Nat Commun , IF:14.919 , 2024 Apr , V15 (1) : P3253 doi: 10.1038/s41467-024-47678-7
A fine-scale Arabidopsis chromatin landscape reveals chromatin conformation-associated transcriptional dynamics.
Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China.; Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China.; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA.; Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA.; Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK. yiliang.ding@jic.ac.uk.; Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China. zhanghk045@nenu.edu.cn.
Plants, as sessile organisms, deploy transcriptional dynamics for adapting to extreme growth conditions such as cold stress. Emerging evidence suggests that chromatin architecture contributes to transcriptional regulation. However, the relationship between chromatin architectural dynamics and transcriptional reprogramming in response to cold stress remains unclear. Here, we apply a chemical-crosslinking assisted proximity capture (CAP-C) method to elucidate the fine-scale chromatin landscape, revealing chromatin interactions within gene bodies closely associated with RNA polymerase II (Pol II) densities across initiation, pausing, and termination sites. We observe dynamic changes in chromatin interactions alongside Pol II activity alterations during cold stress, suggesting local chromatin dynamics may regulate Pol II activity. Notably, cold stress does not affect large-scale chromatin conformations. We further identify a comprehensive promoter-promoter interaction (PPI) network across the genome, potentially facilitating co-regulation of gene expression in response to cold stress. Our study deepens the understanding of chromatin conformation-associated gene regulation in plant response to cold.
PMID: 38627396
Plant Cell , IF:11.277 , 2024 Apr doi: 10.1093/plcell/koae116
The chill coalition: A key regulatory node connecting salicylic acid and brassinosteroids in freezing tolerance.
Assistant Features Editor, The Plant Cell, American Society of Plant Biologists, USA.; Laboratory of Functional Plant Biology, Department of Biology, Faculty of Sciences, Ghent University, Gent B-9000, Belgium.
PMID: 38626212
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
mBio , IF:7.867 , 2024 Apr : 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
Food Chem , IF:7.514 , 2024 Apr , V438 : P138005 doi: 10.1016/j.foodchem.2023.138005
Metabolic profiling of Oryza sativa seedlings under chilling stress using nanoliter electrospray ionization mass spectrometry.
College of Life Sciences, Jiangxi Normal University, Nanchang 330022, PR China; School of Life Sciences, Nanchang Normal University, Nanchang, 330031, PR China; School of Life Sciences, Nanchang University, Nanchang 330031, PR China.; College of Life Sciences, Jiangxi Normal University, Nanchang 330022, PR China.; School of Life Sciences, Nanchang Normal University, Nanchang, 330031, PR China.; School of Life Sciences, Nanchang University, Nanchang 330031, PR China.; School of Life Sciences, Nanchang University, Nanchang 330031, PR China. Electronic address: lluo2@126.com.
Low temperatures significantly impact on rice (Oryza sativa) yield and quality. Traditional metabolomic techniques, often involving time-consuming chromatography-mass spectrometry procedures, are currently in use. This study investigated metabolomic responses of rice seedlings under low-temperature stress using nanoliter electrospray ionization mass spectrometry (nanoESI-MS) in combination with multivariate analysis. Results revealed distinct metabolic profiles in 'Qiutianxiaoting' (japonica) and '93-11' (indica) rice seedlings. Among the 36 identified compounds in rice, seven key metabolites, comprising l-glutamic acid, asparagine, tryptophan, citric acid, alpha-linolenic acid, malic acid, and inositol, were identified as responsive to cold stress. Notably, malic acid content reached 1332.40 mug/g dry weight in Qiutianxiaoting and 1444.13 mug/g in 93-11. Both the qualitative and quantitative results of nanoESI-MS were further confirmed through gas chromatography-mass spectrometry validation. The findings highlight the potential of nanoESI-MS for rapidly characterizing crucial metabolites across diverse plant species under exposure to stress.
PMID: 37983997
Plant Cell Environ , IF:7.228 , 2024 Apr doi: 10.1111/pce.14922
Appropriate induction of TOC1 ensures optimal MYB44 expression in ABA signaling and stress response in Arabidopsis.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China.; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China.; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China.
Plants possess the remarkable ability to integrate the circadian clock with various signalling pathways, enabling them to quickly detect and react to both external and internal stress signals. However, the interplay between the circadian clock and biological processes in orchestrating responses to environmental stresses remains poorly understood. TOC1, a core component of the plant circadian clock, plays a vital role in maintaining circadian rhythmicity and participating in plant defences. Here, our study reveals a direct interaction between TOC1 and the promoter region of MYB44, a key gene involved in plant defence. TOC1 rhythmically represses MYB44 expression, thereby ensuring elevated MYB44 expression at dawn to help the plant in coping with lowest temperatures during diurnal cycles. Additionally, both TOC1 and MYB44 can be induced by cold stress in an Abscisic acid (ABA)-dependent and independent manner. TOC1 demonstrates a rapid induction in response to lower temperatures compared to ABA treatment, suggesting timely flexible regulation of TOC1-MYB44 regulatory module by the circadian clock in ensuring a proper response to diverse stresses and maintaining a balance between normal physiological processes and energy-consuming stress responses. Our study elucidates the role of TOC1 in effectively modulating expression of MYB44, providing insights into the regulatory network connecting the circadian clock, ABA signalling, and stress-responsive genes.
PMID: 38654596
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
Plant Cell Environ , IF:7.228 , 2024 Apr , V47 (4) : P1334-1347 doi: 10.1111/pce.14816
A transcriptional regulation of ERF15 contributes to ABA-mediated cold tolerance in tomato.
Hainan Institute, Zhejiang University, Sanya, China.; Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou, China.
Cold stress is a major meteorological threat to crop growth and yield. Abscisic acid (ABA) plays important roles in plant cold tolerance by activating the expression of cold-responsive genes; however, the underlying transcriptional regulatory module remains unknown. Here, we demonstrated that the cold- and ABA-responsive transcription factor ETHYLENE RESPONSE FACTOR 15 (ERF15) positively regulates ABA-mediated cold tolerance in tomato. Exogenous ABA treatment significantly enhanced cold tolerance in wild-type tomato plants but failed to rescue erf15 mutants from cold stress. Transcriptome analysis showed that ERF15 was associated with the expression of cold-responsive transcription factors such as CBF1 and WRKY6. Further RT-qPCR assays confirmed that the ABA-induced increased in CBF1 and WRKY6 transcripts was suppressed in erf15 mutants when the plants were subjected to cold treatment. Moreover, yeast one-hybrid assays, dual-luciferase assays and electrophoretic mobility shift assays demonstrated that ERF15 activated the transcription of CBF1 and WRKY6 by binding their promoters. Silencing CBF1 or WRKY6 significantly decreased cold tolerance. Overall, our study identified the role of ERF15 in conferring ABA-mediated cold tolerance in tomato plants by activating CBF1 and WRKY6 expression. This study not only broadens our knowledge of the mechanism of ABA-mediated cold tolerance in plants but also highlights ERF15 as an ideal target gene for cold-tolerant crop breeding.
PMID: 38221812
Plant Cell Environ , IF:7.228 , 2024 Apr , V47 (4) : P1185-1206 doi: 10.1111/pce.14796
ERF54 regulates cold tolerance in Rosa multiflora through DREB/COR signalling pathways.
Discipline of Ornamental Horticulture, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A & F University, Hangzhou, Zhejiang, China.; Discipline of Landscape Architecture, College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, Henan, China.
Ethylene-responsive factors (ERFs) participate in a wide range of physiological and biological processes. However, many of the functions of ERFs in cold stress responses remain unclear. We, therefore, characterised the cold responses of RmERF54 in Rosa multiflora, a rose-related cold-tolerant species. Overexpression of RmERF54, which is a nuclear transcription factor, increases the cold resistance of transgenic tobacco and rose somatic embryos. In contrast, virus-induced gene silencing (VIGS) of RmERF54 increased cold susceptibility of R. multiflora. The overexpression of RmERF54 resulted in extensive transcriptional reprogramming of stress response and antioxidant enzyme systems. Of these, the levels of transcripts encoding the PODP7 peroxidase and the cold-related COR47 protein showed the largest increases in the somatic embryos with ectopic expression of RmERF54. RmERF54 binds to the promoters of the RmPODP7 and RmCOR47 genes and activates expression. RmERF54-overexpressing lines had higher antioxidant enzyme activities and considerably lower levels of reactive oxygen species. Opposite effects on these parameters were observed in the VIGS plants. RmERF54 was identified as a target of Dehydration-Responsive-Element-Binding factor (RmDREB1E). Taken together, provide new information concerning the molecular mechanisms by which RmERF54 regulates cold tolerance.
PMID: 38164066
Plant Cell Environ , IF:7.228 , 2024 Apr , V47 (4) : P1379-1396 doi: 10.1111/pce.14813
Allelic variation of PmCBF03 contributes to the altitude and temperature adaptability in Japanese apricot (Prunus mume Sieb. et Zucc.).
Fruit Tree Biotechnology Laboratory, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China.; Department of Pomology, College of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China.; Department of Special Fruit Tree Germplasm Resources, Yunnan Green Food Development Center, Kunming, Yunnan, China.
Japanese apricot is an important subtropical deciduous fruit tree in China, widely distributed in different altitude areas. How does it adapt to the different temperature environments in these areas? In this study, we identified a low-temperature transcription factor PmCBF03 on chromosome 7 through adaptive analysis of populations at different altitudes, which has an early termination single nucleotide polymorphism mutation. There were two different types of variation, PmCBF03(A) type in high-altitude areas and PmCBF03(T) type in low-altitude areas. PmCBF03(A) gene increased the survival rate, Fv/Fm values, antioxidant enzyme activity, and expression levels of antioxidant enzyme genes, and reducing electrolyte leakage and accumulation of reactive oxygen species in transgenic Arabidopsis under low temperature and freezing stress. Simultaneously, PmCBF03(A) gene promoted the dormancy of transgenic Arabidopsis seeds than wild-type. Biochemical analysis demonstrated that PmCBF03(A) directly bound to the DRE/CRT element in the promoters of the PmCOR413, PmDAM6 and PmABI5 genes, promoting their transcription and enhanced the cold resistance and dormancy of the overexpressing PmCBF03(A) lines. While PmCBF03(T) gene is unable to bind to the promoters of PmDAM6 and PmABI5 genes, leading to early release of dormancy to adapt to the problem of insufficient chilling requirement in low-altitude areas.
PMID: 38221869
Plant Cell Environ , IF:7.228 , 2024 Apr doi: 10.1111/pce.14917
Freezing treatment under light conditions leads to a dramatic enhancement of freezing tolerance in cold-acclimated Arabidopsis.
The United Graduate School of Agricultural and Sciences, Iwate University, Morioka, Iwate, Japan.; Department of Plant-bioscience, Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan.
Overwintering plants survive subzero temperatures by cold acclimation (CA), wherein they acquire freezing tolerance through short-term exposure to low temperatures above 0 degrees C. The freezing tolerance of CA plants increases when they are subsequently exposed to mild subzero temperatures, a phenomenon known as second-phase cold hardening (2PH). Here, we explored the molecular mechanism and physiological conditions of 2PH. The results show that, compared with supercooling, a freezing treatment during 2PH after CA enhanced the freezing tolerance of Arabidopsis. This required CA as a pretreatment, and was designated as second-phase freezing acclimation (2PFA). Light increased the effect of 2PFA to enhance freezing tolerance after CA. C-repeat binding factor and cold-regulated genes were downregulated by light during the 2PFA treatment, a different transcription profile from that during CA. The freezing tolerance of 2PFA plants was decreased by the presence of the photosynthetic electron transfer inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea during the 2PFA treatment. Compared with wild-type plants, phototropin1,2 and phyb mutants showed lower freezing tolerance after 2PFA treatment. These results show that exposure to freezing after CA increases freezing tolerance as a secondary process, and that freezing under light conditions further increases freezing tolerance via pathways involving photoreceptors and photosynthetic electron transfer.
PMID: 38630014
Microbiol Spectr , IF:7.171 , 2024 Apr , V12 (4) : Pe0242523 doi: 10.1128/spectrum.02425-23
Differential effects of winter cold stress on soil bacterial communities, metabolites, and physicochemical properties in two varieties of Tetrastigma hemsleyanum Diels & Gilg in reclaimed land.
Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China.; Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.; Hangzhou Agricultural and Rural Affairs Guarantee Center, Hangzhou, China.; Qingliangfeng Lvyuan Vegetable Professional Cooperative, Hangzhou, China.; Institute of Biotechnology, Zhejiang University, Hangzhou, China.; School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China.
Tetrastigma hemsleyanum Diels & Gilg (TDG) has been recently planted in reclaimed lands in Zhejiang Province, China, to increase reclaimed land use. Winter cold stress seriously limits the growth and development of TDG and has become the bottleneck limiting the TDG planting industry. To investigate the defense mechanisms of TDG toward winter cold stress when grown on reclaimed land, a combined analysis of soil bacterial communities, metabolites, and physicochemical properties was conducted in this study. Significant differences were observed in the composition of soil bacterial communities, metabolites, and properties in soils of a cold-tolerant variety (A201201) compared with a cold-intolerant variety (B201810). The fresh weight (75.8% of tubers) and dry weight (73.6%) of A201201 were significantly higher than those of B201810. The 16S rRNA gene amplicon sequencing of soil bacteria showed that Gp5 (25.3%), Gemmatimonas (19.6%), Subdivision3 (16.7%), Lacibacterium (11.9%), Gp4 (11.8%), Gp3 (10.4%), Gp6 (7.0%), and WPS-1 (1.2%) were less common, while Chryseolinea (10.6%) were more common in A201201 soils than B201810 soils. Furthermore, linear discriminant analysis of effect size identified 35 bacterial biomarker taxa for both treatments. Co-occurrence network analyses also showed that the structures of the bacterial communities were more complex and stable in A201201 soils compared to B201810 soils. In addition, ultra-high-performance liquid chromatography coupled to mass spectrometry analysis indicated the presence of significantly different metabolites in the two soil treatments, with 10 differentially expressed metabolites (DEMs) (8 significantly upregulated by 9.2%-391.3% and 2 significantly downregulated by 25.1%-73.4%) that belonged to lipids and lipid-like molecules, organic acids and derivatives, and benzenoids. The levels of those DEMs were significantly correlated with the relative abundances of nine bacterial genera. Also, redundancy discriminant analysis revealed that the main factors affecting changes in the bacterial community composition were available potassium (AK), microbial biomass nitrogen (MBN), microbial biomass carbon (MBC), alkaline hydrolysis nitrogen (AHN), total nitrogen (TN), available phosphorus (AP), and soil organic matter (SOM). The main factors affecting changes in the metabolite profiles were AK, MBC, MBN, AHN, pH, SOM, TN, and AP. Overall, this study provides new insights into the TDG defense mechanisms involved in winter cold stress responses when grown on reclaimed land and practical guidelines for achieving optimal TDG production.IMPORTANCEChina has been undergoing rapid urbanization, and land reclamation is regarded as a viable option to balance occupation and compensation. In general, the quality of reclaimed land cannot meet plant or even cultivation requirements due to poor soil fertility and high gravel content. However, Tetrastigma hemsleyanum Diels & Gilg (TDG), extensively used in Chinese herbal medicine, can grow well in stony soils with few nutrients. So, to increase reclaimed land use, TDG has been cultivated on reclaimed lands in Zhejiang Province, China, recently. However, the artificial cultivation of TDG is often limited by winter cold stress. The aim of this study was to find out how TDG on reclaimed land deal with winter cold stress by looking at the bacterial communities, metabolites, and physicochemical properties of the soil, thereby guiding production in practice.
PMID: 38470484
J Integr Plant Biol , IF:7.061 , 2024 Apr , V66 (4) : P660-682 doi: 10.1111/jipb.13585
OsNAC5 orchestrates OsABI5 to fine-tune cold tolerance in rice.
College of Agronomy, Anhui Agricultural University, Hefei, 230036, China.; Hainan Institute, Yazhou Bay Sci-Tech City, Zhejiang University, Sanya, 572025, China.; National Key Laboratory of Rice Biology, Advanced Seed Institute, Zhejiang University, Hangzhou, 311225, China.; State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China.; Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
Due to its tropical origins, rice (Oryza sativa) is susceptible to cold stress, which poses severe threats to production. OsNAC5, a NAC-type transcription factor, participates in the cold stress response of rice, but the detailed mechanisms remain poorly understood. Here, we demonstrate that OsNAC5 positively regulates cold tolerance at germination and in seedlings by directly activating the expression of ABSCISIC ACID INSENSITIVE 5 (OsABI5). Haplotype analysis indicated that single nucleotide polymorphisms in a NAC-binding site in the OsABI5 promoter are strongly associated with cold tolerance. OsNAC5 also enhanced OsABI5 stability, thus regulating the expression of cold-responsive (COR) genes, enabling fine-tuned control of OsABI5 action for rapid, precise plant responses to cold stress. DNA affinity purification sequencing coupled with transcriptome deep sequencing identified several OsABI5 target genes involved in COR expression, including DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTOR 1A (OsDREB1A), OsMYB20, and PEROXIDASE 70 (OsPRX70). In vivo and in vitro analyses suggested that OsABI5 positively regulates COR gene transcription, with marked COR upregulation in OsNAC5-overexpressing lines and downregulation in osnac5 and/or osabi5 knockout mutants. This study extends our understanding of cold tolerance regulation via OsNAC5 through the OsABI5-CORs transcription module, which may be used to ameliorate cold tolerance in rice via advanced breeding.
PMID: 37968901
J Exp Bot , IF:6.992 , 2024 Apr , V75 (8) : P2266-2279 doi: 10.1093/jxb/erae007
PlantC2U: deep learning of cross-species sequence landscapes predicts plastid C-to-U RNA editing in plants.
Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China.
In plants, C-to-U RNA editing mainly occurs in plastid and mitochondrial transcripts, which contributes to a complex transcriptional regulatory network. More evidence reveals that RNA editing plays critical roles in plant growth and development. However, accurate detection of RNA editing sites using transcriptome sequencing data alone is still challenging. In the present study, we develop PlantC2U, which is a convolutional neural network, to predict plastid C-to-U RNA editing based on the genomic sequence. PlantC2U achieves >95% sensitivity and 99% specificity, which outperforms the PREPACT tool, random forests, and support vector machines. PlantC2U not only further checks RNA editing sites from transcriptome data to reduce possible false positives, but also assesses the effect of different mutations on C-to-U RNA editing based on the flanking sequences. Moreover, we found the patterns of tissue-specific RNA editing in the mangrove plant Kandelia obovata, and observed reduced C-to-U RNA editing rates in the cold stress response of K. obovata, suggesting their potential regulatory roles in plant stress adaptation. In addition, we present RNAeditDB, available online at https://jasonxu.shinyapps.io/RNAeditDB/. Together, PlantC2U and RNAeditDB will help researchers explore the RNA editing events in plants and thus will be of broad utility for the plant research community.
PMID: 38190348
Int J Biol Macromol , IF:6.953 , 2024 Apr , V264 (Pt 1) : P130429 doi: 10.1016/j.ijbiomac.2024.130429
Characteristics of ZjCIPKs and ZjbHLH74-ZjCIPK5 regulated cold tolerance in jujube.
College of Horticulture, Hebei Agricultural University, Baoding 071001, Hebei, China.; College of Life Science, Hebei Agricultural University, Baoding 071001, Hebei, China.; 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.
CIPKs are kind of serine/threonine (Ser/Thr) protein kinases which play important roles in response to biotic and abiotic stresses, and in plant growth and development. However, CIPKs in jujube (Ziziphus jujuba Mill.) had limited information, especially regarding their response to cold stress. In the current study, a total of 18 ZjCIPKs were identified in jujube genome which unevenly distributed on seven chromosomes. Conserved motif and gene structural analysis depicted them with conserved DEGLSA and APE motifs and similar structures. Phylogenetic analysis indicated that CIPKs were classified into five subgroups (I-V). In addition, three pairs of ZjCIPKs exhibited tandem duplication while the segmental duplication of ZjCIPKs was not identified. Study on the cis-acting elements indicted that stress or hormone related cis-acting elements were distributed unevenly on ZjCIPKs promoters and most ZjCIPKs were down- or up-regulated by the cold stress. VIGS induced silencing of ZjCIPK5 decreased the cold tolerance of sour jujube. Subcellular location analysis showed ZjCIPK5 located in nucleus. Moreover, transcription factor ZjbHLH74 which was induced at 6 h under cold stress could interact with the promoter of ZjCIPK5 to regulate jujube cold tolerance. These findings provided insights to a molecular basis of CIPK5 in jujube cold tolerance breeding for future.
PMID: 38428762
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 Apr , V118 (2) : P549-564 doi: 10.1111/tpj.16624
Cold-induced deposition of bivalent H3K4me3-H3K27me3 modification and nucleosome depletion in Arabidopsis.
Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, 610101, Sichuan, China.; Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu, 610101, Sichuan, China.; Department of Plant Biology, Department of Horticulture, Michigan State University AgBioResearch, Michigan State University, East Lansing, Michigan, 48824, USA.
Epigenetic regulation of gene expression plays a crucial role in plant development and environmental adaptation. The H3K4me3 and H3K27me3 have not only been discovered in the regulation of gene expression in multiple biological processes but also in responses to abiotic stresses in plants. However, evidence for the presence of both H3K4me3 and H3K27me3 on the same nucleosome is sporadic. Cold-induced deposition of bivalent H3K4me3-H3K27me3 modifications and nucleosome depletion over a considerable number of active genes is documented in potato tubers and provides clues on an additional role of the bivalent modifications. Limited by the available information of genes encoding PcG/TrxG proteins as well as their corresponding mutants in potatoes, the molecular mechanism underlying the cold-induced deposition of the bivalent mark remains elusive. In this study, we found a similar deposition of the bivalent H3K4me3-H3K27me3 mark over 2129 active genes in cold-treated Arabidopsis Col-0 seedlings. The expression levels of the bivalent mark-associated genes tend to be independent of bivalent modification levels. However, these genes were associated with greater chromatin accessibility, presumably to provide a distinct chromatin environment for gene expression. In mutants clf28 and lhp1, failure to deposit H3K27me3 in active genes upon cold treatment implies that the CLF is potentially involved in cold-induced deposition of H3K27me3, with assistance from LHP1. Failure to deposit H3K4me3 during cold treatment in atx1-2 suggests a regulatory role of ATX1 in the deposition of H3K4me3. In addition, we observed a cold-induced global reduction in nucleosome occupancy, which is potentially mediated by LHP1 in an H3K27me3-dependent manner.
PMID: 38184780
Int J Mol Sci , IF:5.923 , 2024 Apr , V25 (8) doi: 10.3390/ijms25084458
VvJAZ13 Positively Regulates Cold Tolerance in Arabidopsis and Grape.
College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China.
Cold stress adversely impacts grape growth, development, and yield. Therefore, improving the cold tolerance of grape is an urgent task of grape breeding. The Jasmonic acid (JA) pathway responsive gene JAZ plays a key role in plant response to cold stress. However, the role of JAZ in response to low temperatures in grape is unclear. In this study, VvJAZ13 was cloned from the 'Pinot Noir' (Vitis vinefera cv. 'Pinot Noir') grape, and the potential interacting protein of VvJAZ13 was screened by yeast two-hybrid (Y2H). The function of VvJAZ13 under low temperature stress was verified by genetic transformation. Subcellular localization showed that the gene was mainly expressed in cytoplasm and the nucleus. Y2H indicated that VvF-box, VvTIFY5A, VvTIFY9, Vvbch1, and VvAGD13 may be potential interacting proteins of VvJAZ13. The results of transient transformation of grape leaves showed that VvJAZ13 improved photosynthetic capacity and reduced cell damage by increasing maximum photosynthetic efficiency of photosystem II (Fv/Fm), reducing relative electrolyte leakage (REL) and malondialdehyde (MDA), and increasing proline content in overexpressed lines (OEs), which played an active role in cold resistance. Through the overexpression of VvJAZ13 in Arabidopsis thaliana and grape calli, the results showed that compared with wild type (WT), transgenic lines had higher antioxidant enzyme activity and proline content, lower REL, MDA, and hydrogen peroxide (H(2)O(2)) content, and an improved ability of scavenging reactive oxygen species. In addition, the expression levels of CBF1-2 and ICE1 genes related to cold response were up-regulated in transgenic lines. To sum up, VvJAZ13 is actively involved in the cold tolerance of Arabidopsis and grape, and has the potential to be a candidate gene for improving plant cold tolerance.
PMID: 38674041
Int J Mol Sci , IF:5.923 , 2024 Apr , V25 (7) doi: 10.3390/ijms25074088
Overexpression of a Fragaria vesca NAM, ATAF, and CUC (NAC) Transcription Factor Gene (FvNAC29) Increases Salt and Cold Tolerance in Arabidopsis thaliana.
Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.; Horticulture Branch of Heilongjiang Academy of Agricultural Sciences, Harbin 150040, China.
The NAC (NAM, ATAF1/2, CUC2) family of transcription factors (TFs) is a vital transcription factor family of plants. It controls multiple parts of plant development, tissue formation, and abiotic stress response. We cloned the FvNAC29 gene from Fragaria vesca (a diploid strawberry) for this research. There is a conserved NAM structural domain in the FvNAC29 protein. The highest homology between FvNAC29 and PaNAC1 was found by phylogenetic tree analysis. Subcellular localization revealed that FvNAC29 is localized onto the nucleus. Compared to other tissues, the expression level of FvNAC29 was higher in young leaves and roots. In addition, Arabidopsis plants overexpressing FvNAC29 had higher cold and high-salinity tolerance than the wild type (WT) and unloaded line with empty vector (UL). The proline and chlorophyll contents of transgenic Arabidopsis plants, along with the activities of the antioxidant enzymes like catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) under 200 mM NaCl treatment or -8 degrees C treatment, were higher than those activities of the control. Meanwhile, malondialdehyde (MDA) and the reactive oxygen species (ROS) content were higher in the WT and UL lines. FvNAC29 improves transgenic plant resistance to cold and salt stress by regulating the expression levels of AtRD29a, AtCCA1, AtP5CS1, and AtSnRK2.4. It also improves the potential to tolerate cold stress by positively regulating the expression levels of AtCBF1, AtCBF4, AtCOR15a, and AtCOR47. These findings suggest that FvNAC29 may be related to the processes and the molecular mechanisms of F. vesca response to high-salinity stress and LT stress, providing a comprehensive understanding of the NAC TFs.
PMID: 38612898
Metabolites , IF:4.932 , 2024 Apr , V14 (4) doi: 10.3390/metabo14040223
Cryoprotectant-Mediated Cold Stress Mitigation in Litchi Flower Development: Transcriptomic and Metabolomic Perspectives.
College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China.
Temperature is vital in plant growth and agricultural fruit production. Litchi chinensis Sonn, commonly known as litchi, is appreciated for its delicious fruit and fragrant blossoms and is susceptible to stress when exposed to low temperatures. This study investigates the effect of two cryoprotectants that counteract cold stress during litchi flowering, identifies the genes that generate the cold resistance induced by the treatments, and hypothesizes the roles of these genes in cold resistance. Whole plants were treated with Bihu and Liangli cryoprotectant solutions to protect inflorescences below 10 degrees C. The soluble protein, sugar, fructose, sucrose, glucose, and proline contents were measured during inflorescence. Sucrose synthetase, sucrose phosphate synthetase, antioxidant enzymes (SOD, POD, CAT), and MDA were also monitored throughout the flowering stage. Differentially expressed genes (DEGs), gene ontology, and associated KEGG pathways in the transcriptomics study were investigated. There were 1243 DEGs expressed after Bihu treatment and 1340 in the control samples. Signal transduction pathways were associated with 39 genes in the control group and 43 genes in the Bihu treatment group. The discovery of these genes may contribute to further research on cold resistance mechanisms in litchi. The Bihu treatment was related to 422 low-temperature-sensitive differentially accumulated metabolites (DAMs), as opposed to 408 DAMs in the control, mostly associated with lipid metabolism, organic oxidants, and alcohols. Among them, the most significant differentially accumulated metabolites were involved in pathways such as beta-alanine metabolism, polycyclic aromatic hydrocarbon biosynthesis, linoleic acid metabolism, and histidine metabolism. These results showed that Bihu treatment could potentially promote these favorable traits and increase fruit productivity compared to the Liangli and control treatments. More genomic research into cold stress is needed to support the findings of this study.
PMID: 38668352
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 Sci , IF:4.729 , 2024 Apr , V341 : P112012 doi: 10.1016/j.plantsci.2024.112012
The cold-responsive C-repeat binding factors in Betula platyphylla Suk. positively regulate cold tolerance.
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, Heilongjiang, China.; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, Heilongjiang, China. Electronic address: chensu@nefu.edu.cn.
Cold stress is one of the most destructive abiotic stresses limiting plant growth and development. CBF (C-repeat binding factor) transcription factors and their roles in cold response have been identified in Arabidopsis as well as several other plant species. However, the biological functions and related molecular mechanisms of CBFs in birch (Betula platyphylla Suk.) remain undetermined. In this study, five cold-responsive BpCBF genes, BpCBF1, BpCBF2, BpCBF7, BpCBF10 and BpCBF12 were cloned. Via protoplast transformation, BpCBF7 was found to be localized in nucleus. The result of yeast one hybrid assay validated the binding of BpCBF7 to the CRT/DRE (C-repeat/dehydration responsive element) elements in the promoter of BpERF1.1 gene. By overexpressing and repressing BpCBFs in birch plants, it was proven that BpCBFs play positive roles in the cold tolerance. At the metabolic level, BpCBFs OE lines had lower ROS accumulation, as well as higher activities of antioxidant enzymes (SOD, POD and CAT) and higher accumulation of protective substances (soluble sugar, soluble protein and proline). Via yeast one hybrid and co-transformation of effector and reporter vectors assay, it was proven that BpCBF7 can regulate the expression of BpERF5 and BpZAT10 genes by directly binding to their promoters. An interacting protein of BpCBF7, BpWRKY17, was identified by yeast two hybrid library sequencing and the interaction was validated with in vivo methods. These results indicates that BpCBFs can increase the cold tolerance of birch plants, partly by gene regulation and protein interaction. This study provides a reference for the research on CBF transcription factors and genetic improvement of forest trees upon abiotic stresses.
PMID: 38311248
Plant Physiol Biochem , IF:4.27 , 2024 Apr , 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 Apr , 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
Saudi J Biol Sci , IF:4.219 , 2024 Apr , V31 (4) : P103959 doi: 10.1016/j.sjbs.2024.103959
Insights into cucumber (Cucumis sativus) genetics: Genome-wide discovery and computational analysis of the Calreticulin Domain-Encoding gene (CDEG) family.
Department of Biology, College of Science and Humanities, Prince Sattam bin Abdulaziz University, Alkharj 11942, Saudi Arabia.
Cucumber is an essential vegetable crop throughout the world. Cucumber development is vital for accomplishing both quality and productivity requirements. Meanwhile, numerous factors have resulted in substantial cucumber losses. However, the calreticulin domain-encoding genes (CDEGs) in cucumber were not well-characterized and had little function. In the genome-wide association study (GWAS), we recognized and characterized the CDEGs in Cucumis sativus (cucumber). Through a comprehensive study of C. sativus, our research has unveiled the presence of three unique genes, denoted as CsCRTb, CsCRT3, and CsCNX1, unevenly distributed on three chromosomes in the genome of C. sativus. In accordance to the phylogenetic investigation, these genes may be categorized into three subfamilies. Based on the resemblance with AtCDE genes, we reorganized the all CsCDE genes in accordance with international nomenclature. The expression analysis and cis-acting components revealed that each of CsCDE gene promoter region enclosed number of cis-elements connected with hormone and stress response. According to subcellular localization studies demonstrated that, they were found in deferent locations of the cell such as endoplasmic reticulum, plasma membrane, golgi apparatus, and vacuole, according to subcellular localization studies. Chromosomal distribution analysis and synteny analysis demonstrated the probability of segmental or tandem duplications within the cucumber CDEG gene family. Additionally, miRNAs displayed diverse modes of action, including mRNA cleavage and translational inhibition. We used the RNA seq data to analyze the expression of CDEG genes in response to cold stress and also improved cold tolerance, which was brought on by treating cucumber plants to an exogenous chitosan oligosaccharide spray. Our investigation revealed that these genes responded to this stress in a variety of ways, demonstrating that they may adapt quickly to environmental changes in cucumber plants. This study provides a base for further understanding in reference to CDE gene family and reveals that genes play significant functions in cucumber stress responses.
PMID: 38404540
BMC Plant Biol , IF:4.215 , 2024 Apr , V24 (1) : P342 doi: 10.1186/s12870-024-05027-2
Discovery of gene regulation mechanisms associated with uniconazole-induced cold tolerance in banana using integrated transcriptome and metabolome analysis.
Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.; Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China. guochenglin0278@126.com.
BACKGROUND: The gibberellic acid (GA) inhibitor, uniconazole, is a plant growth regulator commonly used in banana cultivation to promote dwarfing but also enhances the cold resistance in plants. However, the mechanism of this induced cold resistance remains unclear. RESULTS: We confirmed that uniconazole induced cold tolerance in bananas and that the activities of Superoxide dismutase and Peroxidase were increased in the uniconazole-treated bananas under cold stress when compared with the control groups. The transcriptome and metabolome of bananas treated with or without uniconazole were analyzed at different time points under cold stress. Compared to the control group, differentially expressed genes (DEGs) between adjacent time points in each uniconazole-treated group were enriched in plant-pathogen interactions, MAPK signaling pathway, and plant hormone signal transduction, which were closely related to stimulus-functional responses. Furthermore, the differentially abundant metabolites (DAMs) between adjacent time points were enriched in flavone and flavonol biosynthesis and linoleic acid metabolism pathways in the uniconazole-treated group than those in the control group. Temporal analysis of DEGs and DAMs in uniconazole-treated and control groups during cold stress showed that the different expression patterns in the two groups were enriched in the linoleic acid metabolism pathway. In addition to strengthening the antioxidant system and complex hormonal changes caused by GA inhibition, an enhanced linoleic acid metabolism can protect cell membrane stability, which may also be an important part of the cold resistance mechanism of uniconazole treatment in banana plants. CONCLUSIONS: This study provides information for understanding the mechanisms underlying inducible cold resistance in banana, which will benefit the production of this economically important crop.
PMID: 38671368
BMC Plant Biol , IF:4.215 , 2024 Apr , V24 (1) : P266 doi: 10.1186/s12870-024-04983-z
Cold-stress induced metabolomic and transcriptomic changes in leaves of three mango varieties with different cold tolerance.
Guangxi Key Laboratory of Biology for Mongo, Baise University, Baise, 533000, China.; College of Agriculture and Food Engineering, Baise University, Baise, 533000, China.; Guangxi Key Laboratory of Biology for Mongo, Baise University, Baise, 533000, China. yufengli@bsuc.cn.; College of Agriculture and Food Engineering, Baise University, Baise, 533000, China. yufengli@bsuc.cn.
BACKGROUND: Mango (Mangifera indica L.) is grown in Hainan, Guangdong, Yunnan, Sichuan, and Fujian provinces and Guanxi autonomous region of China. However, trees growing in these areas suffer severe cold stress during winter, which affects the yield. To this regard, data on global metabolome and transcriptome profiles of leaves are limited. Here, we used combined metabolome and transcriptome analyses of leaves of three mango cultivars with different cold stress tolerance, i.e. Jinhuang (J)-tolerant, Tainung (T) and Guiremang No. 82 (G)-susceptible, after 24 (LF), 48 (MF) and 72 (HF) hours of cold. RESULTS: A total of 1,323 metabolites belonging to 12 compound classes were detected. Of these, amino acids and derivatives, nucleotides and derivatives, and lipids accumulated in higher quantities after cold stress exposure in the three cultivars. Notably, Jinhuang leaves showed increasing accumulation trends of flavonoids, terpenoids, lignans and coumarins, and alkaloids with exposure time. Among the phytohormones, jasmonic acid and abscisic acid levels decreased, while N6-isopentenyladenine increased with cold stress time. Transcriptome analysis led to the identification of 22,526 differentially expressed genes. Many genes enriched in photosynthesis, antenna proteins, flavonoid, terpenoid (di- and sesquiterpenoids) and alkaloid biosynthesis pathways were upregulated in Jihuang leaves. Moreover, expression changes related to phytohormones, MAPK (including calcium and H(2)O(2)), and the ICE-CBF-COR signalling cascade indicate involvement of these pathways in cold stress responses. CONCLUSION: Cold stress tolerance in mango leaves is associated with regulation of primary and secondary metabolite biosynthesis pathways. Jasmonic acid, abscisic acid, and cytokinins are potential regulators of cold stress responses in mango leaves.
PMID: 38600447
BMC Plant Biol , IF:4.215 , 2024 Apr , V24 (1) : P256 doi: 10.1186/s12870-024-04922-y
Comparative physiology and transcriptome response patterns in cold-tolerant and cold-sensitive varieties of Solanum melongena.
Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China.; Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, China.; Sichuan Province Engineering Technology Research Center of Vegetables, Chengdu, 611934, China.; Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China. saasfangchao@163.com.; Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, China. saasfangchao@163.com.; Sichuan Province Engineering Technology Research Center of Vegetables, Chengdu, 611934, China. saasfangchao@163.com.
BACKGROUND: Climate change has led to severe cold events, adversely impacting global crop production. Eggplant (Solanum melongena L.), a significant economic crop, is highly susceptible to cold damage, affecting both yield and quality. Unraveling the molecular mechanisms governing cold resistance, including the identification of key genes and comprehensive transcriptional regulatory pathways, is crucial for developing new varieties with enhanced tolerance. RESULTS: In this study, we conducted a comparative analysis of leaf physiological indices and transcriptome sequencing results. The orthogonal partial least squares discriminant analysis (OPLS-DA) highlighted peroxidase (POD) activity and soluble protein as crucial physiological indicators for both varieties. RNA-seq data analysis revealed that a total of 7024 and 6209 differentially expressed genes (DEGs) were identified from variety "A" and variety "B", respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment of DEGs demonstrated that the significant roles of starch and sucrose metabolism, glutathione metabolism, terpenoid synthesis, and energy metabolism (sucrose and starch metabolism) were the key pathways in eggplant. Weighted gene co-expression network analysis (WGCNA) shown that the enrichment of numerous cold-responsive genes, pathways, and soluble proteins in the MEgrep60 modules. Core hub genes identified in the co-expression network included POD, membrane transporter-related gene MDR1, abscisic acid-related genes, growth factor enrichment gene DELLA, core components of the biological clock PRR7, and five transcription factors. Among these, the core transcription factor MYB demonstrated co-expression with signal transduction, plant hormone, biosynthesis, and metabolism-related genes, suggesting a pivotal role in the cold response network. CONCLUSION: This study integrates physiological indicators and transcriptomics to unveil the molecular mechanisms responsible for the differences in cold tolerance between the eggplant cold-tolerant variety "A" and the cold-sensitive variety "B". These mechanisms include modulation of reactive oxygen species (ROS), elevation in osmotic carbohydrate and free proline content, and the expression of terpenoid synthesis genes. This comprehensive understanding contributes valuable insights into the molecular underpinnings of cold stress tolerance, ultimately aiding in the improvement of crop cold tolerance.
PMID: 38594627
BMC Plant Biol , IF:4.215 , 2024 Apr , V24 (1) : P230 doi: 10.1186/s12870-024-04903-1
Physiological and transcriptomic comparisons shed light on the cold stress response mechanisms of Dendrobium spp.
Sanya Institute of China Agricultural University, Sanya, Hainan, 572025, China.; Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, 100193, Beijing, China.; Tropical Crops Genetic Resources Institute, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Chines Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China.; Hainan Engineering Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, 571737, Danzhou, Hainan, China.; Tropical Crops Genetic Resources Institute, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Chines Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China. yinjunmei2011@sina.com.; Hainan Engineering Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, 571737, Danzhou, Hainan, China. yinjunmei2011@sina.com.; Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571101, Sanya, China. yinjunmei2011@sina.com.; Sanya Institute of China Agricultural University, Sanya, Hainan, 572025, China. chqzhang@cau.edu.cn.; Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, 100193, Beijing, China. chqzhang@cau.edu.cn.
BACKGROUND: Dendrobium spp. comprise a group of tropical orchids with ornamental and medicinal value. Dendrobium spp. are sensitive to low temperature, and the underlying cold response regulatory mechanisms in this group are unclear. To understand how these plants respond to cold stress, we compared the transcriptomic responses of the cold-tolerant cultivar 'Hongxing' (HX) and the cold-sensitive cultivar 'Sonia Hiasakul' (SH) to cold stress. RESULTS: Chemometric results showed that the physiological response of SH in the later stages of cold stress is similar to that of HX throughout the cold treatment. Orthogonal partial least squares discriminant analysis (OPLS-DA) revealed that soluble protein content and peroxidase activity are key physiological parameters for assessing the cold tolerance of these two Dendrobium spp. cultivars. Additionally, weighted gene co-expression network analysis (WGCNA) results showed that many cold response genes and metabolic pathways significantly associated with the physiological indices were enriched in the 12 detected modules. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) enrichment analyses of the 105 hub genes showed that Dendrobium spp. adapt to cold stress by regulating signal transduction, phytohormones, transcription factors, protein translation and modification, functional proteins, biosynthesis and metabolism, cell structure, light, and the circadian clock. Hub genes of the cold stress response network included the remorin gene pp34, the abscisic acid signaling pathway-related genes PROTEIN PHOSPATASE 2 C (PP2C), SNF1-RELATED PROTEIN KINASE 2 (SnRK2), ABRE-BINDING FACTOR 1 (ABF1) and SKI-INTERACTING PROTEIN 17 (SKIP17), the Ca(2+) signaling-related GTP diphosphokinase gene CRSH1, the carbohydrate-related gene STARCH SYNTHASE 2 (SS2), the cell wall biosynthesis gene CINNAMYL ALCOHOL DEHYDROGENASE (CAD7), and the endocytosis-related gene VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 52 A (VPS52A). CONCLUSIONS: The cold-responsive genes and metabolic pathways of Dendrobium spp. revealed in this study provide important insight to enable the genetic enhancement of cold tolerance in Dendrobium spp., and to facilitate cold tolerance breeding in related plants.
PMID: 38561687
BMC Genomics , IF:3.969 , 2024 Apr , V25 (1) : P370 doi: 10.1186/s12864-024-10265-7
Genome-wide identification of polyamine metabolism and ethylene synthesis genes in Chenopodium quinoa Willd. and their responses to low-temperature stress.
Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201, Kunming, China.; College of Horticulture and Landscape, Yunnan Agricultural University, 650201, Kunming, China.; College of Agronomy and Biotechnology, Yunnan Agricultural University, 650201, Kunming, China. yngfg@sina.cn.; College of Agronomy and Biotechnology, Yunnan Agricultural University, 650201, Kunming, China.
BACKGROUND: Quinoa (Chenopodium quinoa Willd.) is valued for its nutritional richness. However, pre-harvest sprouting poses a significant threat to yield and grain quality. This study aims to enhance our understanding of pre-harvest sprouting mitigation strategies, specifically through delayed sowing and avoiding rainy seasons during quinoa maturation. The overarching goal is to identify cold-resistant varieties and unravel the molecular mechanisms behind the low-temperature response of quinoa. We employed bioinformatics and genomics tools for a comprehensive genome-wide analysis of polyamines (PAs) and ethylene synthesis gene families in quinoa under low-temperature stress. RESULTS: This involved the identification of 37 PA biosynthesis and 30 PA catabolism genes, alongside 227 ethylene synthesis. Structural and phylogenetic analyses showcased conserved patterns, and subcellular localization predictions indicated diverse cellular distributions. The results indicate that the PA metabolism of quinoa is closely linked to ethylene synthesis, with multiple genes showing an upregulation in response to cold stress. However, differential expression within gene families suggests a nuanced regulatory network. CONCLUSIONS: Overall, this study contributes valuable insights for the functional characterization of the PA metabolism and ethylene synthesis of quinoa, which emphasize their roles in plant low-temperature tolerance and providing a foundation for future research in this domain.
PMID: 38627628
Plants (Basel) , IF:3.935 , 2024 Apr , V13 (8) doi: 10.3390/plants13081152
Genome-Wide Analysis Elucidates the Roles of GhTIR1/AFB Genes Reveals the Function of Gh_D08G0763 (GhTIR1) in Cold Stress in G. hirsutum.
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.; Western Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Changji 831100, China.; Institute of Cotton Research, Shanxi Agricultural University, Yuncheng 044000, China.; Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng 475000, China.; Sanya Institute of Henan University, Sanya 572025, China.
This study identified 13 GhTIR1/AFB members in G. hirsutum through bioinformatics methods and divided them into three subgroups by phylogenetic tree analysis. Motif and gene structure analysis showed that the genes in this family were highly conserved. Promoter cis-acting element analysis found that the promoters of GhTIR1/AFBs contained a large number of cis-acting elements in response to growth and development and abiotic stress. Further RT-qPCR results showed that GhTIR1/AFB genes responded to various abiotic stresses such as IAA, ABA, cold, and heat, and the expression levels of each gene changed obviously, especially Gh_D08G0763 (GhTIR1), which responded significantly to cold injury. Using VIGS (virus-induced gene silencing) technology to silence Gh_D08G0763 in the cold-tolerant cotton variety ZM36, it was found that the resistance of ZM36 to cold damage was significantly reduced. The physiological response mechanism of the Gh_D08G0763 in resisting cold damage was further analyzed through trypan blue staining of leaves and determination of enzyme activity levels. This study provided effective genetic resources for cotton cold-tolerance breeding.
PMID: 38674561
Plants (Basel) , IF:3.935 , 2024 Apr , V13 (8) doi: 10.3390/plants13081118
Genome-Wide Identification of BrCMF Genes in Brassica rapa and Their Expression Analysis under Abiotic Stresses.
College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271000, China.; Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
CCT MOTIF FAMILY (CMF) genes belong to the CCT gene family and have been shown to play a role in diverse processes, such as flowering time and yield regulation, as well as responses to abiotic stresses. CMF genes have not yet been identified in Brassica rapa. A total of 25 BrCMF genes were identified in this study, and these genes were distributed across eight chromosomes. Collinearity analysis revealed that B. rapa and Arabidopsis thaliana share many homologous genes, suggesting that these genes have similar functions. According to sequencing analysis of promoters, several elements are involved in regulating the expression of genes that mediate responses to abiotic stresses. Analysis of the tissue-specific expression of BrCMF14 revealed that it is highly expressed in several organs. The expression of BrCMF22 was significantly downregulated under salt stress, while the expression of BrCMF5, BrCMF7, and BrCMF21 was also significantly reduced under cold stress. The expression of BrCMF14 and BrCMF5 was significantly increased under drought stress, and the expression of BrCMF7 was upregulated. Furthermore, protein-protein interaction network analysis revealed that A. thaliana homologs of BrCMF interacted with genes involved in the abiotic stress response. In conclusion, BrCMF5, BrCMF7, BrCMF14, BrCMF21, and BrCMF22 appear to play a role in responses to abiotic stresses. The results of this study will aid future investigations of CCT genes in B. rapa.
PMID: 38674527
Plants (Basel) , IF:3.935 , 2024 Apr , V13 (8) doi: 10.3390/plants13081100
Exogenous Spermidine Alleviated Low-Temperature Damage by Affecting Polyamine Metabolism and Antioxidant Levels in Apples.
Key Laboratory of Fruit Quality Development and Regulation of Liaoning Province, College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China.; Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China.
Low-temperature stress significantly limits the growth, development, and geographical distribution of apple cultivation. Spermidine (Spd), a known plant growth regulator, plays a vital role in the plant's response to abiotic stress. Yet, the mechanisms by which exogenous Spd enhances cold resistance in apples remain poorly understood. Therefore, the present study analyzed the effects of exogenous Spd on antioxidant enzyme activity, polyamine metabolism, and related gene expression levels of 1-year-old apple branches under low-temperature stress. Treatment with exogenous Spd was found to stabilize branch tissue biofilms and significantly reduce the levels of reactive oxygen species by elevating proline content and boosting the activity of antioxidants such as superoxide dismutase. It also upregulated the activities of arginine decarboxylase, S-adenosylmethionine decarboxylase, and spermidine synthase and the expression levels of MdADC1, MdSAMDC1, and MdSPDS1 under low-temperature stress and led to the accumulation of large amounts of Spd and spermine. Moreover, compared with the 2 mmol.L(-1) Spd treatment, the 1 mmol.L(-1) Spd treatment increased the expression levels of cold-responsive genes MdCBF1/2/3, MdCOR47, and MdKIN1, significantly. The findings suggest that exogenous Spd can enhance cold resistance in apple branches significantly. This enhancement is achieved by modulating polyamine metabolism and improving antioxidant defense mechanisms, which could be exploited to improve apple cultivation under cold stress conditions.
PMID: 38674509
Plants (Basel) , IF:3.935 , 2024 Apr , V13 (8) doi: 10.3390/plants13081055
Jasmonates Promote beta-Amylase-Mediated Starch Degradation to Confer Cold Tolerance in Tomato Plants.
School of Life Sciences, Liaocheng University, Liaocheng 252000, China.
Cold stress severely restricts growth and development, reduces yields, and impairs quality in tomatoes (Solanum lycopersicum). Amylase-associated starch degradation and soluble sugar accumulation have been implicated in adaptation and resistance to abiotic stress. Here, we report a beta-amylase (BAM) gene, SlBAM3, which plays a central role in tomato cold tolerance. The expression of SlBAM3 was triggered by cold stress. SlBAM3 knockout using the CRISPR/Cas9 system retarded starch degradation and reduced soluble sugar accumulation in tomato plants, eventually attenuating cold tolerance. Expression analysis revealed that the SlBAM3 transcript level was boosted by MeJA. Furthermore, MYC2, an essential component of the JA signaling pathway, could bind to the SlBAM3 promoter and directly activate SlBAM3 transcription, as revealed by yeast one-hybrid and dual LUC assays. In addition, the suppression of MYC2 resulted in increased starch accumulation, decreased soluble sugar content, and reduced tolerance to cold stress in tomato plants. Taken together, these findings demonstrate that JA positively regulates beta-amylase-associated starch degradation through the MYC2-SlBAM3 module in tomato during cold stress. The results of the present work expand our understanding of the mechanisms underlying BAM gene activation and starch catabolism under cold stress. The regulatory module of SlBAM3 can be further utilized to breed tomato cultivars with enhanced cold tolerance.
PMID: 38674464
Plants (Basel) , IF:3.935 , 2024 Apr , V13 (7) doi: 10.3390/plants13071016
MicroRNA Profiling Revealed the Mechanism of Enhanced Cold Resistance by Grafting in Melon (Cucumis melo L.).
College of Horticulture, Hebei Agricultural University, Baoding 071000, China.; Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding 071000, China.; Ministry of Education of China-Hebei Province Joint Innovation Center for Efficient Green Vegetable Industry, Baoding 071000, China.
Grafting is widely used to improve the resistance to abiotic stresses in cucurbit plants, but the effect and molecular mechanism of grafting on cold stress are still unknown in melon. In this study, phenotypic characteristics, physiological indexes, small-RNA sequencing and expression analyses were performed on grafted plants with pumpkin rootstock (PG) and self-grafted plants (SG) to explore the mechanism of changed cold tolerance by grafting in melon. Compared with SG plants, the cold tolerance was obviously enhanced, the malondialdehyde (MDA) content was significantly decreased and the activities of antioxidant enzymes (superoxide dismutase, SOD; catalase, CAT; peroxidase, POD) were significantly increased in PG plants. Depend on differentially expressed miRNA (DEM) identification and expression pattern analyses, cme-miR156b, cme-miR156f and chr07_30026 were thought to play a key role in enhancing low-temperature resistance resulting from grafting. Subsequently, 24, 37 and 17 target genes of cme-miR156b, cme-miR156f and chr07_30026 were respectively predicted, and 21 target genes were co-regulated by cme-miR156b and cme-miR156f. Among these 57 unique target genes, the putative promoter of 13 target genes contained the low-temperature responsive (LTR) cis-acting element. The results of qRT-PCR indicated that six target genes (MELO3C002370, MELO3C009217, MELO3C018972, MELO3C016713, MELO3C012858 and MELO3C000732) displayed the opposite expression pattern to their corresponding miRNAs. Furthermore, MELO3C002370, MELO3C016713 and MELO3C012858 were significantly downregulated in cold-resistant cultivars and upregulated in cold-sensitive varieties after cold stimulus, and they acted as the key negative regulators of low-temperature response in melon. This study revealed three key miRNAs and three putative target genes involved in the cold tolerance of melon and provided a molecular basis underlying how grafting improved the low-temperature resistance of melon plants.
PMID: 38611545
Plants (Basel) , IF:3.935 , 2024 Mar , V13 (7) doi: 10.3390/plants13071002
The Physiological Response of Apricot Flowers to Low-Temperature Stress.
College of Horticulture, Shanxi Agricultural University, Taigu, Jinzhong 030801, China.
The growth and development of apricot flower organs are severely impacted by spring frosts. To better understand this process, apricot flowers were exposed to temperatures ranging from 0 degrees C to -8 degrees C, including a control at 18 degrees C, in artificial incubators to mimic diverse low-temperature environments. We aimed to examine their physiological reactions to cold stress, with an emphasis on changes in phenotype, membrane stability, osmotic substance levels, and antioxidant enzyme performance. Results reveal that cold stress induces significant browning and cellular damage, with a sharp increase in browning rate and membrane permeability below -5 degrees C. Soluble sugars and proteins initially rise as osmoprotectants, but their content decreases at lower temperatures. Proline content consistently increases, suggesting a protective role. Antioxidant enzyme activities, including catalase (CAT), peroxidase (POD), superoxide dismutase (SOD), and ascorbate peroxidase (APX), exhibit a complex pattern, with initial increases followed by declines at more severe cold conditions. Correlation and principal component analyses highlight the interplay between these responses, indicating a multifaceted adaptation strategy. The findings contribute to the understanding of apricot cold tolerance and inform breeding efforts for improved crop resilience.
PMID: 38611530
Gene , IF:3.688 , 2024 Apr : 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
Plant Biol (Stuttg) , IF:3.081 , 2024 Apr 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
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
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
Plant Commun , 2024 Apr : P100923 doi: 10.1016/j.xplc.2024.100923
NAC056 transcription factor confers freezing tolerance by positively regulating the expression of CBFs and NIA1 in Arabidopsis.
Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, No. 300 Fenglin Road, Shanghai 200032, China. Electronic address: ppxu@cemps.ac.cn.; State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China.; Department of Food Science, College of Hospitality Management, Shanghai Business School, Shanghai 200235, China.; Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, No. 300 Fenglin Road, Shanghai 200032, China.
It is well known that freezing stress can seriously affect the growth and development of plants. However, the mechanisms of these effects and plant response to freezing stress need to be further explored. Here, we identified a NAC family transcription factor (TF) NAC056 that can promote freezing tolerance. The NAC056 mRNA level was obviously induced by freezing stress in roots. We showed that the nac056 mutant compromised freezing tolerance. NAC056 acts positively in response to freezing by directly promoting the key CBF pathway genes. Interestingly, we found that the CBF1 regulates nitrate assimilation by regulating the nitrate reductase gene, NIA1, in plants, therefore, NAC056-CBF1-NIA1 form a regulatory module for the assimilation of nitrate and the growth of roots under freezing stress. In addition, 35S::NAC056 transgenic plants promoted freezing tolerance. The cbfs triple mutant could partly reverse the 35S::NAC056-induced freezing tolerance. Thus, NAC056 confers freezing tolerance through the CBF pathway. Therefore, NAC056 mediates the response of plants to balance plant growth and freezing stress tolerance.
PMID: 38637986