Genome-Wide Identification and Characterization of Cysteine-Rich Receptor-Like Protein Kinase Genes in Tomato and Their Expression Profile in Response to Heat Stress

During plant growth, development and stress adaption, receptor-like protein kinases (RLKs) are essential components in perceiving and integrating extracellular stimuli and transmitting the signals to activate the downstream signaling pathways. Cysteine-rich receptor-like protein kinases (CRKs) are a large subfamily of RLKs and their roles in modulating plant disease resistance are well elucidated. However, the roles of CRKs in plant abiotic stress responses, especially heat stress, are largely unknown. In this study, 35 SlCRK genes were identified in tomato (Solanum lycopersicum) based on the multiple sequence alignment and phylogenetic relationships. SlCRK genes are tandemly distributed on seven chromosomes and have similar exon–intron organization and common conserved motifs. Various phytohormone responsive, stress responsive cis-regulatory elements and heat shock elements are predicted in the promoter regions of SlCRK genes. Transcriptome analysis of tomato fruits under heat stress revealed that most SlCRK genes were downregulated upon heat treatment. GO enrichment analyses of genes that were co-expressed with SlCRK members have identified various stress responses related and proteasomal protein catabolic process related genes, which may be involved in heat stress signaling. Overall, our results provide valuable information for further research on the roles of SlCRKs in response to abiotic stress, especially heat stress.

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Systematic discovery and characterization of stress-related microRNA genes in Oryza sativa

Biologia ◽

10.1515/biolog-2015-0001 ◽

2015 ◽

Vol 70 (1) ◽

Cited By ~ 1

Author(s):

Kai Bin Xie ◽

Xue Zhou ◽

Tian Hai Zhang ◽

Bao Long Zhang ◽

Li Ming Chen ◽

...

Keyword(s):

Abiotic Stress ◽

Stress Responses ◽

Systematic Investigation ◽

Chemical Toxicity ◽

Promoter Regions ◽

Crop Species ◽

Translation Inhibition ◽

Microrna Genes ◽

Insight Into

AbstractAbiotic stresses including drought, salinity, extreme temperatures, chemical toxicity and oxidative are the natural status of the environment to exert serious threats to agriculture. Abiotic stress-related microRNAs (ASmiRNAs) are a group of microRNAs (miRNAs) regulating stress responses in plants. However, the systematic investigation of ASmiRNAs is limited in Rice (O. sativa), a typical abiotic stress-resistant crop species. In the present work, we systematically investigated ASmiRNAs in silico. First, we identified 177 putative ASmiRNAs in O.sativa. Second, we found most ASmiRNAs were driven by TATA-promoter and most stress-related miRNA promoter regions contained the stress-related elements. Third, we found many ASmiRNAs families were species/family specific and a set of miRNAs might derive from genomic repeat-sequences in O. sativa. Finally, we found the ASmiRNAs in O. sativa target 289 genes with 1050 predicted target sites in which 98% sites have cleavage activity and 2% sites have translation inhibition activity. In conclusion, our findings provide an insight into both the function and evolution of ASmiRNAs and improve our understanding on the mechanism of abiotic stress resistance in O. sativa.

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Genome-wide promoter analysis, homology modeling and protein interaction network of Dehydration Responsive Element Binding (DREB) gene family in Solanum tuberosum

PLoS ONE ◽

10.1371/journal.pone.0261215 ◽

2021 ◽

Vol 16 (12) ◽

pp. e0261215

Author(s):

Qurat-ul ain-Ali ◽

Nida Mushtaq ◽

Rabia Amir ◽

Alvina Gul ◽

Muhammad Tahir ◽

...

Keyword(s):

Abiotic Stress ◽

Gene Family ◽

Stress Responses ◽

Promoter Analysis ◽

Molecular Mechanisms ◽

Regulatory Elements ◽

Start Codon ◽

Gene Promoters ◽

Responsive Element ◽

Dreb Gene

Dehydration Responsive Element Binding (DREB) regulates the expression of numerous stress-responsive genes, and hence plays a pivotal role in abiotic stress responses and tolerance in plants. The study aimed to develop a complete overview of the cis-acting regulatory elements (CAREs) present in S. tuberosum DREB gene promoters. A total of one hundred and four (104) cis-regulatory elements (CREs) were identified from 2.5kbp upstream of the start codon (ATG). The in-silico promoter analysis revealed variable sets of cis-elements and functional diversity with the predominance of light-responsive (30%), development-related (20%), abiotic stress-responsive (14%), and hormone-responsive (12%) elements in StDREBs. Among them, two light-responsive elements (Box-4 and G-box) were predicted in 64 and 61 StDREB genes, respectively. Two development-related motifs (AAGAA-motif and as-1) were abundant in StDREB gene promoters. Most of the DREB genes contained one or more Myeloblastosis (MYB) and Myelocytometosis (MYC) elements associated with abiotic stress responses. Hormone-responsive element i.e. ABRE was found in 59 out of 66 StDREB genes, which implied their role in dehydration and salinity stress. Moreover, six proteins were chosen corresponding to A1-A6 StDREB subgroups for secondary structure analysis and three-dimensional protein modeling followed by model validation through PROCHECK server by Ramachandran Plot. The predicted models demonstrated >90% of the residues in the favorable region, which further ensured their reliability. The present study also anticipated pocket binding sites and disordered regions (DRs) to gain insights into the structural flexibility and functional annotation of StDREB proteins. The protein association network determined the interaction of six selected StDREB proteins with potato proteins encoded by other gene families such as MYB and NAC, suggesting their similar functional roles in biological and molecular pathways. Overall, our results provide fundamental information for future functional analysis to understand the precise molecular mechanisms of the DREB gene family in S. tuberosum.

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Identification of conserved and novel miRNAs responsive to heat stress in flowering Chinese cabbage using high-throughput sequencing

Scientific Reports ◽

10.1038/s41598-019-51443-y ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Waqas Ahmed ◽

Yanshi Xia ◽

Hua Zhang ◽

Ronghua Li ◽

Guihua Bai ◽

...

Keyword(s):

Heat Stress ◽

Abiotic Stress ◽

High Throughput ◽

Chinese Cabbage ◽

Stress Responses ◽

High Throughput Sequencing ◽

Differential Expression Analysis ◽

Plant Responses ◽

Limited Information ◽

Flowering Chinese Cabbage

Abstract Plant microRNAs (miRNAs) are noncoding and endogenous key regulators that play significant functions in regulating plant responses to stress, and plant growth and development. Heat stress is a critical abiotic stress that reduces the yield and quality of flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee). However, limited information is available on whether miRNAs are involved in the regulation of heat stress in B. campestris. A high-throughput sequencing approach was used to identify novel and conserved heat-responsive miRNAs in four small RNA libraries of flowering Chinese cabbage using leaves collected at 0 h, 1 h, 6 h and 12 h after a 38 °C heat-stress treatment. The analysis identified 41 conserved miRNAs (belonging to 19 MIR families), of which MIR156, MIR159, MIR168, MIR171 and MIR1885 had the most abundant molecules. Prediction and evaluation of novel miRNAs using the unannotated reads resulted in 18 candidate miRNAs. Differential expression analysis showed that most of the identified miRNAs were downregulated in heat-treated groups. To better understand functional importance, bioinformatic analysis predicted 432 unique putative target miRNAs involved in cells, cell parts, catalytic activity, cellular processes and abiotic stress responses. Furthermore, the Kyoto Encyclopedia of Genes and Genomes maps of flowering Chinese cabbage identified the significant role of miRNAs in stress adaptation and stress tolerance, and in several mitogen-activated protein kinases signaling pathways including cell death. This work presents a comprehensive study of the miRNAs for understanding the regulatory mechanisms and their participation in the heat stress of flowering Chinese cabbage.

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A comprehensive analysis of cotton VQ gene superfamily reveals their potential and extensive roles in regulating cotton abiotic stress

10.21203/rs.3.rs-38226/v1 ◽

2020 ◽

Author(s):

Shuxun Yu ◽

Pengyun Chen ◽

Fei wei ◽

Shuaishuai Cheng ◽

Liang Ma ◽

...

Keyword(s):

Abiotic Stress ◽

Stress Responses ◽

Expression Patterns ◽

Regulatory Elements ◽

Abiotic Stress Response ◽

Salt And Drought Stress ◽

Solid Foundation ◽

Underlying Mechanisms ◽

Peg Stress ◽

Insight Into

Abstract Background Valine-glutamine (VQ) motif-containing proteins play important roles in plant growth, development and abiotic stress response. For many plant species, the VQ genes have been identified and their functions have been described. However, little is known about the origin, evolution, and functions (and underlying mechanisms) of the VQ family genes in cotton. Results In this study, we comprehensively analyzed the characteristics of 268 VQ genes from four Gossypium genomes and found that the VQ proteins evolved into ten clades, and each clade had a similar structural and conservative motif. The expansion of the VQ gene was mainly through segmental duplication, followed by dispersal. Expression analysis revealed that the VQ genes play important roles in response to salt and drought stress, especially GhVQ18 and GhVQ84 were significantly high expression in PEG stress and salt stress. Further analysis showed that GhVQ genes were co-expressed with GhWRKY transcription factors (TFs), and microRNAs (miRNAs) could hybridize to their cis-regulatory elements. Conclusions The results in this study broaden our understanding of the VQ gene family in plants, and the analysis of the structure, conserved elements, and expression patterns of the VQ genes provide a solid foundation for exploring their specific functions in the abiotic stress responses in cotton. Our study provides significant insight into the potential functions of VQ genes in cotton.

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Modulation of GmFAD3 expression alters responses to abiotic stress in soybean

10.22541/au.160569953.30220980/v1 ◽

2020 ◽

Author(s):

Ajay Singh ◽

Mahesh Kumar ◽

Susheel Raina ◽

Milind Ratnaparkhe ◽

Jagadish Rane ◽

...

Keyword(s):

Heat Stress ◽

Abiotic Stress ◽

Fatty Acid ◽

Stress Tolerance ◽

Salinity Stress ◽

Stress Responses ◽

Fatty Acid Desaturase ◽

Stress Conditions ◽

Omega 3 ◽

Soybean Plants

FAD3 play important roles in modulating membrane fluidity in response to various abiotic stresses. However, a comprehensive analysis of FAD3 in drought, salinity and heat stress tolerance is lacking in soybean. The present study assessed the functional role of fatty acid desaturase 3 to abiotic stress responses in soybean. We used Bean Pod Mottle Virus -based vector to alter expression of Glycine max omega-3 fatty acid desaturase . Higher levels of recombinant BPMV-GmFAD3 transcripts were detected in overexpressing soybean plants. Overexpression of GmFAD3 in soybean resulted in increased levels of jasmonic acid and higher expression of GmWRKY54 as compared to mock-inoculated, vector-infected and FAD3-silenced soybean plants under drought and salinity stress conditions. FAD3 overexpressing plants showed higher levels of chlorophyll content, leaf SPAD value, relative water content, chlorophyll fluorescence, transpiration rate, carbon assimilation rate, proline content and also cooler canopy under drought and salinity stress conditions as compared to mock-inoculated, vector-infected and FAD3-silenced soybean plants. Results from current study revealed that GmFAD3 overexpressing soybean plants exhibited drought and salinity stress tolerance although tolerance to heat stress was reduced. On the other hand, soybean plants silenced for GmFAD3 exhibited tolerance to heat stress, but were vulnerable to drought and salinity stress

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Molecular Cloning, Expression and Insilco Analysis of Drought Stress Inducible MYB Transcription Factor Encoding Gene From C4 Plant Eleusine Coracana

10.21203/rs.3.rs-955905/v1 ◽

2021 ◽

Author(s):

MEGHA BHATT

Keyword(s):

Gene Expression ◽

Abiotic Stress ◽

Drought Stress ◽

Molecular Cloning ◽

Stress Responses ◽

Promoter Region ◽

Regulatory Elements ◽

Full Length ◽

Growth And Yield ◽

Yield Potential

Abstract Drought is one of the key abiotic stresses that critically influences the crops by restraining their growth and yield potential. Being sessile, plant tackle the detrimental effects of drought stress via modulating the cellular state by changing the gene expression. Such alteration of gene expression is essentially driven by the transcriptional syndicate. Transcription factors (TF) are the key regulatory protein that controls the expression of their target gene by binding to the cis-regulatory elements present in the promoter region. Myb-TF subiquitously present in all eukaryotes belong to one of the largest TF family, and play wide array of biological functions in plants including anthocyanin biosynthesis, vasculature system, cell signaling, seed maturation and abiotc stress responses. In the present study, isolation, and molecular cloning of full length Myb TF from Eleusine corocana has been performed. The isolated full-length coding sequence has 1053 bp and 350 aa was submitted to NCBI (Accession number MT312253). The transcript level of EcMYB increases under different abiotic stress treatment including dehydration, salinity, and high temperature stress. The promoter region of EcMyb1 was found to be enriched in stress-responsive cis-regulatory elements such as DRE, HSE, ABRE etc. In phylogenetic analysis, EcMyb1 appeared to have high homology with its monocot orthologs particularly Sateria italica, Hordeum vulgare, Saccharum barberi and Oryza sativa. The three-dimension protein structure was generated based on homology modeling and structural aspects were discussed. Further, Insilco analysis was conducted to explore the physiological properties, subcellular localization, potential post-translational modification sites (phosphorylation and glycosylation sites), and molecular and biological function of full-length protein. Overall, the expression profiling and Insilco analysis of EcMyb1 strongly indicated its potential role in abiotic stress response in Eleusine corocana.

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Comparative Genome-wide Analysis and Expression Profiling of Histone Acetyltransferases and Histone Deacetylases Involved in the Response to Drought in Wheat

10.21203/rs.3.rs-123885/v1 ◽

2020 ◽

Author(s):

Hua Li ◽

Huajie Liu ◽

Xinxin Pei ◽

Hongyu Chen ◽

Xiao Li ◽

...

Keyword(s):

Drought Stress ◽

Stress Responses ◽

Histone Deacetylases ◽

Gene Expression Analysis ◽

Regulatory Elements ◽

Wheat Genome ◽

Histone Acetyltransferases ◽

Promoter Regions ◽

Conserved Domain ◽

Genome Wide

Abstract Background: Histone acetyltransferases (HATs) and histone deacetylases (HDACs) contribute to plant growth, development, and stress responses. A number of HAT and HDAC genes have been identified in several plants. However, wheat HATs and HDACs have not been comprehensively characterized. In this study, we identified TaHATs and TaHDACs in the wheat genome using bioinformatics tools. Result: In total, 30 TaHAT genes and 53 TaHDAC genes were detected in the wheat genome. As described in other plants, TaHATs were classified into four subfamilies (i.e., GNAT, p300/CBP, MYST, and TAFII250) and TaHDACs were divided into three subfamilies (i.e., RPD3/HDA1, HD2, and SIR2). Phylogenetic and conserved domain analyses showed that TaHATs and TaHDACs are highly similar to those in Arabidopsis and rice; however, divergence and expansion from Arabidopsis and rice were also observed. We detected many stress-related cis-regulatory elements in the promoter regions of these genes (i.e., ABRE, STRE, MYB et al.). Further, based on a comparative expression analyses of three varieties with different degrees of drought resistance under drought stress, we found that TaHAG2, TaHAG3, TaHAC2, TaHDA18, TaHDT1, and TaHDT2 are likely regulate drought stress in wheat. Conclusions: In this study, TaHATs and TaHDACs from the wheat genome were identified. Three TaHATs and three TaHDACs were very likely to regulate drought stress based on a promoter analysis and gene expression analysis. These results provide a foundation for further research on the regulation of acetylation in wheat and its role in the response to drought stress.

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Receptor-Like Protein Kinases Function Upstream of MAPKs in Regulating Plant Development

International Journal of Molecular Sciences ◽

10.3390/ijms21207638 ◽

2020 ◽

Vol 21 (20) ◽

pp. 7638

Author(s):

Zhe Wang ◽

Xiaoping Gou

Keyword(s):

Protein Kinases ◽

Plant Development ◽

Stress Responses ◽

Higher Plants ◽

Signal Molecules ◽

Signal Pathways ◽

Downstream Signaling ◽

Mapk Cascades ◽

Growth Development ◽

Upstream Regulators

Mitogen-activated protein kinases (MAPKs) are a group of protein kinase broadly involved in various signal pathways in eukaryotes. In plants, MAPK cascades regulate growth, development, stress responses and immunity by perceiving signals from the upstream regulators and transmitting the phosphorylation signals to the downstream signaling components. To reveal the interactions between MAPK cascades and their upstream regulators is important for understanding the functional mechanisms of MAPKs in the life span of higher plants. Typical receptor-like protein kinases (RLKs) are plasma membrane-located to perceive endogenous or exogenous signal molecules in regulating plant growth, development and immunity. MAPK cascades bridge the extracellular signals and intracellular transcription factors in many RLK-mediated signaling pathways. This review focuses on the current findings that RLKs regulate plant development through MAPK cascades and discusses questions that are worth investigating in the near future.

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In silico analysis and expression profiling of S-domain receptor-like kinases (SD-RLKs) under different abiotic stresses in Arabidopsis thaliana

BMC Genomics ◽

10.1186/s12864-021-08133-9 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Raju Mondal ◽

Subhankar Biswas ◽

Akanksha Srivastava ◽

Suvajit Basu ◽

Maitri Trivedi ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Abiotic Stress ◽

Signaling Pathways ◽

Differential Expression ◽

Stress Responses ◽

Abiotic Stresses ◽

Expression Patterns ◽

Light Stress ◽

Regulatory Elements ◽

Qrt Pcr

Abstract Background S-domain receptor-like kinases (SD-RLKs) are an important and multi-gene subfamily of plant receptor-like/pelle kinases (RLKs), which are known to play a significant role in the development and immune responses of Arabidopsis thaliana. The conserved cysteine residues in the extracellular domain of SD-RLKs make them interesting candidates for sensing reactive oxygen species (ROS), assisting oxidative stress mitigation and associated signaling pathways during abiotic stresses. However, how closely SD-RLKs are interrelated to abiotic stress mitigation and signaling remains unknown in A. thaliana. Results This study was initiated by examining the chromosomal localization, phylogeny, sequence and differential expression analyses of 37 SD-RLK genes using publicly accessible microarray datasets under cold, osmotic stress, genotoxic stress, drought, salt, UV-B, heat and wounding. Out of 37 SD-RLKs, 12 genes displayed differential expression patterns in both the root and the shoot tissues. Promoter structure analysis suggested that these 12 SD-RLK genes harbour several potential cis-regulatory elements (CREs), which are involved in regulating multiple abiotic stress responses. Based on these observations, we investigated the expression patterns of 12 selected SD-RLKs under ozone, wounding, oxidative (methyl viologen), UV-B, cold, and light stress at different time points using semi-qRT-PCR. Of these 12 SD-SRKs, the genes At1g61360, At1g61460, At1g61380, and At4g27300 emerged as potential candidates that maintain their expression in most of the stress treatments till exposure for 12 h. Expression patterns of these four genes were further verified under similar stress treatments using qRT-PCR. The expression analysis indicated that the gene At1g61360, At1g61380, and At1g61460 were mostly up-regulated, whereas the expression of At4g27300 either up- or down-regulated in these conditions. Conclusions To summarize, the computational analysis and differential transcript accumulation of SD-RLKs under various abiotic stresses suggested their association with abiotic stress tolerance and related signaling in A. thaliana. We believe that a further detailed study will decipher the specific role of these representative SD-RLKs in abiotic stress mitigation vis-a-vis signaling pathways in A. thaliana.

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Arabidopsis Target of Rapamycin Coordinates With Transcriptional and Epigenetic Machinery to Regulate Thermotolerance

Frontiers in Plant Science ◽

10.3389/fpls.2021.741965 ◽

2021 ◽

Vol 12 ◽

Author(s):

Mohan Sharma ◽

Muhammed Jamsheer K. ◽

Brihaspati Narayan Shukla ◽

Manvi Sharma ◽

Prakhar Awasthi ◽

...

Keyword(s):

Heat Stress ◽

Stress Responses ◽

Target Of Rapamycin ◽

Dependent Manner ◽

Heat Shock Factors ◽

Promoter Regions ◽

Stress Protection ◽

Epigenetic Machinery ◽

Adaptation To Heat

Global warming exhibits profound effects on plant fitness and productivity. To withstand stress, plants sacrifice their growth and activate protective stress responses for ensuring survival. However, the switch between growth and stress is largely elusive. In the past decade, the role of the target of rapamycin (TOR) linking energy and stress signalling is emerging. Here, we have identified an important role of Glucose (Glc)-TOR signalling in plant adaptation to heat stress (HS). Glc via TOR governs the transcriptome reprogramming of a large number of genes involved in heat stress protection. Downstream to Glc-TOR, the E2Fa signalling module regulates the transcription of heat shock factors through direct recruitment of E2Fa onto their promoter regions. Also, Glc epigenetically regulates the transcription of core HS signalling genes in a TOR-dependent manner. TOR acts in concert with p300/CREB HISTONE ACETYLTRANSFERASE1 (HAC1) and dictates the epigenetic landscape of HS loci to regulate thermotolerance. Arabidopsis plants defective in TOR and HAC1 exhibited reduced thermotolerance with a decrease in the expression of core HS signalling genes. Together, our findings reveal a mechanistic framework in which Glc-TOR signalling through different modules integrates stress and energy signalling to regulate thermotolerance.

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