Plant Cell , IF:11.277 , 2024 Feb doi: 10.1093/plcell/koae050
Molecular dissection of an intronic enhancer governing cold-induced expression of the vacuolar invertase gene in potato.
Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, Anhui Province, China.; Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.; United States Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, Wisconsin 53706, USA.; Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu 610101, Sichuan Province, China.; Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu 610101, Sichuan Province, China.; Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA.; Department of Postharvest Science, The Volcani Institute, ARO, Rishon LeZion, Israel.; Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, USA.; Michigan State University AgBioResearch, East Lansing, Michigan 48824, USA.; Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA.
Potato (Solanum tuberosum) is the third most important food crop in the world. Potato tubers must be stored at cold temperatures to minimize sprouting and losses due to disease. However, cold temperatures strongly induce the expression of the potato vacuolar invertase gene (VInv) and cause reducing sugar accumulation. This process, referred to as "cold-induced sweetening", is a major postharvest problem for the potato industry. We discovered that the cold-induced expression of VInv is controlled by a 200-bp enhancer, VInvIn2En, located in its second intron. We identified several DNA motifs in VInvIn2En that bind transcription factors involved in the plant cold stress response. Mutation of these DNA motifs abolished VInvIn2En function as a transcriptional enhancer. We developed VInvIn2En deletion lines in both diploid and tetraploid potato using clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9)-mediated gene editing. VInv transcription in cold-stored tubers was significantly reduced in the deletion lines. Interestingly, the VInvIn2En sequence is highly conserved among distantly related Solanum species, including tomato (Solanum lycopersicum) and other non-tuber-bearing species. We conclude that the VInv gene as well as the VInvIn2En enhancer have adopted distinct roles in the cold stress response in tubers of tuber-bearing Solanum species.
PMID: 38374801
Plant Cell , IF:11.277 , 2024 Feb doi: 10.1093/plcell/koae039
Pan-transcriptomic analysis reveals alternative splicing control of cold tolerance in rice.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China.; Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China.
Plants have evolved complex mechanisms to adapt to harsh environmental conditions. Rice (Oryza sativa) is a staple food crop that is sensitive to low temperatures. However, its cold stress responses remain poorly understood, thus limiting possibilities for crop engineering to achieve greater cold tolerance. In this study, we constructed a rice pan-transcriptome and characterized its transcriptional regulatory landscape in response to cold stress. We performed Iso-Seq and RNA-Seq of 11 rice cultivars subjected to a time-course cold treatment. Our analyses revealed that alternative splicing-regulated gene expression plays a significant role in the cold stress response. Moreover, we identified CATALASE C (OsCATC) and Os03g0701200 as candidate genes for engineering enhanced cold tolerance. Importantly, we uncovered central roles for the two serine-arginine-rich proteins OsRS33 and OsRS2Z38 in cold tolerance. Our analysis of cold tolerance and resequencing data from a diverse collection of 165 rice cultivars suggested that OsRS2Z38 may be a key selection gene in japonica domestication for cold adaptation, associated with the adaptive evolution of rice. This study systematically investigated the distribution, dynamic changes, and regulatory mechanisms of alternative splicing in rice under cold stress. Overall, our work generates a rich resource with broad implications for understanding the genetic basis of cold response mechanisms in plants.
PMID: 38345423
Proc Natl Acad Sci U S A , IF:11.205 , 2024 Feb , V121 (6) : Pe2317461121 doi: 10.1073/pnas.2317461121
A large-effect fitness trade-off across environments is explained by a single mutation affecting cold acclimation.
Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907.; Center for Plant Biology, Purdue University, West Lafayette, IN 47907.; Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala SE-752 36, Sweden.; Department of Biochemistry, Purdue University, West Lafayette, IN 47907.; Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523.
Identifying the genetic basis of local adaptation and fitness trade-offs across environments is a central goal of evolutionary biology. Cold acclimation is an adaptive plastic response for surviving seasonal freezing, and costs of acclimation may be a general mechanism for fitness trade-offs across environments in temperate zone species. Starting with locally adapted ecotypes of Arabidopsis thaliana from Italy and Sweden, we examined the fitness consequences of a naturally occurring functional polymorphism in CBF2. This gene encodes a transcription factor that is a major regulator of cold-acclimated freezing tolerance and resides within a locus responsible for a genetic trade-off for long-term mean fitness. We estimated the consequences of alternate genotypes of CBF2 on 5-y mean fitness and fitness components at the native field sites by comparing near-isogenic lines with alternate genotypes of CBF2 to their genetic background ecotypes. The effects of CBF2 were validated at the nucleotide level using gene-edited lines in the native genetic backgrounds grown in simulated parental environments. The foreign CBF2 genotype in the local genetic background reduced long-term mean fitness in Sweden by more than 10%, primarily via effects on survival. In Italy, fitness was reduced by more than 20%, primarily via effects on fecundity. At both sites, the effects were temporally variable and much stronger in some years. The gene-edited lines confirmed that CBF2 encodes the causal variant underlying this genetic trade-off. Additionally, we demonstrated a substantial fitness cost of cold acclimation, which has broad implications for potential maladaptive responses to climate change.
PMID: 38289961
Curr Biol , IF:10.834 , 2024 Feb doi: 10.1016/j.cub.2024.01.045
Structural changes in cell wall pectic polymers contribute to freezing tolerance induced by cold acclimation in plants.
Graduate School of Science & Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan. Electronic address: dtakahashi@mail.saitama-u.ac.jp.; Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan.; Graduate School of Science & Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan.; La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, Bundoora, VIC 3086, Australia.; Department of Biochemistry & Molecular Biology, Faculty of Science, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan.; School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuda-cho, Midori-ku, Yokohama 226-8503, Japan.; Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany.
Subzero temperatures are often lethal to plants. Many temperate herbaceous plants have a cold acclimation mechanism that allows them to sense a drop in temperature and prepare for freezing stress through accumulation of soluble sugars and cryoprotective proteins. As ice formation primarily occurs in the apoplast (the cell wall space), cell wall functional properties are important for plant freezing tolerance. Although previous studies have shown that the amounts of constituent sugars of the cell wall, in particular those of pectic polysaccharides, are altered by cold acclimation, the significance of this change during cold acclimation has not been clarified. We found that beta-1,4-galactan, which forms neutral side chains of the acidic pectic rhamnogalacturonan-I, accumulates in the cell walls of Arabidopsis and various freezing-tolerant vegetables during cold acclimation. The gals1 gals2 gals3 triple mutant, which has reduced beta-1,4-galactan in the cell wall, exhibited impaired freezing tolerance compared with wild-type Arabidopsis during initial stages of cold acclimation. Expression of genes involved in the galactan biosynthesis pathway, such as galactan synthases and UDP-glucose 4-epimerases, was induced during cold acclimation in Arabidopsis, explaining the galactan accumulation. Cold acclimation resulted in a decrease in extensibility and an increase in rigidity of the cell wall in the wild type, whereas these changes were not observed in the gals1 gals2 gals3 triple mutant. These results indicate that the accumulation of pectic beta-1,4-galactan contributes to acquired freezing tolerance by cold acclimation, likely via changes in cell wall mechanical properties.
PMID: 38335960
J Hazard Mater , IF:10.588 , 2024 Feb , V463 : P132802 doi: 10.1016/j.jhazmat.2023.132802
Performance and mechanism of SMX removal by an electrolysis-integrated ecological floating bed at low temperatures: A new perspective of plant activity, iron plaque, and microbial functions.
Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.; School of Life Sciences, Anhui Medical University, Hefei 230032, China.; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China.; State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing 100012, China. Electronic address: lushy2000@163.com.; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China. Electronic address: lxh7786@ouc.edu.cn.; State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
Improvements in plant activity and functional microbial communities are important to ensure the stability and efficiency of pollutant removal measures in cold regions. Although electrochemistry is known to accelerate pollutant degradation, cold stress acclimation of plants and the stability and activity of plant-microbial synergism remain poorly understood. The sulfamethoxazole (SMX) removal, iron plaque morphology, plant activity, microbial community, and function responses were investigated in an electrolysis-integrated ecological floating bed (EFB) at 6 +/- 2 ℃. Electrochemistry significantly improved SMX removal and plant activity. Dense and uniform iron plaque was found on root surfaces in L-E-Fe which improved the plant adaptability at low temperatures and provided more adsorption sites for bacteria. The microbial community structure was optimized and the key functional bacteria for SMX degradation (e.g., Actinobacteriota, Pseudomonas) were enriched. Electrochemistry improves the relative abundance of enzymes related to energy metabolism, thereby increasing energy responses to SMX and low temperatures. Notably, electrochemistry improved the expression of target genes (sadB and sadC, especially sadC) involved in SMX degradation. Electrochemistry enhances hydrogen bonding and electrostatic interactions between SMX and sadC, thereby enhancing SMX degradation and transformation. This study provides a deeper understanding of the electrochemical stability of antibiotic degradation at low temperatures.
PMID: 37922584
New Phytol , IF:10.151 , 2024 Mar , V241 (5) : P2143-2157 doi: 10.1111/nph.19514
COG3 confers the chilling tolerance to mediate OsFtsH2-D1 module in rice.
Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.; University of Chinese Academy of Sciences, Beijing, 100049, China.; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
The chilling stress induced by the global climate change harms rice production, especially at seedling and booting stage, which feed half the population of the world. Although there are key quantitative trait locus genes identified in the individual stage, few genes have been reported and functioned at both stages. Utilizing chromosome segment substitution lines (CSSLs) and a combination of map-based cloning and phenotypes of the mutants and overexpression lines, we identified the major gene Chilling-tolerance in Geng/japonica rice 3 (COG3) of q chilling-tolerance at the booting and seedling stage 11 (qCTBS11) conferred chilling tolerance at both seedling and booting stages. COG3 was significantly upregulated in Nipponbare under chilling treatment compared with its expression in 93-11. The loss-of-function mutants cog3 showed a reduced chilling tolerance. On the contrary, overexpression enhanced chilling tolerance. Genome evolution and genetic analysis suggested that COG3 may have undergone strong selection in temperate japonica during domestication. COG3, a putative calmodulin-binding protein, physically interacted with OsFtsH2 at chloroplast. In cog3-1, OsFtsH2-mediated D1 degradation was impaired under chilling treatment compared with wild-type. Our results suggest that COG3 is necessary for maintaining OsFtsH2 protease activity to regulate chilling tolerance at the booting and seedling stage.
PMID: 38173177
Plant Biotechnol J , IF:9.803 , 2024 Mar , V22 (3) : P751-758 doi: 10.1111/pbi.14221
Fine-tuning rice heading date through multiplex editing of the regulatory regions of key genes by CRISPR-Cas9.
State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm Resources, Nanjing Agricultural University, Nanjing, China.; Institute of Lianyungang Agricultural Science of Xuhuai Area/Lianyungang Institute of Agricultural Sciences, Lianyungang, China.; National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
Heading date (or flowering time) is a key agronomic trait that affects seasonal and regional adaption of rice cultivars. An unoptimized heading date can either not achieve a high yield or has a high risk of encountering abiotic stresses. There is a strong demand on the mild to moderate adjusting the heading date in breeding practice. Genome editing is a promising method which allows more precise and faster changing the heading date of rice. However, direct knock out of major genes involved in regulating heading date will not always achieve a new germplasm with expected heading date. It is still challenging to quantitatively adjust the heading date of elite cultivars with best adaption for broader region. In this study, we used a CRISPR-Cas9 based genome editing strategy called high-efficiency multiplex promoter-targeting (HMP) to generate novel alleles at cis-regulatory regions of three major heading date genes: Hd1, Ghd7 and DTH8. We achieved a series of germplasm with quantitative variations of heading date by editing promoter regions and adjusting the expression levels of these genes. We performed field trials to screen for the best adapted lines for different regions. We successfully expanded an elite cultivar Ningjing8 (NJ8) to a higher latitude region by selecting a line with a mild early heading phenotype that escaped from cold stress and achieved high yield potential. Our study demonstrates that HMP is a powerful tool for quantitatively regulating rice heading date and expanding elite cultivars to broader regions.
PMID: 37932934
Plant Biotechnol J , IF:9.803 , 2024 Feb , V22 (2) : P413-426 doi: 10.1111/pbi.14195
Banana MaNAC1 activates secondary cell wall cellulose biosynthesis to enhance chilling resistance in fruit.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, South China Agricultural University, Guangzhou, China.; Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China.
Chilling injury has a negative impact on the quantity and quality of crops, especially subtropical and tropical plants. The plant cell wall is not only the main source of biomass production, but also the first barrier to various stresses. Therefore, improving the understanding of the alterations in cell wall architecture is of great significance for both biomass production and stress adaptation. Herein, we demonstrated that the cell wall principal component cellulose accumulated during chilling stress, which was caused by the activation of MaCESA proteins. The sequence-multiple comparisons show that a cold-inducible NAC transcriptional factor MaNAC1, a homologue of Secondary Wall NAC transcription factors, has high sequence similarity with Arabidopsis SND3. An increase in cell wall thickness and cellulosic glucan content was observed in MaNAC1-overexpressing Arabidopsis lines, indicating that MaNAC1 participates in cellulose biosynthesis. Over-expression of MaNAC1 in Arabidopsis mutant snd3 restored the defective secondary growth of thinner cell walls and increased cellulosic glucan content. Furthermore, the activation of MaCESA7 and MaCESA6B cellulose biosynthesis genes can be directly induced by MaNAC1 through binding to SNBE motifs within their promoters, leading to enhanced cellulose content during low-temperature stress. Ultimately, tomato fruit showed greater cold resistance in MaNAC1 overexpression lines with thickened cell walls and increased cellulosic glucan content. Our findings revealed that MaNAC1 performs a vital role as a positive modulator in modulating cell wall cellulose metabolism within banana fruit under chilling stress.
PMID: 37816143
Plant Physiol , IF:8.34 , 2024 Jan , V194 (2) : P1075-1090 doi: 10.1093/plphys/kiad578
Transcription factor SlWRKY50 enhances cold tolerance in tomato by activating the jasmonic acid signaling.
National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, P.R. China.
Tomato (Solanum lycopersicum) is a cold-sensitive crop but frequently experiences low-temperature stimuli. However, tomato responses to cold stress are still poorly understood. Our previous studies have shown that using wild tomato (Solanum habrochaites) as rootstock can significantly enhance the cold resistance of grafted seedlings, in which a high concentration of jasmonic acids (JAs) in scions exerts an important role, but the mechanism of JA accumulation remains unclear. Herein, we discovered that tomato SlWRKY50, a Group II WRKY transcription factor that is cold inducible, responds to cold stimuli and plays a key role in JA biosynthesis. SlWRKY50 directly bound to the promoter of tomato allene oxide synthase gene (SlAOS), and overexpressing SlWRKY50 improved tomato chilling resistance, which led to higher levels of Fv/Fm, antioxidative enzymes, SlAOS expression, and JA accumulation. SlWRKY50-silenced plants, however, exhibited an opposite trend. Moreover, diethyldithiocarbamate acid (a JA biosynthesis inhibitor) foliar treatment drastically reduced the cold tolerance of SlWRKY50-overexpression plants to wild-type levels. Importantly, SlMYC2, the key regulator of the JA signaling pathway, can control SlWRKY50 expression. Overall, our research indicates that SlWRKY50 promotes cold tolerance by controlling JA biosynthesis and that JA signaling mediates SlWRKY50 expression via transcriptional activation by SlMYC2. Thus, this contributes to the genetic knowledge necessary for developing cold-resistant tomato varieties.
PMID: 37935624
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 Feb doi: 10.1111/pce.14845
MrERF039 transcription factor plays an active role in the cold response of Medicago ruthenica as a sugar molecular switch.
Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, College of Life Sciences, Inner Mongolia University, Hohhot, China.; Inner Mongolia Academy of Science and Technology, Hohhot, China.
Cold stress severely restricts plant development, causing significant agricultural losses. We found a critical transcription factor network in Medicago ruthenica was involved in plant adaptation to low-temperature. APETALA2/ethylene responsive factor (AP2/ERF) transcription factor MrERF039 was transcriptionally induced by cold stress in M. ruthenica. Overexpression of MrERF039 significantly increased the glucose and maltose content, thereby improving the tolerance of M. ruthenica. MrERF039 could bind to the DRE cis-acting element in the MrCAS15A promoter. Additionally, the methyl group of the 14th amino acid in MrERF039 was required for binding. Transcriptome analysis showed that MrERF039 acted as a sugar molecular switch, regulating numerous sugar transporters and sugar metabolism-related genes. In addition, we found that MrERF039 could directly regulate beta-amylase gene, UDP glycosyltransferase gene, and C2H2 zinc finger protein gene expression. In conclusion, these findings suggest that high expression of MrERF039 can significantly improve the cold tolerance of M. ruthenica root tissues during cold acclimation. Our results provide a new theoretical basis and candidate genes for breeding new legume forage varieties with high resistance.
PMID: 38318779
J Exp Bot , IF:6.992 , 2024 Feb doi: 10.1093/jxb/erae045
The Circadian Clock And Thermal Regulation In Plants: Novel Findings On The Role Of Positive Circadian Clock-Regulators In Temperature Responses.
Fundacion Instituto Leloir-IIBBA/CONICET, Av. Patricias Argentinas 435, Ciudad Autonoma de Buenos Aires, Argentina.
The impact of rising global temperatures on crop yields is a serious concern, and developing heat-resistant crop varieties is crucial for mitigating the effects of climate change on agriculture. To achieve this, a better understanding of the molecular basis of the thermal responses in plants is necessary. The circadian clock plays a central role in modulating plant biology in synchrony with environmental changes including temperature fluctuations. Recent studies have uncovered the role of transcriptional activators of the core circadian network in temperature responses. This expert view highlights key novel findings regarding the role of RVE and LNK gene families in regulating gene expression patterns and plant growth under different temperature conditions, ranging from regular diurnal oscillations to extreme stress temperatures. These findings reinforce the essential role of the circadian clock in plant adaptation to changing temperatures and provide a basis for future studies on crop improvement.
PMID: 38373194
Int J Biol Macromol , IF:6.953 , 2024 Feb , V257 (Pt 1) : P128617 doi: 10.1016/j.ijbiomac.2023.128617
Genome-wide identification and expression profiling of the WRKY gene family reveals abiotic stress response mechanisms in Platycodon grandiflorus.
College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China.; College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China; Institute of Conservation and Development of Traditional Chinese Medicine Resources, Anhui Academy of Chinese Medicine, Hefei 230012, China; Anhui Province Key Laboratory of Research & Development of Chinese Medicine, Hefei 230012, China. Electronic address: zlp_ahtcm@126.com.; College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China; Institute of Pharmaceutics, Anhui Academy of Chinese Medicine, Hefei, China; Anhui Province Key Laboratory of Pharmaceutical Technology and Application, Anhui University of Chinese Medicine, Hefei, China; MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, China. Electronic address: guishy0520@ahtcm.edu.cn.
The WRKY family of transcription factors (TFs) is an important gene family involved in abiotic stress responses. Although the roles of WRKY TFs in plant abiotic stress responses are well studied, little is known about the stress-induced changes in WRKY family in Platycodon grandiflorus. 42 PgWRKY genes in seven subgroups were identified in the P. grandiflorus genome. The content of eight platycodins in P. grandiflorus was investigated under cold, heat, and drought stresses. Platycodin D levels significantly increased under three abiotic stresses, while the content changes of other platycodins varied. Transcriptome analysis showed that different WRKY family members exhibited varied expression patterns under different abiotic stresses. PgWRKY20, PgWRKY26, and PgWRKY39 were identified as three key candidates for temperature and drought stress responses, and were cloned and analysed for sequence characteristics, gene structure, subcellular localisation, and expression patterns. The RT-qPCR results showed that PgWRKY26 expression significantly increased after heat stress for 48 h, cold stress for 6 h, and drought stress for 2 d (DS_2 d). The PgWRKY39 expression level significantly increased at DS_2 d. This study provides a theoretical basis for clarifying the molecular mechanism of the abiotic stress responses of the WRKY gene family in P. grandiflorus.
PMID: 38070802
Plant J , IF:6.417 , 2024 Mar , V117 (5) : P1377-1391 doi: 10.1111/tpj.16568
CaSnRK2.4-mediated phosphorylation of CaNAC035 regulates abscisic acid synthesis in pepper (Capsicum annuum L.) responding to cold stress.
College of Horticulture, Northwest A&F University, Yangling, 712100, China.; Department of Horticulture, The University of Haripur, Haripur, 22620, Pakistan.; College of Horticulture, Hunan Agricultural University, Changshai, 410125, China.; Shaanxi Engineering Research Center for Vegetables, Yangling, 712100, China.
Plant NAC transcription factors play a crucial role in enhancing cold stress tolerance, yet the precise molecular mechanisms underlying cold stress remain elusive. In this study, we identified and characterized CaNAC035, an NAC transcription factor isolated from pepper (Capsicum annuum) leaves. We observed that the expression of the CaNAC035 gene is induced by both cold and abscisic acid (ABA) treatments, and we elucidated its positive regulatory role in cold stress tolerance. Overexpression of CaNAC035 resulted in enhanced cold stress tolerance, while knockdown of CaNAC035 significantly reduced resistance to cold stress. Additionally, we discovered that CaSnRK2.4, a SnRK2 protein, plays an essential role in cold tolerance. In this study, we demonstrated that CaSnRK2.4 physically interacts with and phosphorylates CaNAC035 both in vitro and in vivo. Moreover, the expression of two ABA biosynthesis-related genes, CaAAO3 and CaNCED3, was significantly upregulated in the CaNAC035-overexpressing transgenic pepper lines. Yeast one-hybrid, Dual Luciferase, and electrophoretic mobility shift assays provided evidence that CaNAC035 binds to the promoter regions of both CaAAO3 and CaNCED3 in vivo and in vitro. Notably, treatment of transgenic pepper with 50 mum Fluridone (Flu) enhanced cold tolerance, while the exogenous application of ABA at a concentration of 10 mum noticeably reduced cold tolerance in the virus-induced gene silencing line. Overall, our findings highlight the involvement of CaNAC035 in the cold response of pepper and provide valuable insights into the molecular mechanisms underlying cold tolerance. These results offer promising prospects for molecular breeding strategies aimed at improving cold tolerance in pepper and other crops.
PMID: 38017590
Plant J , IF:6.417 , 2024 Mar , V117 (5) : P1317-1329 doi: 10.1111/tpj.16562
A C2H2-type zinc finger protein ZAT12 of Poncirus trifoliata acts downstream of CBF1 to regulate cold tolerance.
National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China.; Hubei Key Laboratory of Germplasm Innovation and Utilization of Fruit Trees, Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.; College of Life Sciences, Gannan Normal University, Ganzhou, 341000, China.
The Cys2/His2 (C2H2)-type zinc finger family has been reported to regulate multiple aspects of plant development and abiotic stress response. However, the role of C2H2-type zinc finger proteins in cold tolerance remains largely unclear. Through RNA-sequence analysis, a cold-responsive zinc finger protein, named as PtrZAT12, was identified and isolated from trifoliate orange (Poncirus trifoliata L. Raf.), a cold-hardy plant closely related to citrus. Furthermore, we found that PtrZAT12 was markedly induced by various abiotic stresses, especially cold stress. PtrZAT12 is a nuclear protein, and physiological analysis suggests that overexpression of PtrZAT12 conferred enhanced cold tolerance in transgenic tobacco (Nicotiana tabacum) plants, while knockdown of PtrZAT12 by virus-induced gene silencing (VIGS) increased the cold sensitivity of trifoliate orange and repressed expression of genes involved in stress tolerance. The promoter of PtrZAT12 harbors a DRE/CRT cis-acting element, which was verified to be specifically bound by PtrCBF1 (Poncirus trifoliata C-repeat BINDING FACTOR1). VIGS-mediated silencing of PtrCBF1 reduced the relative expression levels of PtrZAT12 and decreased the cold resistance of trifoliate orange. Based on these results, we propose that PtrZAT12 is a direct target of CBF1 and plays a positive role in modulation of cold stress tolerance. The knowledge gains new insight into a regulatory module composed of CBF1-ZAT12 in response to cold stress and advances our understanding of cold stress response in plants.
PMID: 38017362
Plant J , IF:6.417 , 2024 Jan doi: 10.1111/tpj.16654
A normalization method that controls for total RNA abundance affects the identification of differentially expressed genes, revealing bias toward morning-expressed responses.
Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA.; Department of Agriculture and Natural Resources, Delaware State University, Dover, Delaware, USA.; Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, 79410, USA.; Department of Science and Technology, The Good Food Institute, Washington, District of Columbia, 20090, USA.; Department of Agronomy, Kansas State University, Manhattan, Kansas, 66506, USA.
RNA-Sequencing is widely used to investigate changes in gene expression at the transcription level in plants. Most plant RNA-Seq analysis pipelines base the normalization approaches on the assumption that total transcript levels do not vary between samples. However, this assumption has not been demonstrated. In fact, many common experimental treatments and genetic alterations affect transcription efficiency or RNA stability, resulting in unequal transcript abundance. The addition of synthetic RNA controls is a simple correction that controls for variation in total mRNA levels. However, adding spike-ins appropriately is challenging with complex plant tissue, and carefully considering how they are added is essential to their successful use. We demonstrate that adding external RNA spike-ins as a normalization control produces differences in RNA-Seq analysis compared to traditional normalization methods, even between two times of day in untreated plants. We illustrate the use of RNA spike-ins with 3' RNA-Seq and present a normalization pipeline that accounts for differences in total transcriptional levels. We evaluate the effect of normalization methods on identifying differentially expressed genes in the context of identifying the effect of the time of day on gene expression and response to chilling stress in sorghum.
PMID: 38289828
Int J Mol Sci , IF:5.923 , 2024 Feb , V25 (4) doi: 10.3390/ijms25042064
Identification and Molecular Characterization of the CAMTA Gene Family in Solanaceae with a Focus on the Expression Analysis of Eggplant Genes under Cold Stress.
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.
Calmodulin-binding transcription activator (CAMTA) is an important calmodulin-binding protein with a conserved structure in eukaryotes which is widely involved in plant stress response, growth and development, hormone signal transduction, and other biological processes. Although CAMTA genes have been identified and characterized in many plant species, a systematic and comprehensive analysis of CAMTA genes in the Solanaceae genome is performed for the first time in this study. A total of 28 CAMTA genes were identified using bioinformatics tools, and the biochemical/physicochemical properties of these proteins were investigated. CAMTA genes were categorized into three major groups according to phylogenetic analysis. Tissue-expression profiles indicated divergent spatiotemporal expression patterns of SmCAMTAs. Furthermore, transcriptome analysis of SmCAMTA genes showed that exposure to cold induced differential expression of many eggplant CAMTA genes. Yeast two-hybrid and bimolecular fluorescent complementary assays suggested an interaction between SmCAMTA2 and SmERF1, promoting the transcription of the cold key factor SmCBF2, which may be an important mechanism for plant cold resistance. In summary, our results provide essential information for further functional research on Solanaceae family genes, and possibly other plant families, in the determination of the development of plants.
PMID: 38396743
Int J Mol Sci , IF:5.923 , 2024 Feb , V25 (3) doi: 10.3390/ijms25031877
Genome-Wide Identification of the GhANN Gene Family and Functional Validation of GhANN11 and GhANN4 under Abiotic Stress.
State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.; Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China.
Annexins (ANNs) are a structurally conserved protein family present in almost all plants. In the present study, 27 GhANNs were identified in cotton and were unevenly distributed across 14 chromosomes. Transcriptome data and RT-qPCR results revealed that multiple GhANNs respond to at least two abiotic stresses. Similarly, the expression levels of GhANN4 and GhANN11 were significantly upregulated under heat, cold, and drought stress. Using virus-induced gene silencing (VIGS), functional characterization of GhANN4 and GhANN11 revealed that, compared with those of the controls, the leaf wilting of GhANN4-silenced plants was more obvious, and the activities of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) were lower under NaCl and PEG stress. Moreover, the expression of stress marker genes (GhCBL3, GhDREB2A, GhDREB2C, GhPP2C, GhRD20-2, GhCIPK6, GhNHX1, GhRD20-1, GhSOS1, GhSOS2 and GhSnRK2.6) was significantly downregulated in GhANN4-silenced plants after stress. Under cold stress, the growth of the GHANN11-silenced plants was significantly weaker than that of the control plants, and the activities of POD, SOD, and CAT were also lower. However, compared with those of the control, the elasticity and orthostatic activity of the GhANN11-silenced plants were greater; the POD, SOD, and CAT activities were higher; and the GhDREB2C, GhHSP, and GhSOS2 expression levels were greater under heat stress. These results suggest that different GhANN family members respond differently to different types of abiotic stress.
PMID: 38339155
Int J Mol Sci , IF:5.923 , 2024 Feb , V25 (3) doi: 10.3390/ijms25031776
Comparative Analysis of Chloroplast Pan-Genomes and Transcriptomics Reveals Cold Adaptation in Medicago sativa.
Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China.; International Agriculture Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China.; Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China.; National Engineering Research Center for Ornamental Horticulture, Yunnan Flower Breeding Key Laboratory, Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China.
Alfalfa (Medicago sativa) is a perennial forage legume that is widely distributed all over the world; therefore, it has an extremely complex genetic background. Though population structure and phylogenetic studies have been conducted on a large group of alfalfa nuclear genomes, information about the chloroplast genomes is still lacking. Chloroplast genomes are generally considered to be conservative and play an important role in population diversity analysis and species adaptation in plants. Here, 231 complete alfalfa chloroplast genomes were successfully assembled from 359 alfalfa resequencing data, on the basis of which the alfalfa chloroplast pan-genome was constructed. We investigated the genetic variations of the alfalfa chloroplast genome through comparative genomic, genetic diversity, phylogenetic, population genetic structure, and haplotype analysis. Meanwhile, the expression of alfalfa chloroplast genes under cold stress was explored through transcriptome analysis. As a result, chloroplast genomes of 231 alfalfa lack an IR region, and the size of the chloroplast genome ranges from 125,192 bp to 126,105 bp. Using population structure, haplotypes, and construction of a phylogenetic tree, it was found that alfalfa populations could be divided into four groups, and multiple highly variable regions were found in the alfalfa chloroplast genome. Transcriptome analysis showed that tRNA genes were significantly up-regulated in the cold-sensitive varieties, while rps7, rpl32, and ndhB were down-regulated, and the editing efficiency of ycf1, ycf2, and ndhF was decreased in the cold-tolerant varieties, which may be due to the fact that chloroplasts store nutrients through photosynthesis to resist cold. The huge number of genetic variants in this study provide powerful resources for molecular markers.
PMID: 38339052
Int J Mol Sci , IF:5.923 , 2024 Jan , V25 (3) doi: 10.3390/ijms25031663
The Effect of Ethephon on Ethylene and Chlorophyll in Zoysia japonica Leaves.
College of Grassland Science, Beijing Forestry University, Beijing 100083, China.
Zoysia japonica (Zoysia japonica Steud.) is a kind of warm-season turfgrass with many excellent characteristics. However, the shorter green period and longer dormancy caused by cold stress in late autumn and winter are the most limiting factors affecting its application. A previous transcriptome analysis revealed that ethephon regulated genes in chlorophyll metabolism in Zoysia japonica under cold stress. Further experimental data are necessary to understand the effect and underlying mechanism of ethephon in regulating the cold tolerance of Zoysia japonica. The aim of this study was to evaluate the effects of ethephon by measuring the enzyme activity, intermediates content, and gene expression related to ethylene biosynthesis, signaling, and chlorophyll metabolism. In addition, the ethylene production rate, chlorophyll content, and chlorophyll a/b ratio were analyzed. The results showed that ethephon application in a proper concentration inhibited endogenous ethylene biosynthesis, but eventually promoted the ethylene production rate due to its ethylene-releasing nature. Ethephon could promote chlorophyll content and improve plant growth in Zoysia japonica under cold-stressed conditions. In conclusion, ethephon plays a positive role in releasing ethylene and maintaining the chlorophyll content in Zoysia japonica both under non-stressed and cold-stressed conditions.
PMID: 38338942
Front Plant Sci , IF:5.753 , 2024 , V15 : P1286908 doi: 10.3389/fpls.2024.1286908
Fatty acid unsaturation improves germination of upland cotton (Gossypium hirsutum) under cold stress.
Department of Plant and Soil Science, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX, United States.
INTRODUCTION: The level of fatty acid unsaturation in seeds is one of the major determinants of cold germination ability, particularly in oilseeds. The presence of cis double bonds in unsaturated fatty acids creates bends that lowers their melting temperatures compared to saturated fatty acids. Unsaturated fatty acids with low melting points mobilize faster at low temperatures providing seeds with sufficient energy for germination. METHODOLOGY: To investigate the effects of fatty acid unsaturation on the ability of cotton seeds to germinate under cold conditions, four recombinant inbred lines (RILs) of cotton with unique fatty acid profiles were evaluated using a set of developmental and biochemical assays at 12 degrees C (critically low temperature), 15 degrees C (cardinal minimum temperature) and 30 degrees C (optimum temperature). Furthermore, whole seed lipidome profiling using liquid chromatography with mass spectrometry was done to compare the lipid compositional changes at 12 degrees C and 30 degrees C after imbibing cotton seeds of all the six genotypes for 0 hours, 3 hours and 6 hours. RESULTS AND DISCUSSION: The RILs with higher unsaturation/saturation ratios registered robust germination performance, lower solute leakage, and optimum water uptake rates under cold stress. Imbibition at 30 degrees C for 8 hours before cold exposure significantly improved the germination of cold sensitive genotypes, indicating that the first few hours of water uptake are critical for cold stress. Whole seed lipidome profiling of all the genotypes specifically associated cold germination ability with higher unsaturation levels of phospholipids during early imbibition. The presence of cis double bonds in phospholipids creates kinks that maintain the fluidity of cell membranes under low temperature. Membrane flexibility under cold conditions is essential for facilitating key germination events including membrane organization and respiration. The current results highlight the importance of fatty acid composition in cold germination ability of upland cotton.
PMID: 38379948
Front Plant Sci , IF:5.753 , 2023 , V14 : P1310459 doi: 10.3389/fpls.2023.1310459
Freezing stress response of wild and cultivated chickpeas.
Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada.
Chickpea is an economically and nutritionally important grain legume globally, however, cold stress has adverse effects on its growth. In cold countries, like Canada where the growing season is short, having cold stress-tolerant varieties is crucial. Crop wild relatives of chickpea, especially Cicer reticulatum, can survive in suboptimal environments and are an important resource for crop improvement. In this study, we explored the performance of eleven C. reticulatum wild accessions and two chickpea cultivars, CDC Leader and CDC Consul, together with a cold sensitive check ILC533 under freezing stress. Freezing tolerance was scored based on a 1-9 scale. The wild relatives, particularly Kesen_075 and CudiA_152, had higher frost tolerance compared to the cultivars, which all died after frost treatment. We completed transcriptome analysis via mRNA sequencing to assess changes in gene expression in response to freezing stress and identified 6,184 differentially expressed genes (DEGs) in CDC Consul, and 7,842 DEGs in Kesen_075. GO (gene ontology) analysis of the DEGs revealed that those related to stress responses, endogenous and external stimuli responses, secondary metabolite processes, and photosynthesis were significantly over-represented in CDC Consul, while genes related to endogenous stimulus responses and photosynthesis were significantly over-represented in Kesen_075. These results are consistent with Kesen_075 being more tolerant to freezing stress than CDC Consul. Moreover, our data revealed that the expression of CBF pathway-related genes was impacted during freezing conditions in Kesen_075, and expression of these genes is believed to alleviate the damage caused by freezing stress. We identified genomic regions associated with tolerance to freezing stress in an F2 population derived from a cross between CDC Consul and Kesen_075 using QTL-seq analysis. Eight QTLs (P<0.05) on chromosomes Ca3, Ca4, Ca6, Ca7, Ca8, and two QTLs (P<0.01) on chromosomes Ca4 and Ca8, were associated with tolerance to freezing stress. Interestingly, 58 DEGs co-located within these QTLs. To our knowledge, this is the first study to explore the transcriptome and QTLs associated with freezing tolerance in wild relatives of chickpea under controlled conditions. Altogether, these findings provide comprehensive information that aids in understanding the molecular mechanism of chickpea adaptation to freezing stress and further provides functional candidate genes that can assist in breeding of freezing-stress tolerant varieties.
PMID: 38375446
Front Plant Sci , IF:5.753 , 2024 , V15 : P1285879 doi: 10.3389/fpls.2024.1285879
Full-length transcriptome reveals the pivotal role of ABA and ethylene in the cold stress response of Tetrastigma hemsleyanum.
Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, China.; Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China.; Institute of Crop Science and Ecology, Hangzhou Academy of Agricultural Sciences, Hangzhou, China.
Tetrastigma hemsleyanum is a valuable herb widely used in Chinese traditional and modern medicine. Winter cold severely limits the artificial cultivation of this plant, but the physiological and molecular mechanisms upon exposure to cold stress in T. hemsleyanum are unclear. T. hemsleyanum plants with different geographical origins exhibit large differences in response to cold stress. In this research study, using T. hemsleyanum ecotypes that exhibit frost tolerance (FR) and frost sensitivity (FS), we analyzed the response of cottage seedlings to a simulated frost treatment; plant hormones were induced with both short (2 h) and long (9 h) frost treatments, which were used to construct the full-length transcriptome and obtained 76,750 transcripts with all transcripts mapped to 28,805 genes, and 27,215 genes, respectively, annotated to databases. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed enrichment in plant hormone signaling pathways. Further analysis shows that differently expressed genes (DEGs) concentrated on calcium signaling, ABA biosynthesis and signal transduction, and ethylene in response to cold stress. We also found that endogenous ABA and ethylene content were increased after cold treatment, and exogenous ABA and ethylene significantly improved cold tolerance in both ecotypes. Our results elucidated the pivotal role of ABA and ethylene in response to cold stress in T. hemsleyanum and identified key genes.
PMID: 38357266
Int J Food Microbiol , IF:5.277 , 2024 Jan , V410 : P110479 doi: 10.1016/j.ijfoodmicro.2023.110479
Diverse Listeria monocytogenes in-house clones are present in a dynamic frozen vegetable processing environment.
FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Technopark 1D, 3430 Tulln, Austria. Electronic address: nadja.pracser@ffoqsi.at.; Unit of Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria. Electronic address: andreas.zaiser@vetmeduni.ac.at.; Unit of Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.; Austrian National Reference Laboratory for Listeria monocytogenes, Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Beethovenstrasse 6, 8010 Graz, Austria. Electronic address: ariane.pietzka@ages.at.; FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Technopark 1D, 3430 Tulln, Austria; Unit of Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria. Electronic address: martin.wagner@vetmeduni.ac.at.; Unit of Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria. Electronic address: kathrin.rychli@vetmeduni.ac.at.
Listeria (L.) monocytogenes is of global concern for food safety as the listeriosis-causing pathogen is widely distributed in the food processing environments, where it can survive for a long time. Frozen vegetables contaminated with L. monocytogenes were recently identified as the source of two large listeriosis outbreaks in the EU and US. So far, only a few studies have investigated the occurrence and behavior of Listeria in frozen vegetables and the associated processing environment. This study investigates the occurrence of L. monocytogenes and other Listeria spp. in a frozen vegetable processing environment and in frozen vegetable products. Using whole genome sequencing (WGS), the distribution of sequence types (MLST-STs) and core genome sequence types (cgMLST-CT) of L. monocytogenes were assessed, and in-house clones were identified. Comparative genomic analyses and phenotypical characterization of the different MLST-STs and isolates were performed, including growth ability under low temperatures, as well as survival of freeze-thaw cycles. Listeria were widely disseminated in the processing environment and five in-house clones namely ST451-CT4117, ST20-CT3737, ST8-CT1349, ST8-CT6243, ST224-CT5623 were identified among L. monocytogenes isolates present in environmental swab samples. Subsequently, the identified in-house clones were also detected in product samples. Conveyor belts were a major source of contamination in the processing environment. A wide repertoire of stress resistance markers supported the colonization and survival of L. monocytogenes in the frozen vegetable processing facility. The presence of ArgB was significantly associated with in-house clones. Significant differences were also observed in the growth rate between different MLST-STs at low temperatures (4 degrees C and 10 degrees C), but not between in-house and non-in-house isolates. All isolates harbored major virulence genes such as full length InlA and InlB and LIPI-1, yet there were differences between MLST-STs in the genomic content. The results of this study demonstrate that WGS is a strong tool for tracing contamination sources and transmission routes, and for identifying in-house clones. Further research targeting the co-occurring microbiota and the presence of biofilms is needed to fully understand the mechanism of colonization and persistence in a food processing environment.
PMID: 37977080
Biomolecules , IF:4.879 , 2024 Feb , V14 (2) doi: 10.3390/biom14020182
Characterization of NAC Gene Family in Ammopiptanthus mongolicus and Functional Analysis of AmNAC24, an Osmotic and Cold-Stress-Induced NAC Gene.
Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China.; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China.; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.; College of Life Sciences, Beijing Normal University, Beijing 100080, China.
The NAC family of transcription factors (TFs) is recognized as a significant group within the plant kingdom, contributing crucially to managing growth and development processes in plants, as well as to their response and adaptation to various environmental stressors. Ammopiptanthus mongolicus, a temperate evergreen shrub renowned for its remarkable resilience to low temperatures and drought stress, presents an ideal subject for investigating the potential involvement of NAC TFs in stress response mechanisms. Here, the structure, evolution, and expression profiles of NAC family TFs were analyzed systematically, and a cold and osmotic stress-induced member, AmNAC24, was selected and functionally characterized. A total of 86 NAC genes were identified in A. mongolicus, and these were divided into 15 groups. Up to 48 and 8 NAC genes were generated by segmental duplication and tandem duplication, respectively, indicating that segmental duplication is a predominant mechanism in the expansion of the NAC gene family in A. mongolicus. A considerable amount of NAC genes, including AmNAC24, exhibited upregulation in response to cold and osmotic stress. This observation is in line with the detection of numerous cis-acting elements linked to abiotic stress response in the promoters of A. mongolicus NAC genes. Subcellular localization revealed the nuclear residence of the AmNAC24 protein, coupled with demonstrable transcriptional activation activity. AmNAC24 overexpression enhanced the tolerance of cold and osmotic stresses in Arabidopsis thaliana, possibly by maintaining ROS homeostasis. The present study provided essential data for understanding the biological functions of NAC TFs in plants.
PMID: 38397419
Plant Sci , IF:4.729 , 2024 Feb , 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 Feb , V207 : P108405 doi: 10.1016/j.plaphy.2024.108405
The histone deacetylase SRT2 enhances the tolerance of chrysanthemum to low temperatures through the ROS scavenging system.
Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China. Electronic address: 1498916871@qq.com.; Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China. Electronic address: 415519757@qq.com.; Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China. Electronic address: 1085469002@qq.com.; Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China. Electronic address: 3353580058@qq.com.; Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China. Electronic address: 1614452019@qq.com.; Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China. Electronic address: 1210337813@qq.com.; Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China. Electronic address: 15008200632@163.com.; Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China. Electronic address: 13305@sicau.edu.cn.; Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China. Electronic address: 14069@sicau.edu.cn.; Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China. Electronic address: 13786@sicau.edu.cn.; Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan, 611130, China. Electronic address: qinglinliu@126.com.
Low temperatures can severely affect plant growth and reduce their ornamental value. A family of plant histone deacetylases allows plants to cope with both biotic and abiotic stresses. In this study, we screened and cloned the cDNA of DgSRT2 obtained from transcriptome sequencing of chrysanthemum leaves under low-temperature stress. Sequence analysis showed that DgSRT2 belongs to the sirtuin family of histone deacetylases. We obtained the stable transgenic chrysanthemum lines OE-2 and OE-12. DgSRT2 showed tissue specificity in wild-type chrysanthemum and was most highly expressed in leaves. Under low-temperature stress, the OE lines showed higher survival rates, proline content, solute content, and antioxidant enzyme activities, and lower relative electrolyte leakage, malondialdehyde, hydrogen peroxide, and superoxide ion accumulation than the wild-type lines. This work suggests that DgSRT2 can serve as an essential gene for enhancing cold resistance in plants. In addition, a series of cold-responsive genes in the OE line were compared with WT. The results showed that DgSRT2 exerted a positive regulatory effect by up-regulating the transcript levels of cold-responsive genes. The above genes help to increase antioxidant activity, maintain membrane stability and improve osmoregulation, thereby enhancing survival under cold stress. It can be concluded from the above work that DgSRT2 enhances chrysanthemum tolerance to low temperatures by scavenging the ROS system.
PMID: 38354529
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 Feb , V24 (1) : P101 doi: 10.1186/s12870-024-04775-5
Enhancing cold resistance in Banana (Musa spp.) through EMS-induced mutagenesis, L-Hyp pressure selection: phenotypic alterations, biomass composition, and transcriptomic insights.
National Key Laboratory for Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, Hainan, 572024/571101, China.; College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.; Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.; College of Horticulture, Hainan University, Haikou, 571101, Hainan, China.; Collage of Tropical Crop, Yunnan Agricultural University, Puer, 611101, Yunnan, China.; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.; National Key Laboratory for Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, Hainan, 572024/571101, China. jingyanglee@163.com.; Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China. jingyanglee@163.com.
BACKGROUND: The cultivation of bananas encounters substantial obstacles, particularly due to the detrimental effects of cold stress on their growth and productivity. A potential remedy that has gained attention is the utilization of ethyl mesylate (EMS)-induced mutagenesis technology, which enables the creation of a genetically varied group of banana mutants. This complex procedure entails subjecting the mutants to further stress screening utilizing L-Hyp in order to identify those exhibiting improved resistance to cold. This study conducted a comprehensive optimization of the screening conditions for EMS mutagenesis and L-Hyp, resulting in the identification of the mutant cm784, which exhibited remarkable cold resistance. Subsequent investigations further elucidated the physiological and transcriptomic responses of cm784 to low-temperature stress. RESULTS: EMS mutagenesis had a substantial effect on banana seedlings, resulting in modifications in shoot and root traits, wherein a majority of seedlings exhibited delayed differentiation and limited elongation. Notably, mutant leaves displayed altered biomass composition, with starch content exhibiting the most pronounced variation. The application of L-Hyp pressure selection aided in the identification of cold-resistant mutants among seedling-lethal phenotypes. The mutant cm784 demonstrated enhanced cold resistance, as evidenced by improved survival rates and reduced symptoms of chilling injury. Physiological analyses demonstrated heightened activities of antioxidant enzymes and increased proline production in cm784 when subjected to cold stress. Transcriptome analysis unveiled 946 genes that were differentially expressed in cm784, with a notable enrichment in categories related to 'Carbohydrate transport and metabolism' and 'Secondary metabolites biosynthesis, transport, and catabolism'. CONCLUSION: The present findings provide insights into the molecular mechanisms that contribute to the heightened cold resistance observed in banana mutants. These mechanisms encompass enhanced carbohydrate metabolism and secondary metabolite biosynthesis, thereby emphasizing the adaptive strategies employed to mitigate the detrimental effects induced by cold stress.
PMID: 38331759
Tree Physiol , IF:4.196 , 2024 Feb doi: 10.1093/treephys/tpae019
Comparative transcriptomics of the chilling stress response in two Asian mangrove species Bruguiera gymnorhiza and Rhizophora apiculata.
Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Daxuedonglu 100, Nanning, 530004 China.; Institute of Ecology and Evolution, 5289 University of Oregon, Eugene, OR 97403, USA.; State Key Laboratory of Conservation and Utilization of Subtropical Agro-bio-resources, College of Forestry, Guangxi University Daxuedonglu 100, Nanning 530004, Guangxi, China.; Crop Eco-physiology, Texas A&M AgriLife Research and Extension Center, 1619 Garner Field Rd, Uvalde, TX 78801, USA.; Department of Biological Sciences, Louisiana State University (LSU), Louisiana, LA 70803, United States.; School of Biological Sciences, University of Western Australia, 35 Stirling Highway,Perth, WA 6009, Australia.; Smithsonian Environmental Research Center, Smithsonian Institution, 647 Contees Wharf Road, Edgewater, MD 21037.; School of Environmental and Geographical Sciences, University of Nottingham Malaysia Campus, Semenyih, Malaysia.
Low temperatures largely determine the geographic limits of plant species by reducing survival and growth. Interspecific differences in the geographic distribution of mangrove species have been associated with cold tolerance, with exclusively tropical species being highly cold-sensitive and subtropical species being relatively cold-tolerant. To identify species-specific adaptations to low temperatures, we compared the chilling stress response of two widespread Indo-West Pacific mangrove species from Rhizophoraceae with differing latitudinal range limits-Bruguiera gymnorhiza (subtropical range limit) and Rhizophora apiculata (tropical range limit). For both species, we measured the maximum photochemical efficiency of photosystem II (Fv/Fm) as a proxy for the physiological condition of the plants and examined gene expression profiles during chilling at 15 degrees C and 5 degrees C. At 15 degrees C, B. gymnorhiza maintained a significantly higher Fv/Fm than R. apiculata. However, at 5 degrees C, both species displayed equivalent Fv/Fm values. Thus, species-specific differences in chilling tolerance were only found at 15 degrees C, and both species were sensitive to chilling at 5 degrees C. At 15 degrees C, B. gymnorhiza down-regulated genes related to the light reactions of photosynthesis and up-regulated a gene involved in cyclic electron flow regulation, while R. apiculata down-regulated more RuBisCo related genes. At 5 degrees C, both species repressed genes related to CO2 assimilation. The down-regulation of genes related to light absorption and up-regulation of genes related to cyclic electron flow regulation are photoprotective mechanisms that likely contributed to the greater PSII photochecmical efficiency of B. gymnorhiza at 15 degrees C. The results of this study provide evidence that the distributional range limits and potentially the expansion rates of plant species are associated with differences in the regulation of photosynthesis and photoprotective mechanisms under low temperatures.
PMID: 38366388
Tree Physiol , IF:4.196 , 2024 Feb , V44 (1) doi: 10.1093/treephys/tpad117
Freeze dehydration vs supercooling in tree stems: physical and physiological modelling.
Universite Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France.
Frost resistance is the major factor affecting the distribution of plant species at high latitude and elevation. The main effects of freeze-thaw cycles are damage to living cells and formation of gas embolism in tree xylem vessels. Lethal intracellular freezing can be prevented in living cells by two mechanisms, such as dehydration and deep supercooling. We developed a multiphysics numerical model coupling water flow, heat transfer and phase change, considering different cell types in plant tissues, to study the dynamics and extent of cell dehydration, xylem pressure changes and stem diameter changes in response to freezing and thawing. Results were validated using experimental data for stem diameter changes of walnut trees (Juglans regia). The effect of cell mechanical properties was found to be negligible as long as the intracellular tension developed during dehydration was sufficiently low compared with the ice-induced cryostatic suction. The model was finally used to explore the coupled effects of relevant physiological parameters (initial water and sugar content) and environmental conditions (air temperature variations) on the dynamics and extent of dehydration. It revealed configurations where cell dehydration could be sufficient to protect cells from intracellular freezing, and situations where supercooling was necessary. This model, freely available with this paper, could easily be extended to explore different anatomical structures, different species and more complex physical processes.
PMID: 37738582
Biochimie , IF:4.079 , 2024 Mar , V218 : P76-84 doi: 10.1016/j.biochi.2023.08.004
Transmembrane and PAS domains of the histidine kinase Hik33 as regulators of cold and light responses in the cyanobacterium Synechocystis sp. PCC 6803.
K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow, 127276, Russia.; K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow, 127276, Russia. Electronic address: losda@ippras.ru.
The PAS (Per-ARNT-Sim) domain is a sensory protein regulatory module found in archaea, prokaryotes, and eukaryotes. Histidine and serine/threonine protein kinases, chemo- and photoreceptors, circadian rhythm regulators, ion channels, phosphodiesterases, and other cellular response regulators are among these proteins. Hik33 is a multifunctional sensory histidine kinase that is implicated in cyanobacterial responses to cold, salt, hyperosmotic, and oxidative stressors. The functional roles of individual Hik33 domains in signal transduction were investigated in this study. Synechocystis Hik33 deletion variants were developed, in which either both or a portion of the transmembrane domains and/or the PAS domain were deleted. Cold stress was applied to the mutant strains either under illumination or in the dark. The findings show that the transmembrane domains govern temperature responses, whereas PAS domain may be involved in regulation of downstream gene expression in light-dependent manner.
PMID: 37567357
BMC Genomics , IF:3.969 , 2024 Feb , V25 (1) : P149 doi: 10.1186/s12864-024-10060-4
Comparative phylogenetic analysis of the mediator complex subunit in asparagus bean (Vigna unguiculata ssp. sesquipedialis) and its expression profile under cold stress.
College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China.; Mianyang Academy of Agricultural Sciences, Mianyang, 621000, China.; College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China. huanxiuli62@163.com.
BACKGROUND: The mediator complex subunits (MED) constitutes a multiprotein complex, with each subunit intricately involved in crucial aspects of plant growth, development, and responses to stress. Nevertheless, scant reports pertain to the VunMED gene within the context of asparagus bean (Vigna unguiculata ssp. sesquipedialis). Establishing the identification and exploring the responsiveness of VunMED to cold stress forms a robust foundation for the cultivation of cold-tolerant asparagus bean cultivars. RESULTS: Within this study, a comprehensive genome-wide identification of VunMED genes was executed in the asparagus bean cultivar 'Ningjiang3', resulting in the discovery of 36 distinct VunMED genes. A phylogenetic analysis encompassing 232 MED genes from diverse species, including Arabidopsis, tomatoes, soybeans, mung beans, cowpeas, and asparagus beans, underscored the highly conserved nature of MED gene sequences. Throughout evolutionary processes, each VunMED gene underwent purification and neutral selection, with the exception of VunMED19a. Notably, VunMED9/10b/12/13/17/23 exhibited structural variations discernible across four cowpea species. Divergent patterns of temporal and spatial expression were evident among VunMED genes, with a prominent role attributed to most genes during early fruit development. Additionally, an analysis of promoter cis-acting elements was performed, followed by qRT-PCR assessments on roots, stems, and leaves to gauge relative expression after exposure to cold stress and subsequent recovery. Both treatments induced transcriptional alterations in VunMED genes, with particularly pronounced effects observed in root-based genes following cold stress. Elucidating the interrelationships between subunits involved a preliminary understanding facilitated by correlation and principal component analyses. CONCLUSIONS: This study elucidates the pivotal contribution of VunMED genes to the growth, development, and response to cold stress in asparagus beans. Furthermore, it offers a valuable point of reference regarding the individual roles of MED subunits.
PMID: 38321384
Gene , IF:3.688 , 2024 Feb , V896 : P148041 doi: 10.1016/j.gene.2023.148041
Low-temperature perception and modulations in Ocimum basilicum commercial cultivar CIM-Shishir: Biosynthetic potential with insight towards climate-smart resilience.
CSIR- Human Resource Development Centre Campus, Academy of Scientific and Innovative Research (AcSIR), Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India.; Biotechnology Division, CSIR- Central Institute for Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, 226016, India. Electronic address: sunita.dhawan@cimap.res.in.; Genetics and Plant Breeding Division, CSIR- Central Institute for Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, 226015, India.; Analytical Chemistry Division, CSIR- Central Institute for Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, 226015, India.
The newly released interspecific hybrid variety CIM-Shishir, resulting from a cross between Ocimum basilicum and Ocimum kilimandscharicum claims to be a multicut, lodging resistant, cold tolerant, high essential oil yielding with linalool rich variety. It has a purple-green stem and has a unique feature and advantage of better survival in the winter season than other O. basilicum varieties, illustrating its physiological mechanisms for cold tolerance. In this study, we subjected both the CIM-Shishir variety and a control plant to cold stress to investigate the impact of low temperatures on various physiological, trichome developments, secondary metabolite constitution aspects related to essential oil production, and gene expression. The analysis revealed a significantly higher density and altered morphology of trichomes on the leaf surface of the variety subjected to low temperatures, indicating its adaptation to cold conditions. Furthermore, when comparing the treated plants under low-temperature stress, it was observed that the relative electrolyte leakage and Malondialdehyde (MDA) contents substantially increased in the control in contrast to the CIM-Shishir variety. This finding suggests that CIM-Shishir exhibits superior cold tolerance. Additionally, an increase in proline content was noted in the variety exposed to low temperatures compared to the control. Moreover, the chlorophyll and anthocyanin content gradually increased with prolonged exposure to low-temperature stress in the newly developed variety, indicating its ability to maintain photosynthetic capacity and adapt to cold conditions. The activities of superoxide dismutase (SOD) also increased under low-temperature conditions in the CIM-Shishir variety, further highlighting its cold tolerance behaviour. In our research, we investigated the comprehensive molecular mechanisms of cold response in Ocimum. We analyzed the expression of key genes associated with cold tolerance in two plant groups: the newly developed hybrid variety known as CIM-Shishir Ocimum, which exhibits cold tolerance, and the control plants susceptible to cold climates that include WRKY53, ICE1, HOS1, COR47, LOS15, DREB5, CBF4, LTI6, KIN, and ERD2. These genes exhibited significantly higher expression levels in the CIM-Shishir variety compared to the control, shedding light on the genetic basis of its cold tolerance. The need for climate-smart, resilient high-yielding genotype is of high importance due to varied climatic conditions as this will hit the yield drastically and further to the economic sectors including farmers and many industries that are dependent on the bioactive constituents of Ocimum.
PMID: 38036074
Gene , IF:3.688 , 2024 Jan , V893 : P147908 doi: 10.1016/j.gene.2023.147908
Identification and expression analysis of miR396 and its target genes in Jerusalem artichoke under temperature stress.
College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.; College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China. Electronic address: zszhou@njau.edu.cn.
The highly conserved miR396 plays a pivotal role in the growth, development, and responses to abiotic and biotic stresses in plants. However, research on miR396 and its targets in Jerusalem artichoke remains largely unexplored. In this study, we employed bioinformatics and experimental techniques, such as cloning and qRT-PCR, to investigate the regulatory role of miR396 on its targets, leveraging our lab's transcriptomic and degradomic data of Jerusalem artichoke. Specifically, we initially cloned and characterized the precursors (htu-MIR396a/b/c) and mature sequences (htu-miR396a/b/c) of three miR396 isoforms. Subsequently, we identified nine target genes, including seven Growth-Regulating Factors (GRFs) (HtGRF3/4/6/9/10/12/13), one WRKY transcription factor (HtWRKY40), and one Scarecrow-like (SCL) transcription factor (HtSCL33). Finally, we conducted an analysis of their expression patterns across various tissues and their responses to temperature stress. Notably, htu-MIR396s exhibited high expression in seedling stems, while htu-miR396s predominantly expressed in seedling leaves. Moreover, HtWRKY40 and HtSCL33 displayed higher expression levels than HtGRFs in most tissues, except leaves. Remarkably, HtGRF4/6/10/12/13 exhibited higher expression in leaves than in roots and stems during seedling growth. Furthermore, during tuber development, HtGRF4/6/10, HtWRKY40, and HtSCL33 were highly expressed, while HtGRF3/9/12/13 showed relatively lower expression levels. Under heat stress (42℃), htu-MIR396 expression was up-regulated, and htu-miR396 showed dynamic expression patterns in seedlings, resulting in the induction of HtGRF4/6/10/12/13 in leaves and HtSCL33 in roots, while HtWRKY40 in leaves was repressed. Conversely, under cold stress (4℃), htu-MIR396s showed fluctuating expression levels, and htu-miR396s were up-regulated in seedlings. Notably, HtGRF4/13 and HtSCL33 in seedlings were reduced, whereas HtGRF6 in roots and HtWRKY40 in leaves were enhanced. These findings offer valuable insights into the functional roles of miR396-target interactions under abiotic stress in Jerusalem artichoke.
PMID: 37858744
J Plant Physiol , IF:3.549 , 2024 Feb , V294 : P154192 doi: 10.1016/j.jplph.2024.154192
Freezing temperature effects on photosystem II in Antarctic lichens evaluated by chlorophyll fluorescence.
Doctoral School of Exact and Natural Sciences, Jagiellonian University in Cracow, Lojasiewicza 11, Krakow, 30-348, Poland; M. Smoluchowski Institute of Physics, Jagiellonian University in Cracow, Lojasiewicza 11, Krakow, 30-348, Poland. Electronic address: aleksandra.andrzejowska@doctoral.uj.edu.pl.; Masaryk University, Faculty of Science, Department of Experimental Biology, Laboratory of Photosynthetic Processes, Kamenice 5, 625 00, Brno, Czech Republic; Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management (FFWT), Zemedelska 3, 613 00, Brno, Cerna Pole, Czech Republic.; Masaryk University, Faculty of Science, Department of Experimental Biology, Laboratory of Photosynthetic Processes, Kamenice 5, 625 00, Brno, Czech Republic; National Antarctic Scientific Centre, Ministry of Education and Science of Ukraine, Taras Shevchenko Blvd. 16, 01601, Kyiv, Ukraine; Institute for Problems of Cryobiology and Cryomedicine, National Academy of Sciences of Ukraine, 23, Pereyaslavska, Kharkiv, 61016, Ukraine.; M. Smoluchowski Institute of Physics, Jagiellonian University in Cracow, Lojasiewicza 11, Krakow, 30-348, Poland.; Masaryk University, Faculty of Science, Department of Experimental Biology, Laboratory of Photosynthetic Processes, Kamenice 5, 625 00, Brno, Czech Republic.
This study explores and compares the limits for photosynthesis in subzero temperatures of six Antarctic lichens: Sphaerophorus globosus, Caloplaca regalis, Umbilicaria antarctica, Pseudephebe minuscula, Parmelia saxatilis and Lecania brialmontii combining linear cooling and chlorophyll fluorescence methods. The results revealed triphasic S-curves in the temperature response of the maximum quantum yield (F(V)/F(M)) and effective quantum yield of photosystem II (Phi(PSII)) for all species. All investigated species showed a high level of cryoresistance with critical temperatures (T(c)) below -20 degrees C. However, record low T(c) temperatures have been discovered for L. brialmotii (-54 degrees C for F(V)/F(M) and -40 degrees C for Phi(PSII)) and C. regalis (-52 degrees C for F(V)/F(M) and -38 degrees C for Phi(PSII)). Additionally, the yield differentials (F(V)/F(M) - Phi(PSII)) in functions of temperature revealed one or two peaks, with the larger one occurring for temperatures below -20 degrees C for the above-mentioned species. Finally, Kautsky kinetics were measured and compared at different temperatures (20 degrees C, 10 degrees C, 0 degrees C and -10 degrees C and then -10 degrees C after 1 h of incubation). This research serves as a foundation for further developing investigations into the biophysical mechanisms by which photosynthesis is carried out at subzero temperatures.
PMID: 38382176
Funct Plant Biol , IF:3.101 , 2024 Feb doi: 10.1071/FP23248
Melatonin as a master regulatory hormone for genetic responses to biotic and abiotic stresses in model plant Arabidopsis thaliana: a comprehensive review.
Melatonin is a naturally occurring biologically active amine produced by plants, animals and microbes. This review explores the biosynthesis of melatonin in plants, with a particular focus on its diverse roles in Arabidopsis thaliana, a model species. Melatonin affects abiotic and biotic stress resistance in A. thaliana. Exogenous and endogenous melatonin is addressed in association with various conditions, including cold stress, high light stress, intense heat and infection with Botrytis cinerea or Pseudomonas, as well as in seed germination and lateral root formation. Furthermore, melatonin confers stress resistance in Arabidopsis by initiating the antioxidant system, remedying photosynthesis suppression, regulating transcription factors involved with stress resistance (CBF, DREB, ZAT, CAMTA, WRKY33, MYC2, TGA) and other stress-related hormones (abscisic acid, auxin, ethylene, jasmonic acid and salicylic acid). This article additionally addresses other precursors, metabolic components, expression of genes (COR, CBF, SNAT, ASMT, PIN, PR1, PDF1.2 and HSFA) and proteins (JAZ, NPR1) associated with melatonin and reducing both biological and environmental stressors. Furthermore, the future perspective of melatonin rich agri-crops is explored to enhance plant tolerance to abiotic and biotic stresses, maximise crop productivity and enhance nutritional worth, which may help improve food security.
PMID: 38310885
J Insect Physiol , IF:2.354 , 2024 Mar , V153 : P104619 doi: 10.1016/j.jinsphys.2024.104619
Plasticity of cold and heat stress tolerance induced by hardening and acclimation in the melon thrips.
Beijing Key Laboratory for Forest Pests Control, Beijing Forestry University, Beijing 100083, China; Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.; Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.; Beijing Key Laboratory for Forest Pests Control, Beijing Forestry University, Beijing 100083, China. Electronic address: minch@bjfu.edu.cn.; Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia. Electronic address: ary@unimelb.edu.au.; Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China. Electronic address: shujun268@163.com.
Extreme temperatures threaten species under climate change and can limit range expansions. Many species cope with changing environments through plastic changes. This study tested phenotypic changes in heat and cold tolerance under hardening and acclimation in the melon thrips, Thrips palmi Karny (Thysanoptera: Thripidae), an agricultural pest of many vegetables. We first measured the critical thermal maximum (CT(max)) of the species by the knockdown time under static temperatures and found support for an injury accumulation model of heat stress. The inferred knockdown time at 39 degrees C was 82.22 min. Rapid heat hardening for 1 h at 35 degrees C slightly increased CT(max) by 1.04 min but decreased it following exposure to 31 degrees C by 3.46 min and 39 degrees C by 6.78 min. Heat acclimation for 2 and 4 days significantly increased CT(max) at 35 degrees C by 1.83, and 6.83 min, respectively. Rapid cold hardening at 0 degrees C and 4 degrees C for 2 h, and cold acclimation at 10 degrees C for 3 days also significantly increased cold tolerance by 6.09, 5.82, and 2.00 min, respectively, while cold hardening at 8 degrees C for 2 h and acclimation at 4 degrees C and 10 degrees C for 5 days did not change cold stress tolerance. Mortality at 4 degrees C for 3 and 5 days reached 24.07 % and 43.22 % respectively. Our study showed plasticity for heat and cold stress tolerance in T. palmi, but the thermal and temporal space for heat stress induction is narrower than for cold stress induction.
PMID: 38301801
Noncoding RNA , 2024 Feb , V10 (1) doi: 10.3390/ncrna10010013
The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling.
Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.; Sashi Bhusan Rath Government Autonomous Women's College, Brahmapur 760001, India.; Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.; Department of Plant, Soil and Microbial Science, Michigan State University, East Lansing, MI 48824, USA.
Plant species utilize a variety of regulatory mechanisms to ensure sustainable productivity. Within this intricate framework, numerous non-coding RNAs (ncRNAs) play a crucial regulatory role in plant biology, surpassing the essential functions of RNA molecules as messengers, ribosomal, and transfer RNAs. ncRNAs represent an emerging class of regulators, operating directly in the form of small interfering RNAs (siRNAs), microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). These ncRNAs exert control at various levels, including transcription, post-transcription, translation, and epigenetic. Furthermore, they interact with each other, contributing to a variety of biological processes and mechanisms associated with stress resilience. This review primarily concentrates on the recent advancements in plant ncRNAs, delineating their functions in growth and development across various organs such as root, leaf, seed/endosperm, and seed nutrient development. Additionally, this review broadens its scope by examining the role of ncRNAs in response to environmental stresses such as drought, salt, flood, heat, and cold in plants. This compilation offers updated information and insights to guide the characterization of the potential functions of ncRNAs in plant growth, development, and stress resilience in future research.
PMID: 38392968
Mol Breed , 2024 Mar , V44 (3) : P18 doi: 10.1007/s11032-024-01457-w
PbrCSP1, a pollen tube-specific cold shock domain protein, is essential for the growth and cold resistance of pear pollen tubes.
State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, 210095 China. ROR: https://ror.org/05td3s095. GRID: grid.27871.3b. ISNI: 0000 0000 9750 7019; Jiangsu Engineering Research Center for Pear, Nanjing Agricultural University, Nanjing, 210014 China. ROR: https://ror.org/05td3s095. GRID: grid.27871.3b. ISNI: 0000 0000 9750 7019; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China. ROR: https://ror.org/001f9e125. GRID: grid.454840.9. ISNI: 0000 0001 0017 5204
Cold shock domain proteins (CSPs), initially identified in Escherichia coli, have been demonstrated to play a positive role in cold resistance. Previous studies in wheat, rice, and Arabidopsis have indicated the functional conservation of CSPs in cold resistance between bacteria and higher plants. However, the biological functions of PbrCSPs in pear pollen tubes, which represent the fragile reproductive organs highly sensitive to low temperature, remain largely unknown. In this study, a total of 22 CSPs were identified in the seven Rosaceae species, with a focus on characterizing four PbrCSPs in pear (Pyrus bretschneideri Rehder). All four PbrCSPs were structurally conserved and responsive to the abiotic stresses, such as cold, high osmotic, and abscisic acid (ABA) treatments. PbrCSP1, which is specifically expressed in pear pollen tubes, was selected for further research. PbrCSP1 was localized in both the cytoplasm and nucleus. Suppressing the expression of PbrCSP1 significantly inhibited the pollen tube growth in vitro. Conversely, overexpression of PbrCSP1 promoted the growth of pear pollen tubes under the normal condition and, notably, under the cold environment at 4 degrees C. These findings highlight an essential role of PbrCSP1 in facilitating the normal growth and enhancing cold resistance in pear pollen tubes. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11032-024-01457-w.
PMID: 38390031
Biochem Biophys Rep , 2024 Mar , V37 : P101620 doi: 10.1016/j.bbrep.2023.101620
Trancriptome data mining in combination with co-expression network analysis identifies the functional modules and critical regulators in Hordeum vulgare L. in response to cold stress.
Department of Genomics, Branch for Northwest & West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran.; Faculty of Agriculture (Meshgin-Shahr Campus), University of Mohaghegh Ardabili, Ardabil, Iran.
Cold stress, as an abiotic stress, is one of the most limiting factors which pose a great threat to the plant's productivity. To understand the transcriptional regulation and connectivity pattern of genes involved in barley cold stress responses, co-expression network analysis was performed based on the global transcriptome profiling. The microarray datasets related to cold stress treatments were retrieved from the Gene Expression Omnibus (GEO) and Array express databases. Four microarray datasets related to cold stress-responsive transcriptome in barley were included in our study. Gene co-expression analysis was constructed using WGCNA method. Module-Trait Relationships (MTR) analysis and hub genes determination and validation were carried out. Finally, transcription factor and kinase regulatory networks were Inferred using machine learning algorithm. The co-expression modules were determined using beta index = 10. In total 13 co-expressed modules were identified with an average size of 153 genes. Functional enrichment based on gene ontology (GO) showed that each of the stress related significant modules were enriched in different biological processes. Annotation of significant modules identifies some TFs and Kinases such as ethylene-responsive transcription factor 1-like, transcription factor PCL1-like, transcription factor MYC2, WRKY, serine/threonine-protein kinase PBL7, and receptor-like protein kinase At2g42960 were contributed in barley cold stress response. Our analysis highlighted the functional importance of ABA signaling pathway, ROS signaling, defensive and protective proteins, degrading protein, Ca2(+) related signaling, ribosome-mediated translation and etc. in responding of barley to cold stress condition. The current findings add substantially to our understanding of the cold responsive underlying mechanism of barley which can serve in future studies and breeding programs.
PMID: 38155945