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Khatun MS, Islam MSU, Shing P, Zohra FT, Rashid SB, Rahman SM, Sarkar MAR. Genome-wide identification and characterization of FORMIN gene family in potato (Solanum tuberosum L.) and their expression profiles in response to drought stress condition. PLoS One 2024; 19:e0309353. [PMID: 39186738 DOI: 10.1371/journal.pone.0309353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 08/11/2024] [Indexed: 08/28/2024] Open
Abstract
Formin proteins, characterized by the FH2 domain, are critical in regulating actin-driven cellular processes and cytoskeletal dynamics during abiotic stress. However, no genome-wide analysis of the formin gene family has yet to be conducted in the economically significant plant potato (Solanum tuberosum L.). In this study, 26 formin genes were identified and characterized in the potato genome (named as StFH), each containing the typical FH2 domain and distributed across the ten chromosomes. The StFH was categorized into seven subgroups (A-G) and the gene structure and motif analysis demonstrated higher structural similarities within the subgroups. Besides, the StFH exhibited ancestry and functional similarities with Arabidopsis. The Ka/Ks ratio indicated that StFH gene pairs were evolving through purifying selection, with five gene pairs exhibiting segmental duplications and two pairs exhibiting tandem duplications. Subcellular localization analysis suggested that most of the StFH genes were located in the chloroplast and plasma membrane. Moreover, 54 cis-acting regulatory elements (CAREs) were identified in the promoter regions, some of which were associated with stress responses. According to gene ontology analysis, the majority of the StFH genes were involved in biological processes, with 63 out of 74 GO terms affecting actin polymerization. Six major transcription factor families, including bZIP, C2H2, ERF, GATA, LBD, NAC, and HSF, were identified that were involved in the regulation of StFH genes in various abiotic stresses, including drought. Further, the 60 unique microRNAs targeted 24 StFH by regulating gene expression in response to drought stress were identified. The expression of StFH genes in 14 different tissues, particularly in drought-responsive tissues such as root, stem, shoot apex, and leaf, underscores their significance in managing drought stress. RNA-seq analysis of the drought-resistant Qingshu No. 9 variety revealed the potential role of up-regulated genes, including StFH2, StFH10, StFH19, and StFH25, in alleviating drought stress. Overall, these findings provide crucial insights into the response to drought stress in potatoes and can be utilized in breeding programs to develop potato cultivars with enhanced drought-tolerant traits.
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Affiliation(s)
- Mst Sumaiya Khatun
- Laboratory of Functional Genomics and Proteomics, Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Shohel Ul Islam
- Laboratory of Functional Genomics and Proteomics, Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Pollob Shing
- Laboratory of Functional Genomics and Proteomics, Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Fatema Tuz Zohra
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Shuraya Beente Rashid
- Laboratory of Functional Genomics and Proteomics, Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Shaikh Mizanur Rahman
- Laboratory of Functional Genomics and Proteomics, Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Abdur Rauf Sarkar
- Laboratory of Functional Genomics and Proteomics, Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
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Xia P, Zhang Y, Zhang X. The Potential Relevance of PnDREBs to Panax notoginseng Nitrogen Sensitiveness. Biochem Genet 2024; 62:2631-2651. [PMID: 37999875 DOI: 10.1007/s10528-023-10567-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023]
Abstract
The dehydration response element-binding (DREB) transcription factor is a subfamily of AP2/ERF. It actively responds to various abiotic stresses in plants. As one of the representative plants, Panax notoginseng is sensitive to Nitrogen (N). Here, bioinformatics analysis, the identification, chromosomal location, phylogeny, structure, cis-acting elements, and collinearity of PnDREBs were analyzed. In addition, the expression levels of PnDREBs were analyzed by quantitative reverse transcription PCR. In this study, 54 PnDREBs were identified and defined as PnDREB1 to PnDREB54. They were divided into 6 subfamilies (A1-A6). And 44 PnDREBs were irregularly distributed on 10 of 12 chromosomes. Each group showed specific motifs and exon-intron structures. By predicting cis-acting elements, the PnDREBs may participate in biotic stress, abiotic stress, and hormone induction. Collinear analysis showed that fragment duplication events were beneficial to the amplification and evolution of PnDREB members. The expression of PnDREBs showed obvious tissue specificity in its roots, flowers, and leaves. In addition, under the action of ammonium nitrogen and nitrate nitrogen at the 15 mM level, the level of PnDREB genes expression in roots varied to different degrees. In this study, we identified and characterized PnDREBs for the first time, and analyzed that PnDREBs may be related to the response of P. Notoginseng to N sensitiveness. The results of this study lay a foundation for further research on the function of PnDREBs in P. Notoginseng.
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Affiliation(s)
- Pengguo Xia
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China.
| | - Yan Zhang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Xuemin Zhang
- Tianjin TASLY Modern Chinese Medicine Resources Co., Ltd., Tianjin, 300402, People's Republic of China
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Wang D, Zeng Y, Yang X, Nie S. Characterization of DREB family genes in Lotus japonicus and LjDREB2B overexpression increased drought tolerance in transgenic Arabidopsis. BMC PLANT BIOLOGY 2024; 24:497. [PMID: 39075356 PMCID: PMC11285619 DOI: 10.1186/s12870-024-05225-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 05/30/2024] [Indexed: 07/31/2024]
Abstract
BACKGROUND Drought stress affects plant growth and development. DREB proteins play important roles in modulating plant growth, development, and stress responses, particularly under drought stress. To study the function of DREB transcription factors (TFs), we screened key DREB-regulating TFs for drought in Lotus japonicus. RESULTS Forty-two DREB TFs were identified, and phylogenetic analysis of proteins from L. japonicus classified them into five subfamilies (A1, A2, A4, A5, A6). The gene motif composition of the proteins is conserved within the same subfamily. Based on the cis-acting regulatory element analysis, we identified many growth-, hormone-, and stress-responsive elements within the promoter regions of DREB. We further analyzed the expression pattern of four genes in the A2 subfamily in response to drought stress. We found that the expression of most of the LjDREB A2 subfamily genes, especially LjDREB2B, was induced by drought stress. We further generated LjDREB2B overexpression transgenic Arabidopsis plants. Under drought stress, the growth of wild-type (WT) and overexpressing LjDREB2B (OE) Arabidopsis lines was inhibited; however, OE plants showed better growth. The malondialdehyde content of LjDREB2B overexpressing lines was lower than that of the WT plants, whereas the proline content and antioxidant enzyme activities in the OE lines were significantly higher than those in the WT plants. Furthermore, after drought stress, the expression levels of AtP5CS1, AtP5CS2, AtRD29A, and AtRD29B in the OE lines were significantly higher than those in the WT plants. CONCLUSIONS Our results facilitate further functional analysis of L. japonicus DREB. LjDREB2B overexpression improves drought tolerance in transgenic Arabidopsis. These results indicate that DREB holds great potential for the genetic improvement of drought tolerance in L. japonicus.
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Affiliation(s)
- Dan Wang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, China
| | - Yuanyuan Zeng
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, China
| | - Xiuxiu Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, China
| | - Shuming Nie
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, China.
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Hu X, Liang J, Wang W, Cai C, Ye S, Wang N, Han F, Wu Y, Zhu Q. Comprehensive genome-wide analysis of the DREB gene family in Moso bamboo (Phyllostachys edulis): evidence for the role of PeDREB28 in plant abiotic stress response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1248-1270. [PMID: 37566437 DOI: 10.1111/tpj.16420] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/16/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023]
Abstract
Dehydration response element binding (DREB) proteins are vital for plant abiotic stress responses, but the understanding of DREBs in bamboo, an important sustainable non-timber forest product, is limited. Here we conducted a comprehensive genome-wide analysis of the DREB gene family in Moso bamboo, representing the most important running bamboo species in Asia. In total, 44 PeDREBs were identified, and information on their gene structures, protein motifs, phylogenetic relationships, and stress-related cis-regulatory elements (CREs) was provided. Based on the bioinformatical analysis, we further analyzed PeDREBs from the A5 group and found that four of five PeDREB transcripts were induced by salt, drought, and cold stresses, and their proteins could bind to stress-related CREs. Among these, PeDREB28 was selected as a promising candidate for further functional characterization. PeDREB28 is localized in nucleus, has transcriptional activation activity, and could bind to the DRE- and coupling element 1- (CE1) CREs. Overexpression of PeDREB28 in Arabidopsis and bamboo improved plant abiotic stress tolerance. Transcriptomic analysis showed that broad changes due to the overexpression of PeDREB28. Furthermore, 628 genes that may act as the direct PeDREB28 downstream genes were identified by combining DAP-seq and RNA-seq analysis. Moreover, we confirmed that PeDREB28 could bind to the promoter of pyrabactin-resistance-like gene (DlaPYL3), which is a homolog of abscisic acid receptor in Arabidopsis, and activates its expression. In summary, our study provides important insights into the DREB gene family in Moso bamboo, and contributes to their functional verification and genetic engineering applications in the future.
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Affiliation(s)
- Xin Hu
- Basic Forestry and Proteomics Center (BFPC), HaiXia Institute for Science and Technology, College of Forestry, Fujian Agriculture and Forestry University, 350002, Fujian, China
| | - Jianxiang Liang
- Basic Forestry and Proteomics Center (BFPC), HaiXia Institute for Science and Technology, College of Forestry, Fujian Agriculture and Forestry University, 350002, Fujian, China
| | - Wenjia Wang
- Basic Forestry and Proteomics Center (BFPC), HaiXia Institute for Science and Technology, College of Forestry, Fujian Agriculture and Forestry University, 350002, Fujian, China
| | - Changyang Cai
- Basic Forestry and Proteomics Center (BFPC), HaiXia Institute for Science and Technology, College of Forestry, Fujian Agriculture and Forestry University, 350002, Fujian, China
| | - Shanwen Ye
- Basic Forestry and Proteomics Center (BFPC), HaiXia Institute for Science and Technology, College of Forestry, Fujian Agriculture and Forestry University, 350002, Fujian, China
| | - Nannan Wang
- Basic Forestry and Proteomics Center (BFPC), HaiXia Institute for Science and Technology, College of Forestry, Fujian Agriculture and Forestry University, 350002, Fujian, China
| | - Fangying Han
- Basic Forestry and Proteomics Center (BFPC), HaiXia Institute for Science and Technology, College of Forestry, Fujian Agriculture and Forestry University, 350002, Fujian, China
| | - Yuxin Wu
- Basic Forestry and Proteomics Center (BFPC), HaiXia Institute for Science and Technology, College of Forestry, Fujian Agriculture and Forestry University, 350002, Fujian, China
| | - Qiang Zhu
- Basic Forestry and Proteomics Center (BFPC), HaiXia Institute for Science and Technology, College of Forestry, Fujian Agriculture and Forestry University, 350002, Fujian, China
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Jing Q, Chen A, Lv Z, Dong Z, Wang L, Meng X, Feng Y, Wan Y, Su C, Cui Y, Xu W, Hou H, Zhu X. Systematic Analysis of Galactinol Synthase and Raffinose Synthase Gene Families in Potato and Their Expression Patterns in Development and Abiotic Stress Responses. Genes (Basel) 2023; 14:1344. [PMID: 37510251 PMCID: PMC10379439 DOI: 10.3390/genes14071344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 06/19/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023] Open
Abstract
Raffinose family oligosaccharides (RFOs) are very important for plant growth, development, and abiotic stress tolerance. Galactinol synthase (GolS) and raffinose synthase (RFS) are critical enzymes involved in RFO biosynthesis. However, the whole-genome identification and stress responses of their coding genes in potato remain unexplored. In this study, four StGolS and nine StRFS genes were identified and classified into three and five subgroups, respectively. Remarkably, a total of two StGolS and four StRFS genes in potato were identified to form collinear pairs with those in both Arabidopsis and tomato, respectively. Subsequent analysis revealed that StGolS4 exhibited significantly high expression levels in transport-related tissues, PEG-6000, and ABA treatments, with remarkable upregulation under salt stress. Additionally, StRFS5 showed similar responses to StGolS4, but StRFS4 and StRFS8 gene expression increased significantly under salt treatment and decreased in PEG-6000 and ABA treatments. Overall, these results lay a foundation for further research on the functional characteristics and molecular mechanisms of these two gene families in response to ABA, salt, and drought stresses, and provide a theoretical foundation and new gene resources for the abiotic-stress-tolerant breeding of potato.
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Affiliation(s)
- Quankai Jing
- School of Horticulture, Anhui Agricultural University, Hefei 230000, China
| | - Airu Chen
- School of Horticulture, Anhui Agricultural University, Hefei 230000, China
| | - Zhaoyan Lv
- School of Horticulture, Anhui Agricultural University, Hefei 230000, China
| | - Zhihao Dong
- School of Horticulture, Anhui Agricultural University, Hefei 230000, China
| | - Lixia Wang
- School of Horticulture, Anhui Agricultural University, Hefei 230000, China
| | - Xiaoke Meng
- School of Horticulture, Anhui Agricultural University, Hefei 230000, China
| | - Yue Feng
- School of Horticulture, Anhui Agricultural University, Hefei 230000, China
| | - Yu Wan
- School of Horticulture, Anhui Agricultural University, Hefei 230000, China
| | - Chengyun Su
- School of Horticulture, Anhui Agricultural University, Hefei 230000, China
| | - Yanjie Cui
- School of Horticulture, Anhui Agricultural University, Hefei 230000, China
| | - Wenjuan Xu
- School of Horticulture, Anhui Agricultural University, Hefei 230000, China
| | - Hualan Hou
- School of Horticulture, Anhui Agricultural University, Hefei 230000, China
| | - Xiaobiao Zhu
- School of Horticulture, Anhui Agricultural University, Hefei 230000, China
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Su J, Song S, Wang Y, Zeng Y, Dong T, Ge X, Duan H. Genome-wide identification and expression analysis of DREB family genes in cotton. BMC PLANT BIOLOGY 2023; 23:169. [PMID: 36997878 PMCID: PMC10061749 DOI: 10.1186/s12870-023-04180-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Dehydration responsive element-binding (DREB) transcription factors are widely present in plants, and involve in signalling transduction, plant growth and development, and stress response. DREB genes have been characterized in multiple species. However, only a few DREB genes have been studied in cotton, one of the most important fibre crops. Herein, the genome‑wide identification, phylogeny, and expression analysis of DREB family genes are performed in diploid and tetraploid cotton species. RESULTS In total, 193, 183, 80, and 79 putative genes containing the AP2 domain were identified using bioinformatics approaches in G. barbadense, G. hirsutum, G. arboretum, and G. raimondii, respectively. Phylogenetic analysis showed that based on the categorization of Arabidopsis DREB genes, 535 DREB genes were divided into six subgroups (A1-A6) by using MEGA 7.0. The identified DREB genes were distributed unevenly across 13/26 chromosomes of A and/or D genomes. Synteny and collinearity analysis confirmed that during the evolution, the whole genome duplications, segmental duplications, and/or tandem duplications occurred in cotton DREB genes, and then DREB gene family was further expanded. Further, the evolutionary trees with conserved motifs, cis-acting elements, and gene structure of cotton DREB gene family were predicted, and these results suggested that DREB genes might be involved in the hormone and abiotic stresses responses. The subcellular localization showed that in four cotton species, DREB proteins were predominantly located in the nucleus. Further, the analysis of DREB gene expression was carried out by real-time quantitative PCR, confirming that the identified DREB genes of cotton were involved in response to early salinity and osmotic stress. CONCLUSIONS Collectively, our results presented a comprehensive and systematic understanding in the evolution of cotton DREB genes, and demonstrated the potential roles of DREB family genes in stress and hormone response.
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Affiliation(s)
- Jiuchang Su
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Shanglin Song
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Yiting Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Yunpeng Zeng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Tianyu Dong
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Hongying Duan
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
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Maqsood H, Munir F, Amir R, Gul A. Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family in Solanum lycopersicum. FRONTIERS IN PLANT SCIENCE 2022; 13:1031679. [PMID: 36507398 PMCID: PMC9731513 DOI: 10.3389/fpls.2022.1031679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/25/2022] [Indexed: 06/12/2023]
Abstract
Tomato is a drought-sensitive crop which has high susceptibility to adverse climatic changes. Dehydration-responsive element-binding (DREB) are significant plant transcription factors that have a vital role in regulating plant abiotic stress tolerance by networking with DRE/CRT cis-regulatory elements in response to stresses. In this study, bioinformatics analysis was performed to conduct the genome-wide identification and characterization of DREB genes and promoter elements in Solanum lycopersicum. In genome-wide coverage, 58 SlDREB genes were discovered on 12 chromosomes that justified the criteria of the presence of AP2 domain as conserved motifs. Intron-exon organization and motif analysis showed consistency with phylogenetic analysis and confirmed the absence of the A3 class, thus dividing the SlDREB genes into five categories. Gene expansion was observed through tandem duplication and segmental duplication gene events in SlDREB genes. Ka/Ks values were calculated in ortholog pairs that indicated divergence time and occurrence of purification selection during the evolutionary period. Synteny analysis demonstrated that 32 out of 58 and 47 out of 58 SlDREB genes were orthologs to Arabidopsis and Solanum tuberosum, respectively. Subcellular localization predicted that SlDREB genes were present in the nucleus and performed primary functions in DNA binding to regulate the transcriptional processes according to gene ontology. Cis-acting regulatory element analysis revealed the presence of 103 motifs in 2.5-kbp upstream promoter sequences of 58 SlDREB genes. Five representative SlDREB proteins were selected from the resultant DREB subgroups for 3D protein modeling through the Phyre2 server. All models confirmed about 90% residues in the favorable region through Ramachandran plot analysis. Moreover, active catalytic sites and occurrence in disorder regions indicated the structural and functional flexibility of SlDREB proteins. Protein association networks through STRING software suggested the potential interactors that belong to different gene families and are involved in regulating similar functional and biological processes. Transcriptome data analysis has revealed that the SlDREB gene family is engaged in defense response against drought and heat stress conditions in tomato. Overall, this comprehensive research reveals the identification and characterization of SlDREB genes that provide potential knowledge for improving abiotic stress tolerance in tomato.
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Affiliation(s)
| | - Faiza Munir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
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Khurshid K, Akram A, Ali A, Munir F, Gul A, Haider G, Qayyum Z, Amir R. Genome wide identification and characterization of nodulation related genes in Arachis hypogaea. PLoS One 2022; 17:e0273768. [PMID: 36084097 PMCID: PMC9462762 DOI: 10.1371/journal.pone.0273768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 08/16/2022] [Indexed: 11/18/2022] Open
Abstract
Nitrogen is an important plant nutrient that has a significant role in crop yield. Hence, to fulfill the needs of sustainable agriculture, it is necessary to improve biological nitrogen fixation in leguminous crops. Nod inducing gene families plays a crucial role in the interaction between rhizobia and legumes, leading to biological nitrogen fixation. However, nod inducing genes identification and characterization has not yet been performed in Arachis hypogaea. In this study, identification and genome-wide analysis of nod inducing genes are performed so that to explore their potential functions in the Arachis hypogaea for the first time. Nod genes were comprehensively analyzed by phylogenetic clustering analysis, gene structure determination, detection of conserved motifs, subcellular localization, conserved motifs, cis-acting elements and promoter region analysis. This study identified 42 Nod inducing genes in Arachis hypogaea, their sequences were submitted to NCBI and accession numbers were obtained. Potential involvement of these genes in biological nitrogen fixation has been unraveled, such as, phylogenetic analysis revealed that nod inducing genes evolved independently in Arachis hypogaea, the amino acid structures exhibited 20 highly conserved motifs, the proteins are present at different locations in cells and the gene structures revealed that all the genes are full-length genes with upstream intronic regions. Further, the promoter analysis determined a large number of cis-regulatory elements involved in nodulation. Moreover, this study not only provides identification and characterization of genes underlying developmental and functional stages of nodulation and biological nitrogen fixation but also lays the foundation for further revelation of nod inducing gene family. Besides, identification and structural analysis of these genes in Arachis hypogaea may provide a theoretical basis for the study of evolutionary relationships in future analysis.
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Affiliation(s)
- Kiran Khurshid
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Anum Akram
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Ahmad Ali
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Faiza Munir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Alvina Gul
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Ghulam Haider
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Zuhra Qayyum
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Rabia Amir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
- * E-mail: ,
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Pan R, Buitrago S, Peng Y, Fatouh Abou-Elwafa S, Wan K, Liu Y, Wang R, Yang X, Zhang W. Genome-wide identification of cold-tolerance genes and functional analysis of IbbHLH116 gene in sweet potato. Gene X 2022; 837:146690. [PMID: 35738441 DOI: 10.1016/j.gene.2022.146690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/05/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022] Open
Abstract
Sweet potato (Ipomoea batatas L.) originated from South America; therefore, it is vulnerable to low temperature. Here, the evolutionary analysis of 22 cold-responsive genes in 35 plant species revealed that the identified MYC-type basic helix-loop-helix (bHLH) transcription factors exhibit diverse structures. We found that the number of bHLH gene family members was significantly lower than that of cold-tolerant species. We further systematically evaluated the gene structure, promoter analysis, synteny analysis, and expression pattern of 28 bHLH gene family members in sweet potato. The basic helix-loop-helix protein 116 (IbbHLH116) has the closest phylogeny to the AtICE1 protein of A. thaliana. However, the IbbHLH116 protein from cold-tolerant variety FS18 showed a 37.90% of sequence homology with AtICE1 protein. Subcellular localization analysis showed that IbbHLH116 is localized in the nucleus. The transcripts of IbbHLH116 were highly accumulated in cold-tolerant genotype FS18, particularly in new leaves and stems, compared to the cold-sensitive genotype NC1 under cold stress. Overexpression of IbbHLH116 in the wild type (Col-0) A. thaliana significantly enhanced cold tolerance in transgenic plants by regulating activities of oxidative protective enzymes, such as peroxidase (POD), superoxide dismutase (SOD), and the contents of malondialdehyde (MDA), proline and soluble proteins. Moreover, overexpression of IbbHLH116 in ice1 mutant A. thaliana fully rescued the cold-sensitive phenotype by promoting the expression of C-repeat binding factors 3 (CBF3). Overexpression of IbbHLH116 in the sweet potato callus also induced the expression of CBF3 under low temperature. These results imply that IbbHLH116 can perform the function of the ICE1 gene in conferring cold tolerance in sweet potato.
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Affiliation(s)
- Rui Pan
- Research Center of Crop Stresses Resistance Technologies/ Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou 434025, China
| | - Sebastian Buitrago
- Research Center of Crop Stresses Resistance Technologies/ Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou 434025, China
| | - Ying Peng
- Research Center of Crop Stresses Resistance Technologies/ Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou 434025, China
| | | | - Kui Wan
- Research Center of Crop Stresses Resistance Technologies/ Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou 434025, China
| | - Yi Liu
- Research Center of Crop Stresses Resistance Technologies/ Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou 434025, China; Hubei Sweet potato Engineering and Technology Research Centre, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Rongsen Wang
- Research Center of Crop Stresses Resistance Technologies/ Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou 434025, China
| | - Xinsun Yang
- Hubei Sweet potato Engineering and Technology Research Centre, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Wenying Zhang
- Research Center of Crop Stresses Resistance Technologies/ Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou 434025, China.
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ain-Ali QU, Mushtaq N, Amir R, Gul A, Tahir M, Munir F. Genome-wide promoter analysis, homology modeling and protein interaction network of Dehydration Responsive Element Binding (DREB) gene family in Solanum tuberosum. PLoS One 2021; 16:e0261215. [PMID: 34914734 PMCID: PMC8675703 DOI: 10.1371/journal.pone.0261215] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/27/2021] [Indexed: 12/24/2022] Open
Abstract
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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Affiliation(s)
- Qurat-ul ain-Ali
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Nida Mushtaq
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Rabia Amir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Alvina Gul
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Muhammad Tahir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Faiza Munir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
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