Plant Cell , IF:11.277 , 2022 Jan , V34 (1) : P514-534 doi: 10.1093/plcell/koab267
Prediction of conserved and variable heat and cold stress response in maize using cis-regulatory information.
Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA.; School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia.; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA.
Changes in gene expression are important for responses to abiotic stress. Transcriptome profiling of heat- or cold-stressed maize genotypes identifies many changes in transcript abundance. We used comparisons of expression responses in multiple genotypes to identify alleles with variable responses to heat or cold stress and to distinguish examples of cis- or trans-regulatory variation for stress-responsive expression changes. We used motifs enriched near the transcription start sites (TSSs) for thermal stress-responsive genes to develop predictive models of gene expression responses. Prediction accuracies can be improved by focusing only on motifs within unmethylated regions near the TSS and vary for genes with different dynamic responses to stress. Models trained on expression responses in a single genotype and promoter sequences provided lower performance when applied to other genotypes but this could be improved by using models trained on data from all three genotypes tested. The analysis of genes with cis-regulatory variation provides evidence for structural variants that result in presence/absence of transcription factor binding sites in creating variable responses. This study provides insights into cis-regulatory motifs for heat- and cold-responsive gene expression and defines a framework for developing models to predict expression responses across multiple genotypes.
PMID: 34735005
J Integr Plant Biol , IF:7.061 , 2022 Jan doi: 10.1111/jipb.13216
Integration of light and temperature signaling pathways in plants.
State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.; Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania, 18766, USA.
As two of the most important environmental factors, light and temperature regulate almost all aspects of plant growth and development. Under natural conditions, light is accompanied by warm temperatures and darkness by cooler temperatures, suggesting that light and temperature are tightly-associated signals for plants. Indeed, accumulating evidence shows that plants have evolved a wide range of mechanisms to simultaneously perceive and respond to dynamic changes in light and temperature. Notably, the photoreceptor phytochrome B (phyB) was recently shown to function as a thermosensor, thus reinforcing the notion that light and temperature signaling pathways are tightly associated in plants. In this review, we summarize and discuss the current understanding of the molecular mechanisms integrating light and temperature signaling pathways in plants, with the emphasis on recent progress in temperature sensing, light control of plant freezing tolerance, and thermomorphogenesis. We also discuss the questions that are crucial for a further understanding of the interactions between light and temperature signaling pathways in plants. This article is protected by copyright. All rights reserved.
PMID: 34984823
J Exp Bot , IF:6.992 , 2022 Jan , V73 (1) : P307-323 doi: 10.1093/jxb/erab392
OsATL38 mediates mono-ubiquitination of the 14-3-3 protein OsGF14d and negatively regulates the cold stress response in rice.
Department of Systems Biology and Division of Life Science, Yonsei University, Seoul 03722, Korea.; Institute of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea.
One of the major regulatory pathways that permits plants to convert an external stimulus into an internal cellular response within a short period of time is the ubiquitination pathway. In this study, OsATL38 was identified as a low temperature-induced gene that encodes a rice homolog of Arabidopsis Toxicos en Levadura RING-type E3 ubiquitin (Ub) ligase, which was predominantly localized to the plasma membrane. OsATL38-overexpressing transgenic rice plants exhibited decreased tolerance to cold stress as compared with wild-type rice plants. In contrast, RNAi-mediated OsATL38 knockdown transgenic progeny exhibited markedly increased tolerance to cold stress relative to that of wild-type plants, which indicated a negative role of OsATL38 in response to cold stress. Yeast two-hybrid, in vitro pull-down, and co-immunoprecipitation assays revealed that OsATL38 physically interacted with OsGF14d, a rice 14-3-3 protein. An in vivo target ubiquitination assay indicated that OsGF14d was mono-ubiquitinated by OsATL38. osgf14d knockout mutant plants were more sensitive to cold stress than wild-type rice plants, indicating that OsGF14d is a positive factor in the response to cold stress. These results provide evidence that the RING E3 Ub ligase OsATL38 negatively regulates the cold stress response in rice via mono-ubiquitination of OsGF14d 14-3-3 protein.
PMID: 34436579
Hortic Res , IF:6.793 , 2022 Jan doi: 10.1093/hr/uhab063
Galactinol synthase 1 improves cucumber performance under cold stress by enhancing assimilate translocation.
College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China.
Cucumber (Cucumis sativus L.) predominately translocates raffinose family oligosaccharides (RFOs) in the phloem and accumulates RFOs in leaves. Galactinol synthase (GolS) catalyzes the critical step of RFO biosynthesis, and determining the functional diversity of multiple GolS isoforms in cucumber is of scientific significance. In this study, we found that all four isoforms of CsGolS in the cucumber genome were upregulated by different abiotic stresses. beta-glucuronidase staining and tissue separation experiments suggested that CsGolS1 is expressed in vascular tissues, whereas the other three CsGolSs are located in mesophyll cells. Further investigation indicates that CsGolS1 plays double roles in both assimilate loading and stress response in minor veins, which could increase the RFO concentration in the phloem sap and then improve assimilate transport under adverse conditions. Cold-induced minor vein-specific overexpression of CsGolS1 enhanced the assimilate translocation efficiency and accelerated the growth rates of sink leaves, fruits and whole plants under cold stress. Finally, our results demonstrate a previously unknown response to adverse environments and provide a potential biotechnological strategy to improve the stress resistance of cucumber.
PMID: 35048123
Hortic Res , IF:6.793 , 2022 Jan doi: 10.1093/hr/uhab028
DgMYB2 improves cold resistance in chrysanthemum by directly targeting DgGPX1.
Department of Ornamental Horticulture, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, Sichuan 611130, People's Republic of China.
MYB transcription factors play important roles in plant responses to cold stress, but the associated underlying mechanisms remain unclear. In this study, a cold-induced MYB transcription factor, DgMYB2, was isolated from chrysanthemum (Chrysanthemum morifolium Ramat). DgMYB2 was localized to the nucleus and exhibited transactivational activity. Overexpression of DgMYB2 improved cold tolerance in chrysanthemum, while cold tolerance in the antisense suppression lines decreased compared to that of the wild type. Additionally, electrophoretic mobility shift assays, chromatin immunoprecipitation, luciferase complementary imaging analysis, and dual-luciferase reporter gene detection experiments confirmed that DgMYB2 directly targets DgGPX1 and increases the activity of glutathione peroxidase to reduce the accumulation of reactive oxygen species, thereby improving cold resistance in chrysanthemum.
PMID: 35039835
Int J Mol Sci , IF:5.923 , 2022 Jan , V23 (2) doi: 10.3390/ijms23020981
Cold Response Transcriptome Analysis of the Alternative Splicing Events Induced by the Cold Stress in D. catenatum.
The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.; CAS Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla 666303, China.; University of Chinese Academy of Sciences, Beijing 100049, China.; College of Horticulture and Landscape, Yunnan Agricultural University, Kunming 650500, China.
Dendrobium catenatum Lindl is a valuable medicinal herb and gardening plant due to its ornamental value and special medical value. Low temperature is a major bottleneck restricting D. catenatum expansion towards the north, which influences the quality and yield of D. catenatum. In this study, we analysed the cold response of D. catenatum by RNA-Seq. A total of 4302 differentially expressed genes were detected under cold stress, which were mainly linked to protein kinase activity, membrane transport and the glycan biosynthesis and metabolism pathway. We also identified 4005 differential alternative events in 2319 genes significantly regulated by cold stress. Exon skipping and intron retention were the most common alternative splicing isoforms. Numerous genes were identified that differentially modulated under cold stress, including cold-induced transcription factors and splicing factors mediated by AS (alternative splicing). GO enrichment analysis found that differentially alternatively spliced genes without differential expression levels were related to RNA/mRNA processing and spliceosomes. DAS (differentially alternative splicing) genes with different expression levels were mainly enriched in protein kinase activity, plasma membrane and cellular response to stimulus. We further identified and cloned DcCBP20 in D. catenatum; we found that DcCBP20 promotes the generation of alternative splicing variants in cold-induced genes under cold stress via genetic experiments and RT-PCR. Taken together, our results identify the main cold-response pathways and alternative splicing events in D. catenatum responding to cold treatment and that DcCBP20 of D. catenatum get involved in regulating the AS and gene expression of cold-induced genes during this process. Our study will contribute to understanding the role of AS genes in regulating the cold stress response in D. catenatum.
PMID: 35055168
Int J Mol Sci , IF:5.923 , 2022 Jan , V23 (2) doi: 10.3390/ijms23020648
Genome Wide Identification of Respiratory Burst Oxidase Homolog (Rboh) Genes in Citrus sinensis and Functional Analysis of CsRbohD in Cold Tolerance.
School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China.; Joint International Research Laboratory of Agriculture and Agri-Product Safety (The Ministry of Education), Yangzhou University, Yangzhou 225009, China.; Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China.
Respiratory burst oxidase homologs (Rbohs) are critical enzymes involved in the generation of reactive oxygen species (ROS) that play an important role in plant growth and development as well as various biotic and abiotic stresses in plants. Thus far, there have been few reports on the characterization of the Rboh gene family in Citrus. In this study, seven Rboh genes (CsRbohA~CsRbohG) were identified in the Citrus sinensis genome. The CsRboh proteins were predicted to localize to the cell membrane. Most CsRbohs contained four conserved domains, an EF-hand domain, and a transmembrane region. Phylogenetic analysis demonstrated that the CsRbohs were divided into five groups, suggesting potential distinct functions and evolution. The expression profiles revealed that these seven CsRboh genes displayed tissue-specific expression patterns, and five CsRboh genes were responsive to cold stress. Fourteen putative cis-acting elements related to stress response, hormone response, and development regulation were present within the promoters of CsRboh genes. The in-silico microRNA target transcript analyses indicated that CsRbohE might be targeted by csi-miR164. Further functional and physiological analyses showed that the knockdown of CsRbohD in trifoliate orange impaired resistance to cold stress. As a whole, our results provide valuable information for further functional studies of the CsRboh genes in response to cold stress.
PMID: 35054832
Int J Mol Sci , IF:5.923 , 2022 Jan , V23 (2) doi: 10.3390/ijms23020606
ERF Transcription Factor OsBIERF3 Positively Contributes to Immunity against Fungal and Bacterial Diseases but Negatively Regulates Cold Tolerance in Rice.
State Key Laboratory of Rice Biology, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.; State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
We previously showed that overexpression of the rice ERF transcription factor gene OsBIERF3 in tobacco increased resistance against different pathogens. Here, we report the function of OsBIERF3 in rice immunity and abiotic stress tolerance. Expression of OsBIERF3 was induced by Xanthomonas oryzae pv. oryzae, hormones (e.g., salicylic acid, methyl jasmonate, 1-aminocyclopropane-1-carboxylic acid, and abscisic acid), and abiotic stress (e.g., drought, salt and cold stress). OsBIERF3 has transcriptional activation activity that depends on its C-terminal region. The OsBIERF3-overexpressing (OsBIERF3-OE) plants exhibited increased resistance while OsBIERF3-suppressed (OsBIERF3-Ri) plants displayed decreased resistance to Magnaporthe oryzae and X. oryzae pv. oryzae. A set of genes including those for PRs and MAPK kinases were up-regulated in OsBIERF3-OE plants. Cell wall biosynthetic enzyme genes were up-regulated in OsBIERF3-OE plants but down-regulated in OsBIERF3-Ri plants; accordingly, cell walls became thicker in OsBIERF3-OE plants but thinner in OsBIERF3-Ri plants than WT plants. The OsBIERF3-OE plants attenuated while OsBIERF3-Ri plants enhanced cold tolerance, accompanied by altered expression of cold-responsive genes and proline accumulation. Exogenous abscisic acid and 1-aminocyclopropane-1-carboxylic acid, a precursor of ethylene biosynthesis, restored the attenuated cold tolerance in OsBIERF3-OE plants while exogenous AgNO3, an inhibitor of ethylene action, significantly suppressed the enhanced cold tolerance in OsBIERF3-Ri plants. These data demonstrate that OsBIERF3 positively contributes to immunity against M. oryzae and X. oryzae pv. oryzae but negatively regulates cold stress tolerance in rice.
PMID: 35054806
Int J Mol Sci , IF:5.923 , 2022 Jan , V23 (2) doi: 10.3390/ijms23020728
Effects of the Chloroplast Fructose-1,6-Bisphosphate Aldolase Gene on Growth and Low-Temperature Tolerance of Tomato.
Horticulture Department, Hebei Agriculture University, Baoding 071000, China.; Horticulture Department, Shandong Agriculture University, Tai'an 271018, China.; State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China.; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Tomato (Solanum lycopersicum) is one of the most important greenhouse vegetables, with a large cultivated area across the world. However, in northern China, tomato plants often suffer from low-temperature stress in solar greenhouse cultivation, which affects plant growth and development and results in economic losses. We previously found that a chloroplast aldolase gene in tomato, SlFBA4, plays an important role in the Calvin-Benson cycle (CBC), and its expression level and activity can be significantly altered when subjected to low-temperature stress. To further study the function of SlFBA4 in the photosynthesis and chilling tolerance of tomato, we obtained transgenic tomato plants by the over-expression and RNA interference (RNAi) of SlFBA4. The over-expression of SlFBA4 led to higher fructose-1,6-bisphosphate aldolase activity, net photosynthetic rate (Pn) and activity of other enzymes in the CBC than wild type. Opposite results were observed in the RNAi lines. Moreover, an increase in thousand-seed weight, plant height, stem diameter and germination rate in optimal and sub-optimal temperatures was observed in the over-expression lines, while opposite effects were observed in the RNAi lines. Furthermore, over-expression of SlFBA4 increased Pn and enzyme activity and decreased malonaldehyde (MDA) content under chilling conditions. On the other hand, Pn and MDA content were more severely influenced by chilling stress in the RNAi lines. These results indicate that SlFBA4 plays an important role in tomato growth and tolerance to chilling stress.
PMID: 35054921
Front Plant Sci , IF:5.753 , 2021 , V12 : P763284 doi: 10.3389/fpls.2021.763284
Jasmonate and Melatonin Act Synergistically to Potentiate Cold Tolerance in Tomato Plants.
School of Life Sciences, Liaocheng University, Liaocheng, China.; College of Forestry, Northwest A&F University, Xianyang, China.
Both jasmonic acid (JA) and melatonin (MT) have been demonstrated to play positive roles in cold tolerance, however, whether and how they crosstalk in the cold responses in plants remain elusive. Here, we report that JA and MT act synergistically in the cold tolerance in tomato plants (Solanum lycopersicum). It was found that JA and MT were both substantially accumulated in response to cold stress and foliar applications of methyl jasmonate (MeJA) and MT promoted cold tolerance as evidenced by increased Fv/Fm, decreased relative electrolyte leakage (EL) and declined H2O2 accumulation in tomato plants. Inhibition of MT biosynthesis attenuated MeJA-induced cold tolerance, while inhibition of JA biosynthesis reduced MT accumulation in tomato plants under cold conditions. Furthermore, qRT-PCR analysis showed that the expressions of two MT biosynthetic genes, SlSNAT and SlAMST, were strongly induced by MeJA, whereas suppression of SlMYC2, a master JA signaling regulator, abated the expressions of SlSNAT and SlAMST under cold stress. Additionally, suppression of SlMYC2 reduced MT accumulation, decreased Fv/Fm and increased EL in cold-stressed tomato plants. Interestingly, exogenous MT promoted JA accumulation, while inhibition of MT biosynthesis significantly reduced JA accumulation in tomato plants under the cold condition. Taken together, these results suggest that JA and MT act cooperatively in cold tolerance and form a positive feedback loop, amplifying the cold responses of tomato plants. Our findings might be translated into the development of cold-resistant tomato cultivars by genetically manipulating JA and MT pathways.
PMID: 35069620
J Agric Food Chem , IF:5.279 , 2022 Jan , V70 (2) : P687-698 doi: 10.1021/acs.jafc.1c06915
Different Phenylalanine Pathway Responses to Cold Stress Based on Metabolomics and Transcriptomics in Tartary Buckwheat Landraces.
College of Life and Environmental Sciences, Minzu University of China, Beijing 100088, China.; College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518000, China.; State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.; Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing 100081, China.; Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing 100081, China.
Tartary buckwheat (Fagopyrum tataricum) is strongly adapted to growth in adverse environments. In Liangshan, the Yi people cultivate different Tartary buckwheat landraces in different habitats. In this study, we aimed to understand the molecular differences in transcriptomic and metabolomic responses underlying cold tolerance between two Tartary buckwheat landraces (TM and RG) cultivated at different altitudes. After cold treatment, TM showed normal growth in the seedling stage and had significantly higher total flavonoids (16.53 mg/g, 1.47 times), rutin (5.73 mg/g, 1.32 times), and quercetin (0.08 mg/g, 2.67 times), which were higher than those in RG. In addition, TM showed higher-level changes in carbon and nitrogen metabolism than RG. Combined transcriptome and metabolomic analyses showed that phenylpropanoid biosynthesis was upregulated after cold treatment, and in TM, rutin synthesis was upregulated with a higher-level response to cold stress. RG showed higher expression in anthocyanins in response to cold stress. In addition, 24 structural genes involved in flavonoid synthesis, including 6 PAL, 3 C4H, 2 4CL, 2 CHS, 1 CHI, 3 F3H, 3 DFR, 1 FLS, 1 F3'H, and 4 GTR genes, were identified. These results will provide sufficient information for breeding Tartary buckwheat with high cold tolerance and constructing rutin high-yield varieties based on genetic engineering.
PMID: 34989558
Plant Cell Physiol , IF:4.927 , 2022 Jan , V63 (1) : P19-29 doi: 10.1093/pcp/pcab135
Citrus sinensis CBF1 Functions in Cold Tolerance by Modulating Putrescine Biosynthesis through Regulation of Arginine Decarboxylase.
Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
C-repeat (CRT) binding factors (CBFs) are well known to act as crucial transcription factors that function in cold stress response. Arginine decarboxylase (ADC)- mediated putrescine (Put) biosynthesis has been reported to be activated in plants exposed to cold conditions, but it remains elusive whether CBFs can regulate ADC expression and Put accumulation. In this study, we show that cold upregulated ADC gene (Citrus sinensis ADC;CsADC) and elevated endogenous Put content in sweet orange (C.sinensis). The promoter of CsADC contains two CRT sequences that are canonical elements recognized by CBFs. Sweet orange genome contains four CBFs (CsCBF1-4), in which CsCBF1 was significantly induced by cold. CsCBF1, located in the nucleus, was demonstrated to bind directly and specifically to the promoter of CsADC and acted as a transcriptional activator. Overexpression of CsCBF1 led to notable elevation of CsADC and Put levels in sweet orange transgenic plants, along with remarkably enhanced cold tolerance, relative to the wild type. However, pretreatment with D-arginine, an ADC inhibitor, caused a prominent reduction of endogenous Put levels in the overexpressing lines, accompanied by greatly compromised cold tolerance. Taken together, these results demonstrate that the CBF1 of sweet orange directly regulates ADC expression and modulates Put synthesis for orchestrating the cold tolerance. Our findings shed light on the transcriptional regulation of Put accumulation through targeting the ADC gene in the presence of cold stress. Meanwhile, this study illustrates a new mechanism underlying the CBF-mediated cold stress response.
PMID: 34478552
BMC Plant Biol , IF:4.215 , 2022 Jan , V22 (1) : P44 doi: 10.1186/s12870-022-03437-8
Transcriptional and physiological data revealed cold tolerance in a photo-thermo sensitive genic male sterile line Yu17S.
Biotechnology Research Institute, Chongqing Academy of Agricultural Sciences/Chongqing Key Laboratory of Adversity Agriculture, Chongqing, 401329, China.; Chongqing Rationing Rice Research Center, Chongqing Academy of Agricultural Sciences, Chongqing, 402160, China.; Chongqing Rationing Rice Research Center, Chongqing Academy of Agricultural Sciences, Chongqing, 402160, China. ycty2006@126.com.
BACKGROUND: Rice is highly sensitive to chilling stress during the seedling stage. However, the adaptable photo-thermo sensitive genic male sterile (PTGMS) rice line, Yu17S, exhibits tolerance to low temperatures. Currently, the molecular characteristics of Yu17S are unclear. RESULTS: To evaluate the molecular mechanisms behind cold responses in rice seedlings, a comparative transcriptome analysis was performed in Yu17S during seedling development under normal temperature and low temperature conditions. In total, 9317 differentially expressed genes were detected. Gene ontology and pathway analyses revealed that these genes were involved mostly in photosynthesis, carotenoid biosynthesis, carbohydrate metabolism and plant hormone signal transduction. An integrated analysis of specific pathways combined with physiological data indicated that rice seedlings improved the performance of photosystem II when exposed to cold conditions. Genes involved in starch degradation and sucrose metabolism were activated in rice plants exposed to cold stress treatments, which was accompanied by the accumulation of soluble sugar, trehalose, raffinose and galactinol. Furthermore, chilling stress induced the expression of phytoene desaturase, 15-cis-zeta-carotene isomerase, zeta-carotene desaturase, carotenoid isomerase and beta-carotene hydroxylase; this was coupled with the activation of carotenoid synthase activity and increases in abscisic acid (ABA) levels in rice seedlings. CONCLUSIONS: Our results suggest that Yu17S exhibited better tolerance to cold stress with the activation of carotenoid synthase activity and increasing of ABA levels, and as well as the expression of photosynthesis-related genes under cold condition in rice seedlings.
PMID: 35062884
BMC Plant Biol , IF:4.215 , 2022 Jan , V22 (1) : P25 doi: 10.1186/s12870-021-03371-1
Genome-wide identification of the Liriodendron chinense WRKY gene family and its diverse roles in response to multiple abiotic stress.
Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.; College of Biology and the Environment, Nanjing Forestry University, Nanjing, China.; Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China. chenjh@njfu.edu.cn.
BACKGROUND: Liriodendron chinense (Lchi) is a tree species within the Magnoliaceae family and is considered a basal angiosperm. The too low or high temperature or soil drought will restrict its growth as the adverse environmental conditions, thus improving L. chinense abiotic tolerance was the key issues to study. WRKYs are a major family of plant transcription factors known to often be involved in biotic and abiotic stress responses. So far, it is still largely unknown if and how the LchiWRKY gene family is tied to regulating L. chinense stress responses. Therefore, studying the involvement of the WRKY gene family in abiotic stress regulation in L. chinense could be very informative in showing how this tree deals with such stressful conditions. RESULTS: In this research, we performed a genome-wide analysis of the Liriodendron chinense (Lchi) WRKY gene family, studying their classification relationships, gene structure, chromosomal locations, gene duplication, cis-element, and response to abiotic stress. The 44 members of the LchiWRKY gene family contain a significant amount of sequence diversity, with their lengths ranging from 525 bp to 40,981 bp. Using classification analysis, we divided the 44 LchiWRKY genes into three phylogenetic groups (I, II, II), with group II then being further divided into five subgroups (IIa, IIb, IIc, IId, IIe). Comparative phylogenetic analysis including the WRKY families from 17 plant species suggested that LchiWRKYs are closely related to the Magnolia Cinnamomum kanehirae WRKY family, and has fewer family members than higher plants. We found the LchiWRKYs to be evenly distributed across 15 chromosomes, with their duplication events suggesting that tandem duplication may have played a major role in LchiWRKY gene expansion model. A Ka/Ks analysis indicated that they mainly underwent purifying selection and distributed in the group IId. Motif analysis showed that LchiWRKYs contained 20 motifs, and different phylogenetic groups contained conserved motif. Gene ontology (GO) analysis showed that LchiWRKYs were mainly enriched in two categories, i.e., biological process and molecular function. Two group IIc members (LchiWRKY10 and LchiWRKY37) contain unique WRKY element sequence variants (WRKYGKK and WRKYGKS). Gene structure analysis showed that most LchiWRKYs possess 3 exons and two different types of introns: the R- and V-type which are both contained within the WRKY domain (WD). Additional promoter cis-element analysis indicated that 12 cis-elements that play different functions in environmental adaptability occur across all LchiWRKY groups. Heat, cold, and drought stress mainly induced the expression of group II and I LchiWRKYs, some of which had undergone gene duplication during evolution, and more than half of which had three exons. LchiWRKY33 mainly responded to cold stress and LchiWRKY25 mainly responded to heat stress, and LchiWRKY18 mainly responded to drought stress, which was almost 4-fold highly expressed, while 5 LchiWRKYs (LchiWRKY5, LchiWRKY23, LchiWRKY14, LchiWRKY27, and LchiWRKY36) responded equally three stresses with more than 6-fold expression. Subcellular localization analysis showed that all LchiWRKYs were localized in the nucleus, and subcellular localization experiments of LchiWRKY18 and 36 also showed that these two transcription factors were expressed in the nucleus. CONCLUSIONS: This study shows that in Liriodendron chinense, several WRKY genes like LchiWRKY33, LchiWRKY25, and LchiWRKY18, respond to cold or heat or drought stress, suggesting that they may indeed play a role in regulating the tree's response to such conditions. This information will prove a pivotal role in directing further studies on the function of the LchiWRKY gene family in abiotic stress response and provides a theoretical basis for popularizing afforestation in different regions of China.
PMID: 35012508
BMC Plant Biol , IF:4.215 , 2022 Jan , V22 (1) : P26 doi: 10.1186/s12870-021-03381-z
Transcriptome analysis provides new insights into plants responses under phosphate starvation in association with chilling stress.
School of life sciences, Tianjin University, No.92 Weijin Road, Nankai District, 300072, Tianjin, China.; Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, No. 3888 Chenhua Road, 201602, Shanghai, P. R. China.; Department of Biosciences, COMSATS University Islamabad, Park road, 45550, Islamabad, Pakistan. ayesha.tahir@comsats.edu.pk.; School of life sciences, Tianjin University, No.92 Weijin Road, Nankai District, 300072, Tianjin, China. jun.kang@tju.edu.cn.
BACKGROUND: Chilling temperature reduces the rate of photosynthesis in plants, which is more pronounced in association with phosphate (Pi) starvation. Previous studies showed that Pi resupply improves recovery of the rate of photosynthesis in plants much better under combination of dual stresses than in non-chilled samples. However, the underlying mechanism remains poorly understood. RESULTS: In this study, RNA-seq analysis showed the expression level of 41 photosynthetic genes in plant roots increased under phosphate starvation associated with 4 degrees C (-P 4 degrees C) compared to -P 23 degrees C. Moreover, iron uptake increased significantly in the stem cell niche (SCN) of wild type (WT) roots in -P 4 degrees C. In contrast, lower iron concentrations were found in SCN of aluminum activated malate transporter 1 (almt1) and its transcription factor, sensitive to protein rhizotoxicity 1 (stop1) mutants under -P 4 degrees C. The Fe content examined by ICP-MS analysis in -P 4 degrees C treated almt1 was 98.5 ng/microg, which was only 17% of that of seedlings grown under -P 23 degrees C. Average plastid number in almt1 root cells under -P 4 degrees C was less than -P 23 degrees C. Furthermore, stop1 and almt1 single mutants both exhibited increased primary root elongation than WT under combined stresses. In addition, dark treatment blocked the root elongation phenotype of stop1 and almt1. CONCLUSIONS: Induction of photosynthetic gene expression and increased iron accumulation in roots is required for plant adjustment to chilling in association with phosphate starvation.
PMID: 35016604
BMC Plant Biol , IF:4.215 , 2022 Jan , V22 (1) : P35 doi: 10.1186/s12870-021-03420-9
More opportunities more species: Pleistocene differentiation and northward expansion of an evergreen broad-leaved tree species Machilus thunbergii (Lauraceae) in Southeast China.
Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China.; Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China. yixuankou@163.com.; Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.; Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China. pinus-rubus@163.com.
BACKGROUND: The broad continuum between tropical and temperate floras in Eastern Asia (EAS) are thought to be one of the main factors responsible for a prominent species diversity anomaly of temperate plants between EAS and eastern North America (ENS). However, how the broad continuum and niche evolution between tropical and temperate floras in EAS contributes to lineage divergence and species diversity remains largely unknown. RESULTS: Population genetic structure, demography, and determinants of genetic structure [i.e., isolation-by-distance (IBD), isolation-by-resistance (IBR), and isolation-by-environment (IBE)] of Machilus thunbergii Sieb. et Zucc. (Lauraceae) were evaluated by examining sequence variation of ten low-copy nuclear genes across 43 populations in southeast China. Climatic niche difference and potential distributions across four periods (Current, mid-Holocene, the last glacial maximum, the last interglacial) of two genetic clusters were determined by niche modelling. North and south clusters of populations in M. thunbergii were revealed and their demarcation line corresponds well with the northern boundary of tropical zone in China of Zhu & Wan. The divergence time between the clusters and demographic expansion of M. thunbergii occurred after the mid-Pleistocene climate transition (MPT, 0.8-1.2 Ma). Migration rates between clusters were asymmetrical, being much greater from north to south than the reverse. Significant effects of IBE, but non-significant effects of IBD and IBR on population genetic divergence were detected. The two clusters have different ecological niches and require different temperature regimes. CONCLUSIONS: The north-south genetic differentiation may be common across the temperate-tropical boundary in southeast China. Divergent selection under different temperature regimes (possibly above and below freezing temperature in winter) could account for this divergence pattern. The broad continuum between tropical and temperate floras in EAS may have provided ample opportunities for tropical plant lineages to acquire freezing tolerance and to colonize the temperate regions during the late-Cenozoic global cooling. Our findings shed deeper insights into the high temperate plant species diversity in EAS.
PMID: 35038992
FEMS Microbiol Ecol , IF:4.194 , 2022 Jan , V98 (1) doi: 10.1093/femsec/fiab161
Ecology and potential functions of plant-associated microbial communities in cold environments.
Center Agriculture Food Environment (C3A), University of Trento, via E. Mach 1, 38098 San Michele all'Adige, Italy.; Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy.
Complex microbial communities are associated with plants and can improve their resilience under harsh environmental conditions. In particular, plants and their associated communities have developed complex adaptation strategies against cold stress. Although changes in plant-associated microbial community structure have been analysed in different cold regions, scarce information is available on possible common taxonomic and functional features of microbial communities across cold environments. In this review, we discuss recent advances in taxonomic and functional characterization of plant-associated microbial communities in three main cold regions, such as alpine, Arctic and Antarctica environments. Culture-independent and culture-dependent approaches are analysed, in order to highlight the main factors affecting the taxonomic structure of plant-associated communities in cold environments. Moreover, biotechnological applications of plant-associated microorganisms from cold environments are proposed for agriculture, industry and medicine, according to biological functions and cold adaptation strategies of bacteria and fungi. Although further functional studies may improve our knowledge, the existing literature suggest that plants growing in cold environments harbor complex, host-specific and cold-adapted microbial communities, which may play key functional roles in plant growth and survival under cold conditions.
PMID: 34910139
Planta , IF:4.116 , 2022 Jan , V255 (2) : P45 doi: 10.1007/s00425-022-03828-z
Stress memory responses and seed priming correlate with drought tolerance in plants: an overview.
Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, 53115, Bonn, Germany.; College of Bioengineering, Sichuan University of Science & Engineering, Zigong, 643000, China.; Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, Hubei, China.; Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, 53115, Bonn, Germany. dbartels@uni-bonn.de.
MAIN CONCLUSION: Environmental-friendly techniques based on plant stress memory, cross-stress tolerance, and seed priming help sustainable agriculture by mitigating negative effects of dehydration stress. The frequently uneven rainfall distribution caused by global warming will lead to more irregular and multiple abiotic stresses, such as heat stress, dehydration stress, cold stress or the combination of these stresses. Dehydration stress is one of the major environmental factors affecting the survival rate and productivity of plants. Hence, there is an urgent need to develop improved resilient varieties. Presently, technologies based on plant stress memory, cross-stress tolerance and priming of seeds represent fruitful and promising areas of future research and applied agricultural science. In this review, we will provide an overview of plant drought stress memory from physiological, biochemical, molecular and epigenetic perspectives. Drought priming-induced cross-stress tolerance to cold and heat stress will be discussed and the application of seed priming will be illustrated for different species.
PMID: 35066685
Planta , IF:4.116 , 2022 Jan , V255 (2) : P39 doi: 10.1007/s00425-021-03809-8
Cold stress and freezing tolerance negatively affect the fitness of Arabidopsis thaliana accessions under field and controlled conditions.
Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany.; Department of Chemistry and Bioscience, Aalborg University, 9220, Aalborg East, Denmark.; Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany. zuther@mpimp-golm.mpg.de.
MAIN CONCLUSION: Higher acclimated freezing tolerance improved winter survival, but reduced reproductive fitness of Arabidopsis thaliana accessions under field and controlled conditions. Low temperature is one of the most important abiotic factors influencing plant fitness and geographical distribution. In addition, cold stress is known to influence crop yield and is therefore of great economic importance. Increased freezing tolerance can be acquired by the process of cold acclimation, but this may be associated with a fitness cost. To assess the influence of cold stress on the fitness of plants, long-term field trials over 5 years were performed with six natural accessions of Arabidopsis thaliana ranging from very tolerant to very sensitive to freezing. Fitness parameters, as seed yield and 1000 seed mass, were measured and correlation analyses with temperature and freezing tolerance data performed. The results were compared with fitness parameters from controlled chamber experiments over 3 years with application of cold priming and triggering conditions. Winter survival and seed yield per plant were positively correlated with temperature in field experiments. In addition, winter survival and 1000 seed mass were correlated with the cold-acclimated freezing tolerance of the selected Arabidopsis accessions. The results provide strong evidence for a trade-off between higher freezing tolerance and reproductive fitness in A. thaliana, which might have ecological impacts in the context of global warming.
PMID: 35032192
Plants (Basel) , IF:3.935 , 2022 Jan , V11 (2) doi: 10.3390/plants11020199
Metabolic and Physiological Regulation of Aspartic Acid-Mediated Enhancement of Heat Stress Tolerance in Perennial Ryegrass.
College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing 210095, China.; Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA.
Aspartate is the most critical amino acid in the aspartate metabolic pathway, which is associated with multiple metabolic pathways, such as protein synthesis, nucleotide metabolism, TCA cycle, glycolysis, and hormone biosynthesis. Aspartate also plays an important role in plant resistance to abiotic stress, such as cold stress, drought stress, salt stress or heavy metal stress. This study found that the chlorophyll content and antioxidant active enzyme content (SOD, CAT, POD and APX) of perennial ryegrass treated with 2 mM aspartate were significantly higher than those treated with water under heat stress. The electrolyte leakage rate, MDA content and peroxide levels (O(2-) and H2O2) of perennial ryegrass treated with aspartate were significantly lower than those of perennial ryegrass treated with water, indicating that exogenous aspartate increases the content of chlorophyll, maintain the integrity of cell membrane system, and enhances SOD-CAT antioxidant pathway to eliminate the oxidative damage caused by ROS in perennial ryegrass under heat stress. Furthermore, exogenous aspartate could enhance the TCA cycle, the metabolism of the amino acids related to the TCA cycle, and pyrimidine metabolism to enhance the heat tolerance of perennial ryegrass.
PMID: 35050087
Gene , IF:3.688 , 2022 Jan , V807 : P145952 doi: 10.1016/j.gene.2021.145952
Identification of key genes and molecular mechanisms associated with temperature stress in lentil.
Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran. Electronic address: sohrabi.sa@fa.lu.ac.ir.; Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran. Electronic address: ismaili.a@lu.ac.ir.; Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran. Electronic address: nazarian.f@lu.ac.ir.; Department of Biology, School of Sciences, Razi University, Kermanshah, Iran. Electronic address: h.fallahi@razi.ac.ir.; Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran. Electronic address: hoseini.za@fa.lu.ac.ir.
Extreme temperature is one of the serious threats to crop production in present and future scenarios of global climate changes. Lentil (Lens culinaris) is an important crop, and there is a serious lack of genetic information regarding environmental and temperature stresses responses. This study is the first report of evaluation of key genes and molecular mechanisms related to temperature stresses in lentil using the RNA sequencing technique. De novo transcriptome assembly created 44,673 contigs and differential gene expression analysis revealed 7494 differentially expressed genes between the temperature stresses and control group. Basic annotation of generated transcriptome assembly in our study led to the identification of 2765 novel transcripts that have not been identified yet in lentil genome draft v1.2. In addition, several unigenes involved in mechanisms of temperature sensing, calcium and hormone signaling and DNA-binding transcription factor activity were identified. Also, common mechanisms in response to temperature stresses, including the proline biosynthesis, the photosynthetic light reactions balancing, chaperone activity and circadian rhythms, are determined by the hub genes through the protein-protein interaction networks analysis. Deciphering the mechanisms of extreme temperature tolerance would be a new way for developing crops with enhanced plasticity against climate change. In general, this study has identified set of mechanisms and various genes related to cold and heat stresses which will be useful in better understanding of the lentil's reaction to temperature stresses.
PMID: 34500049
Mol Genet Genomics , IF:3.291 , 2022 Jan doi: 10.1007/s00438-021-01839-1
Genome-wide analysis and transcriptional reprogrammings of MYB superfamily revealed positive insights into abiotic stress responses and anthocyanin accumulation in Carthamus tinctorius L.
Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China.; Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China. xiuming1211@163.com.; Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China. yaona1103@126.com.
The MYB transcription factors comprise one of the largest superfamilies in plants that have been implicated in the regulation of plant-specific metabolites and responses to biotic and abiotic stresses. Here, we present the first comprehensive genome-wide analysis and functional characterization of the CtMYB family in Carthamus tinctorius. A total of 272 CtMYBs were identified and classified into 12 subgroups using comparative phylogenetic analysis with Arabidopsis and rice orthologs. The overview of conserved motifs, gene structures, and cis elements as well as the expression pattern of CtMYB genes indicated the diverse roles of these transcription factors during plant growth, regulation of secondary metabolites, and various abiotic stress responses. The subcellular localization and transactivation analysis of four CtMYB proteins indicated predominant localization in the nuclei with enhanced transcriptional activation in yeast. The expression of CtMYB63 induced with various abiotic stress conditions showed upregulation in its transcription level. In addition, the expression analysis of the core structural genes of anthocyanin biosynthetic pathway under drought and cold stress in CtMYB63 overexpressed transgenic lines also supports the notion of CtMYB63 transcriptional reprogramming in response to abiotic stress by upregulating the anthocyanin biosynthesis. Together, our findings revealed the underlying regulatory mechanism of CtMYB TF network involving enhanced cold and drought stress tolerance through activating the rapid biosynthesis of anthocyanin in C. tinctorius. This study also presents useful insights towards the establishment of new strategies for crop improvements.
PMID: 34978004
Comput Biol Chem , IF:2.877 , 2022 Jan , V97 : P107622 doi: 10.1016/j.compbiolchem.2022.107622
Identification of leucine-rich repeat receptor-like protein kinase (LRR-RLK) genes in paper mulberry and their potential roles in response to cold stress.
Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.; Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China. Electronic address: pengxianjun@ibcas.ac.cn.; Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China. Electronic address: shshen@ibcas.ac.cn.
Leucine-rich repeat receptor-like protein kinases (LRR-RLKs) represent the largest group of receptor-like kinases in plants, which have been previously reported to play vital roles in plant growth, development, stress adaptation and signal transduction. However, there is lack of comprehensive analysis of this family in paper mulberry (Broussonetia papyrifera). In the present investigation, a genome-wide scan revealed the presence of 236 LRR-RLK genes in paper mulberry, which were classified into 21 subgroups based on the maximum-likelihood phylogenetic tree. Gene structure and conserved motif analyses suggested genes in the same subgroup had highly consistent motif composition and intron/exon arrangement, but were divergent among subgroups. Total of 223 BpLRR-RLK genes were unevenly distributed across all 13 chromosomes, while the remaining 13 genes were localized to the unassembled scaffolds. Tandem and segmental duplications were confirmed to contribute to the expansion of BpLRR-RLK family. Further Ka/Ks showed that the duplicated BpLRR-RLKs had experienced strong purifying selection. The global promoter composition, transcriptome and phosphorylation analysis indicated that many of BpLRR-RLKs were associated with plant development, biotic and abiotic stress response, especially for cold stress. Furthermore, protein-protein interaction network was constructed for the 127 and 14 BpLRR-RLKs that responded to cold stress at the transcriptomics and phosphorylation level, respectively. All these findings will facilitate the studies on the evolutionary history of the LRR-RLK gene family in paper mulberry, also establish a solid foundation to further explore the potential functions of LRR-RLK genes in higher plants, particularly with regards to cold resistance.
PMID: 35033836