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

BMC Genomics ◽  
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.

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

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.

scholarly journals Specific functions for Mediator complex subunits from different modules in the transcriptional response of Arabidopsis thaliana to abiotic stress

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Tim Crawford ◽  
Fazeelat Karamat ◽  
Nóra Lehotai ◽  
Matilda Rentoft ◽  
Jeanette Blomberg ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Abiotic Stress ◽  
Signaling Pathways ◽  
Stress Responses ◽  
Target Genes ◽  
Biochemical Characterization ◽  
Transcriptional Response ◽  
Stress Conditions ◽  
Important Player ◽  
Adverse Environmental Conditions

AbstractAdverse environmental conditions are detrimental to plant growth and development. Acclimation to abiotic stress conditions involves activation of signaling pathways which often results in changes in gene expression via networks of transcription factors (TFs). Mediator is a highly conserved co-regulator complex and an essential component of the transcriptional machinery in eukaryotes. Some Mediator subunits have been implicated in stress-responsive signaling pathways; however, much remains unknown regarding the role of plant Mediator in abiotic stress responses. Here, we use RNA-seq to analyze the transcriptional response of Arabidopsis thaliana to heat, cold and salt stress conditions. We identify a set of common abiotic stress regulons and describe the sequential and combinatorial nature of TFs involved in their transcriptional regulation. Furthermore, we identify stress-specific roles for the Mediator subunits MED9, MED16, MED18 and CDK8, and putative TFs connecting them to different stress signaling pathways. Our data also indicate different modes of action for subunits or modules of Mediator at the same gene loci, including a co-repressor function for MED16 prior to stress. These results illuminate a poorly understood but important player in the transcriptional response of plants to abiotic stress and identify target genes and mechanisms as a prelude to further biochemical characterization.

scholarly journals Identification of the Golden-2-like transcription factors gene family in Gossypium hirsutum

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12484
Author(s):  
Zilin Zhao ◽  
Jiaran Shuang ◽  
Zhaoguo Li ◽  
Huimin Xiao ◽  
Yuling Liu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Response ◽  
Gossypium Hirsutum ◽  
Gene Family ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Abiotic Stress Response ◽  
Qrt Pcr

Background Golden2-Like (GLK) transcription factors are a type of transcriptional regulator in plants. They play a pivotal role in the plant physiological activity process and abiotic stress response. Methods In this study, the potential function of GLK family genes in Gossypium hirsutum was studied based on genomic identification, phylogenetic analysis, chromosome mapping and cis-regulatory elements prediction. Gene expression of nine key genes were analyzed by qRT-PCR experiments. Results Herein, we identified a total of 146 GhGLK genes in Gossypium hirsutum, which were unevenly distributed on each of the chromosomes. There were significant differences in the number and location of genes between the At sub-genome and the Dt sub-genome. According to the phylogenetic analysis, they were divided into ten subgroups, each of which had very similar number and structure of exons and introns. Some cis-regulatory elements were identified through promoter analysis, including five types of elements related to abiotic stress response, five types of elements related to phytohormone and five types of elements involved in growth and development. Based on public transcriptome data analysis, we identified nine key GhGLKs involved in salt, cold, and drought stress. The qRT-PCR results showed that these genes had different expression patterns under these stress conditions, suggesting that GhGLK genes played an important role in abiotic stress response. This study laid a theoretical foundation for the screening and functional verification of genes related to stress resistance of GLK gene family in cotton.

scholarly journals Genome-wide characterization and evolutionary analysis of heat stress transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.)

2019 ◽  
Author(s):  
Mingjia Tang ◽  
Liang Xu ◽  
Yan Wang ◽  
Wanwan Cheng ◽  
Xiaobo Luo ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Raphanus Sativus ◽  
Crop Production ◽  
Expression Patterns ◽  
Protein Domain ◽  
Evolutionary Analysis ◽  
Raphanus Sativus L

Abstract Background Abiotic stresses due to climate change pose a great threat to crop production. Heat shock transcription factors (HSFs) are vital regulators that play key roles in protecting plants against various abiotic stresses. Therefore, the identification and characterization of HSFs is imperative to dissect the mechanism responsible for plant stress responses. Although the HSF gene family has been extensively studied in several plant species, its characterization, evolutionary history and expression patterns in the radish (Raphanus sativus L.) remain limited. Results In this study, 33 RsHSF genes were obtained from the radish genome, which were classified into three main groups and 12 subgroups based on HSF protein domain structure. Chromosomal localization analysis revealed that 28 of 33 RsHSF genes were located on nine chromosomes, and 10 duplicated RsHSF genes were grouped into eight gene pairs by whole genome duplication (WGD). Moreover, there were 23 or 9 pairs of orthologous HSFs were identified between radish and Arabidopsis or rice, respectively. Comparative analysis revealed a close relationship among radish, Chinese cabbage and Arabidopsis. RNA-seq data showed that eight RsHSF genes, including RsHSF-03, were highly expressed in the leaf, root, cortex, cambium and xylem, results that these genes might be involved in plant growth and development. Further, quantitative real-time polymerase chain reaction (RT-qPCR) indicated that the expression patterns of 12 RsHSF genes varied upon exposure to different abiotic stresses, including heat, salt, and heavy metals. This data indicated that the RsHSFs may be involved in abiotic stress response. Conclusions These results could provide fundamental insights into the characteristics and evolution of the HSF family and facilitate further dissection of the molecular mechanism responsible for radish abiotic stress responses.

scholarly journals Genome-wide characterization and evolutionary analysis of heat stress transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.)

2019 ◽  
Author(s):  
Mingjia Tang ◽  
Liang Xu ◽  
Yan Wang ◽  
Wanwan Cheng ◽  
Xiaobo Luo ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Raphanus Sativus ◽  
Crop Production ◽  
Expression Patterns ◽  
Protein Domain ◽  
Evolutionary Analysis ◽  
Raphanus Sativus L

Abstract Background Abiotic stresses due to climate change pose a great threat to crop production. Heat shock transcription factors (HSFs) are vital regulators that play key roles in protecting plants against various abiotic stresses. Therefore, the identification and characterization of HSFs is imperative to dissect the mechanism responsible for plant stress responses. Although the HSF gene family has been extensively studied in several plant species, its characterization, evolutionary history and expression patterns in the radish (Raphanus sativus L.) remain limited. Results In this study, 33 RsHSF genes were obtained from the radish genome, which were classified into three main groups and 12 subgroups based on HSF protein domain structure. Chromosomal localization analysis revealed that 28 of 33 RsHSF genes were located on nine chromosomes, and 10 duplicated RsHSF genes were grouped into eight gene pairs by whole genome duplication (WGD). Moreover, there were 23 or 9 pairs of orthologous HSFs were identified between radish and Arabidopsis or rice, respectively. Comparative analysis revealed a close relationship among radish, Chinese cabbage and Arabidopsis. RNA-seq data showed that eight RsHSF genes, including RsHSF-03, were highly expressed in the leaf, root, cortex, cambium and xylem, results that these genes might be involved in plant growth and development. Further, quantitative real-time polymerase chain reaction (RT-qPCR) indicated that the expression patterns of 12 RsHSF genes varied upon exposure to different abiotic stresses, including heat, salt, and heavy metals. This data indicated that the RsHSFs may be involved in abiotic stress response. Conclusions These results could provide fundamental insights into the characteristics and evolution of the HSF family and facilitate further dissection of the molecular mechanism responsible for radish abiotic stress responses.

scholarly journals Genome-wide characterization and evolutionary analysis of heat stress transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.)

2019 ◽  
Author(s):  
Mingjia Tang ◽  
Liang Xu ◽  
Yan Wang ◽  
Wanwan Cheng ◽  
Xiaobo Luo ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Raphanus Sativus ◽  
Crop Production ◽  
Expression Patterns ◽  
Protein Domain ◽  
Evolutionary Analysis ◽  
Raphanus Sativus L

Abstract Background Abiotic stresses due to climate change pose a great threat to crop production. Heat shock transcription factors (HSFs) are vital regulators that play key roles in protecting plants against various abiotic stresses. Therefore, the identification and characterization of HSFs is imperative to dissect the mechanism responsible for plant stress responses. Although the HSF gene family has been extensively studied in several plant species, its characterization, evolutionary history and expression patterns in the radish (Raphanus sativus L.) remain limited. Results In this study, 33 RsHSF genes were obtained from the radish genome, which were classified into three main groups and 12 subgroups based on HSF protein domain structure. Chromosomal localization analysis revealed that 28 of 33 RsHSF genes were located on nine chromosomes, and 10 duplicated RsHSF genes were grouped into eight gene pairs by whole genome duplication (WGD). Moreover, there were 23 or 9 pairs of orthologous HSFs were identified between radish and Arabidopsis or rice, respectively. Comparative analysis revealed a close relationship among radish, Chinese cabbage and Arabidopsis. RNA-seq data showed that eight RsHSF genes, including RsHSF-03, were highly expressed in the leaf, root, cortex, cambium and xylem, results that these genes might be involved in plant growth and development. Further, quantitative real-time polymerase chain reaction (RT-qPCR) indicated that the expression patterns of 12 RsHSF genes varied upon exposure to different abiotic stresses, including heat, salt, and heavy metals. This data indicated that the RsHSFs may be involved in abiotic stress response. Conclusions These results could provide fundamental insights into the characteristics and evolution of the HSF family and facilitate further dissection of the molecular mechanism responsible for radish abiotic stress responses.

scholarly journals Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.)

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Mingjia Tang ◽  
Liang Xu ◽  
Yan Wang ◽  
Wanwan Cheng ◽  
Xiaobo Luo ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Heat Shock ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Raphanus Sativus ◽  
Expression Patterns ◽  
Protein Domain ◽  
Evolutionary Analysis ◽  
Heat Shock Transcription Factors

Abstract Background Abiotic stresses due to climate change pose a great threat to crop production. Heat shock transcription factors (HSFs) are vital regulators that play key roles in protecting plants against various abiotic stresses. Therefore, the identification and characterization of HSFs is imperative to dissect the mechanism responsible for plant stress responses. Although the HSF gene family has been extensively studied in several plant species, its characterization, evolutionary history and expression patterns in the radish (Raphanus sativus L.) remain limited. Results In this study, 33 RsHSF genes were obtained from the radish genome, which were classified into three main groups based on HSF protein domain structure. Chromosomal localization analysis revealed that 28 of 33 RsHSF genes were located on nine chromosomes, and 10 duplicated RsHSF genes were grouped into eight gene pairs by whole genome duplication (WGD). Moreover, there were 23 or 9 pairs of orthologous HSFs were identified between radish and Arabidopsis or rice, respectively. Comparative analysis revealed a close relationship among radish, Chinese cabbage and Arabidopsis. RNA-seq data showed that eight RsHSF genes including RsHSF-03, were highly expressed in the leaf, root, cortex, cambium and xylem, indicating that these genes might be involved in plant growth and development. Further, quantitative real-time polymerase chain reaction (RT-qPCR) indicated that the expression patterns of 12 RsHSF genes varied upon exposure to different abiotic stresses including heat, salt, and heavy metals. These results indicated that the RsHSFs may be involved in abiotic stress response. Conclusions These results could provide fundamental insights into the characteristics and evolution of the HSF family and facilitate further dissection of the molecular mechanism responsible for radish abiotic stress responses.

scholarly journals Arabidopsis thaliana Trihelix Transcription factor AST1 mediates abiotic stress tolerance by binding to a novel AGAG-box and some GT motifs

2017 ◽  
Author(s):  
Hongyun Xu ◽  
Lin He ◽  
Yong Guo ◽  
Xinxin Shi ◽  
Dandan Zang ◽  
...  
Keyword(s):  
Reactive Oxygen Species ◽  
Abiotic Stress ◽  
Stress Tolerance ◽  
Stress Responses ◽  
Abiotic Stress Tolerance ◽  
Light Stress ◽  
Reactive Oxygen ◽  
Oxygen Species ◽  
Qrt Pcr ◽  
Helix Loop Helix

AbstractTrihelix transcription factors are characterized by containing a conserved trihelix (helix-loop-helix-loop-helix) domain that bind to GT elements required for light response, play roles in light stress, and also in abiotic stress responses. However, only few of them have been functionally characterised. In the present study, we characterized the function of AST1 (Arabidopsis SIP1 clade Trihelix1) in response to abiotic stress. AST1 shows transcriptional activation activity, and its expression is induced by osmotic and salt stress. The genes regulated by AST1 were identified using qRT-PCR and transcriptome assays. A conserved sequence highly present in the promoters of genes regulated by AST1 was identified, which is bound by AST1, and termed AGAG-box with the sequence [A/G][G/A][A/T]GAGAG. Additionally, AST1 also binds to some GT motifs including GGTAATT, TACAGT, GGTAAAT and GGTAAA, but failed in binding to GTTAC and GGTTAA. Chromatin immunoprecipitation combined with qRT-PCR analysis suggested that AST1 binds to AGAG-box and/or some GT motifs to regulate the expression of stress tolerance genes, resulting in reduced reactive oxygen species, Na+ accumulation, stomatal apertures, lipid peroxidation, cell death and water loss rate, and increased proline content and reactive oxygen species scavenging capability. These physiological changes mediated by AST1 finally improve abiotic stress tolerance.

scholarly journals Genome-wide identification and analysis of WRKY gene family in maize provide insights into regulatory network in response to abiotic stresses

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Wenjing Hu ◽  
Qiaoyu Ren ◽  
Yali Chen ◽  
Guoliang Xu ◽  
Yexiong Qian
Keyword(s):  
Transcription Factor ◽  
Abiotic Stress ◽  
Gene Family ◽  
Stress Responses ◽  
Regulatory Network ◽  
Abiotic Stresses ◽  
Interaction Analysis ◽  
Expression Patterns ◽  
Wrky Transcription Factor ◽  
Rna Seq

Abstract Background The WRKY transcription factor family plays significant roles in biotic and abiotic stress responses, which has been associated with various biological processes in higher plants. However, very little is known regarding the structure and function of WRKY genes in maize. Results In this study, a total of 140 ZmWRKY proteins encoded by 125 ZmWRKY genes were eventually identified in maize. On the basis of features of molecular structure and a comparison of phylogenetic relationships of WRKY transcription factor families from Arabidopsis, rice and maize, all 140 ZmWRKY proteins in maize were divided into three main groups (Groups I, II and III) and the Group II was further classified into five subgroups. The characteristics of exon-intron structure of these putative ZmWRKY genes and conserved protein motifs of their encoded ZmWRKY proteins were also presented respectively, which was in accordance with the group classification results. Promoter analysis suggested that ZmWRKY genes shared many abiotic stress-related elements and hormone-related elements. Gene duplication analysis revealed that the segmental duplication and purifying selection might play a significant role during the evolution of the WRKY gene family in maize. Using RNA-seq data, transcriptome analysis indicated that most of ZmWRKY genes displayed differential expression patterns at different developmental stages of maize. Further, by quantitative real-time PCR analysis, twenty-one ZmWRKY genes were confirmed to respond to two different abiotic stress treatments, suggesting their potential roles in various abiotic stress responses. In addition, RNA-seq dataset was used to conduct weighted gene co-expression network analysis (WGCNA) in order to recognize gene subsets possessing similar expression patterns and highly correlated with each other within different metabolic networks. Further, subcellular localization prediction, functional annotation and interaction analysis of ZmWRKY proteins were also performed to predict their interactions and associations involved in potential regulatory network. Conclusions Taken together, the present study will serve to present an important theoretical basis for further exploring function and regulatory mechanism of ZmWRKY genes in the growth, development, and adaptation to abiotic stresses in maize.

scholarly journals Response of phytohormone mediated plant homeodomain (PHD) family to abiotic stress in upland cotton (Gossypium hirsutum spp.)

2020 ◽  
Author(s):  
Huanhuan Wu ◽  
Lei Zheng ◽  
Ghulam Qanmber ◽  
Mengzhen Guo ◽  
Zhi Wang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Plant Hormones ◽  
Abiotic Stresses ◽  
Growth And Development ◽  
Upland Cotton ◽  
Expression Patterns ◽  
Plant Tolerance ◽  
Qrt Pcr ◽  
A Genome ◽  
Plant Homeodomain

Abstract Background The sequencing and annotations of cotton genomes provide strong theoretical support to reveal more physiological phenomena and functions. Plant homeodomain (PHD) protein family have been reported to be involved in regulating diverse biological processes in plants. However, their functions have not yet been carried out in cotton. Results In this study, we performed a genome-wide analysis of the PHD genes in cotton, including the chromosomal location, phylogenetic relationship, gene structure, and conserved domains. Using a phylogenetic analysis, we divided the 297 PHD genes into five subgroups. The GhPHDs were unevenly distributed across all 26 chromosomes in upland cotton, and whole genome duplication events analyses showed that purifying selection might contributed greatly to the maintenance of function in the GhPHD family. Expression pattern analysis based on RNA-seq data and qRT-PCR results showed that the most of GhPHD genes have significant tissue-specific spatial and temporal expression patterns, indicating GhPHD have multiple functions in growth and development. We further summarized the cis -acting elements in response to abiotic stresses and plant hormones, and treated cotton seedlings with abiotic stresses and plant hormones, respectively. Then, GhPHD gene expression level were detected by qRT-PCR, which indicated that GhPHD could response to stresses and plant hormones. Co-expression network analysis also indicated that GhPHDs were essential for plant growth and development, and phytohormone mediate GhPHD response to abiotic stress can improve plant tolerance to adverse environment. Conclusion This study provides useful information to facilitate the further study of the function of the GhPHD family.

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