2 can efficiently facilitate the transport of rutin into vacuoles, thereby enhancing flavonoids accumulation. These findings suggest that FtABCC2 is a promising candidate for molecular-assisted breeding aimed at developing high-flavonoid TB varieties.
PMID: 38740160
Int J Biol Macromol , IF:6.953 , 2024 May , V268 (Pt 1) : P131804 doi: 10.1016/j.ijbiomac.2024.131804
VvERF117 positively regulates grape cold tolerance through direct regulation of the antioxidative gene BAS1.
College of Enology, Northwest A&F University, Yangling, Shaanxi 712100.; College of Enology, Northwest A&F University, Yangling, Shaanxi 712100. Electronic address: wangxianhang@nwafu.edu.cn.; College of Enology, Northwest A&F University, Yangling, Shaanxi 712100. Electronic address: xizhumei@nwsuaf.edu.cn.
Cold stress significantly threatens grape quality, yield, and geographical distribution. Although ethylene-responsive factors (ERFs) are recognized for their pivotal roles in cold stress, the regulatory mechanisms of many ERFs contributing to tolerance remain unclear. In this study, we identified the cold-responsive gene VvERF117 and elucidated its positive regulatory function in cold tolerance. VvERF117 exhibits transcriptional activity and localizes to the nucleus. VvERF117 overexpression improved cold tolerance in transgenic Arabidopsis, grape calli, and grape leaves, whereas VvERF117 silencing increased cold sensitivity in grape calli and leaves. Furthermore, VvERF117 overexpression remarkably upregulated the expression of several stress-related genes. Importantly, BAS1, encoding a 2-Cys peroxidase (POD), was confirmed as a direct target gene of VvERF117. Meanwhile, compared to the wild-type, POD activity and H(2)O(2) content were remarkably increased and decreased in VvERF117-overexpressing grape calli and leaves, respectively. Conversely, VvERF117 silencing displayed the opposite trend in grape calli and leaves under cold stress. These findings indicate that VvERF117 plays a positive role in cold resistance by, at least in part, enhancing antioxidant capacity through regulating the POD-encoding gene VvBAS1, leading to effective mitigation of reactive oxygen species.
PMID: 38670186
Int J Biol Macromol , IF:6.953 , 2024 May , V266 (Pt 2) : P131293 doi: 10.1016/j.ijbiomac.2024.131293
Characterisation of the MLP genes in peach postharvest cold storage and the regulatory role of PpMLP10 in the chilling stress response.
College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.; Laboratory of Plant Molecular Genetics and Crop Gene Editing, School of Life Sciences, Linyi University, Linyi 276000, China.; Laboratory of Plant Molecular Genetics and Crop Gene Editing, School of Life Sciences, Linyi University, Linyi 276000, China. Electronic address: liuhenglydx@163.com.; Laboratory of Plant Molecular Genetics and Crop Gene Editing, School of Life Sciences, Linyi University, Linyi 276000, China. Electronic address: wangshucai@lyu.edu.cn.
The major latex proteins/ripening-related proteins are a subfamily of the Bet v 1 protein superfamily and are commonly involved in plant development and responses to various stresses. However, the functions of MLPs in the postharvest cold storage of fruits remain uninvestigated. Herein, we identified 30 MLP genes in the peach (Prunus persica) genome that were clustered into three subgroups. Chromosomal location analysis revealed that the PpMLP genes were unevenly distributed on five of the eight peach chromosomes. Synteny analysis of the MLP genes between peach and seven other plant species (five dicotyledons and two monocotyledons) explored their evolutionary characteristics. Furthermore, the PpMLP promoters contained cis-elements for multiple hormones and stress responses. Gene expression analysis revealed that PpMLPs participated in chilling stress responses. Ectopic expression of PpMLP10 in Arabidopsis improved chilling stress tolerance by decreasing membrane damage and maintaining membrane stability. Additional research confirmed that PpWRKY2 participates in PpMLP10-mediated chilling stress by binding to its promoter. Collectively, these results suggest the role of PpMLP10 in enhancing chilling stress tolerance, which is significant for decreasing chilling injury during the postharvest cold storage of peaches.
PMID: 38565368
Protein Sci , IF:6.725 , 2024 May , V33 (5) : Pe4989 doi: 10.1002/pro.4989
Functional in vitro diversity of an intrinsically disordered plant protein during freeze-thawing is encoded by its structural plasticity.
Max-Planck Institute of Molecular Plant Physiology, Potsdam, Germany.; Physical Biochemistry, University of Potsdam, Potsdam, Germany.; Department of Chemistry, University of Bergen, Bergen, Norway.; Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.; Julich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8: Neutron Scattering and Biological Matter), Forschungszentrum Julich GmbH, Julich, Germany.; Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universitat Munchen, Garching, Germany.; Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.; Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.; Australian Nuclear Science and Technology Organization (ANSTO), Kirrawee, New South Wales, Australia.; Institute of Physical Chemistry, RWTH Aachen University, Aachen, Germany.
Intrinsically disordered late embryogenesis abundant (LEA) proteins play a central role in the tolerance of plants and other organisms to dehydration brought upon, for example, by freezing temperatures, high salt concentration, drought or desiccation, and many LEA proteins have been found to stabilize dehydration-sensitive cellular structures. Their conformational ensembles are highly sensitive to the environment, allowing them to undergo conformational changes and adopt ordered secondary and quaternary structures and to participate in formation of membraneless organelles. In an interdisciplinary approach, we discovered how the functional diversity of the Arabidopsis thaliana LEA protein COR15A found in vitro is encoded in its structural repertoire, with the stabilization of membranes being achieved at the level of secondary structure and the stabilization of enzymes accomplished by the formation of oligomeric complexes. We provide molecular details on intra- and inter-monomeric helix-helix interactions, demonstrate how oligomerization is driven by an alpha-helical molecular recognition feature (alpha-MoRF) and provide a rationale that the formation of noncanonical, loosely packed, right-handed coiled-coils might be a recurring theme for homo- and hetero-oligomerization of LEA proteins.
PMID: 38659213
Plant J , IF:6.417 , 2024 May doi: 10.1111/tpj.16812
MORN motif-containing protein OsMORN1 and OsMORN2 are crucial for rice pollen viability and cold tolerance.
Seed Science Center, The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.; Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510640, China.; Hainan Research Institute, Zhejiang University, Sanya, 572025, China.
The pollen viability directly affects the pollination process and the ultimate grain yield of rice. Here, we identified that the MORN motif-containing proteins, OsMORN1 and OsMORN2, had a crucial role in maintaining pollen fertility. Compared with the wild type (WT), the pollen viability of the osmorn1 and osmorn2 mutants was reduced, and pollen germination was abnormal, resulting in significantly lower spikelet fertility, seed-setting rate, and grain yield per plant. Further investigation revealed that OsMORN1 was localized to the Golgi apparatus and lipid droplets. Lipids associated with pollen viability underwent alterations in osmorn mutants, such as the diacylglyceride (18:3_18:3) was 5.1-fold higher and digalactosyldiacylglycerol (18:2_18:2) was 5.2-fold lower in osmorn1, while the triacylglycerol (TG) (16:0_18:2_18:3) was 8.3-fold higher and TG (16:0_18:1_18:3) was 8.5-fold lower in osmorn2 than those in WT. Furthermore, the OsMORN1/2 was found to be associated with rice cold tolerance, as osmorn1 and osmorn2 mutants were more sensitive to chilling stress than WT. The mutants displayed increased hydrogen peroxide accumulation, reduced antioxidant enzyme activities, elevated malondialdehyde content, and a significantly decreased seedling survival rate. Lipidomics analysis revealed distinct alterations in lipids under low temperature, highlighting significant changes in TG (18:2_18:3_18:3) and TG (18:4_18:2_18:2) in osmorn1, TG (16:0_18:2_18:2) and PI (17:2_18:3) in osmorn2 compared to the WT. Therefore, it suggested that OsMORN1 and OsMORN2 regulate both pollen viability and cold tolerance through maintaining lipid homeostasis.
PMID: 38761113
Plant J , IF:6.417 , 2024 Jun , V118 (5) : P1241-1257 doi: 10.1111/tpj.16654
A normalization method that controls for total RNA abundance affects the identification of differentially expressed genes, revealing bias toward morning-expressed responses.
Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA.; Department of Agriculture and Natural Resources, Delaware State University, Dover, Delaware, USA.; Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, 79410, USA.; Department of Science and Technology, The Good Food Institute, Washington, District of Columbia, 20090, USA.; Department of Agronomy, Kansas State University, Manhattan, Kansas, 66506, USA.
RNA-Sequencing is widely used to investigate changes in gene expression at the transcription level in plants. Most plant RNA-Seq analysis pipelines base the normalization approaches on the assumption that total transcript levels do not vary between samples. However, this assumption has not been demonstrated. In fact, many common experimental treatments and genetic alterations affect transcription efficiency or RNA stability, resulting in unequal transcript abundance. The addition of synthetic RNA controls is a simple correction that controls for variation in total mRNA levels. However, adding spike-ins appropriately is challenging with complex plant tissue, and carefully considering how they are added is essential to their successful use. We demonstrate that adding external RNA spike-ins as a normalization control produces differences in RNA-Seq analysis compared to traditional normalization methods, even between two times of day in untreated plants. We illustrate the use of RNA spike-ins with 3' RNA-Seq and present a normalization pipeline that accounts for differences in total transcriptional levels. We evaluate the effect of normalization methods on identifying differentially expressed genes in the context of identifying the effect of the time of day on gene expression and response to chilling stress in sorghum.
PMID: 38289828
Int J Mol Sci , IF:5.923 , 2024 May , V25 (9) doi: 10.3390/ijms25094991
Influence of Cold Stress on Physiological and Phytochemical Characteristics and Secondary Metabolite Accumulation in Microclones of Juglans regia L.
Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan.; Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan.; Faculty of Chemistry, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan.
The current study investigated the impact of cold stress on the morphological, physiological, and phytochemical properties of Juglans regia L. (J. regia) using in vitro microclone cultures. The study revealed significant stress-induced changes in the production of secondary antioxidant metabolites. According to gas chromatography-mass spectrometry (GC-MS) analyses, the stress conditions profoundly altered the metabolism of J. regia microclones. Although the overall spectrum of metabolites was reduced, the production of key secondary antioxidant metabolites significantly increased. Notably, there was a sevenfold (7x) increase in juglone concentration. These findings are crucial for advancing walnut metabolomics and enhancing our understanding of plant responses to abiotic stress factors. Additionally, study results aid in identifying the role of individual metabolites in these processes, which is essential for developing strategies to improve plant resilience and tolerance to adverse conditions.
PMID: 38732208
Front Plant Sci , IF:5.753 , 2024 , V15 : P1396666 doi: 10.3389/fpls.2024.1396666
Effect of cold stress on photosynthetic physiological characteristics and molecular mechanism analysis in cold-resistant cotton (ZM36) seedlings.
College of Agriculture, Shihezi University, Shihezi, Xinjiang, China.; Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science/Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Shihezi, Xinjiang, China.; Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang, China.; Western Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Changji, China.
Low temperature and cold damage seriously hinder the growth, development, and morphogenesis of cotton seedlings. However, the response mechanism of cotton seedlings under cold stress still lacks research. In this study, transcriptome sequencing, gas exchange parameters, and rapid chlorophyll fluorescence parameters were analyzed in leaves of cold-tolerant upland cotton variety "ZM36" under different temperature stress [25 degrees C (T25, CK), 15 degrees C (T15), 10 degrees C (T10), and 4 degrees C (T4)]. The results showed that the net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), PSII potential maximum photochemical efficiency (Fv/Fm), and performance index (PIabs) of cotton leaves significantly decreased, and the intercellular CO(2) concentration (Ci) and Fo/Fm significantly increased under cold stress. The transcriptome sequencing analysis showed that a total of 13,183 DEGs were involved in the response of cotton seedlings at each temperature point (T25, T15, T10, and T4), mainly involving five metabolic pathways-the phosphatidylinositol signaling system, photosynthesis, photosynthesis antenna protein, carbon fixation in photosynthetic organisms, and carotenoid synthesis. The 1,119 transcription factors were discovered among all the DEGs. These transcription factors involve 59 families, of which 15.8% of genes in the NAC family are upregulated. Through network regulatory analysis, the five candidate genes GhUVR8 (GH_A05G3668), GhPLATZ (GH_A09G2161), GhFAD4-1 (GH_A01G0758), GhNFYA1 (GH_A02G1336), and GhFAD4-2 (GH_D01G0766) were identified in response to cold stress. Furthermore, suppressing the expression level of GhPLATZ by virus-induced gene silencing led to the reduction of low temperature resistance, implying GhPLATZ as a positive regulator of low temperature tolerance. The findings of the study revealed a piece of the complex response mechanism of the cold-tolerant variety "ZM36" to different cold stresses and excavated key candidate genes for low temperature response, which provided support for accelerating the selection and breeding of cotton varieties with low temperature tolerance.
PMID: 38803600
Front Plant Sci , IF:5.753 , 2024 , V15 : P1402521 doi: 10.3389/fpls.2024.1402521
The metabolism of amino acids, AsA and abscisic acid induced by strigolactone participates in chilling tolerance in postharvest zucchini fruit.
College of Agriculture and Agricultural Engineering, Liaocheng University, Liaocheng, China.; College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China.
Zucchini fruit are notably susceptible to chilling injury when stored at low temperatures. The purpose of this experimental investigation was to assess the influence of strigolactone (ST) (5 mumol L(-1)) on mitigating chilling injury and the metabolic changes in amino acids, ascorbic acid, and abscisic acid in zucchini fruit stored at 4 degrees C. Research findings demonstrated that ST-treated zucchini fruit displayed a significantly higher tolerance to chilling stress compared to the control group. Postharvest ST treatment led to a decrease in weight loss, accompanied by reduced levels of malondialdehyde and relative ion leakage compared to the untreated group. ST immersion significantly boosted the metabolic pathways associated with proline and arginine, affecting both the enzymatic reactions and gene expressions, thus cumulatively increasing the internal concentrations of these amino acids in zucchini fruit. Zucchini treated with ST exhibited an increased concentration of gamma-aminobutyric acid (GABA) as a result of augmented activities and elevated transcriptional levels of glutamate decarboxylase (GAD), GABA transaminase (GAT), and succinate semialdehyde dehydrogenase (SSD). In the ST-treated sample, the elevated enzymatic activities and enhanced gene expressions within the ascorbic acid (AsA) biosynthesis pathway worked together to sustain AsA accumulation. The application of ST resulted in a rise in abscisic acid (ABA) concentration, which correspondingly correlated with the induction of both activities and gene expression levels of crucial enzymes involved in ABA metabolism. Our findings revealed that submerging zucchini fruit in ST could be a highly effective strategy for boosting their chilling tolerance. The alleviation in chilling injury induced by ST may be attributed to the modulation of proline, arginine, GABA, AsA and ABA metabolism.
PMID: 38807778
Genomics , IF:5.736 , 2024 May , V116 (4) : P110871 doi: 10.1016/j.ygeno.2024.110871
Dynamic DNA methylation modifications in the cold stress response of cassava.
School of Life Sciences, Nantong University, Nantong 226019, China; Xinglin College, Nantong University, Qidong 226236, China.; Qingdao Smart Rural Development Service Center, Qingdao 266000, China.; Xinglin College, Nantong University, Qidong 226236, China.; Department of Biology, East Carolina University, Greenville, NC 27858, USA.; School of Life Sciences, Nantong University, Nantong 226019, China. Electronic address: kwang5@ntu.edu.cn.; School of Life Sciences, Nantong University, Nantong 226019, China. Electronic address: jinleihan@ntu.edu.cn.
Cassava, a crucial tropical crop, faces challenges from cold stress, necessitating an exploration of its molecular response. Here, we investigated the role of DNA methylation in moderating the response to moderate cold stress (10 degrees C) in cassava. Using whole-genome bisulfite sequencing, we examined DNA methylation patterns in leaf blades and petioles under control conditions, 5 h, and 48 h of cold stress. Tissue-specific responses were observed, with leaf blades exhibiting subtle changes, while petioles displayed a pronounced decrease in methylation levels under cold stress. We identified cold stress-induced differentially methylated regions (DMRs) that demonstrated both tissue and treatment specificity. Importantly, these DMRs were enriched in genes with altered expression, implying functional relevance. The cold-response transcription factor ERF105 associated with DMRs emerged as a significant and conserved regulator across tissues and treatments. Furthermore, we investigated DNA methylation dynamics in transposable elements, emphasizing the sensitivity of MITEs with bHLH binding motifs to cold stress. These findings provide insights into the epigenetic regulation of response to cold stress in cassava, contributing to an understanding of the molecular mechanisms underlying stress adaptation in this tropical plant.
PMID: 38806102
Theor Appl Genet , IF:5.699 , 2024 May , V137 (6) : P135 doi: 10.1007/s00122-024-04643-8
Low frequency of the wild-type freezing-tolerance LsCBF7 allele among lettuce population suggests a negative selection during domestication and breeding.
U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD, 20705, USA. Sunchung.park@usda.gov.; Horticulture Dept, University of Arkansas, Fayetteville, AR, 72701, USA.; U.S. Department of Agriculture, Agricultural Research Service, Salinas, CA, 93905, USA.
Sustainable winter production in lettuce requires freezing tolerant varieties. This study identified a wild-type allele of LsCBF7 that could contribute to freezing tolerance improvement in lettuce. Lettuce is one of the most consumed vegetables globally. While ideally grown in 13-21 degrees C, its cultivation extends into winter in milder climates. However, occasional freezing temperatures can significantly reduce yields. Therefore, the development of freezing-tolerant lettuce varieties has become a long-term goal of lettuce breeding programs. Despite its significance, our understanding of freezing tolerance in lettuce remains limited. Plants have evolved a coping mechanism against freezing, known as cold acclimation, whereby they can increase freezing tolerance when pre-exposed to low nonfreezing temperatures. The CBF pathway is well-known for its central role in cold acclimation. Previously, we identified 14 CBF genes in lettuce and discovered that one of them, LsCBF7, had a loss-of-function mutation. In this study, we uncovered that accessions from colder regions carried the wild-type allele of LsCBF7 and this allele likely contributed to increased freezing tolerance, with 14% of the lettuce population carrying this allele. Interestingly, in wild lettuce (L. serriola) that is considered a progenitor of cultivated lettuce, this wild-type allele was much more common, with a frequency of 90%. This finding suggests that this wild-type allele may have undergone negative selection during the domestication or breeding of lettuce. Our data strongly indicate that this allele could be linked to early bolting, an undesirable trait in lettuce, which may have driven the negative selection. While this wild-type allele shows promise for improving freezing tolerance in lettuce, it is crucial to decouple it from the early bolting trait to fully harness its potential in lettuce breeding.
PMID: 38761248
Rice (N Y) , IF:4.783 , 2024 May , V17 (1) : P34 doi: 10.1186/s12284-024-00713-z
OsLSC6 Regulates Leaf Sheath Color and Cold Tolerance in Rice Revealed by Metabolite Genome Wide Association Study.
Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China.; Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction By Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China. lichen@gdaas.cn.
Plant metabolites including anthocyanins play an important role in the growth of plants, as well as in regulating biotic and abiotic stress responses to the environment. Here we report comprehensive profiling of 3315 metabolites and a further metabolic-based genome-wide association study (mGWAS) based on 292,485 SNPs obtained from 311 rice accessions, including 160 wild and 151 cultivars. We identified hundreds of common variants affecting a large number of secondary metabolites with large effects at high throughput. Finally, we identified a novel gene namely OsLSC6 (Oryza sativa leaf sheath color 6), which encoded a UDP 3-O-glucosyltransferase and involved in the anthocyanin biosynthesis of Cyanidin-3-Galc (sd1825) responsible for leaf sheath color, and resulted in significant different accumulation of sd1825 between wild (purple) and cultivars (green). The results of knockout transgenic experiments showed that OsLSC6 regulated the biosynthesis and accumulation of sd1825, controlled the purple leaf sheath. Our further research revealed that OsLSC6 also confers resistance to cold stress during the seedling stage in rice. And we identified that a SNP in OsLSC6 was responsible for the leaf sheath color and chilling tolerance, supporting the importance of OsLSC6 in plant adaption. Our study could not only demonstrate that OsLSC6 is a vital regulator during anthocyanin biosynthesis and abiotic stress responses, but also provide a powerful complementary tool based on metabolites-to-genes analysis by mGWAS for functional gene identification andpromising candidate in future rice breeding and improvement.
PMID: 38739288
Plant Sci , IF:4.729 , 2024 May , V342 : P112020 doi: 10.1016/j.plantsci.2024.112020
Physiological and transcriptomic analysis revealed that the accumulation of reactive oxygen species caused the low temperature sensitivity of Liriodendron x sinoamericanum.
State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in the Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China.; State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in the Southern China, Nanjing Forestry University, Nanjing 210037, China.; State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in the Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China. Electronic address: jshi@njfu.edu.cn.; State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in the Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China. Electronic address: chenjh@njfu.edu.cn.
Liriodendron x sinoamericanum is widely cultivated in southern China as an excellent wood and garden ornamental trees. However, its intolerance to low temperature limits its application to high latitudes. Understanding the molecular mechanism of low temperature sensitivity of Liriodendron x sinoamericanum is very important for its further application. In this study, combined with physiological and transcriptomic analysis, it was revealed that low temperature stress can lead to water loss and decreased photosynthetic capacity of Liriodendron x sinoamericanum leaves. The accelerated accumulation of reactive oxygen species (ROS) caused by the imbalance of cell REDOX homeostasis is one of the important reasons for the low temperature sensitivity. Further analysis showed that several transcription factors could be involved in regulating the synthesis and degradation of ROS, among which LsNAC72 and LsNAC73a could regulate the accumulation of O(2)(-) and H(2)O(2) in leaves by affecting the expression level of LsAPX, LsSOD, LsPAO, and LsPOD.
PMID: 38311251
Plant Cell Rep , IF:4.57 , 2024 May , V43 (6) : P151 doi: 10.1007/s00299-024-03236-5
Overexpression of VaBAM3 from Vitis amurensis enhances seedling cold tolerance by promoting soluble sugar accumulation and reactive oxygen scavenging.
College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China.; College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China. maojuan@gsau.edu.cn.; State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China. maojuan@gsau.edu.cn.; College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China. bhch@gsau.edu.cn.; State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China. bhch@gsau.edu.cn.
The VaBAM3 cloned from Vitis amurensis can enhance the cold tolerance of overexpressed plants, but VaBAM3 knock out by CRISPR/Cas9 system weakened grape callus cold tolerance. In grape production, extreme cold conditions can seriously threaten plant survival and fruit quality. Regulation of starch content by beta-amylase (BAM, EC: 3.2.1.2) contributes to cold tolerance in plants. In this study, we cloned the VaBAM3 gene from an extremely cold-tolerant grape, Vitis amurensis, and overexpressed it in tomato and Arabidopsis plants, as well as in grape callus for functional characterization. After exposure to cold stress, leaf wilting in the VaBAM3-overexpressing tomato plants was slightly less pronounced than that in wild-type tomato plants, and these plants were characterized by a significant accumulation of autophagosomes. Additionally, the VaBAM3-overexpressing Arabidopsis plants had a higher freezing tolerance than the wild-type counterparts. Under cold stress conditions, the activities of total amylase, BAM, peroxidase, superoxide dismutase, and catalase in VaBAM3-overexpressing plants were significantly higher than those in the corresponding wild-type plants. Furthermore, sucrose, glucose, and fructose contents in these lines were similarly significantly higher, whereas starch contents were reduced in comparison to the levels in the wild-type plants. Furthermore, we detected high CBF and COR gene expression levels in cold-stressed VaBAM3-overexpressing plants. Compared with those in VaBAM3-overexpressing grape callus, the aforementioned indicators tended to change in the opposite direction in grape callus with silenced VaBAM3. Collectively, our findings indicate that heterologous overexpression of VaBAM3 enhanced cold tolerance of plants by promoting the accumulation of soluble sugars and scavenging of excessive reactive oxygen species. These findings provide a theoretical basis for the cultivation of cold-resistant grape and support creation of germplasm resources for this purpose.
PMID: 38802546
Plant Cell Rep , IF:4.57 , 2024 May , V43 (6) : P142 doi: 10.1007/s00299-024-03226-7
Genome-wide identification of the plant homeodomain-finger family in rye and ScPHD5 functions in cold tolerance and flowering time.
Institute of Animal Molecular Biotechnology, Korea University, Seoul, 02841, Korea.; Department of Plant Biotechnology, Korea University, Seoul, 02841, Korea.; Ojeong Plant Breeding Research Center, Korea University, Seoul, 02841, Korea.; Department of Plant Biotechnology, Korea University, Seoul, 02841, Korea. seoag@korea.ac.kr.; Ojeong Plant Breeding Research Center, Korea University, Seoul, 02841, Korea. seoag@korea.ac.kr.
111 PHD genes were newly identified in rye genome and ScPHD5's role in regulating cold tolerance and flowering time was suggested. Plant homeodomain (PHD)-finger proteins regulate the physical properties of chromatin and control plant development and stress tolerance. Although rye (Secale cereale L.) is a major winter crop, PHD-finger proteins in rye have not been studied. Here, we identified 111 PHD genes in the rye genome that exhibited diverse gene and protein sequence structures. Phylogenetic tree analysis revealed that PHDs were genetically close in monocots and diverged from those in dicots. Duplication and synteny analyses demonstrated that ScPHDs have undergone several duplications during evolution and that high synteny is conserved among the Triticeae species. Tissue-specific and abiotic stress-responsive gene expression analyses indicated that ScPHDs were highly expressed in spikelets and developing seeds and were responsive to cold and drought stress. One of these genes, ScPHD5, was selected for further functional characterization. ScPHD5 was highly expressed in the spike tissues and was localized in the nuclei of rye protoplasts and tobacco leaves. ScPHD5-overexpressing Brachypodium was more tolerant to freezing stress than wild-type (WT), with increased CBF and COR gene expression. Additionally, these transgenic plants displayed an extremely early flowering phenotype that flowered more than two weeks earlier than the WT, and vernalization genes, rather than photoperiod genes, were increased in the WT. RNA-seq analysis revealed that diverse stress response genes, including HSPs, HSFs, LEAs, and MADS-box genes, were also upregulated in transgenic plants. Our study will help elucidate the roles of PHD genes in plant development and abiotic stress tolerance in rye.
PMID: 38744747
Physiol Plant , IF:4.5 , 2024 May-Jun , V176 (3) : Pe14352 doi: 10.1111/ppl.14352
Metabolic changes in tomato plants caused by psychrotolerant Antarctic endophytic bacteria might be implicated in cold stress mitigation.
Center Agriculture Food Environment (C3A), University of Trento, San Michele all'Adige, Trento, Italy.; Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Tulln, Austria.; Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.; Core Facility Bioactive Molecules: Screening and Analysis, University of Natural Resources and Life Sciences, Tulln, Austria.
Climate change is responsible for mild winters and warm springs that can induce premature plant development, increasing the risk of exposure to cold stress with a severe reduction in plant growth. Tomato plants are sensitive to cold stress and beneficial microorganisms can increase their tolerance. However, scarce information is available on mechanisms stimulated by bacterial endophytes in tomato plants against cold stress. This study aimed to clarify metabolic changes stimulated by psychrotolerant endophytic bacteria in tomato plants exposed to cold stress and annotate compounds possibly associated with cold stress mitigation. Tomato seeds were inoculated with two bacterial endophytes isolated from Antarctic Colobanthus quitensis plants (Ewingella sp. S1.OA.A_B6 and Pseudomonas sp. S2.OTC.A_B10) or with Paraburkholderia phytofirmans PsJN, while mock-inoculated seeds were used as control. The metabolic composition of tomato plants was analyzed immediately after cold stress exposure (4 degrees C for seven days) or after two and four days of recovery at 25 degrees C. Under cold stress, the content of malondialdehyde, phenylalanine, ferulic acid, and p-coumaric acid was lower in bacterium-inoculated compared to mock-inoculated plants, indicating a reduction of lipid peroxidation and the stimulation of phenolic compound metabolism. The content of two phenolic compounds, five putative phenylalanine-derived dipeptides, and three further phenylalanine-derived compounds was higher in bacterium-inoculated compared to mock-inoculated samples under cold stress. Thus, psychrotolerant endophytic bacteria can reprogram polyphenol metabolism and stimulate the accumulation of secondary metabolites, like 4-hydroxybenzoic and salicylic acid, which are presumably involved in cold stress mitigation, and phenylalanine-derived dipeptides possibly involved in plant stress responses.
PMID: 38764037
Physiol Plant , IF:4.5 , 2024 May-Jun , V176 (3) : Pe14332 doi: 10.1111/ppl.14332
Genome-wide characterization of cytochrome P450 genes reveals the potential roles in fruit ripening and response to cold stress in tomato.
Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, China.; Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs of China, Hangzhou, China.; Hainan Institute, Zhejiang University, Sanya, China.
Plant cytochrome P450 (CYP) superfamily, the largest enzyme metabolism family, has been identified in many species and plays a vital role in plant development and stress response via secondary metabolite biosynthesis. A comprehensive identification and functional investigation of CYPs in tomato plants would contribute to deeper understanding of their biological significance. In this study, 268 tomato CYP genes were identified and found to be unevenly located on 12 chromosomes. Based on the phylogenetic analysis, these 268 SlCYPs were classed into two distinct clades (A-type and non-A-type) and nine clans, including 48 families. Moreover, 67 tandem and 22 WGD (whole genome duplication)/segmental duplication events were detected, of which 12 SlCYP genes experienced both WGD/segmental and tandem duplication events, indicating that tandem duplication plays a major role in the expansion of the SlCYP family. Besides, 48 pairs containing 41 SlCYP and 44 AtCYP genes were orthologous, while 216 orthologous pairs were obtained between tomato and potato. The expression level of all SlCYP genes in tomato tissues at different development stages was analyzed, and most expressed SlCYPs showed a tissue-specific pattern. Meanwhile, 143 differentially expressed SlCYPs were identified under cold stress. Furthermore, the RT-qPCR results indicated that SlCYPs may be involved in fruit ripening and cold tolerance in tomato seedlings. These findings provide valuable insights into the evolutionary relationships and functional characteristics of SlCYPs, which can be utilized for further investigation of fruit metabolic pathways and cold tolerance in tomato.
PMID: 38710502
Ann Bot , IF:4.357 , 2024 May doi: 10.1093/aob/mcae072
High freezing sensitivity of legumes relative to other herbaceous species in northern temperate plant communities.
University of Western Ontario, Department of Biology, 1151 Richmond St. N, London, ON N6A 5B7, Canada.
BACKGROUND AND AIMS: Reduced snow cover and increased air temperature variability are predicted to expose overwintering herbaceous plants to more severe freezing in some northern temperate regions. Legumes are a key functional group that may exhibit lower freezing tolerance than other species these regions, but this trend only has been observed for non-native legumes. Our aim was to confirm if this trend is restricted to non-native legumes or whether native legumes in these regions also exhibit low freezing tolerance. METHODS: First, we transplanted legumes (five non-native species and four native species) into either an old field (non-native) or a prairie (native) and used snow removal to expose the plots to increased soil freezing. Second, we grew plants in mesocosms (old field) and pots (prairie species) and exposed them in controlled environment chambers to a range of freezing treatments (control, 0, -5 or -10 degrees C) in winter or spring. We assessed freezing responses by comparing differences in biomass, cover and nodulation between freezing (or snow removal) treatments and controls. KEY RESULTS: Among legume species, lower freezing tolerance was positively correlated with a lower proportion of nodulated plants and active nodules, and under controlled conditions, freezing-induced reductions in aboveground biomass were lower on average in native legumes than in non-native legumes. Nevertheless, both non-native and native legume (except Desmodium canadense) exhibited greater reductions in biomass in response to increased freezing than their non-leguminous neighbors, both in controlled environments and in the field. CONCLUSIONS: These results demonstrate that both native and non-native legumes exhibit low freezing tolerance relative to other herbaceous species in northern temperate plant communities. By reducing legume biomass and nodulation, increased soil freezing could reduce N inputs into these systems.
PMID: 38742700
Plant Physiol Biochem , IF:4.27 , 2024 May , V212 : P108743 doi: 10.1016/j.plaphy.2024.108743
Genome-wide identification and role of HSFs in antioxidant response of hot water treated zucchini fruit during cold storage.
College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China.; College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China. Electronic address: pjin@njau.edu.cn.
Zucchini squashes are cold-sensitive and vulnerable to chilling injury (CI) resulting from reactive oxygen species (ROS) and hot water (HW) immersing effectively reduce CI symptoms during cold storage. However, mechanism involved in reduced ROS due to HW treatment has not been characterized well. In this study, tender green zucchini fruit were treated with HW for 15 min at 45 +/- 1 degrees C and stored for 15 d at 4 +/- 1 degrees C and above 90 % relative humidity. Results showed substantial reduction in CI index, electrolyte leakage, malonaldehyde (MDA) contents and ROS accumulation along with increased activity of ROS-scavenging enzymes due to HW treatment. To gain insight into the molecular mechanism involved in antioxidant defense system, transcriptomic analysis revealed that heat shock factors (HSF) accumulated due to HW treatment regulated the ROS pathway during cold stress. CpHSFA4a was one of the highly expressed transcription factors (TF) due to HW treatment that regulated the transcription of ROS enzymes related genes. CpHSFA4a bind actively with heat shock element (HSE) in promoter regions of CpSOD, CpCAT, CpAPX1, CpAPX2, and CpAPX3, activated and increased the expression of these genes. In conclusion, HW treatment alleviated the CI by maintaining ROS homeostasis through CpHSFA4a mediated ROS pathway in zucchini squashes during cold storage.
PMID: 38788295
Plant Physiol Biochem , IF:4.27 , 2024 Jun , V211 : P108726 doi: 10.1016/j.plaphy.2024.108726
CsMIEL1 effectively inhibits the accumulation of anthocyanins under low temperatures in tea plants (Camelliasinensis).
School of Biological and Environmental Engineering, Chaohu University, Chaohu Regional Collaborative Technology Service Center for Rural Revitalization, Hefei, 23800, China; State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.; State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.; School of Life Science, Anhui Agricultural University, Hefei, 230036, China.; School of Biological and Environmental Engineering, Chaohu University, Chaohu Regional Collaborative Technology Service Center for Rural Revitalization, Hefei, 23800, China.; College of Education, De La Salle University-Dasmarinas, Cavite, Philippines.; State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China. Electronic address: jiangxiaolan@ahau.edu.cn.; School of Life Science, Anhui Agricultural University, Hefei, 230036, China. Electronic address: gaolp62@126.com.; State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China. Electronic address: xiatao62@126.com.
Tea is one of the most prevalent non-alcoholic beverages. The leaves of tea plants hyperaccumulate anthocyanins under cold stress, resulting in enhanced bitterness. Previously, we determined that the RING-type E3 ubiquitin ligase CsMIEL1 from the tea plant (Camellia sinensis (L.) O. Kuntze) is involved in the response to stress conditions. This study aimed to determine the role of CsMIEL1 in anthocyanin accumulation at the post-translational modification level. The results showed that the heterologous expression of CsMIEL1 led to an 86% decrease in anthocyanin levels, resulting in a significant decrease in the mRNA levels of related genes in Arabidopsis at low temperatures but no significant differences in other phenotypes. Furthermore, multi-omics analysis and yeast two-hybrid library screening were performed to identify potential downstream targets of CsMIEL1. The results showed that the overexpression of CsMIEL1 resulted in 45% (448) of proteins being differentially expressed, of which 8% (36) were downregulated in A.thaliana, and most of these differentially expressed proteins (DEPs) were clustered in the plant growth and secondary metabolic pathways. Among the 71 potential targets that may interact with CsMIEL1, CsMYB90 and CsGSTa, which are related to anthocyanin accumulation, were selected. In subsequent analyses, these two proteins were verified to interact with CsMIEL1 via yeast two-hybrid (Y2H) and pull-down analyses in vitro. In summary, we explored the potential mechanism by which the E3 ligase relieves anthocyanin hyperaccumulation at low temperatures in tea plants. These results provide a new perspective on the mechanisms of anthocyanin regulation and the molecular breeding of tea plants.
PMID: 38744083
Plant Physiol Biochem , IF:4.27 , 2024 Jun , V211 : P108679 doi: 10.1016/j.plaphy.2024.108679
Integrated anatomical structure, physiological, and transcriptomic analyses to identify differential cold tolerance responses of Ziziphus jujuba mill. 'Yueguang' and its autotetraploid 'Hongguang'.
College of Horticulture, Hebei Agricultural University, Baoding, 071001, Hebei, China.; Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China. Electronic address: tanggangliang@ms.xjb.ac.cn.; Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Teheran, Iran.; College of Horticulture, Hebei Agricultural University, Baoding, 071001, Hebei, China. Electronic address: jujubeliu@163.com.; College of Horticulture, Hebei Agricultural University, Baoding, 071001, Hebei, China. Electronic address: wanglxht@163.com.
Cold stress is a limiting stress factor that limits plant distribution and development; however, polyploid plants have specific characteristics such as higher resistance to abiotic stress, especially cold stress, that allow them to overcome this challenge. The cultivated cultivar Ziziphus jujuba Mill. 'Yueguang' (YG) and its autotetraploid counterpart 'Hongguang' (HG) exhibit differential cold tolerance. However, the underlying molecular mechanism and methods to enhance their cold tolerance remain unknown. Anatomical structure and physiological analysis indicated YG had a higher wood bark ratio, and xylem ratio under cold treatment compared to HG. However, the half-lethal temperature (LT(50)), cortex ratio, and malondialdehyde (MDA) content were significantly decreased in YG than HG, which indicated YG was cold tolerant than HG. Transcriptome analysis showed that 2084, 1725, 2888, and 2934 differentially expressed genes (DEGs) were identified in HC vs YC, H20 vs Y20, Y20 vs YC, and H20 vs HC treatment, respectively. Meanwhile, KEGG enrichment analysis of DEGs showed that several metabolic pathways, primarily plant hormone signal transduction and the MAPK signaling pathway, were involved in the differential regulation of cold tolerance between YG and HG. Furthermore, exogenous abscisic acid (ABA) and brassinolide (BR) treatments could improve their cold tolerance through increased SOD and POD activities, decreased relative electrical conductivity, and MDA content. All of these findings suggested that plant hormone signal transduction, particularly ABA and BR, might have an important role in the regulation of differential cold tolerance between YG and HG, laying the foundation for further improving cold tolerance in jujube and examining the molecular mechanisms underlying differences in cold tolerance among different ploidy cultivars.
PMID: 38714127
Plant Physiol Biochem , IF:4.27 , 2024 May , V210 : P108643 doi: 10.1016/j.plaphy.2024.108643
Polystyrene nanoplastics in soil impair drought priming-induced low temperature tolerance in wheat.
Key Laboratory of Black Soil Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.; Key Laboratory of Black Soil Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China.; Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.; Key Laboratory of Black Soil Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: lixiangnan@iga.ac.cn.
Drought priming is known to enhance plant low temperature tolerance, whereas polystyrene nanoplastic contamination exerts detrimental effects on plant growth. This study investigates the less-explored influence of nanoplastic contamination on cold stress tolerance in drought-primed plants. We compared the photosynthetic carbon assimilation, carbohydrate metabolism, reactive oxygen species metabolism, and grain yield between the non-primed and drought-primed wheat grown in both nanoplastic-contaminated and healthy soils. Our results reveal that the beneficial effects of drought priming on photosynthetic carbon assimilation and the efficiency of the "water-water" cycle were compromised in the presence of nanoplastics (nPS). Additionally, nPS exposure disturbed carbohydrate metabolism, which impeded source-to-sink transport of sugar and resulted in reduced grain yield in drought-primed plants under low temperature conditions. These findings unveil the suppression of nPS on drought-primed low-temperature tolerance (DPLT) in wheat plants, suggesting an intricate interplay between the induction of stress tolerance and responses to nPS contamination. The study raises awareness about a potential challenge for future crop production.
PMID: 38653097
Plant Physiol Biochem , IF:4.27 , 2024 May , V210 : P108576 doi: 10.1016/j.plaphy.2024.108576
Integrated analysis of ATAC-seq and transcriptomic reveals the ScDof3-ScproC molecular module regulating the cold acclimation capacity of potato.
National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, PR China; Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, PR China; Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, PR China.; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642, PR China.; National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, PR China; Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, PR China; Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, PR China. Electronic address: songbotao@mail.hzau.edu.cn.
Low temperature severely affects the geographical distribution and production of potato, which may incur cold damage in early spring or winter. Cultivated potatoes, mainly derived from Solanum tuberosum, are sensitive to freezing stress, but wild species of potato such as S. commersonii exhibit both constitutive freezing tolerance and/or cold acclimation tolerance. Hence, such wild species could assist in cold hardiness breeding. Yet the key transcription factors and their downstream functional genes that confer freezing tolerance are far from clear, hindering the breeding process. Here, we used ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) alongside RNA-seq to investigate the variation in chromatin accessibility and patterns of gene expression in freezing-tolerant CMM5 (S. commersonii), before and after its cold treatment. Our results suggest that after exposure to cold, transcription factors including Dof3, ABF2, PIF4, and MYB4 were predicted to further control the genes active in the synthetic/metabolic pathways of plant hormones, namely abscisic acid, polyamine, and reductive glutathione (among others). This suggests these transcription factors could regulate freezing tolerance of CMM5 leaves. In particular, ScDof3 was proven to regulate the expression of ScproC (pyrroline-5-carboxylate reductase, P5CR) according to dual-LUC assays. Overexpressing ScDof3 in Nicotiana benthamiana leaves led to an increase in both the proline content and expression level of NbproC (homolog of ScproC). These results demonstrate the ScDof3-ScproC module regulates the proline content and thus promotes freezing tolerance in potato. Our research provides valuable genetic resources to further study the molecular mechanisms underpinning cold tolerance in potato.
PMID: 38608502
BMC Plant Biol , IF:4.215 , 2024 May , V24 (1) : P442 doi: 10.1186/s12870-024-05099-0
Integrated transcriptomic and metabolomic analysis provides insights into cold tolerance in lettuce (Lactuca sativa L.).
Shanghai Agrobiological Gene Center, Shanghai, 201106, China.; Institute of Biothermal Science and Technology, School of Health Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, 200093, China.; Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu National Agricultural Science and Technology Center, Chengdu, 610213, China.; Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu National Agricultural Science and Technology Center, Chengdu, 610213, China. zhangli10@caas.cn.; Shanghai Agrobiological Gene Center, Shanghai, 201106, China. wsw@sagc.org.cn.; Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China. wsw@sagc.org.cn.; Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China.
The popular leafy vegetable lettuce (Lactuca sativa L.) is susceptible to cold stress during the growing season, which slows growth rate, causes leaf yellowing and necrosis, and reduced yield and quality. In this study, transcriptomic and metabolomic analyses of two cold-resistant lettuce cultivars (GWAS-W42 and F11) and two cold-sensitive lettuce cultivars (S13K079 and S15K058) were performed to identify the mechanisms involved in the cold response of lettuce. Overall, transcriptome analysis identified 605 differentially expressed genes (DEGs), including significant enrichment of genes involved in the flavonoid and flavonol (CHS, CHI, F3H, FLS, CYP75B1, HCT, etc.) biosynthetic pathways related to oxidation-reduction and catalytic activity. Untargeted metabolomic analysis identified fifteen flavonoid metabolites and 28 other metabolites potentially involved in the response to cold stress; genistein, quercitrin, quercetin derivatives, kaempferol derivatives, luteolin derivatives, apigenin and their derivatives accumulate at higher levels in cold-resistant cultivars. Moreover, MYBs, bHLHs, WRKYs and Dofs also play positive role in the low temperature response, which affected the expression of structural genes contributing to the variation of metabolites between the resistant and sensitive. These results provide valuable evidence that the metabolites and genes involved in the flavonoid biosynthetic pathway play important roles in the response of lettuce to cold stress.
PMID: 38778262
BMC Plant Biol , IF:4.215 , 2024 May , V24 (1) : P433 doi: 10.1186/s12870-024-05111-7
Genome-wide characterization of LEA gene family reveals a positive role of BnaA.LEA6.a in freezing tolerance in rapeseed (Brassica napus L.).
College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China.; College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China. hexinzhsh@126.com.
BACKGROUND: Freezing stress is one of the major abiotic stresses that causes extensive damage to plants. LEA (Late embryogenesis abundant) proteins play a crucial role in plant growth, development, and abiotic stress. However, there is limited research on the function of LEA genes in low-temperature stress in Brassica napus (rapeseed). RESULTS: Total 306 potential LEA genes were identified in B. rapa (79), B. oleracea (79) and B. napus (148) and divided into eight subgroups. LEA genes of the same subgroup had similar gene structures and predicted subcellular locations. Cis-regulatory elements analysis showed that the promoters of BnaLEA genes rich in cis-regulatory elements related to various abiotic stresses. Additionally, RNA-seq and real-time PCR results indicated that the majority of BnaLEA family members were highly expressed in senescent tissues of rapeseed, especially during late stages of seed maturation, and most BnaLEA genes can be induced by salt and osmotic stress. Interestingly, the BnaA.LEA6.a and BnaC.LEA6.a genes were highly expressed across different vegetative and reproductive organs during different development stages, and showed strong responses to salt, osmotic, and cold stress, particularly freezing stress. Further analysis showed that overexpression of BnaA.LEA6.a increased the freezing tolerance in rapeseed, as evidenced by lower relative electrical leakage and higher survival rates compared to the wild-type (WT) under freezing treatment. CONCLUSION: This study is of great significance for understanding the functions of BnaLEA genes in freezing tolerance in rapeseed and offers an ideal candidate gene (BnaA.LEA6.a) for molecular breeding of freezing-tolerant rapeseed cultivars.
PMID: 38773359
BMC Plant Biol , IF:4.215 , 2024 May , V24 (1) : P373 doi: 10.1186/s12870-024-05086-5
A method for mining condition-specific co-expressed genes in Camellia sinensis based on k-means clustering.
Tea Research Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China. xhzheng@zju.edu.cn.; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore. xhzheng@zju.edu.cn.; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore. mutwil@ntu.edu.sg.; Tea Research Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China. zdcy@zju.edu.cn.
BACKGROUND: As one of the world's most important beverage crops, tea plants (Camellia sinensis) are renowned for their unique flavors and numerous beneficial secondary metabolites, attracting researchers to investigate the formation of tea quality. With the increasing availability of transcriptome data on tea plants in public databases, conducting large-scale co-expression analyses has become feasible to meet the demand for functional characterization of tea plant genes. However, as the multidimensional noise increases, larger-scale co-expression analyses are not always effective. Analyzing a subset of samples generated by effectively downsampling and reorganizing the global sample set often leads to more accurate results in co-expression analysis. Meanwhile, global-based co-expression analyses are more likely to overlook condition-specific gene interactions, which may be more important and worthy of exploration and research. RESULTS: Here, we employed the k-means clustering method to organize and classify the global samples of tea plants, resulting in clustered samples. Metadata annotations were then performed on these clustered samples to determine the "conditions" represented by each cluster. Subsequently, we conducted gene co-expression network analysis (WGCNA) separately on the global samples and the clustered samples, resulting in global modules and cluster-specific modules. Comparative analyses of global modules and cluster-specific modules have demonstrated that cluster-specific modules exhibit higher accuracy in co-expression analysis. To measure the degree of condition specificity of genes within condition-specific clusters, we introduced the correlation difference value (CDV). By incorporating the CDV into co-expression analyses, we can assess the condition specificity of genes. This approach proved instrumental in identifying a series of high CDV transcription factor encoding genes upregulated during sustained cold treatment in Camellia sinensis leaves and buds, and pinpointing a pair of genes that participate in the antioxidant defense system of tea plants under sustained cold stress. CONCLUSIONS: To summarize, downsampling and reorganizing the sample set improved the accuracy of co-expression analysis. Cluster-specific modules were more accurate in capturing condition-specific gene interactions. The introduction of CDV allowed for the assessment of condition specificity in gene co-expression analyses. Using this approach, we identified a series of high CDV transcription factor encoding genes related to sustained cold stress in Camellia sinensis. This study highlights the importance of considering condition specificity in co-expression analysis and provides insights into the regulation of the cold stress in Camellia sinensis.
PMID: 38714965
BMC Plant Biol , IF:4.215 , 2024 May , V24 (1) : P376 doi: 10.1186/s12870-024-04889-w
Genome-wide identification of WRKY transcription factors in Casuarina equisetifolia and the function analysis of CeqWRKY11 in response to NaCl/NaHCO(3) stresses.
State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, Zhejiang, 311300, China.; Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, University Road, Tobe Camp, Abbottabad, 22060, Pakistan.; State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, Zhejiang, 311300, China. shenkuiliu@nefu.edu.cn.; State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, Zhejiang, 311300, China. hmren@zafu.edu.cn.
BACKGROUND: Casuarina equisetifolia (C. equisetifolia) is a woody species with many excellent features. It has natural resistance against drought, salt and saline-alkali stresses. WRKY transcription factors (TFs) play significant roles in plant response to abiotic stresses, therefore, molecular characterization of WRKY gene family under abiotic stresses holds great significance for improvement of forest trees through molecular biological tools. At present, WRKY TFs from C. equisetifolia have not been thoroughly studied with respect to their role in salt and saline-alkali stresses response. The current study was conducted to bridge the same knowledge gap. RESULTS: A total of 64 WRKYs were identified in C. equisetifolia and divided into three major groups i.e. group I, II and III, consisting of 10, 42 and 12 WRKY members, respectively. The WRKY members in group II were further divided into 5 subgroups according to their homology with Arabidopsis counterparts. WRKYs belonging to the same group exhibited higher similarities in gene structure and the presence of conserved motifs. Promoter analysis data showed the presence of various response elements, especially those related to hormone signaling and abiotic stresses, such as ABRE (ABA), TGACG (MeJA), W-box ((C/T) TGAC (T/C)) and TC-rich motif. Tissue specific expression data showed that CeqWRKYs were mainly expressed in root under normal growth conditions. Furthermore, most of the CeqWRKYs were up-regulated by NaCl and NaHCO(3) stresses with few of WRKYs showing early responsiveness to both stresses while few others exhibiting late response. Although the expressions of CeqWRKYs were also induced by cold stress, the response was delayed compared with other stresses. Transgenic C. equisetifolia plants overexpressing CeqWRKY11 displayed lower electrolyte leakage, higher chlorophyll content, and enhanced tolerance to both stresses. The higher expression of abiotic stress related genes, especially CeqHKT1 and CeqPOD7, in overexpression lines points to the maintenance of optimum Na(+)/K(+) ratio, and ROS scavenging as possible key molecular mechanisms underlying salt stress tolerance. CONCLUSIONS: Our results show that CeqWRKYs might be key regulators of NaCl and NaHCO(3) stresses response in C. equisetifolia. In addition, positive correlation of CeqWRKY11 expression with increased stress tolerance in C. equisetifolia encourages further research on other WRKY family members through functional genomic tools. The best candidates could be incorporated in other woody plant species for improving stress tolerance.
PMID: 38714947
BMC Plant Biol , IF:4.215 , 2024 May , V24 (1) : P467 doi: 10.1186/s12870-024-05167-5
Winter survival in red clover: experimental evidence for interactions among stresses.
Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, As, N-1432, Norway. ashild.ergon@nmbu.no.; Graminor AS, Hommelstadvegen 60, Ridabu, 2322, Norway.
BACKGROUND: There is a lack of knowledge on the combined effects of different stresses on plants, in particular different stresses that occur during winter in temperate climates. Perennial herbaceous plants in temperate regions are exposed to many different stresses during winter, but except for the fact that cold temperatures induce resistance to a number of them, very little is known about their interaction effects. Knowledge about stress interactions is needed in order to predict effects of climate change on both agricultural production and natural ecosystems, and to develop adaptation strategies, e.g., through plant breeding. Here, we conducted a series of experiments under controlled conditions to study the interactions between cold (low positive temperature), clover rot infection (caused by Sclerotinia trifoliorum) and freezing, in red clover (Trifolium pratense) accessions. We also compared our results with winter survival in field experiments and studied associations between stress and shoot growth. RESULTS: Exposure to low positive temperatures (cold acclimation) induced resistance to clover rot. There was a clear negative interaction effect between freezing stress and clover rot infection, resulting in up to 37% lower survival rate compared to what would have been expected from the additive effect of freezing and infection alone. Freezing tolerance could continue to improve during incubation under artificial snow cover at 3 degrees C in spite of darkness, and we observed compensatory shoot growth following freezing after prolonged incubation. At the accession level, resistance to clover rot was negatively correlated with growth in the field during the previous year at a Norwegian location. It was also negatively correlated with the shoot regrowth of control plants after incubation. Clover rot resistance tests under controlled conditions showed limited correlation with clover rot resistance observed in the field, suggesting that they may reveal variation in more specific resistance mechanisms. CONCLUSIONS: We here demonstrate, for the first time, a strong negative interaction between freezing and infection with a winter pathogen. We also characterize the effects of cold acclimation and incubation in darkness at different temperatures on winter stress tolerance, and present data that support the notion that annual cycles of growth and stress resistance are associated at the genetic level.
PMID: 38807057
BMC Genomics , IF:3.969 , 2024 May , V25 (1) : P479 doi: 10.1186/s12864-024-10403-1
Maize miRNAs and their putative target genes involved in chilling stress response in 5-day old seedlings.
Laboratory for Molecular Genetics and Physiology, Research and Development Department, Maize Research Institute Zemun Polje, Belgrade, Serbia.; Laboratory for Molecular Genetics and Physiology, Research and Development Department, Maize Research Institute Zemun Polje, Belgrade, Serbia. idragana@mrizp.rs.
BACKGROUND: In the context of early sowing of maize as a promising adaptation strategy that could significantly reduce the negative effects of climate change, an in-depth understanding of mechanisms underlying plant response to low-temperature stress is demanded. Although microRNAs (miRNAs) have been recognized as key regulators of plant stress response, research on their role in chilling tolerance of maize during early seedling stages is scarce. Therefore, it is of great significance to explore chilling-responsive miRNAs, reveal their expression patterns and associated target genes, as well as to examine the possible functions of the conserved and novel miRNAs. In this study, the role of miRNAs was examined in 5d-old maize seedlings of one tolerant and one sensitive inbred line exposed to chilling (10/8 degrees C) stress for 6 h and 24 h, by applying high throughput sequencing. RESULTS: A total of 145 annotated known miRNAs belonging to 30 families and 876 potentially novel miRNAs were identified. Differential expression (DE) analysis between control and stress conditions identified 98 common miRNAs for both genotypes at one time point and eight miRNAs at both time points. Target prediction and enrichment analysis showed that the DE zma-miR396, zma-miR156, zma-miR319, and zma-miR159 miRNAs modulate growth and development. Furthermore, it was found that several other DE miRNAs were involved in abiotic stress response: antioxidative mechanisms (zma-miR398), signal transduction (zma-miR156, zma-miR167, zma-miR169) and regulation of water content (zma-miR164, zma-miR394, zma-miR396). The results underline the zma-miRNAs involvement in the modulation of their target genes expression as an important aspect of the plant's survival strategy and acclimation to chilling stress conditions. CONCLUSIONS: To our understanding, this is the first study on miRNAs in 5-d old seedlings' response to chilling stress, providing data on the role of known and novel miRNAs post-transcriptional regulation of expressed genes and contributing a possible platform for further network and functional analysis.
PMID: 38750515
Plants (Basel) , IF:3.935 , 2024 May , V13 (10) doi: 10.3390/plants13101321
A Genome-Wide Analysis of the BAM Gene Family and Identification of the Cold-Responsive Genes in Pomegranate (Punica granatum L.).
School of Life Science, Huaibei Normal University, Huaibei 235000, China.
Beta-amylases (BAMs, EC 3.2.1.2), belonging to a multigene family, play a pivotal role in starch breakdown and are also involved in hormonal and stress responses, notably to cold stress. Pomegranate trees (Punica granatum L.) are adapted to warm climates and are sensitive to cold temperatures. In this study, we analyzed eight PgBAM genes from the pomegranate genome dataset. These members unevenly distributed across chromosomes and were categorized into four groups based on their orthologous members. The motif composition was highly consistent among most members. In contrast, exon numbers and arrangements were conserved within groups or subgroups, whereas significant diversity was observed between different groups. A syntenic analysis revealed that three PgBAM members (PgBAM1/4/5) showed a total of 11 syntenic relationships with the BAM members from Arabidopsis, kiwifruit, and Chinese white pear, respectively. Promoter binding motif prediction suggested potential roles for PgBAMs' genes in light, stress, hormones, and development signaling. Gene expression indicated that PgBAM4 was predominantly expressed in leaves, PgBAM7 in flowers, and PgBAM8 in roots and leaves and during fruit ripening, particularly in pericarp development. A transcriptome analysis identified the starch and sucrose metabolism pathway (map00500) as a key factor in the cold stress response of cold-sensitive cultivar 'Tunisia' seedlings. PgBAM4 exhibited remarkable expression and was closely associated with the cold-responsive BAM genes, characterized by a closer phylogenetic relationship, conserved catalytic residues, and similar secondary and tertiary structures. Moreover, the differences in soluble sugar levels and PgBAM4 expression were closely associated with the varying cold stress resistance observed between 'Tunisia' and 'Sanbai' seedlings. Furthermore, yeast one-hybrid assays confirmed that PgCBF7, a critical transcription factor for enhancing freezing tolerance, binds to the promoter region of PgBAM4. Our findings provide a systematic overview of the PgBAM gene family and shed new light on the regulatory mechanisms underlying cold stress tolerance in pomegranate.
PMID: 38794392
Gene , IF:3.688 , 2024 Jul , V917 : P148467 doi: 10.1016/j.gene.2024.148467
Overexpression of Rhodiola crenulata glutathione peroxidase 5 increases cold tolerance and enhances the pharmaceutical value of the hairy roots.
Pu'er People's Hospital, Yunnan, China; Tianjin Chest Hospital, Tianjin, China; Chest Hospital, Tianjin University, Tianjin, China; Tianjin Medical University, Tianjin, China.; Tianjin Chest Hospital, Tianjin, China; Chest Hospital, Tianjin University, Tianjin, China.; Pu'er People's Hospital, Yunnan, China.; Tianjin Chest Hospital, Tianjin, China; Chest Hospital, Tianjin University, Tianjin, China; Tianjin Medical University, Tianjin, China. Electronic address: sdqmd@tju.edu.cn.; Tianjin Chest Hospital, Tianjin, China; Chest Hospital, Tianjin University, Tianjin, China; Tianjin Medical University, Tianjin, China. Electronic address: Zhigangguo2022@126.com.; School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China. Electronic address: zhanglp@tjcu.edu.cn.
Rhodiola crenulata, a plant of great medicinal value found in cold high-altitude regions, has been excessively exploited due to the difficulty in cultivation. Understanding Rhodiola crenulata's adaptation mechanisms to cold environment can provide a theoretical basis for artificial breeding. Glutathione peroxidases (GPXs), critical enzymes found in plants, play essential roles in antioxidant defense through the ascorbate-glutathione cycle. However, it is unknown whether GPX5 contributes to Rhodiola crenulata's cold tolerance. In this study, we investigated the role of GPX5 in Rhodiola crenulata's cold tolerance mechanisms. By overexpressing Rhodiola crenulata GPX5 (RcGPX5) in yeast and Arabidopsis thaliana, we observed down-regulation of Arabidopsis thaliana GPX5 (AtGPX5) and increased cold tolerance in both organisms. Furthermore, the levels of antioxidants and enzyme activities in the ascorbate-glutathione cycle were elevated, and cold-responsive genes such as AtCBFs and AtCORs were induced. Additionally, RcGPX5 overexpressing lines showed insensitivity to exogenous abscisic acid (ABA), suggesting a negative regulation of the ABA pathway by RcGPX5. RcGPX5 also promoted the expression of several thioredoxin genes in Arabidopsis and interacted with two endogenous genes of Rhodiola crenulata, RcTrx2-3 and RcTrxo1, located in mitochondria and chloroplasts. These findings suggest a significantly different model in Rhodiola crenulata compared to Arabidopsis thaliana, highlighting a complex network involving the function of RcGPX5. Moreover, overexpressing RcGPX5 in Rhodiola crenulata hairy roots positively influenced the salidroside synthesis pathway, enhancing its pharmaceutical value for doxorubicin-induced cardiotoxicity. These results suggested that RcGPX5 might be a key component for Rhodiola crenulata to adapt to cold stress and overexpressing RcGPX5 could enhance the pharmaceutical value of the hairy roots.
PMID: 38615983
Gene , IF:3.688 , 2024 Jun , V913 : P148398 doi: 10.1016/j.gene.2024.148398
Genome-wide analysis of LOG family genes in castor and RcLOG5 enhances drought, salt, and cold stress tolerance in Arabidopsis thaliana.
College of Agriculture, Inner Mongolia Minzu University, Tongliao 028000, China.; College of Agriculture, Inner Mongolia Minzu University, Tongliao 028000, China. Electronic address: xiangdianjun00@126.com.; College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao 028000, China.; College of Agriculture, Inner Mongolia Minzu University, Tongliao 028000, China. Electronic address: liupeng@imun.edu.cn.
The gene encoding the specific phosphohydrolase LONELY GUY (LOG) plays an important role in the activation of cytokinin and the stress response in plant cells. However, the role of LOG genes in castor bean (Ricinus communis) has not been reported. In this study, we identified a total of nine members of the LOG gene family in the castor bean genome and investigated the upregulated expression of the RcLOG5 gene using transcriptome data analysis. We found that the RcLOG5 gene exhibited tissue-specific expression and was activated by polyethylene glycol, NaCl, low temperature, and abscisic acid stress. The subcellular localization results showed that the RcLOG5 gene is mainly located in the cytoplasm. Based on phenotypic and physiological indicators, namely root length, peroxidase activity, and malondialdehyde content, overexpression of the RcLOG5 gene not only improved the drought resistance, salt tolerance, and cold tolerance of transgenic Arabidopsis, but also shortened the dormancy period of the transgenic plants. Transcriptomic sequencing revealed that the overexpression of the RcLOG5 gene led to the enrichment of differentially expressed genes in the glutathione metabolism pathway in transgenic Arabidopsis. Moreover, the overexpression plants had higher levels of glutathione and a higher GSH/GSSG ratio under stress compared to the wild type. Therefore, we inferred that the RcLOG5 gene may be responsible for regulating cell membrane homeostasis by reducing the accumulation of reactive oxygen species through the glutathione pathway. Overall, the overexpression of the RcLOG5 gene positively regulated the stress resistance of transgenic Arabidopsis. This study provides valuable gene resources for breeding stress-tolerant castor bean varieties.
PMID: 38518901
J Plant Physiol , IF:3.549 , 2024 May , V296 : P154233 doi: 10.1016/j.jplph.2024.154233
TaMAPK3 phosphorylates TaCBF and TaICE and plays a negative role in wheat freezing tolerance.
Institute of Animal Molecular Biotechnology, Korea University, Seoul, 02841, South Korea.; Ojeong Plant Breeding Research Center, Korea University, Seoul, 02841, South Korea.; Ojeong Plant Breeding Research Center, Korea University, Seoul, 02841, South Korea; Department of Plant Biotechnology, Korea University, Seoul, 02841, South Korea. Electronic address: seoag@korea.ac.kr.
Freezing temperature during overwintering often kills plants; plants have thus, developed a defense mechanism called 'cold acclimation', in which a number of genes are involved in increasing cell protection and gene expression. Mitogen-activated protein kinase (MAPK) controls proteins' activities by phosphorylation and is involved in numerous metabolic pathways. In this study, we identified the protein interaction between TaMAPK3 and the proteins in the cold response pathway, ICE41, ICE87, and CBFIVd-D9. The subcellular localization and bimolecular fluorescence complement (BiFC) assays revealed that these proteins interact in the nucleus or in the plasma membrane. Furthermore, MAPK3-mediated phosphorylation of ICE41, ICE87, and CBFIVd-D9 was verified using an in vitro phosphorylation assay. TaMAPK3-overexpressing transgenic Brachypodium showed a lower survival rate upon freezing stress and lower proline content during cold acclimation, compared to wild-type plants. Furthermore, cold response gene expression analysis revealed that the expression of these genes was suppressed in the transgenic lines under cold treatment. It was further elucidated that MAPK3 mediates the degradation of ICE and CBF proteins, which implies the negative impact of MAPK3 on the freezing tolerance of plants. This study will help to elucidate the molecular mechanisms of cold tolerance and the activity of MAPK3 in wheat.
PMID: 38554674
AoB Plants , IF:3.276 , 2024 Jun , V16 (3) : Pplae022 doi: 10.1093/aobpla/plae022
Survival analysis of freezing stress in the North American native perennial flax, Linum lewisii.
Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA.; Sunflower Improvement Research Unit, Edward T. Schafer Agricultural Research Center, United Services Department of Agriculture (USDA)-Agricultural Research Service, Fargo, ND 58102, USA.
Abstract. The expansive range of Lewis flax (Linum lewisii), an herbaceous perennial, exposes the species to a diversity of climatic conditions. As interest in the domestication and adoption of perennial crop alternatives grows and interest in this species for natural area restoration continues, the assurance of a commercial plant variety's ability to endure the full range of possible climatic extremes is paramount. This study examines the freezing tolerance of a geographically representative sampling of 44 Lewis flax accessions at winter temperature extremes experienced in the northern Great Plains of the USA. Survival analysis models were adapted to include temperature exposure, in replacement of ordinal time typically used in such models, to produce statistics evaluating reactions to extreme temperatures that Lewis flax would encounter in our field environments. Our results revealed Lewis flax is more freezing tolerant than previously reported, and revealed four accessions with significantly superior genetic freezing tolerance than the released 'Maple Grove' cultivar. Furthermore, regrowth analyses indicate variation among accessions not associated with survival, which could lead to improving regrowth rate and survival simultaneously. These findings and their methodology expand the understanding of Lewis flax adaptation for winter hardiness and offer an efficient, new model that can be used to evaluate freezing tolerance at ordinal temperatures without requiring extensive prior physiological knowledge for a species.
PMID: 38716380
Plant Biol (Stuttg) , IF:3.081 , 2024 Jun , V26 (4) : P532-543 doi: 10.1111/plb.13643
Improving chilling tolerance of peanut seedlings by enhancing antioxidant-modulated ROS scavenging ability, alleviating photosynthetic inhibition, and mobilizing nutrient absorption.
College of Agronomy, Peanut Research Institute, Shenyang Agricultural University, Shenyang, Liaoning Province, China.
Peanut production is threatened by climate change. Damage to seedlings from low temperatures in early spring can limit yield. Plant adaptations to chilling stress remain unclear in peanut seedlings. It is essential to understand how peanut acquires chilling tolerance. We evaluated effects of chilling stress on growth and recovery of peanut seedlings. We compared and analysed biological characteristics, antioxidants, photosynthesis, biochemical and physiological responses, and nutrient absorption at varying levels of chilling. Compared with chilling-sensitive FH18, the reduced impact of chilling stress on chilling-tolerant NH5 was associated with reduced ROS accumulation, higher ascorbate peroxidase activity and soluble sugar content, lower soluble protein content, and smaller reductions in nutrient content during stress. After removal of chilling stress, FH18 had significant accumulation of O(2) (*-) and H(2)O(2), which decreased photosynthesis, nutrient absorption, and transport. ROS-scavenging reduced damage from chilling stress, allowed remobilization of nutrients, improved chilling tolerance, and restored plant functioning after chilling stress removal. These findings provide a reference for targeted research on peanut seedling tolerance to chilling and lay the foundation for bioinformatics-based research on peanut chilling tolerance mechanisms.
PMID: 38597809
Mol Biol Rep , IF:2.316 , 2024 May , V51 (1) : P602 doi: 10.1007/s11033-024-09551-0
Identification and analysis of MAPK cascade gene families of Camellia oleifera and their roles in response to cold stress.
Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, School of Life Sciences, Nanchang University, Nanchang, 330031, China.; Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, School of Life Sciences, Nanchang University, Nanchang, 330031, China. zhangjianlab@126.com.
BACKGROUND: Low-temperature severely limits the growth and development of Camellia oleifera (C. oleifera). The mitogen-activated protein kinase (MAPK) cascade plays a key role in the response to cold stress. METHODS AND RESULTS: Our study aims to identify MAPK cascade genes in C. oleifera and reveal their roles in response to cold stress. In our study, we systematically identified and analyzed the MAPK cascade gene families of C. oleifera, including their physical and chemical properties, conserved motifs, and multiple sequence alignments. In addition, we characterized the interacting networks of MAPKK kinase (MAPKKK)-MAPK kinase (MAPKK)-MAPK in C. oleifera. The molecular mechanism of cold stress resistance of MAPK cascade genes in wild C. oleifera was analyzed by differential gene expression and real-time quantitative reverse transcription-PCR (qRT-PCR). CONCLUSION: In this study, 21 MAPKs, 4 MAPKKs and 55 MAPKKKs genes were identified in the leaf transcriptome of C. oleifera. According to the phylogenetic results, MAPKs were divided into 4 groups (A, B, C and D), MAPKKs were divided into 3 groups (A, B and D), and MAPKKKs were divided into 2 groups (MEKK and Raf). Motif analysis showed that the motifs in each subfamily were conserved, and most of the motifs in the same subfamily were basically the same. The protein interaction network based on Arabidopsis thaliana (A. thaliana) homologs revealed that MAPK, MAPKK, and MAPKKK genes were widely involved in C. oleifera growth and development and in responses to biotic and abiotic stresses. Gene expression analysis revealed that the CoMAPKKK5/CoMAPKKK43/CoMAPKKK49-CoMAPKK4-CoMAPK8 module may play a key role in the cold stress resistance of wild C. oleifera at a high-elevation site in Lu Mountain (LSG). This study can facilitate the mining and utilization of genetic resources of C. oleifera with low-temperature tolerance.
PMID: 38698158
Plant Signal Behav , IF:2.247 , 2024 Dec , V19 (1) : P2318514 doi: 10.1080/15592324.2024.2318514
Insights on the enhancement of chilling tolerance in Rice through over-expression and knock-out studies of OsRBCS3.
Rice Research Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China.; Key Laboratory of Molecular Biology, Heilongjiang University, Harbin, China.
Chilling stress is an important environmental factor that affects rice (Oryza sativa L.) growth and yield, and the booting stage is the most sensitive stage of rice to chilling stress. In this study, we focused on OsRBCS3, a rice gene related to chilling tolerance at the booting stage, which encodes the key enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) small subunit in photosynthesis. The aim of this study was to elucidate the role and mechanism of OsRBCS3 in rice chilling tolerance at the booting stage. The expression levels of OsRBCS3 under chilling stress were compared in two japonica rice cultivars with different chilling tolerances: Kongyu131 (KY131) and Longjing11 (LJ11). A positive correlation was found between OsRBCS3 expression and chilling tolerance. Over-expression (OE) and knock-out (KO) lines of OsRBCS3 were constructed using over-expression and CRISPR/Cas9 technology, respectively, and their chilling tolerance was evaluated at the seedling and booting stages. The results showed that OE lines exhibited higher chilling tolerance than wild-type (WT) lines at both seedling and booting stages, while KO lines showed lower chilling tolerance than WT lines. Furthermore, the antioxidant enzyme activities, malondialdehyde (MDA) content and Rubisco activity of four rice lines under chilling stress were measured, and it was found that OE lines had stronger antioxidant and photosynthetic capacities, while KO lines had the opposite effects. This study validated that OsRBCS3 plays an important role in rice chilling tolerance at the booting stage, providing new molecular tools and a theoretical basis for rice chilling tolerance breeding.
PMID: 38375792
Genetica , IF:1.082 , 2024 May doi: 10.1007/s10709-024-00209-0
Genome-wide identification and expression analysis of the universal stress protein (USP) gene family in Arabidopsis thaliana, Zea mays, and Oryza sativa.
College of Life Sciences and Engineering, Shenyang University, Shenyang, 110000, China. fan_mingxia@foxmail.com.; College of Life Sciences and Engineering, Shenyang University, Shenyang, 110000, China.; Shenyang Institute of Agricultural Science and Technology, Shenyang, 110161, China.; Shenyang Rural Revitalization and Development Center, Shenyang, 110121, China.; Zea Mays Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, China.
The Universal Stress Protein (USP) primarily participates in cellular responses to biotic and abiotic stressors, playing a pivotal role in plant growth, development, and Stress responses to adverse environmental conditions. Totals of 23, 26 and 26 USP genes were recognized in Arabidopsis thaliana, Zea mays, and Oryza sativa, respectively. According to USP genes physicochemical properties, proteins from USP I class were identified as hydrophilic proteins with high stability. Based on phylogenetic analysis, USP genes family were classified into nine groups, USP II were rich in motifs. Additionally, members of the same subgroup exhibited similar numbers of introns/exons, and shared conserved domains, indicating close evolutionary relationships. Motif analysis results demonstrated a high degree of conservation among USP genes. Chromosomal distribution suggested that USP genes might have undergone gene expansion through segmental duplication in Arabidopsis thaliana, Zea mays, and Oryza sativa. Most Ka/Ks ratios were found to be less than 1, suggesting that USP genes in Arabidopsis thaliana, Zea mays, and Oryza sativa have experienced purifying selection. Expression profile analysis revealed that USP genes primarily respond to drought stress in Oryza sativa, temperature, and drought stress in Zea mays, and cold stress in Arabidopsis thaliana. Gene collinearity analysis can reveal correlations between genes, aiding subsequent in-depth investigations. This study sheds new light on the evolution of USP genes in monocots and dicots and lays the foundation for a better understanding of the biological functions of the USP genes family.
PMID: 38789817
J Genet Eng Biotechnol , 2024 Jun , V22 (2) : P100376 doi: 10.1016/j.jgeb.2024.100376
Whole genome resequencing unveils low-temperature stress tolerance specific genomic variations in jute (Corchorus sp.).
Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh.; Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh; Department of Biochemistry and Molecular Biology, National Institute of Science and Technology, Dhaka, Bangladesh.; Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh. Electronic address: haseena@du.ac.bd.; Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh. Electronic address: mriazulislam@du.ac.bd.
Jute (Corchorus sp.), a commercially important and eco-friendly crop, is widely cultivated in Bangladesh, India, and China. Some varieties of this tropical plant such as the Corchorus olitorius. Variety accession no. 2015 (acc. 2015) has been found to be low-temperature tolerant. The current study was designed to explore the genome-wide variations present in the tolerant plant acc. 2015 in comparison to the sensitive farmer popular variety Corchorus olitorius var. O9897 using the whole genome resequencing technique. Among different variations, intergenic Single Nucleotide Polymorphism (SNPs) and Insertion-Deletion (InDels) were found in the highest percentage whereas approximately 3% SNPs and 2% InDels were found in exonic regions in both plants. Gene enrichment analysis indicated the presence of acc. 2015 specific SNPs in the genes encoding peroxidase, ER lumen protein retaining receptor, and hexosyltransferase involved in stress response (GO:0006950) which were not present in sensitive variety O9897. Besides, distinctive copy number variation regions (CNVRs) comprising 120 gene loci were found in acc. 2015 with a gain of function from multiple copy numbers but absent in O9897. Gene ontology analysis revealed these gene loci to possess different receptors like kinases, helicases, phosphatases, transcription factors especially Myb transcription factors, regulatory proteins containing different binding domains, annexin, laccase, acyl carrier protein, potassium transporter, and vesicular transporter proteins that are responsible for low temperature induced adaptation pathways in plants. This work of identifying genomic variations linked to cold stress tolerance traits will help to develop successful markers that will pave the way to develop genetically modified cold-resistant jute lines for year-round cultivation to meet the demand for a sustainable fiber crop economy.
PMID: 38797551
Data Brief , 2024 Jun , V54 : P110319 doi: 10.1016/j.dib.2024.110319
Reference field spectrometric data of albino rice plants.
Hungarian University of Agriculture and Life Sciences, Institute of Environmental Sciences, Research Center for Irrigation and Water Management, Anna-liget str. 35, Szarvas, H-5540, Hungary.; Department of Biotechnology, Cereal Research Non-Profit Ltd., P.O. Box 391, H-6701 Szeged, Hungary.
Remote sensing is the process of detecting and monitoring a plant's characteristics by measuring its reflected and emitted radiation at a distance, typically from a satellite or aircraft. The handheld leaf spectrometers help validate these images at the field scale. This dataset was captured by the CI-710 s SpectraVue Leaf Spectrometer (Cid-Bioscience, Camas, WA, U.S.A.). The absorbance, reflectance, and transmittance of albino plants were measured under natural cold stress in a temperate rice-growing area [1]. The experiment was carried out in field conditions at the seedling stage. The chlorophyll degradation takes place, starting with the yellowing of the leaf until plant death. Albinos and different level of leaf colour mutants are very useful for research and as well as breeding [2]. The symptoms of cool-temperature-induced chlorosis (CTIC) are widely examined in higher plants, especially in rice [3]. Beside laboratory induction, CTIC is appearing natural low temperature in early spring, especially cold-sensitive genotypes, such as indica rice cultivars (e.g. 'Dular') [4]. The dataset contains raw data from 400 nm to 1100 nm with the wavelength data increment of 0.6 nm [5]. These data may provide reliable support to researcher and breeder to make a simple comparison of the extent of chlorophyll degradation.
PMID: 38550228
Dokl Biol Sci , 2024 Jun , V516 (1) : P21-26 doi: 10.1134/S0012496624700935
Potato Solanum tuberosum L. Phytoene Synthase Genes (StPSY1, StPSY2, and StPSY3) Are Involved in the Plant Response to Cold Stress.
Institute of Bioengineering, Federal Research Center "Fundamentals of Biotechnology," Russian Academy of Sciences, 119071, Moscow, Russia. kulakova_97@mail.ru.; Institute of Bioengineering, Federal Research Center "Fundamentals of Biotechnology," Russian Academy of Sciences, 119071, Moscow, Russia.
The structure and phylogeny of the Solanum tuberosum L. phytoene synthase genes StPSY1, StPSY2, and StPSY3 were characterized. Their expression was studied in potato seedlings exposed to cold stress in the dark phase of the diurnal cycle to simulate night cooling. All of the three genes were activated as the temperature decreased, and the greatest response was observed for StPSY1. StPSY3 was for the first time shown to respond to cold stress and photoperiod. A search for cis-regulatory elements was carried out in the promoter regions and 5'-UTRs of the StPSY genes, and the regulation of all three genes proved associated with the response to light. A high level of cold-induced activation of StPSY1 was tentatively attributed to the presence of cis elements associated with sensitivity to cold and ABA.
PMID: 38538824
Plant Commun , 2024 May : P100980 doi: 10.1016/j.xplc.2024.100980
The haplotype-resolved T2T genome assembly of the wild potato species Solanum commersonii provides molecular insights into its freezing tolerance.
School of Life Sciences, Yunnan key Laboratory of Potato Biology, Yunnan Normal University, Southwest United Graduate School, Kunming, Yunnan 650500, China.; Yunnan Key Laboratory of Cell Metabolism and Disease, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, Yunnan 650500, China.; School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, 230036, China.; Yunnan Key Laboratory of Cell Metabolism and Disease, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, Yunnan 650500, China. Electronic address: zhuguangtao@ynnu.edu.cn.; School of Life Sciences, Yunnan key Laboratory of Potato Biology, Yunnan Normal University, Southwest United Graduate School, Kunming, Yunnan 650500, China. Electronic address: zhuguangtao@ynnu.edu.cn.
PMID: 38807365