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 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 Identification and Characterization of Heat-Shock Transcription Factors in Rubber Tree

Forests ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1157 ◽  
Author(s):  
Yan Li ◽  
Wencai Yu ◽  
Yueyi Chen ◽  
Shuguang Yang ◽  
Shaohua Wu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Heat Shock ◽  
Cold Stress ◽  
Expression Patterns ◽  
Rubber Tree ◽  
Protein Motifs ◽  
Heat Shock Transcription Factors ◽  
Genome Wide ◽  
Cold Tolerant ◽  
Oligomerization Domain

Heat-shock transcription factors (Hsfs) play a pivotal role in the response of plants to various stresses. The present study aimed to characterize the Hsf genes in the rubber tree, a primary global source of natural rubber. In this study, 30 Hsf genes were identified in the rubber tree using genome-wide analysis. They possessed a structurally conserved DNA-binding domain and an oligomerization domain. On the basis of the length of the insert region between HR-A and HR-B in the oligomerization domain, the 30 members were clustered into three classes, Classes A (18), B (10), and C (2). Members within the same class shared highly conserved gene structures and protein motifs. The background expression levels of 11 genes in cold-tolerant rubber-tree clone 93-14 were significantly higher than those in cold-sensitive rubber-tree clone Reken501, while four genes exhibited inverse expression patterns. Upon cold stress, 20 genes were significantly upregulated in 93-114. Of the upregulated genes, HbHsfA2b, HbHsfA3a, and HbHsfA7a were also significantly upregulated in three other cold-tolerant rubber-tree clones at one or more time intervals upon cold stress. Their nuclear localization was verified, and the protein–protein interaction network was predicted. This study provides a basis for dissecting Hsf function in the enhanced cold tolerance of the rubber tree.

scholarly journals Genome-Wide Characterization, Expression Profile Analysis of WRKY Family Genes in Santalum album and Functional Identification of Their Role in Abiotic Stress

2019 ◽  
Vol 20 (22) ◽  
pp. 5676 ◽  
Author(s):  
Haifeng Yan ◽  
Mingzhi Li ◽  
Yuping Xiong ◽  
Jianming Wu ◽  
Jaime A. Teixeira da Silva ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Protein Sequences ◽  
Santalum Album ◽  
Biotic And Abiotic Stress ◽  
Functional Identification ◽  
Wrky Protein

WRKY proteins are a large superfamily of transcription factors that are involved in diverse biological processes including development, as well as biotic and abiotic stress responses in plants. WRKY family proteins have been extensively characterized and analyzed in many plant species, including Arabidopsis, rice, and poplar. However, knowledge on WRKY transcription factors in Santalum album is scarce. Based on S. album genome and transcriptome data, 64 SaWRKY genes were identified in this study. A phylogenetic analysis based on the structures of WRKY protein sequences divided these genes into three major groups (I, II, III) together with WRKY protein sequences from Arabidopsis. Tissue-specific expression patterns showed that 37 SaWRKY genes were expressed in at least one of five tissues (leaves, roots, heartwood, sapwood, or the transition zone), while the remaining four genes weakly expressed in all of these tissues. Analysis of the expression profiles of the 42 SaWRKY genes after callus was initiated by salicylic acid (SA) and methyl jasmonate (MeJA) revealed that 25 and 24 SaWRKY genes, respectively, were significantly induced. The function of SaWRKY1, which was significantly up-regulated by SA and MeJA, was analyzed. SaWRKY1 was localized in the nucleus and its overexpression improved salt tolerance in transgenic Arabidopsis. Our study provides important information to further identify the functions of SaWRKY genes and to understand the roles of SaWRKY family genes involved in the development and in SA- and MeJA-mediated stress responses.

scholarly journals The Role of Stress-Responsive Transcription Factors in Modulating Abiotic Stress Tolerance in Plants

Agronomy ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 788 ◽  
Author(s):  
Youngdae Yoon ◽  
Deok Hyun Seo ◽  
Hoyoon Shin ◽  
Hui Jin Kim ◽  
Chul Min Kim ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Tolerance ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Crop Production ◽  
Global Climate ◽  
Abiotic Stress Tolerance ◽  
Plant Responses ◽  
Plant Tolerance

Abiotic stresses, such as drought, high temperature, and salinity, affect plant growth and productivity. Furthermore, global climate change may increase the frequency and severity of abiotic stresses, suggesting that development of varieties with improved stress tolerance is critical for future sustainable crop production. Improving stress tolerance requires a detailed understanding of the hormone signaling and transcriptional pathways involved in stress responses. Abscisic acid (ABA) and jasmonic acid (JA) are key stress-response hormones in plants, and some stress-responsive transcription factors such as ABFs and MYCs function as direct components of ABA and JA signaling, playing a pivotal role in plant tolerance to abiotic stress. In addition, extensive studies have identified other stress-responsive transcription factors belonging to the NAC, AP2/ERF, MYB, and WRKY families that mediate plant response and tolerance to abiotic stress. These suggest that transcriptional regulation of stress-responsive genes is an essential step to determine the mechanisms underlying plant stress responses and tolerance to abiotic stress, and that these transcription factors may be important targets for development of crops with enhanced abiotic stress tolerance. In this review, we briefly describe the mechanisms underlying plant abiotic stress responses, focusing on ABA and JA metabolism and signaling pathways. We then summarize the diverse array of transcription factors involved in plant responses to abiotic stress, while noting their potential applications for improvement of stress tolerance.

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 Transcription factors involved in abiotic stress responses in maize (Zea mays L.) and their roles in enhanced productivity in the post genomics era

2019 ◽  
Author(s):  
Roy Njoroge Kimotho ◽  
Elamin Hafiz Baillo ◽  
Zhengbin Zhang
Keyword(s):  
Zea Mays ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Target Genes ◽  
Animal Feed ◽  
Specific Transcription Factor ◽  
Transcription Factor Genes

Background: Maize (Zea mays L.) is a principal cereal crop cultivated worldwide for human food, animal feed, and more recently as a source of biofuel. However, as a direct consequence of water insufficiency and climate change, frequent occurrences of both biotic and abiotic stresses have been reported in different regions around the world, and recently, this has become a major threat in increasing global maize yields. Plants respond to abiotic stresses by utilizing the activity of transcription factors, which are families of genes coding for specific transcription factor proteins whose target genes form a regulon which is involved in the repression/ activation of genes associated with abiotic stress responses. Therefore, it is of uttermost importance to have a systematic study on each family of the transcription factors, the downstream target genes they regulate, and the specific transcription factor genes which are involved in multiple abiotic stress responses in maize and other main crops. Method: In this review, the main transcription factor families, the specific transcription factor genes and their regulons which are involved in abiotic stress regulation will be momentarily discussed. Great emphasis will be given on maize abiotic stress improvement throughout this review, although other examples from other plants like rice, Arabidopsis, wheat, and barley will be used. Results: We have described in detail the main transcription factor families in maize which take part in abiotic stress responses together with their regulons. Furthermore, we have also briefly described the utilization of high-efficiency technologies in the study and characterization of TFs involved in the abiotic stress regulatory networks in plants with an emphasis on increasing maize production. Examples of these technologies include next-generation sequencing, microarray analysis, machine learning and RNA-Seq technology. Conclusion: In conclusion, it is hoped that all the information provided in this review may in time contribute to the use of TF genes in the research, breeding, and development of new abiotic stress tolerant maize cultivars.

scholarly journals Transcription factors involved in abiotic stress responses in maize (Zea mays L.) and their roles in enhanced productivity in the post genomics era

2019 ◽  
Author(s):  
Roy Njoroge Kimotho ◽  
Elamin Hafiz Baillo ◽  
Zhengbin Zhang
Keyword(s):  
Zea Mays ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Target Genes ◽  
Animal Feed ◽  
Specific Transcription Factor ◽  
Transcription Factor Genes

Background: Maize (Zea mays L.) is a principal cereal crop cultivated worldwide for human food, animal feed, and more recently as a source of biofuel. However, as a direct consequence of water insufficiency and climate change, frequent occurrences of both biotic and abiotic stresses have been reported in different regions around the world, and recently, this has become a major threat in increasing global maize yields. Plants respond to abiotic stresses by utilizing the activity of transcription factors, which are families of genes coding for specific transcription factor proteins whose target genes form a regulon which is involved in the repression/ activation of genes associated with abiotic stress responses. Therefore, it is of uttermost importance to have a systematic study on each family of the transcription factors, the downstream target genes they regulate, and the specific transcription factor genes which are involved in multiple abiotic stress responses in maize and other main crops. Method: In this review, the main transcription factor families, the specific transcription factor genes and their regulons which are involved in abiotic stress regulation will be momentarily discussed. Great emphasis will be given on maize abiotic stress improvement throughout this review, although other examples from other plants like rice, Arabidopsis, wheat, and barley will be used. Results: We have described in detail the main transcription factor families in maize which take part in abiotic stress responses together with their regulons. Furthermore, we have also briefly described the utilization of high-efficiency technologies in the study and characterization of TFs involved in the abiotic stress regulatory networks in plants with an emphasis on increasing maize production. Examples of these technologies include next-generation sequencing, microarray analysis, machine learning and RNA-Seq technology. Conclusion: In conclusion, it is hoped that all the information provided in this review may in time contribute to the use of TF genes in the research, breeding, and development of new abiotic stress tolerant maize cultivars.

scholarly journals A member of wheat class III peroxidase gene family, TaPRX-2A, enhanced the tolerance of salt stress

2020 ◽  
Author(s):  
Peisen Su ◽  
Jun Yan ◽  
Wen Li ◽  
Liang Wang ◽  
Jinxiao Zhao ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Gene Family ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Evolutionary Model ◽  
Evolutionary Analysis ◽  
Class Iii ◽  
Expression Levels ◽  
Stress Related Genes

Abstract Background: Salt and drought are the main abiotic stresses that restrict the yield of crops. Peroxidases (PRXs) are involved in various abiotic stress responses. Furthermore, only few wheat PRXs have been characterized in the mechanism of the abiotic stress response.Results: In this study, a novel wheat peroxidase (PRX) gene named TaPRX-2A, a member of wheat class III PRX gene family, was cloned and its response to salt stress was characterized. Based on the identification and evolutionary analysis of class III PRXs in 12 plants, we proposed an evolutionary model for TaPRX-2A, suggesting that occurrence of some exon fusion events during evolution. We also detected the positive selection of PRX domain in 13 PRXs involving our evolutionary model, and found 2 or 6 positively selected sites during TaPRX-2A evolution. Quantitative reverse transcription–polymerase chain reaction (qRT–PCR) results showed that TaPRX-2A exhibited relatively higher expression levels in root tissue than those exhibited in leaf and stem tissues. TaPRX-2A expression was also induced by abiotic stresses and hormone treatments such as polyethylene glycol 6000, NaCl, hydrogen peroxide (H2O2), salicylic acid (SA), methyljasmonic acid (MeJA) and abscisic acid (ABA). Transgenic wheat plants with overexpression of TaPRX-2A showed higher tolerance to salt stress than wild-type (WT) plants. Confocal microscopy revealed that TaPRX-2A-eGFP was mainly localized in cell nuclei. Survival rate, relative water content, and shoot length were higher in TaPRX-2A-overexpressing wheat than in the WT wheat, whereas root length was not significantly different. The activities of s superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were enhanced in TaPRX-2A-overexpressing wheat compared with those in the WT wheat, resulting in the reduction of reactive oxygen species (ROS) accumulation and malondialdehyde (MDA) content. The expression levels of downstream stress-related genes showed that RD22, TLP4, ABAI, GST22, FeSOD, and CAT exhibited higher expressions in TaPRX-2A-overexpressing wheat than in WT under salt stress.Conclusions: The results show that TaPRX-2A plays a positive role in the response to salt stress by scavenging ROS and regulating stress-related genes.

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