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Zhao S, Qing J, Yang Z, Tian T, Yan Y, Li H, Bai Y. Genome-Wide Identification and Expression Analysis of the HSF Gene Family in Ammopiptanthus mongolicus. Curr Issues Mol Biol 2024; 46:11375-11393. [PMID: 39451558 PMCID: PMC11505871 DOI: 10.3390/cimb46100678] [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: 09/02/2024] [Revised: 10/05/2024] [Accepted: 10/10/2024] [Indexed: 10/26/2024] Open
Abstract
Ammopiptanthus mongolicus is an ancient remnant species from the Mediterranean displaying characteristics such as high-temperature tolerance, drought resistance, cold resistance, and adaptability to impoverished soil. In the case of high-temperature tolerance, heat shock transcription factors (HSFs) are integral transcriptional regulatory proteins exerting a critical role in cellular processes. Despite extensive research on the HSF family across various species, there has been no analysis specifically focused on A. mongolicus. In this study, we identified 24 members of the AmHSF gene family based on the genome database of A. mongolicus, which were unevenly distributed over 9 chromosomes. Phylogenetic analysis showed that these 24 members can be categorized into 5 primary classes consisting of a total of 13 subgroups. Analysis of the physical and chemical properties revealed significant diversity among these proteins. With the exception of the AmHSFB3 protein, which is localized in the cytoplasm, all other AmHSF proteins were found to be situated in the nucleus. Comparison of amino acid sequences revealed that all AmHSF proteins contain a conserved DNA-binding domains structure, and the DNA-binding domains and oligomerization domains of the AmHSF gene exhibit conservation with counterparts across diverse species; we investigated the collinearity of AmHSF genes in relation to those of three other representative species. Through GO enrichment analysis, evidence emerged that AmHSF genes are involved in heat stress responses and may be involved in multiple transcriptional regulatory pathways that coordinate plant growth and stress responses. Finally, through a comprehensive analysis using transcriptome data, we examined the expression levels of 24 AmHSFs under 45 °C. The results revealed significant differences in the expression profiles of AmHSFs at different time intervals during exposure to high temperatures, highlighting their crucial role in responding to heat stress. In summary, these results provide a better understanding of the role and regulatory mechanisms of HSF in the heat stress response of A. mongolicus, meanwhile also establishing a foundation for further exploration of the biological functions of AmHSF in the adversity response of A. mongolicus.
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Affiliation(s)
- Shuai Zhao
- College of Forestry, Inner Mongolia Agricultural University, Hohhot 010019, China; (S.Z.)
| | - Jun Qing
- College of Forestry, Inner Mongolia Agricultural University, Hohhot 010019, China; (S.Z.)
| | - Zhiguo Yang
- Institute of Desertification Studies, Inner Mongolia Academy of Forestry, Hohhot 010019, China
| | - Tian Tian
- College of Forestry, Inner Mongolia Agricultural University, Hohhot 010019, China; (S.Z.)
| | - Yanqiu Yan
- College of Forestry, Inner Mongolia Agricultural University, Hohhot 010019, China; (S.Z.)
| | - Hui Li
- College of Forestry, Inner Mongolia Agricultural University, Hohhot 010019, China; (S.Z.)
| | - Yu’e Bai
- College of Forestry, Inner Mongolia Agricultural University, Hohhot 010019, China; (S.Z.)
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Hao X, He S. Genome-wide identification, classification and expression analysis of the heat shock transcription factor family in Garlic (Allium sativum L.). BMC PLANT BIOLOGY 2024; 24:421. [PMID: 38760734 PMCID: PMC11102281 DOI: 10.1186/s12870-024-05018-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 04/12/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND The heat shock transcription factor (HSF) plays a crucial role in the regulatory network by coordinating responses to heat stress as well as other stress signaling pathways. Despite extensive studies on HSF functions in various plant species, our understanding of this gene family in garlic, an important crop with nutritional and medicinal value, remains limited. In this study, we conducted a comprehensive investigation of the entire garlic genome to elucidate the characteristics of the AsHSF gene family. RESULTS In this study, we identified a total of 17 AsHSF transcription factors. Phylogenetic analysis classified these transcription factors into three subfamilies: Class A (9 members), Class B (6 members), and Class C (2 members). Each subfamily was characterized by shared gene structures and conserved motifs. The evolutionary features of the AsHSF genes were investigated through a comprehensive analysis of chromosome location, conserved protein motifs, and gene duplication events. These findings suggested that the evolution of AsHSF genes is likely driven by both tandem and segmental duplication events. Moreover, the nucleotide diversity of the AsHSF genes decreased by only 0.0002% from wild garlic to local garlic, indicating a slight genetic bottleneck experienced by this gene family during domestication. Furthermore, the analysis of cis-acting elements in the promoters of AsHSF genes indicated their crucial roles in plant growth, development, and stress responses. qRT-PCR analysis, co-expression analysis, and protein interaction prediction collectively highlighted the significance of Asa6G04911. Subsequent experimental investigations using yeast two-hybridization and yeast induction experiments confirmed its interaction with HSP70/90, reinforcing its significance in heat stress. CONCLUSIONS This study is the first to unravel and analyze the AsHSF genes in garlic, thereby opening up new avenues for understanding their functions. The insights gained from this research provide a valuable resource for future investigations, particularly in the functional analysis of AsHSF genes.
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Affiliation(s)
- Xiaomeng Hao
- Institute of Neurobiology, Jining Medical University, Jining, China
| | - Shutao He
- Institute of Biotechnology and Health, Beijing Academy of Science and Technology, Beijing, China.
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Zheng R, Chen J, Peng Y, Zhu X, Niu M, Chen X, Xie K, Huang R, Zhan S, Su Q, Shen M, Peng D, Ahmad S, Zhao K, Liu ZJ, Zhou Y. General Analysis of Heat Shock Factors in the Cymbidium ensifolium Genome Provided Insights into Their Evolution and Special Roles with Response to Temperature. Int J Mol Sci 2024; 25:1002. [PMID: 38256078 PMCID: PMC10815800 DOI: 10.3390/ijms25021002] [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: 11/27/2023] [Revised: 12/27/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Heat shock factors (HSFs) are the key regulators of heat stress responses and play pivotal roles in tissue development and the temperature-induced regulation of secondary metabolites. In order to elucidate the roles of HSFs in Cymbidium ensifolium, we conducted a genome-wide identification of CeHSF genes and predicted their functions based on their structural features and splicing patterns. Our results revealed 22 HSF family members, with each gene containing more than one intron. According to phylogenetic analysis, 59.1% of HSFs were grouped into the A subfamily, while subfamily HSFC contained only two HSFs. And the HSF gene families were differentiated evolutionarily between plant species. Two tandem repeats were found on Chr02, and two segmental duplication pairs were observed on Chr12, Chr17, and Chr19; this provided evidence for whole-genome duplication (WGD) events in C. ensifolium. The core region of the promoter in most CeHSF genes contained cis-acting elements such as AP2/ERF and bHLH, which were associated with plant growth, development, and stress responses. Except for CeHSF11, 14, and 19, each of the remaining CeHSFs contained at least one miRNA binding site. This included binding sites for miR156, miR393, and miR319, which were responsive to temperature and other stresses. The HSF gene family exhibited significant tissue specificity in both vegetative and floral organs of C. ensifolium. CeHSF13 and CeHSF15 showed relatively significant expression in flowers compared to other genes. During flower development, CeHSF15 exhibited markedly elevated expression in the early stages of flower opening, implicating critical regulatory functions in organ development and floral scent-related regulations. During the poikilothermic treatment, CeHSF14 was upregulated over 200-fold after 6 h of heat treatment. CeHSF13 and CeHSF14 showed the highest expression at 6 h of low temperature, while the expression of CeHSF15 and CeHSF21 continuously decreased at a low temperature. The expression patterns of CeHSFs further confirmed their role in responding to temperature stress. Our study may help reveal the important roles of HSFs in plant development and metabolic regulation and show insight for the further molecular design breeding of C. ensifolium.
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Affiliation(s)
- Ruiyue Zheng
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (J.C.); (Y.P.); (X.Z.); (M.N.); (X.C.); (K.X.); (R.H.); (S.Z.); (Q.S.); (D.P.); (S.A.)
| | - Jiemin Chen
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (J.C.); (Y.P.); (X.Z.); (M.N.); (X.C.); (K.X.); (R.H.); (S.Z.); (Q.S.); (D.P.); (S.A.)
| | - Yukun Peng
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (J.C.); (Y.P.); (X.Z.); (M.N.); (X.C.); (K.X.); (R.H.); (S.Z.); (Q.S.); (D.P.); (S.A.)
| | - Xuanyi Zhu
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (J.C.); (Y.P.); (X.Z.); (M.N.); (X.C.); (K.X.); (R.H.); (S.Z.); (Q.S.); (D.P.); (S.A.)
| | - Muqi Niu
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (J.C.); (Y.P.); (X.Z.); (M.N.); (X.C.); (K.X.); (R.H.); (S.Z.); (Q.S.); (D.P.); (S.A.)
| | - Xiuming Chen
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (J.C.); (Y.P.); (X.Z.); (M.N.); (X.C.); (K.X.); (R.H.); (S.Z.); (Q.S.); (D.P.); (S.A.)
| | - Kai Xie
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (J.C.); (Y.P.); (X.Z.); (M.N.); (X.C.); (K.X.); (R.H.); (S.Z.); (Q.S.); (D.P.); (S.A.)
| | - Ruiliu Huang
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (J.C.); (Y.P.); (X.Z.); (M.N.); (X.C.); (K.X.); (R.H.); (S.Z.); (Q.S.); (D.P.); (S.A.)
| | - Suying Zhan
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (J.C.); (Y.P.); (X.Z.); (M.N.); (X.C.); (K.X.); (R.H.); (S.Z.); (Q.S.); (D.P.); (S.A.)
| | - Qiuli Su
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (J.C.); (Y.P.); (X.Z.); (M.N.); (X.C.); (K.X.); (R.H.); (S.Z.); (Q.S.); (D.P.); (S.A.)
| | - Mingli Shen
- College of Life Sciences, Fujian Normal University, Fuzhou 350117, China; (M.S.); (K.Z.)
| | - Donghui Peng
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (J.C.); (Y.P.); (X.Z.); (M.N.); (X.C.); (K.X.); (R.H.); (S.Z.); (Q.S.); (D.P.); (S.A.)
| | - Sagheer Ahmad
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (J.C.); (Y.P.); (X.Z.); (M.N.); (X.C.); (K.X.); (R.H.); (S.Z.); (Q.S.); (D.P.); (S.A.)
| | - Kai Zhao
- College of Life Sciences, Fujian Normal University, Fuzhou 350117, China; (M.S.); (K.Z.)
| | - Zhong-Jian Liu
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (J.C.); (Y.P.); (X.Z.); (M.N.); (X.C.); (K.X.); (R.H.); (S.Z.); (Q.S.); (D.P.); (S.A.)
| | - Yuzhen Zhou
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.Z.); (J.C.); (Y.P.); (X.Z.); (M.N.); (X.C.); (K.X.); (R.H.); (S.Z.); (Q.S.); (D.P.); (S.A.)
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Zhu W, Xue C, Chen M, Yang Q. StHsfB5 Promotes Heat Resistance by Directly Regulating the Expression of Hsp Genes in Potato. Int J Mol Sci 2023; 24:16528. [PMID: 38003725 PMCID: PMC10671264 DOI: 10.3390/ijms242216528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
With global warming, high temperatures have become a major environmental stress that inhibits plant growth and development. Plants evolve several mechanisms to cope with heat stress accordingly. One of the important mechanisms is the Hsf (heat shock factor)-Hsp (heat shock protein) signaling pathway. Therefore, the plant transcription factor Hsf family plays important roles in response to heat stress. All Hsfs can be divided into three classes (A, B, and C). Usually, class-A Hsfs are transcriptional activators, while class-B Hsfs are transcriptional repressors. In potato, our previous work identified 27 Hsfs in the genome and analyzed HsfA3 and HsfA4C functions that promote potato heat resistance. However, the function of HsfB is still elusive. In this study, the unique B5 member StHsfB5 in potato was obtained, and its characterizations and functions were comprehensively analyzed. A quantitative real-time PCR (qRT-PCR) assay showed that StHsfB5 was highly expressed in root, and its expression was induced by heat treatment and different kinds of phytohormones. The subcellular localization of StHsfB5 was in the nucleus, which is consistent with the characterization of transcription factors. The transgenic lines overexpressing StHsfB5 showed higher heat resistance compared with that of the control nontransgenic lines and inhibitory lines. Experiments on the interaction between protein and DNA indicated that the StHsfB5 protein can directly bind to the promoters of target genes small Hsps (sHsp17.6, sHsp21, and sHsp22.7) and Hsp80, and then induce the expressions of these target genes. All these results showed that StHsfB5 may be a coactivator that promotes potato heat resistance ability by directly inducing the expression of its target genes sHsp17.6, sHsp21, sHsp22.7, and Hsp80.
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Affiliation(s)
- Wenjiao Zhu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (C.X.); (M.C.)
| | | | | | - Qing Yang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (C.X.); (M.C.)
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Ceylan Y, Altunoglu YC, Horuz E. HSF and Hsp Gene Families in sunflower: a comprehensive genome-wide determination survey and expression patterns under abiotic stress conditions. PROTOPLASMA 2023; 260:1473-1491. [PMID: 37154904 DOI: 10.1007/s00709-023-01862-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023]
Abstract
Sunflowers belong to the Asteraceae family, which comprises nutrimental and economic oilseed plants. Heat shock proteins (Hsps) are protein families vital for all organisms' growth and survival. Besides the ordinary conditions, the expression of these proteins ascends during abiotic stress factors such as high temperature, salinity, and drought. Using bioinformatics approaches, the current study identified and analyzed HSF and Hsp gene family members in the sunflower (Helianthus annuus L.) plant. HSF, sHsp, Hsp40, Hsp60, Hsp70, Hsp90, and Hsp100 domains were analyzed in the sunflower genome, and 88, 72, 192, 52, 85, 49, and 148 genes were identified, respectively. The motif structures of the proteins in the same phylogenetic tree were similar, and the α-helical form was dominant in all the protein families except for sHsp. The estimated three-dimensional structure of 28 sHsp proteins was determined as β-sheets. Considering protein-protein interactions, the Hsp60-09 protein (38 interactions) was found to be the most interacting protein. The most orthologous gene pairs (58 genes) were identified between Hsp70 genes and Arabidopsis genes. The expression analysis of selected genes was performed under high temperature, drought, and high temperature-drought combined stress conditions in two sunflower cultivars. In stress conditions, gene expressions were upregulated for almost all genes in the first half and first hours at large. The expressions of HanHSF-45 and HanHsp70-29 genes were raised in two cultivars under high temperature and high temperature-drought combined stress conditions. This study presents a blueprint for subsequent research and delivers comprehensive knowledge of this vital protein domain.
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Affiliation(s)
- Yusuf Ceylan
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
- Department of Molecular Biology and Genetics, Faculty of Science, Bartın University, Bartin, Turkey
| | - Yasemin Celik Altunoglu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey.
| | - Erdoğan Horuz
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
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Kanwar M, Chaudhary C, Anand KA, Singh S, Garg M, Mishra SK, Sirohi P, Chauhan H. An insight into Pisum sativum HSF gene family-Genome-wide identification, phylogenetic, expression, and analysis of transactivation potential of pea heat shock transcription factor. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107971. [PMID: 37619269 DOI: 10.1016/j.plaphy.2023.107971] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/23/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023]
Abstract
Field pea (Pisum sativum L, 2n = 14) is a popular temperate legume with high economic value. Heat shock factors (HSFs) are the core element in the regulatory mechanism of heat stress responses. HSFs in pea (P. sativum) have not been characterized and their role remains unclear in different abiotic stresses. To address this knowledge gap, the current study aimed to characterize the HSF gene family in pea. We identified 38 PsHsf members in P. sativum, which are distributed on the seven chromosomes, and based on phylogenetic analysis, we classified them into three representative classes i.e. A, B, and C. Conserved motif and gene structure analysis confirmed a high degree of similarity among the members of the same class. Additionally, identified cis-acting regulatory elements (CAREs) related to abiotic responses, development, growth, and hormone signaling provides crucial insights into the regulatory mechanisms of PsHsfs. Our research revealed instances of gene duplication in PsHsf gene family, suggesting that this mechanism could be driving the expansion of the PsHsf gene family. Moreover, Expression analysis of PsHsfs exhibited upregulation under heat stress (HS), salt stress (SS), and drought stress (DS) showing their phenomenal role in stress conditions. PsHsfs protein interaction network suggested their involvement in stress-responsive mechanisms. Further transactivation potential was checked for spliced variant of PsHsfA2a (PsHsfA2aI, PsHsfA2aII, and PsHsfA2aIII), PsHsfA3, PsHsfA6b, PsHsfA9, PsHsfB1a, and PsHsfB2a. Overall, these findings provide valuable insight into the evolutionary relationship of PsHsf gene family and their role in abiotic stress responses.
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Affiliation(s)
- Meenakshi Kanwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Chanderkant Chaudhary
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Kumar Ankit Anand
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Shilpi Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Menus Garg
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Sumit Kumar Mishra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Parul Sirohi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Harsh Chauhan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India.
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Iqbal MZ, Jia T, Tang T, Anwar M, Ali A, Hassan MJ, Zhang Y, Tang Q, Peng Y. A Heat Shock Transcription Factor TrHSFB2a of White Clover Negatively Regulates Drought, Heat and Salt Stress Tolerance in Transgenic Arabidopsis. Int J Mol Sci 2022; 23:12769. [PMID: 36361560 PMCID: PMC9654841 DOI: 10.3390/ijms232112769] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/19/2022] [Accepted: 10/10/2022] [Indexed: 11/15/2023] Open
Abstract
Heat shock transcription factors (HSF) are divided into classes A, B and C. Class A transcription factors are generally recognized as transcriptional activators, while functional characterization of class B and C heat shock transcription factors have not been fully developed in most plant species. We isolated and characterized a novel HSF transcription factor gene, TrHSFB2a (a class B HSF) gene, from the drought stress-sensitive forage crop species, white clover (Trifolium repens). TrHSFB2a was highly homologous to MtHSFB2b, CarHSFB2a, AtHSFB2b and AtHSFB2a. The expression of TrHSFB2a was strongly induced by drought (PEG6000 15% w/v), high temperature (35 °C) and salt stresses (200 mM L-1 NaCl) in white clover, while subcellular localization analysis showed that it is a nuclear protein. Overexpression of the white clover gene TrHSFB2a in Arabidopsis significantly reduced fresh and dry weight, relative water contents (RWC), maximum photosynthesis efficiency (Fv/Fm) and performance index on the absorption basis (PIABS), while it promoted leaf senescence, relative electrical conductivity (REC) and the contents of malondialdehyde (MDA) compared to a wild type under drought, heat and salt stress conditions of Arabidopsis plants. The silencing of its native homolog (AtHSFB2a) by RNA interference in Arabidopsis thaliana showed opposite trends by significantly increasing fresh and dry weights, RWC, maximum photosynthesis efficiency (Fv/Fm) and performance index on the absorption basis (PIABS) and reducing REC and MDA contents under drought, heat and salt stress conditions compared to wild type Arabidopsis plants. These phenotypic and physiological indicators suggested that the TrHSFB2a of white clover functions as a negative regulator of heat, salt and drought tolerance. The bioinformatics analysis showed that TrHSFB2a contained the core B3 repression domain (BRD) that has been reported as a repressor activator domain in other plant species that might repress the activation of the heat shock-inducible genes required in the stress tolerance process in plants. The present study explores one of the potential causes of drought and heat sensitivity in white clover that can be overcome to some extent by silencing the TrHSFB2a gene in white clover.
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Affiliation(s)
- Muhammad Zafar Iqbal
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tong Jia
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tao Tang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Muhammad Anwar
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
| | - Asif Ali
- Key Laboratory of Southwest Crop Genetic Resources and Genetic Improvement, Ministry of Education, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Muhammad Jawad Hassan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Youzhi Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Qilin Tang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Peng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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Functional Characterization of Heat Shock Factor ( CrHsf) Families Provide Comprehensive Insight into the Adaptive Mechanisms of Canavalia rosea (Sw.) DC. to Tropical Coral Islands. Int J Mol Sci 2022; 23:ijms232012357. [PMID: 36293211 PMCID: PMC9604225 DOI: 10.3390/ijms232012357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Heat shock transcription factors (Hsfs) are key regulators in plant heat stress response, and therefore, they play vital roles in signal transduction pathways in response to environmental stresses, as well as in plant growth and development. Canavalia rosea (Sw.) DC. is an extremophile halophyte with good adaptability to high temperature and salt-drought tolerance, and it can be used as a pioneer species for ecological reconstruction on tropical coral islands. To date, very little is known regarding the functions of Hsfs in the adaptation mechanisms of plant species with specialized habitats, especially in tropical leguminous halophytes. In this study, a genome-wide analysis was performed to identify all the Hsfs in C. rosea based on whole-genome sequencing information. The chromosomal location, protein domain or motif organization, and phylogenetic relationships of 28 CrHsfs were analyzed. Promoter analyses indicated that the expression levels of different CrHsfs were precisely regulated. The expression patterns also revealed clear transcriptional changes among different C. rosea tissues, indicating that the regulation of CrHsf expression varied among organs in a developmental or tissue-specific manner. Furthermore, the expression levels of most CrHsfs in response to environmental conditions or abiotic stresses also implied a possible positive regulatory role of this gene family under abiotic stresses, and suggested roles in adaptation to specialized habitats such as tropical coral islands. In addition, some CrHsfAs were cloned and their possible roles in abiotic stress tolerance were functionally characterized using a yeast expression system. The CrHsfAs significantly enhanced yeast survival under thermal and oxidative stress challenges. Our results contribute to a better understanding of the plant Hsf gene family and provide a basis for further study of CrHsf functions in environmental thermotolerance. Our results also provide valuable information on the evolutionary relationships among CrHsf genes and the functional characteristics of the gene family. These findings are beneficial for further research on the natural ecological adaptability of C. rosea to tropical environments.
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Kao PH, Baiya S, Lai ZY, Huang CM, Jhan LH, Lin CJ, Lai YS, Kao CF. An advanced systems biology framework of feature engineering for cold tolerance genes discovery from integrated omics and non-omics data in soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:1019709. [PMID: 36247545 PMCID: PMC9562094 DOI: 10.3389/fpls.2022.1019709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/06/2022] [Indexed: 06/16/2023]
Abstract
Soybean is sensitive to low temperatures during the crop growing season. An urgent demand for breeding cold-tolerant cultivars to alleviate the production loss is apparent to cope with this scenario. Cold-tolerant trait is a complex and quantitative trait controlled by multiple genes, environmental factors, and their interaction. In this study, we proposed an advanced systems biology framework of feature engineering for the discovery of cold tolerance genes (CTgenes) from integrated omics and non-omics (OnO) data in soybean. An integrative pipeline was introduced for feature selection and feature extraction from different layers in the integrated OnO data using data ensemble methods and the non-parameter random forest prioritization to minimize uncertainties and false positives for accuracy improvement of results. In total, 44, 143, and 45 CTgenes were identified in short-, mid-, and long-term cold treatment, respectively, from the corresponding gene-pool. These CTgenes outperformed the remaining genes, the random genes, and the other candidate genes identified by other approaches in an independent RNA-seq database. Furthermore, we applied pathway enrichment and crosstalk network analyses to uncover relevant physiological pathways with the discovery of underlying cold tolerance in hormone- and defense-related modules. Our CTgenes were validated by using 55 SNP genotype data of 56 soybean samples in cold tolerance experiments. This suggests that the CTgenes identified from our proposed systematic framework can effectively distinguish cold-resistant and cold-sensitive lines. It is an important advancement in the soybean cold-stress response. The proposed pipelines provide an alternative solution to biomarker discovery, module discovery, and sample classification underlying a particular trait in plants in a robust and efficient way.
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Affiliation(s)
- Pei-Hsiu Kao
- Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Supaporn Baiya
- Department of Resource and Environment, Faculty of Science at Sriracha, Kasetsart University, Sriracha, Thailand
| | - Zheng-Yuan Lai
- Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Chih-Min Huang
- Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Li-Hsin Jhan
- Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Chian-Jiun Lin
- Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Ya-Syuan Lai
- Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Feng Kao
- Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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10
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Jianing G, Yuhong G, Yijun G, Rasheed A, Qian Z, Zhiming X, Mahmood A, Shuheng Z, Zhuo Z, Zhuo Z, Xiaoxue W, Jian W. Improvement of heat stress tolerance in soybean ( Glycine max L), by using conventional and molecular tools. FRONTIERS IN PLANT SCIENCE 2022; 13:993189. [PMID: 36226280 PMCID: PMC9549248 DOI: 10.3389/fpls.2022.993189] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/23/2022] [Indexed: 06/12/2023]
Abstract
The soybean is a significant legume crop, providing several vital dietary components. Extreme heat stress negatively affects soybean yield and quality, especially at the germination stage. Continuous change in climatic conditions is threatening the global food supply and food security. Therefore, it is a critical need of time to develop heat-tolerant soybean genotypes. Different molecular techniques have been developed to improve heat stress tolerance in soybean, but until now complete genetic mechanism of soybean is not fully understood. Various molecular methods, like quantitative trait loci (QTL) mapping, genetic engineering, transcription factors (TFs), transcriptome, and clustered regularly interspaced short palindromic repeats (CRISPR), are employed to incorporate heat tolerance in soybean under the extreme conditions of heat stress. These molecular techniques have significantly improved heat stress tolerance in soybean. Besides this, we can also use specific classical breeding approaches and different hormones to reduce the harmful consequences of heat waves on soybean. In future, integrated use of these molecular tools would bring significant results in developing heat tolerance in soybean. In the current review, we have presented a detailed overview of the improvement of heat tolerance in soybean and highlighted future prospective. Further studies are required to investigate different genetic factors governing the heat stress response in soybean. This information would be helpful for future studies focusing on improving heat tolerance in soybean.
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Affiliation(s)
- Guan Jianing
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Gai Yuhong
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Guan Yijun
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Adnan Rasheed
- College of Life Sciences, Changchun Normal University, Changchun, China
| | - Zhao Qian
- College of Life Sciences, Changchun Normal University, Changchun, China
| | - Xie Zhiming
- College of Life Sciences, Baicheng Normal University, Baicheng, China
| | - Athar Mahmood
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Zhang Shuheng
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Zhang Zhuo
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Zhao Zhuo
- College of Life Sciences, Jilin Normal University, Changchun, China
| | - Wang Xiaoxue
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Wei Jian
- College of Life Sciences, Changchun Normal University, Changchun, China
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11
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Yuan T, Liang J, Dai J, Zhou XR, Liao W, Guo M, Aslam M, Li S, Cao G, Cao S. Genome-Wide Identification of Eucalyptus Heat Shock Transcription Factor Family and Their Transcriptional Analysis under Salt and Temperature Stresses. Int J Mol Sci 2022; 23:ijms23148044. [PMID: 35887387 PMCID: PMC9318532 DOI: 10.3390/ijms23148044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/24/2022] Open
Abstract
Heat shock transcription factors (HSFs) activate heat shock protein gene expression by binding their promoters in response to heat stress and are considered to be pivotal transcription factors in plants. Eucalyptus is a superior source of fuel and commercial wood. During its growth, high temperature or other abiotic stresses could impact its defense capability and growth. Hsf genes have been cloned and sequenced in many plants, but rarely in Eucalyptus. In this study, we used bioinformatics methods to analyze and identify Eucalyptus Hsf genes, their chromosomal localization and structure. The phylogenetic relationship and conserved domains of their encoded proteins were further analyzed. A total of 36 Hsf genes were identified and authenticated from Eucalyptus, which were scattered across 11 chromosomes. They could be classified into three classes (A, B and C). Additionally, a large number of stress-related cis-regulatory elements were identified in the upstream promoter sequence of HSF, and cis-acting element analysis indicated that the expression of EgHsf may be regulated by plant growth and development, metabolism, hormones and stress responses. The expression profiles of five representative Hsf genes, EgHsf4, EgHsf9, EgHsf13, EgHsf24 and EgHsf32, under salt and temperature stresses were examined by qRT-PCR. The results show that the expression pattern of class B genes (EgHsf4, EgHsf24 and EgHsf32) was more tolerant to abiotic stresses than that of class A genes (EgHsf9 and EgHsf13). However, the expressions of all tested Hsf genes in six tissues were at different levels. Finally, we investigated the network of interplay between genes, and the results suggest that there may be synergistic effects between different Hsf genes in response to abiotic stresses. We conclude that the Hsf gene family played an important role in the growth and developmental processes of Eucalyptus and could be vital for maintaining cell homeostasis against external stresses. This study provides basic information on the members of the Hsf gene family in Eucalyptus and lays the foundation for the functional identification of related genes and the further investigation of their biological functions in plant stress regulation.
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Affiliation(s)
- Tan Yuan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.Y.); (J.L.); (J.D.); (W.L.); (S.L.)
| | - Jianxiang Liang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.Y.); (J.L.); (J.D.); (W.L.); (S.L.)
| | - Jiahao Dai
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.Y.); (J.L.); (J.D.); (W.L.); (S.L.)
| | - Xue-Rong Zhou
- Commonwealth Scientific Industrial Research Organization (CSIRO) Agriculture Food, Canberra, ACT 2601, Australia;
| | - Wenhai Liao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.Y.); (J.L.); (J.D.); (W.L.); (S.L.)
| | - Mingliang Guo
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.G.); (M.A.)
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mohammad Aslam
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.G.); (M.A.)
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shubin Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.Y.); (J.L.); (J.D.); (W.L.); (S.L.)
| | - Guangqiu Cao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.Y.); (J.L.); (J.D.); (W.L.); (S.L.)
- Correspondence: (G.C.); (S.C.)
| | - Shijiang Cao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.Y.); (J.L.); (J.D.); (W.L.); (S.L.)
- Correspondence: (G.C.); (S.C.)
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12
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Mallick B, Kumari M, Pradhan SK, C P, Acharya GC, Naresh P, Das B, Shashankar P. Genome-wide analysis and characterization of heat shock transcription factors (Hsfs) in common bean (Phaseolus vulgaris L.). Funct Integr Genomics 2022; 22:743-756. [PMID: 35718806 DOI: 10.1007/s10142-022-00875-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/08/2022] [Indexed: 11/28/2022]
Abstract
Heat shock transcription factors (Hsfs) play an essential role as transcriptional regulatory proteins against heat stress by controlling the expression of heat-responsive genes. Common bean is a highly thermosensitive crop, and, therefore, its genome sequence information is segregated, characterized here in terms of heat shock transcription factors and its evolutionary significance. In this study, a complete comprehensive set of 29 non-redundant full-length Hsf genes were identified and characterized from Phaseolus vulgaris L. (PvHsf) genome sequence. Detailed gene information such as chromosomal localization, domain position, motif organization, and exon-intron identification were analyzed. All the 29 PvHsf genes were mapped on 8 out of 11 chromosomes, indicating the gene duplication occurred in the common bean genome. Motif analysis and exon-intron structure were conserved in each group, which showed that the cytoplasmic proteins highly influence the conserved structure of PvHsfs and heat-induced response. The HSF genes were grouped into three classes, i.e., A to C and 14 groups, based on structural features and phylogenetic relationships. Only one pair of paralog sequences suggests that it may be derived from the duplication event during evolution. A comparative genomics study indicated the influence of whole-genome duplication and purifying selection on the common bean genome during development. In silico expression analysis showed the active role of class A and B family during abiotic stress conditions and higher expression in floral organs. The qRT-PCR analysis revealed PvHSFA8 as the master regulator and PvHSFB1A and PvHSFB2A induction during heat exposure in French beans.
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Affiliation(s)
- B Mallick
- Department of Bioinformatics, Orissa University of Agriculture & Technology, Bhubaneswar, India
| | - M Kumari
- ICAR-Research Complex for Eastern Region, RS, Ranchi, India. .,Central Horticultural Experiment Station (ICAR-IIHR), Bhubaneswar, India.
| | - S K Pradhan
- Department of Bioinformatics, Orissa University of Agriculture & Technology, Bhubaneswar, India
| | - Parmeswaran C
- Division of Biotechnology, ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - G C Acharya
- Central Horticultural Experiment Station (ICAR-IIHR), Bhubaneswar, India
| | - P Naresh
- Central Horticultural Experiment Station (ICAR-IIHR), Bhubaneswar, India
| | - Bishnupriya Das
- Central Horticultural Experiment Station (ICAR-IIHR), Bhubaneswar, India
| | - P Shashankar
- Division of Biotechnology, ICAR-National Rice Research Institute, Cuttack, Odisha, India
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13
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Zhao D, Qi X, Zhang Y, Zhang R, Wang C, Sun T, Zheng J, Lu Y. Genome-wide analysis of the heat shock transcription factor gene family in Sorbus pohuashanensis (Hance) Hedl identifies potential candidates for resistance to abiotic stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 175:68-80. [PMID: 35180530 DOI: 10.1016/j.plaphy.2022.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 01/13/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Heat shock transcription factors (Hsfs) are essential regulators of plant responses to abiotic stresses, growth, and development. However, all the Hsf family members have not been identified in Sorbus pohuashanensis. Therefore, the aim of this study was to identify the Hsf family members in S. pohuashanensis and examine their expression under abiotic stress conditions through the integration of gene structure, phylogenetic relationships, chromosome location, and expression patterns. Bioinformatics-based methods, identified 33 Hsfs in S. pohuashanensis. Phylogenetic analysis of Hsfs from S. pohuashanensis and other species revealed that they were more closely related to apples and white pears, followed by Populus trichocarpa, and most distantly related to Arabidopsis. Moreover, the Hsfs were clustered into three major groups: A, B, and C. Gene structure and conserved motif analysis revealed a high degree of conservation among members of the same class. Collinearity analysis revealed that segmental duplication played an essential role in increasing the size of the SpHsfs gene family in S. pohuashanensis. Additionally, several cis-acting elements associated with growth and development, hormone response, and stress were found in the promoter region of SpHsfs genes. Furthermore, expression analysis in various tissues of S. pohuashanensis showed that the genes were closely associated with heat, drought, salt stress, growth, and developmental processes. Overall, these results provide valuable information on the evolutionary relationships of the Hsf gene family. These genes stand as strong functional candidates for further studies on the resistance of S. pohuashanensis to abiotic stresses.
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Affiliation(s)
- Dongxue Zhao
- School of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Xiangyu Qi
- School of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Yan Zhang
- School of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Ruili Zhang
- School of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Cong Wang
- School of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Tianxu Sun
- Shandong Institute of Territorial and Spatial Planning, Jinan, Shandong Province, 250000, China
| | - Jian Zheng
- School of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China.
| | - Yizeng Lu
- Shandong Provincial Center of Forest Tree Germplasm Resources, Jinan, Shandong Province, 250102, China.
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14
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Zhang Q, Geng J, Du Y, Zhao Q, Zhang W, Fang Q, Yin Z, Li J, Yuan X, Fan Y, Cheng X, Du J. Heat shock transcription factor (Hsf) gene family in common bean (Phaseolus vulgaris): genome-wide identification, phylogeny, evolutionary expansion and expression analyses at the sprout stage under abiotic stress. BMC PLANT BIOLOGY 2022; 22:33. [PMID: 35031009 PMCID: PMC8759166 DOI: 10.1186/s12870-021-03417-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 12/28/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND Common bean (Phaseolus vulgaris) is an essential crop with high economic value. The growth of this plant is sensitive to environmental stress. Heat shock factor (Hsf) is a family of antiretroviral transcription factors that regulate plant defense system against biotic and abiotic stress. To date, few studies have identified and bio-analyzed Hsfs in common bean. RESULTS In this study, 30 Hsf transcription factors (PvHsf1-30) were identified from the PFAM database. The PvHsf1-30 belonged to 14 subfamilies with similar motifs, gene structure and cis-acting elements. The Hsf members in Arabidopsis, rice (Oryza sativa), maize (Zea mays) and common bean were classified into 14 subfamilies. Collinearity analysis showed that PvHsfs played a role in the regulation of responses to abiotic stress. The expression of PvHsfs varied across different tissues. Moreover, quantitative real-time PCR (qRT-PCR) revealed that most PvHsfs were differentially expressed under cold, heat, salt and heavy metal stress, indicating that PvHsfs might play different functions depending on the type of abiotic stress. CONCLUSIONS In this study, we identified 30 Hsf transcription factors and determined their location, motifs, gene structure, cis-elements, collinearity and expression patterns. It was found that PvHsfs regulates responses to abiotic stress in common bean. Thus, this study provides a basis for further analysis of the function of PvHsfs in the regulation of abiotic stress in common bean.
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Affiliation(s)
- Qi Zhang
- College of Agriculture, Heilongjiang BaYi Agricultural University, Daqing, 163319, Heilongjaing, China
| | - Jing Geng
- College of Agriculture, Heilongjiang BaYi Agricultural University, Daqing, 163319, Heilongjaing, China
| | - Yanli Du
- College of Agriculture, Heilongjiang BaYi Agricultural University, Daqing, 163319, Heilongjaing, China
- National Coarse Cereals Engineering Research Center, Daqing, 161139, Heilongjiang, China
| | - Qiang Zhao
- College of Agriculture, Heilongjiang BaYi Agricultural University, Daqing, 163319, Heilongjaing, China
| | - Wenjing Zhang
- College of Agriculture, Heilongjiang BaYi Agricultural University, Daqing, 163319, Heilongjaing, China
| | - Qingxi Fang
- College of Agriculture, Heilongjiang BaYi Agricultural University, Daqing, 163319, Heilongjaing, China
| | - Zhengong Yin
- Crop Resources Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, Heilongjiang, China
| | - Jianghui Li
- College of Agriculture, Heilongjiang BaYi Agricultural University, Daqing, 163319, Heilongjaing, China
| | - Xiankai Yuan
- College of Agriculture, Heilongjiang BaYi Agricultural University, Daqing, 163319, Heilongjaing, China
| | - Yaru Fan
- College of Agriculture, Heilongjiang BaYi Agricultural University, Daqing, 163319, Heilongjaing, China
| | - Xin Cheng
- College of Agriculture, Heilongjiang BaYi Agricultural University, Daqing, 163319, Heilongjaing, China
| | - Jidao Du
- College of Agriculture, Heilongjiang BaYi Agricultural University, Daqing, 163319, Heilongjaing, China.
- National Coarse Cereals Engineering Research Center, Daqing, 161139, Heilongjiang, China.
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15
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Rahman A, Sinha KV, Sopory SK, Sanan-Mishra N. Influence of virus-host interactions on plant response to abiotic stress. PLANT CELL REPORTS 2021; 40:2225-2245. [PMID: 34050797 DOI: 10.1007/s00299-021-02718-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/19/2021] [Indexed: 06/12/2023]
Abstract
Environmental factors play a significant role in controlling growth, development and defense responses of plants. Changes in the abiotic environment not only significantly alter the physiological and molecular pathways in plants, but also result in attracting the insect pests that carry a payload of viruses. Invasion of plants by viruses triggers the RNA silencing based defense mechanism in plants. In counter defense the viruses have gained the ability to suppress the host RNA silencing activities. A new paradigm has emerged, with the recognition that plant viruses also have the intrinsic capacity to modulate host plant response to environmental cues, in an attempt to favour their own survival. Thus, plant-virus interactions provide an excellent system to understand the signals in crosstalk between biotic (virus) and abiotic stresses. In this review, we have summarized the basal plant defense responses to pathogen invasion while emphasizing on the role of RNA silencing as a front line of defense response to virus infection. The emerging knowledge indicates overlap between RNA silencing with the innate immune responses during antiviral defense. The suppressors of RNA silencing serve as Avr proteins, which can be recognized by the host R proteins. The defense signals also function in concert with the phytohormones to influence plant responses to abiotic stresses. The current evidence on the role of virus induced host tolerance to abiotic stresses is also discussed.
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Affiliation(s)
- Adeeb Rahman
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Kumari Veena Sinha
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sudhir K Sopory
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
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16
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Genome-Wide Identification and Characterization of Hsf and Hsp Gene Families and Gene Expression Analysis under Heat Stress in Eggplant (Solanum melongema L.). HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7060149] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Under high temperature stress, a large number of proteins in plant cells will be denatured and inactivated. Meanwhile Hsfs and Hsps will be quickly induced to remove denatured proteins, so as to avoid programmed cell death, thus enhancing the thermotolerance of plants. Here, a comprehensive identification and analysis of the Hsf and Hsp gene families in eggplant under heat stress was performed. A total of 24 Hsf-like genes and 117 Hsp-like genes were identified from the eggplant genome using the interolog from Arabidopsis. The gene structure and motif composition of Hsf and Hsp genes were relatively conserved in each subfamily in eggplant. RNA-seq data and qRT-PCR analysis showed that the expressions of most eggplant Hsf and Hsp genes were increased upon exposure to heat stress, especially in thermotolerant line. The comprehensive analysis indicated that different sets of SmHsps genes were involved downstream of particular SmHsfs genes. These results provided a basis for revealing the roles of SmHsps and SmHsp for thermotolerance in eggplant, which may potentially be useful for understanding the thermotolerance mechanism involving SmHsps and SmHsp in eggplant.
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17
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Liang Y, Wang J, Zheng J, Gong Z, Li Z, Ai X, Li X, Chen Q. Genome-Wide Comparative Analysis of Heat Shock Transcription Factors Provides Novel Insights for Evolutionary History and Expression Characterization in Cotton Diploid and Tetraploid Genomes. Front Genet 2021; 12:658847. [PMID: 34168673 PMCID: PMC8217870 DOI: 10.3389/fgene.2021.658847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 03/15/2021] [Indexed: 11/13/2022] Open
Abstract
Heat shock transcription factors (HSFs) are involved in environmental stress response and plant development, such as heat stress and flowering development. According to the structural characteristics of the HSF gene family, HSF genes were classified into three major types (HSFA, HSFB, and HSFC) in plants. Using conserved domains of HSF genes, we identified 621 HSF genes among 13 cotton genomes, consisting of eight diploid and five tetraploid genomes. Phylogenetic analysis indicated that HSF genes among 13 cotton genomes were grouped into two different clusters: one cluster contained all HSF genes of HSFA and HSFC, and the other cluster contained all HSF genes of HSFB. Comparative analysis of HSF genes in Arabidopsis thaliana, Gossypium herbaceum (A1), Gossypium arboreum (A2), Gossypium raimondii (D5), and Gossypium hirsutum (AD1) genomes demonstrated that four HSF genes were inherited from a common ancestor, A0, of all existing cotton A genomes. Members of the HSF gene family in G. herbaceum (A1) genome indicated a significant loss compared with those in G. arboretum (A2) and G. hirsutum (AD1) A genomes. However, HSF genes in G. raimondii (D5) showed relative loss compared with those in G. hirsutum (AD1) D genome. Analysis of tandem duplication (TD) events of HSF genes revealed that protein-coding genes among different cotton genomes have experienced TD events, but only the two-gene tandem array was detected in Gossypium thurberi (D1) genome. The expression analysis of HSF genes in G. hirsutum (AD1) and Gossypium barbadense (AD2) genomes indicated that the expressed HSF genes were divided into two different groups, respectively, and the expressed HSF orthologous genes between the two genomes showed totally different expression patterns despite the implementation of the same abiotic stresses. This work will provide novel insights for the study of evolutionary history and expression characterization of HSF genes in different cotton genomes and a widespread application model for the study of HSF gene families in plants.
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Affiliation(s)
- Yajun Liang
- Xinjiang Academy of Agricultural Science, Urumqi, China.,Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Urumqi, China
| | - Junduo Wang
- Xinjiang Academy of Agricultural Science, Urumqi, China
| | - Juyun Zheng
- Xinjiang Academy of Agricultural Science, Urumqi, China
| | - Zhaolong Gong
- Xinjiang Academy of Agricultural Science, Urumqi, China
| | - Zhiqiang Li
- Adsen Biotechnology Corporation, Urumqi, China
| | - Xiantao Ai
- Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Urumqi, China
| | - Xueyuan Li
- Xinjiang Academy of Agricultural Science, Urumqi, China
| | - Quanjia Chen
- Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Urumqi, China
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18
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Wang L, Liu Y, Chai M, Chen H, Aslam M, Niu X, Qin Y, Cai H. Genome-wide identification, classification, and expression analysis of the HSF gene family in pineapple ( Ananas comosus). PeerJ 2021; 9:e11329. [PMID: 33987013 PMCID: PMC8086565 DOI: 10.7717/peerj.11329] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/31/2021] [Indexed: 11/28/2022] Open
Abstract
Transcription factors (TFs), such as heat shock transcription factors (HSFs), usually play critical regulatory functions in plant development, growth, and response to environmental cues. However, no HSFs have been characterized in pineapple thus far. Here, we identified 22 AcHSF genes from the pineapple genome. Gene structure, motifs, and phylogenetic analysis showed that AcHSF families were distinctly grouped into three subfamilies (12 in Group A, seven in Group B, and four in Group C). The AcHSF promoters contained various cis-elements associated with stress, hormones, and plant development processes, for instance, STRE, WRKY, and ABRE binding sites. The majority of HSFs were expressed in diverse pineapple tissues and developmental stages. The expression of AcHSF-B4b/AcHSF-B4c and AcHSF-A7b/AcHSF-A1c were enriched in the ovules and fruits, respectively. Six genes (AcHSF-A1a , AcHSF-A2, AcHSF-A9a, AcHSF-B1a, AcHSF-B2a, and AcHSF-C1a) were transcriptionally modified by cold, heat, and ABA. Our results provide an overview and lay the foundation for future functional characterization of the pineapple HSF gene family.
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Affiliation(s)
- Lulu Wang
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
| | - Yanhui Liu
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
| | - Mengnan Chai
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
| | - Huihuang Chen
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
| | - Mohammad Aslam
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
| | - Xiaoping Niu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Yuan Qin
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Hanyang Cai
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
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19
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Zhou L, Yu X, Wang D, Li L, Zhou W, Zhang Q, Wang X, Ye S, Wang Z. Genome-wide identification, classification and expression profile analysis of the HSF gene family in Hypericum perforatum. PeerJ 2021; 9:e11345. [PMID: 33996286 PMCID: PMC8106910 DOI: 10.7717/peerj.11345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 04/03/2021] [Indexed: 01/15/2023] Open
Abstract
Heat shock transcription factors (HSFs) are critical regulators of plant responses to various abiotic and biotic stresses, including high temperature stress. HSFs are involved in regulating the expression of heat shock proteins (HSPs) by binding with heat stress elements (HSEs) to defend against high-temperature stress. The H. perforatum genome was recently fully sequenced; this provides a valuable resource for genetic and functional analysis. In this study, 23 putative HpHSF genes were identified and divided into three groups (A, B, and C) based on phylogeny and structural features. Gene structure and conserved motif analyses were performed on HpHSFs members; the DNA-binding domain (DBD), hydrophobic heptad repeat (HR-A/B), and exon-intron boundaries exhibited specific phylogenetic relationships. In addition, the presence of various cis-acting elements in the promoter regions of HpHSFs underscored their regulatory function in abiotic stress responses. RT-qPCR analyses showed that most HpHSF genes were expressed in response to heat conditions, suggesting that HpHSFs play potential roles in the heat stress resistance pathway. Our findings are advantageous for the analysis and research of the function of HpHSFs in high temperature stress tolerance in H. perforatum.
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Affiliation(s)
- Li Zhou
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Xiaoding Yu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Donghao Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Lin Li
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Wen Zhou
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Qian Zhang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Xinrui Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Sumin Ye
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Zhezhi Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
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20
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Shen C, Yuan J. Genome-wide characterization and expression analysis of the heat shock transcription factor family in pumpkin (Cucurbita moschata). BMC PLANT BIOLOGY 2020; 20:471. [PMID: 33054710 PMCID: PMC7557022 DOI: 10.1186/s12870-020-02683-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/01/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND Crop quality and yield are affected by abiotic and biotic stresses, and heat shock transcription factors (Hsfs) are considered to play important roles in regulating plant tolerance under various stresses. To investigate the response of Cucurbita moschata to abiotic stress, we analyzed the genome of C. moschata. RESULTS In this research, a total of 36 C. moschata Hsf (CmHsf) members were identified and classified into three subfamilies (I, II, and III) according to their amino acid sequence identity. The Hsfs of the same subfamily usually exhibit a similar gene structure (intron-exon distribution) and conserved domains (DNA-binding and other functional domains). Chromosome localization analysis showed that the 36 CmHsfs were unevenly distributed on 18 of the 21 chromosomes (except for Cm_Chr00, Cm_Chr08 and Cm_Chr20), among which 18 genes formed 9 duplicated gene pairs that have undergone segmental duplication events. The Ka/Ks ratio showed that the duplicated CmHsfs have mainly experienced strong purifying selection. High-level synteny was observed between C. moschata and other Cucurbitaceae species. CONCLUSIONS The expression profile of CmHsfs in the roots, stems, cotyledons and true leaves revealed that the CmHsfs exhibit tissue specificity. The analysis of cis-acting elements and quantitative real-time polymerase chain reaction (qRT-PCR) revealed that some key CmHsfs were activated by cold stress, heat stress, hormones and salicylic acid. This study lays the foundation for revealing the role of CmHsfs in resistance to various stresses, which is of great significance for the selection of stress-tolerant C. moschata.
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Affiliation(s)
- Changwei Shen
- School of Resources and Environmental Sciences, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Jingping Yuan
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China.
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, 453003, China.
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21
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Janni M, Gullì M, Maestri E, Marmiroli M, Valliyodan B, Nguyen HT, Marmiroli N. Molecular and genetic bases of heat stress responses in crop plants and breeding for increased resilience and productivity. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3780-3802. [PMID: 31970395 PMCID: PMC7316970 DOI: 10.1093/jxb/eraa034] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 01/20/2020] [Indexed: 05/21/2023]
Abstract
To ensure the food security of future generations and to address the challenge of the 'no hunger zone' proposed by the FAO (Food and Agriculture Organization), crop production must be doubled by 2050, but environmental stresses are counteracting this goal. Heat stress in particular is affecting agricultural crops more frequently and more severely. Since the discovery of the physiological, molecular, and genetic bases of heat stress responses, cultivated plants have become the subject of intense research on how they may avoid or tolerate heat stress by either using natural genetic variation or creating new variation with DNA technologies, mutational breeding, or genome editing. This review reports current understanding of the genetic and molecular bases of heat stress in crops together with recent approaches to creating heat-tolerant varieties. Research is close to a breakthrough of global relevance, breeding plants fitter to face the biggest challenge of our time.
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Affiliation(s)
- Michela Janni
- Institute of Bioscience and Bioresources (IBBR), National Research Council (CNR), Via Amendola, Bari, Italy
- Institute of Materials for Electronics and Magnetism (IMEM), National Research Council (CNR), Parco Area delle Scienze, Parma, Italy
| | - Mariolina Gullì
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Elena Maestri
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Marta Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Babu Valliyodan
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
- Lincoln University, Jefferson City, MO, USA
| | - Henry T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
- CINSA Interuniversity Consortium for Environmental Sciences, Parma/Venice, Italy
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22
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Zhang X, Xu W, Ni D, Wang M, Guo G. Genome-wide characterization of tea plant (Camellia sinensis) Hsf transcription factor family and role of CsHsfA2 in heat tolerance. BMC PLANT BIOLOGY 2020; 20:244. [PMID: 32471355 PMCID: PMC7260767 DOI: 10.1186/s12870-020-02462-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 05/24/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND Heat stress factors (Hsfs) play vital roles in signal transduction pathways operating in responses to environmental stresses. However, Hsf gene family has not been thoroughly explored in tea plant (Camellia sinensis L.). RESULTS In this study, we identified 25 CsHsf genes in C. sinensis that were separated by phylogenetic analysis into three sub-families (i.e., A, B, and C). Gene structures, conserved domains and motifs analyses indicated that the CsHsf members in each class were relatively conserved. Various cis-acting elements involved in plant growth regulation, hormone responses, stress responses, and light responses were located in the promoter regions of CsHsfs. Furthermore, degradome sequencing analysis revealed that 7 CsHsfs could be targeted by 9 miRNAs. The expression pattern of each CsHsf gene was significantly different in eight tissues. Many CsHsfs were differentially regulated by drought, salt, and heat stresses, as well as exogenous abscisic acid (ABA) and Ca2+. In addition, CsHsfA2 was located in the nucleus. Heterologous expression of CsHsfA2 improved thermotolerance in transgenic yeast, suggesting its potential role in the regulation of heat stress response. CONCLUSIONS A comprehensive genome-wide analysis of Hsf in C. sinensis present the global identification and functional prediction of CsHsfs. Most of them were implicated in a complex gene regulatory network controlling various abiotic stress responses and signal transduction pathways in tea plants. Additionally, heterologous expression of CsHsfA2 increased thermotolerance of transgenic yeast. These findings provide new insights into the functional divergence of CsHsfs and a basis for further research on CsHsfs functions.
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Affiliation(s)
- Xuyang Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan No. 1, Wuhan, 430070 Hubei Province P. R. China
| | - Wenluan Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan No. 1, Wuhan, 430070 Hubei Province P. R. China
| | - Dejiang Ni
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan No. 1, Wuhan, 430070 Hubei Province P. R. China
| | - Mingle Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan No. 1, Wuhan, 430070 Hubei Province P. R. China
| | - Guiyi Guo
- Henan Key Laboratory of Tea Plant Comprehensive Utilization in South Henan, Xinyang Agriculture and Forestry University, Xinyang, 464000 China
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23
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Xu P, Guo Q, Pang X, Zhang P, Kong D, Liu J. New Insights into Evolution of Plant Heat Shock Factors (Hsfs) and Expression Analysis of Tea Genes in Response to Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2020; 9:E311. [PMID: 32131389 PMCID: PMC7154843 DOI: 10.3390/plants9030311] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 02/18/2020] [Accepted: 02/26/2020] [Indexed: 11/17/2022]
Abstract
Heat shock transcription factor (Hsf) is one of key regulators in plant abotic stress response. Although the Hsf gene family has been identified from several plant species, original and evolution relationship have been fragmented. In addition, tea, an important crop, genome sequences have been completed and function of the Hsf family genes in response to abiotic stresses was not illuminated. In this study, a total of 4208 Hsf proteins were identified within 163 plant species from green algae (Gonium pectorale) to angiosperm (monocots and dicots), which were distributed unevenly into each of plant species tested. The result indicated that Hsf originated during the early evolutionary history of chlorophytae algae and genome-wide genetic varies had occurred during the course of evolution in plant species. Phylogenetic classification of Hsf genes from the representative nine plant species into ten subfamilies, each of which contained members from different plant species, imply that gene duplication had occurred during the course of evolution. In addition, based on RNA-seq data, the member of the Hsfs showed different expression levels in the different organs and at the different developmental stages in tea. Expression patterns also showed clear differences among Camellia species, indicating that regulation of Hsf genes expression varied between organs in a species-specific manner. Furthermore, expression of most Hsfs in response to drought, cold and salt stresses, imply a possible positive regulatory role under abiotic stresses. Expression profiles of nineteen Hsf genes in response to heat stress were also analyzed by quantitative real-time RT-PCR. Several stress-responsive Hsf genes were highly regulated by heat stress treatment. In conclusion, these results lay a solid foundation for us to elucidate the evolutionary origin of plant Hsfs and Hsf functions in tea response to abiotic stresses in the future.
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Affiliation(s)
- Ping Xu
- Department of Tea Science, Zhejiang University, Hangzhou 310058, China;
| | - Qinwei Guo
- Quzhou Academy of Agricultural Sciences, Quzhou 324000, Zhejiang, China;
| | - Xin Pang
- Suzhou Polytechnic Institute of Agriculture, Suzhou 215008, China;
| | - Peng Zhang
- Wulanchabu Academy of Agricultural and Husbandry Sciences, Wulanchabu 012000, Inner Mongolia, China; (P.Z.); (D.K.)
| | - Dejuan Kong
- Wulanchabu Academy of Agricultural and Husbandry Sciences, Wulanchabu 012000, Inner Mongolia, China; (P.Z.); (D.K.)
| | - Jia Liu
- Wulanchabu Academy of Agricultural and Husbandry Sciences, Wulanchabu 012000, Inner Mongolia, China; (P.Z.); (D.K.)
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24
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Zhang L, Chen W, Shi B. Genome-wide analysis and expression profiling of the heat shock transcription factor gene family in Physic Nut ( Jatropha curcas L.). PeerJ 2020; 8:e8467. [PMID: 32071809 PMCID: PMC7007736 DOI: 10.7717/peerj.8467] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/27/2019] [Indexed: 11/20/2022] Open
Abstract
The heat shock transcription factor (Hsf) family, identified as one of the important gene families, participates in plant development process and some stress response. So far, there have been no reports on the research of the Hsf transcription factors in physic nut. In this study, seventeen putative Hsf genes identified from physic nut genome. Phylogenetic analysis manifested these genes classified into three groups: A, B and C. Chromosomal location showed that they distributed eight out of eleven linkage groups. Expression profiling indicated that fourteen JcHsf genes highly expressed in different tissues except JcHsf1, JcHsf6 and JcHsf13. In addition, induction of six and twelve JcHsf genes noted against salt stress and drought stress, respectively, which demonstrated that the JcHsf genes are involved in abiotic stress responses. Our results contribute to a better understanding of the JcHsf gene family and further study of its function.
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Affiliation(s)
- Lin Zhang
- School of Environmental Engineering and Chemistry, Luoyang Institute of Science and Technology, Luoyang, Henan, China
| | - Wei Chen
- School of Environmental Engineering and Chemistry, Luoyang Institute of Science and Technology, Luoyang, Henan, China
| | - Ben Shi
- School of Environmental Engineering and Chemistry, Luoyang Institute of Science and Technology, Luoyang, Henan, China
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25
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Genome-Wide Identification and Characterization of Heat-Shock Transcription Factors in Rubber Tree. FORESTS 2019. [DOI: 10.3390/f10121157] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
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.
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26
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Li W, Wan XL, Yu JY, Wang KL, Zhang J. Genome-Wide Identification, Classification, and Expression Analysis of the Hsf Gene Family in Carnation ( Dianthus caryophyllus). Int J Mol Sci 2019; 20:ijms20205233. [PMID: 31652538 PMCID: PMC6829504 DOI: 10.3390/ijms20205233] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 01/26/2023] Open
Abstract
Heat shock transcription factors (Hsfs) are a class of important transcription factors (TFs) which play crucial roles in the protection of plants from damages caused by various abiotic stresses. The present study aimed to characterize the Hsf genes in carnation (Dianthus caryophyllus), which is one of the four largest cut flowers worldwide. In this study, a total of 17 non-redundant Hsf genes were identified from the D. caryophyllus genome. Specifically, the gene structure and motifs of each DcaHsf were comprehensively analyzed. Phylogenetic analysis of the DcaHsf family distinctly separated nine class A, seven class B, and one class C Hsf genes. Additionally, promoter analysis indicated that the DcaHsf promoters included various cis-acting elements that were related to stress, hormones, as well as development processes. In addition, cis-elements, such as STRE, MYB, and ABRE binding sites, were identified in the promoters of most DcaHsf genes. According to qRT-PCR data, the expression of DcaHsfs varied in eight tissues and six flowering stages and among different DcaHsfs, even in the same class. Moreover, DcaHsf-A1, A2a, A9a, B2a, B3a revealed their putative involvement in the early flowering stages. The time-course expression profile of DcaHsf during stress responses illustrated that all the DcaHsfs were heat- and drought-responsive, and almost all DcaHsfs were down-regulated by cold, salt, and abscisic acid (ABA) stress. Meanwhile, DcaHsf-A3, A7, A9a, A9b, B3a were primarily up-regulated at an early stage in response to salicylic acid (SA). This study provides an overview of the Hsf gene family in D. caryophyllus and a basis for the breeding of stress-resistant carnation.
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Affiliation(s)
- Wei Li
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266000, China.
| | - Xue-Li Wan
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266000, China.
| | - Jia-Yu Yu
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266000, China.
| | - Kui-Ling Wang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266000, China.
| | - Jin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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27
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Li S, Wang R, Jin H, Ding Y, Cai C. Molecular Characterization and Expression Profile Analysis of Heat Shock Transcription Factors in Mungbean. Front Genet 2019; 9:736. [PMID: 30687395 PMCID: PMC6336897 DOI: 10.3389/fgene.2018.00736] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 12/22/2018] [Indexed: 11/30/2022] Open
Abstract
Heat shock transcription factors (Hsfs) are essential elements in plant signal transduction pathways that mediate gene expression in response to various abiotic stresses. Mungbean (Vigna radiata) is an important crop worldwide. The emergence of a genome database now allows for functional analysis of mungbean genes. In this study, we dissect the mungbean Hsfs using genome-wide identification and expression profiles. We characterized a total of 24 VrHsf genes and classified them into three groups (A, B, and C) based on their phylogeny and conserved domain structures. All VrHsf genes exhibit highly conserved exon-intron organization, with two exons and one intron. In addition, all VrHsf proteins contain 16 distinct motifs. Chromosome location analysis revealed that VrHsf genes are located on 8 of the 11 mungbean chromosomes, and that seven duplicated gene pairs had formed among them. Moreover, transcription patterns of VrHsf genes varied in different tissues, indicating their different roles in plant growth and development. We identified multiple stress related cis-elements in VrHsf promoter regions 2 kb upstream of the translation initiation codons, and the expression of most VrHsf genes was altered under different stress conditions, suggesting their potential functions in stress resistance pathways. These molecular characterization and expression profile analyses of VrHsf genes provide essential information for further function investigation.
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Affiliation(s)
- Shuai Li
- Key Lab of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Runhao Wang
- Key Lab of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Hanqi Jin
- Key Lab of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Yanhua Ding
- Key Lab of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Chunmei Cai
- Key Lab of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
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Lohani N, Golicz AA, Singh MB, Bhalla PL. Genome-wide analysis of the Hsf gene family in Brassica oleracea and a comparative analysis of the Hsf gene family in B. oleracea, B. rapa and B. napus. Funct Integr Genomics 2019; 19:515-531. [DOI: 10.1007/s10142-018-0649-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 11/12/2018] [Accepted: 11/19/2018] [Indexed: 02/05/2023]
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29
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Wei Y, Liu G, Chang Y, He C, Shi H. Heat shock transcription factor 3 regulates plant immune response through modulation of salicylic acid accumulation and signalling in cassava. MOLECULAR PLANT PATHOLOGY 2018; 19:2209-2220. [PMID: 29660238 PMCID: PMC6638013 DOI: 10.1111/mpp.12691] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/27/2018] [Accepted: 04/09/2018] [Indexed: 05/05/2023]
Abstract
As the terminal components of signal transduction, heat stress transcription factors (Hsfs) mediate the activation of multiple genes responsive to various stresses. However, the information and functional analysis are very limited in non-model plants, especially in cassava (Manihot esculenta), one of the most important crops in tropical areas. In this study, 32 MeHsfs were identified from the cassava genome; the evolutionary tree, gene structures and motifs were also analysed. Gene expression analysis found that MeHsfs were commonly regulated by Xanthomonas axonopodis pv. manihotis (Xam). Amongst these MeHsfs, MeHsf3 was specifically located in the cell nucleus and showed transcriptionally activated activity on heat stress elements (HSEs). Through transient expression in Nicotiana benthamiana leaves and virus-induced gene silencing (VIGS) in cassava, we identified the essential role of MeHsf3 in plant disease resistance, by regulating the transcripts of Enhanced Disease Susceptibility 1 (EDS1) and pathogen-related gene 4 (PR4). Notably, as regulators of defence susceptibility, MeEDS1 and MePR4 were identified as direct targets of MeHsf3. Moreover, the disease sensitivity of MeHsf3- and MeEDS1-silenced plants could be restored by exogenous salicylic acid (SA) treatment. Taken together, this study highlights the involvement of MeHsf3 in defence resistance through the transcriptional activation of MeEDS1 and MePR4.
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Affiliation(s)
- Yunxie Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesInstitute of Tropical Agriculture and Forestry, Hainan UniversityHaikou 570228China
| | - Guoyin Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesInstitute of Tropical Agriculture and Forestry, Hainan UniversityHaikou 570228China
| | - Yanli Chang
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesInstitute of Tropical Agriculture and Forestry, Hainan UniversityHaikou 570228China
| | - Chaozu He
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesInstitute of Tropical Agriculture and Forestry, Hainan UniversityHaikou 570228China
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesInstitute of Tropical Agriculture and Forestry, Hainan UniversityHaikou 570228China
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Chen B, Feder ME, Kang L. Evolution of heat-shock protein expression underlying adaptive responses to environmental stress. Mol Ecol 2018; 27:3040-3054. [PMID: 29920826 DOI: 10.1111/mec.14769] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/03/2018] [Accepted: 06/07/2018] [Indexed: 12/27/2022]
Abstract
Heat-shock proteins (Hsps) and their cognates are primary mitigators of cell stress. With increasingly severe impacts of climate change and other human modifications of the biosphere, the ability of the heat-shock system to affect evolutionary fitness in environments outside the laboratory and to evolve in response is topic of growing importance. Since the last major reviews, several advances have occurred. First, demonstrations of the heat-shock response outside the laboratory now include many additional taxa and environments. Many of these demonstrations are only correlative, however. More importantly, technical advances in "omic" quantification of nucleic acids and proteins, genomewide association analysis, and manipulation of genes and their expression have enabled the field to move beyond correlation. Several consequent advances are already evident: The pathway from heat-shock gene expression to stress tolerance in nature can be extremely complex, mediated through multiple biological processes and systems, and even multiple species. The underlying genes are more numerous, diverse and variable than previously appreciated, especially with respect to their regulatory variation and epigenetic changes. The impacts and limitations (e.g., due to trade-offs) of natural selection on these genes have become more obvious and better established. At last, as evolutionary capacitors, Hsps may have distinctive impacts on the evolution of other genes and ecological consequences.
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Affiliation(s)
- Bing Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Martin E Feder
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Chidambaranathan P, Jagannadham PTK, Satheesh V, Kohli D, Basavarajappa SH, Chellapilla B, Kumar J, Jain PK, Srinivasan R. Genome-wide analysis identifies chickpea (Cicer arietinum) heat stress transcription factors (Hsfs) responsive to heat stress at the pod development stage. JOURNAL OF PLANT RESEARCH 2018; 131:525-542. [PMID: 28474118 DOI: 10.1007/s10265-017-0948-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/04/2017] [Indexed: 05/15/2023]
Abstract
The heat stress transcription factors (Hsfs) play a prominent role in thermotolerance and eliciting the heat stress response in plants. Identification and expression analysis of Hsfs gene family members in chickpea would provide valuable information on heat stress responsive Hsfs. A genome-wide analysis of Hsfs gene family resulted in the identification of 22 Hsf genes in chickpea in both desi and kabuli genome. Phylogenetic analysis distinctly separated 12 A, 9 B, and 1 C class Hsfs, respectively. An analysis of cis-regulatory elements in the upstream region of the genes identified many stress responsive elements such as heat stress elements (HSE), abscisic acid responsive element (ABRE) etc. In silico expression analysis showed nine and three Hsfs were also expressed in drought and salinity stresses, respectively. Q-PCR expression analysis of Hsfs under heat stress at pod development and at 15 days old seedling stage showed that CarHsfA2, A6, and B2 were significantly upregulated in both the stages of crop growth and other four Hsfs (CarHsfA2, A6a, A6c, B2a) showed early transcriptional upregulation for heat stress at seedling stage of chickpea. These subclasses of Hsfs identified in this study can be further evaluated as candidate genes in the characterization of heat stress response in chickpea.
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Affiliation(s)
- Parameswaran Chidambaranathan
- National Research Centre on Plant Biotechnology, New Delhi, India
- Indian Agricultural Research Institute, New Delhi, India
| | - Prasanth Tej Kumar Jagannadham
- National Research Centre on Plant Biotechnology, New Delhi, India
- Indian Agricultural Research Institute, New Delhi, India
| | - Viswanathan Satheesh
- National Research Centre on Plant Biotechnology, New Delhi, India
- Indian Agricultural Research Institute, New Delhi, India
| | - Deshika Kohli
- National Research Centre on Plant Biotechnology, New Delhi, India
| | | | | | - Jitendra Kumar
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Pradeep Kumar Jain
- National Research Centre on Plant Biotechnology, New Delhi, India
- Indian Agricultural Research Institute, New Delhi, India
| | - R Srinivasan
- National Research Centre on Plant Biotechnology, New Delhi, India.
- Indian Agricultural Research Institute, New Delhi, India.
- Emeritus Scientist, Molecular Biology and Biotechnology, NRC Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India.
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Chen SS, Jiang J, Han XJ, Zhang YX, Zhuo RY. Identification, Expression Analysis of the Hsf Family, and Characterization of Class A4 in Sedum Alfredii Hance under Cadmium Stress. Int J Mol Sci 2018; 19:ijms19041216. [PMID: 29673186 PMCID: PMC5979518 DOI: 10.3390/ijms19041216] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/29/2018] [Accepted: 04/13/2018] [Indexed: 12/25/2022] Open
Abstract
Sedum alfredii Hance, a cadmium (Cd)/zinc (Zn)/lead (Pb) co-hyperaccumulating species, is a promising phytoremediation candidate because it accumulates substantial amounts of heavy metal ions without showing any obvious signs of poisoning. The heat shock transcription factor (Hsf) family plays crucial roles in plant growth, development, and stress responses. Although the roles of some Hsfs in abiotic stress have been well studied in model plants, the Hsf family has not been systematically investigated in heavy metal hyperaccumulators. Here, we comprehensively analyzed the Hsf gene family in S. alfredii based on a transcriptome under Cd stress. There were 22 Hsf members that were identified and phylogenetically clustered into three classes, namely, SaHsfA, SaHsfB, and SaHsfC. All of the three classes shared similar motifs. The expression profiles of the 22 Hsf members showed significant differences: 18 SaHsfs were responsive to Cd stress, as were multiple SaHsp genes, including SaHsp18.1, SaHsp22, SaHsp26.5, SaHsp70, SaHsp90, and SaHsp101. Two class A4 members, SaHsfA4a and SaHsfA4c, exhibited transcriptional activation activities. Overexpression of SaHsfA4a and SaHsfA4c in transgenic yeast indicated an improved tolerance to Cd stress and Cd accumulation. Our results suggest SaHsfs play important regulatory roles in heavy metal stress responses, and provide a reference for further studies on the mechanism of heavy metal stress regulation by SaHsfs.
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Affiliation(s)
- Shuang-Shuang Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China.
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, China.
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China.
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, China.
| | - Xiao-Jiao Han
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China.
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, China.
| | - Yun-Xing Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China.
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, China.
| | - Ren-Ying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China.
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, China.
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Zhang H, Sonnewald U. Differences and commonalities of plant responses to single and combined stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:839-855. [PMID: 28370754 DOI: 10.1111/tpj.13557] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 03/20/2017] [Accepted: 03/27/2017] [Indexed: 05/21/2023]
Abstract
In natural or agricultural environments, plants are constantly exposed to a wide range of biotic and abiotic stresses. Given the forecasted global climate changes, plants will cope with heat waves, drought periods and pathogens at the same time or consecutively. Heat and drought cause opposing physiological responses, while pathogens may or may not profit from climate changes depending on their lifestyle. Several studies have been conducted to find stress-specific signatures or stress-independent commonalities. Previously this has been done by comparing different single stress treatments. This approach has been proven difficult since most studies, comparing single and combined stress conditions, have come to the conclusion that each stress treatment results in specific transcriptional changes. Although transcriptional changes at the level of individual genes are highly variable and stress-specific, central metabolic and signaling responses seem to be common, often leading to an overall reduced plant growth. Understanding how specific transcriptional changes are linked to stress adaptations and identifying central hubs controlling this interaction will be the challenge for the coming years. In this review, we will summarize current knowledge on plant responses to different individual and combined stresses and try to find a common thread potentially underlying these responses. We will begin with a brief summary of known physiological, metabolic, transcriptional and hormonal responses to individual stresses, elucidate potential commonalities and conflicts and finally we will describe results obtained during combined stress experiments. Here we will concentrate on simultaneous application of stress conditions but we will also touch consequences of sequential stress treatments.
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Affiliation(s)
- Haina Zhang
- Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstrasse 5, 91058, Erlangen, Germany
| | - Uwe Sonnewald
- Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstrasse 5, 91058, Erlangen, Germany
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Cai B, Kong X, Zhong C, Sun S, Zhou XF, Jin YH, Wang Y, Li X, Zhu Z, Jin JB. SUMO E3 Ligases GmSIZ1a and GmSIZ1b regulate vegetative growth in soybean . JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:2-14. [PMID: 27762067 PMCID: PMC5248596 DOI: 10.1111/jipb.12504] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 10/18/2016] [Indexed: 05/08/2023]
Abstract
SIZ1 is a small ubiquitin-related modifier (SUMO) E3 ligase that mediates post-translational SUMO modification of target proteins and thereby regulates developmental processes and hormonal and environmental stress responses in Arabidopsis. However, the role of SUMO E3 ligases in crop plants is largely unknown. Here, we identified and characterized two Glycine max (soybean) SUMO E3 ligases, GmSIZ1a and GmSIZ1b. Expression of GmSIZ1a and GmSIZ1b was induced in response to salicylic acid (SA), heat, and dehydration treatment, but not in response to cold, abscisic acid (ABA), and NaCl treatment. Although GmSIZ1a was expressed at higher levels than GmSIZ1b, both genes encoded proteins with SUMO E3 ligase activity in vivo. Heterologous expression of GmSIZ1a or GmSIZ1b rescued the mutant phenotype of Arabidopsis siz1-2, including dwarfism, constitutively activated expression of pathogen-related genes, and ABA-sensitive seed germination. Simultaneous downregulation of GmSIZ1a and GmSIZ1b (GmSIZ1a/b) using RNA interference (RNAi)-mediated gene silencing decreased heat shock-induced SUMO conjugation in soybean. Moreover, GmSIZ1RNAi plants exhibited reduced plant height and leaf size. However, unlike Arabidopsis siz1-2 mutant plants, flowering time and SA levels were not significantly altered in GmSIZ1RNAi plants. Taken together, our results indicate that GmSIZ1a and GmSIZ1b mediate SUMO modification and positively regulate vegetative growth in soybean.
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Affiliation(s)
- Bin Cai
- Key Laboratory of Plant Molecular PhysiologyInstitute of BotanyThe Chinese Academy of SciencesBeijing 100093China
| | - Xiangxiong Kong
- Key Laboratory of Plant Molecular PhysiologyInstitute of BotanyThe Chinese Academy of SciencesBeijing 100093China
| | - Chao Zhong
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China
| | - Suli Sun
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China
| | - Xiao Feng Zhou
- Department of Ornamental HorticultureChina Agricultural UniversityBeijing 100193China
| | - Yin Hua Jin
- Key Laboratory of Plant Molecular PhysiologyInstitute of BotanyThe Chinese Academy of SciencesBeijing 100093China
| | - Youning Wang
- State Key Laboratory of Agricultural MicrobiologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China
| | - Xia Li
- State Key Laboratory of Agricultural MicrobiologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China
| | - Zhendong Zhu
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China
| | - Jing Bo Jin
- Key Laboratory of Plant Molecular PhysiologyInstitute of BotanyThe Chinese Academy of SciencesBeijing 100093China
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Wang P, Song H, Li C, Li P, Li A, Guan H, Hou L, Wang X. Genome-Wide Dissection of the Heat Shock Transcription Factor Family Genes in Arachis. FRONTIERS IN PLANT SCIENCE 2017; 8:106. [PMID: 28220134 PMCID: PMC5292572 DOI: 10.3389/fpls.2017.00106] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 01/18/2017] [Indexed: 05/21/2023]
Abstract
Heat shock transcription factors (Hsfs) are important transcription factors (TFs) in protecting plants from damages caused by various stresses. The released whole genome sequences of wild peanuts make it possible for genome-wide analysis of Hsfs in peanut. In this study, a total of 16 and 17 Hsf genes were identified from Arachis duranensis and A. ipaensis, respectively. We identified 16 orthologous Hsf gene pairs in both peanut species; however HsfXs was only identified from A. ipaensis. Orthologous pairs between two wild peanut species were highly syntenic. Based on phylogenetic relationship, peanut Hsfs were divided into groups A, B, and C. Selection pressure analysis showed that group B Hsf genes mainly underwent positive selection and group A Hsfs were affected by purifying selection. Small scale segmental and tandem duplication may play important roles in the evolution of these genes. Cis-elements, such as ABRE, DRE, and HSE, were found in the promoters of most Arachis Hsf genes. Five AdHsfs and two AiHsfs contained fungal elicitor responsive elements suggesting their involvement in response to fungi infection. These genes were differentially expressed in cultivated peanut under abiotic stress and Aspergillus flavus infection. AhHsf2 and AhHsf14 were significantly up-regulated after inoculation with A. flavus suggesting their possible role in fungal resistance.
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Affiliation(s)
- Pengfei Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Hui Song
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Changsheng Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Pengcheng Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Aiqin Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Hongshan Guan
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Lei Hou
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
- *Correspondence: Lei Hou
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
- College of Life Sciences, Shandong Normal UniversityJinan, China
- Xingjun Wang
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Heat shock transcription factors in banana: genome-wide characterization and expression profile analysis during development and stress response. Sci Rep 2016; 6:36864. [PMID: 27857174 PMCID: PMC5114564 DOI: 10.1038/srep36864] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/21/2016] [Indexed: 12/01/2022] Open
Abstract
Banana (Musa acuminata) is one of the most popular fresh fruits. However, the rapid spread of fungal pathogen Fusarium oxysporum f. sp. cubense (Foc) in tropical areas severely affected banana growth and production. Thus, it is very important to identify candidate genes involved in banana response to abiotic stress and pathogen infection, as well as the molecular mechanism and possible utilization for genetic breeding. Heat stress transcription factors (Hsfs) are widely known for their common involvement in various abiotic stresses and plant-pathogen interaction. However, no MaHsf has been identified in banana, as well as its possible role. In this study, genome-wide identification and further analyses of evolution, gene structure and conserved motifs showed closer relationship of them in every subgroup. The comprehensive expression profiles of MaHsfs revealed the tissue- and developmental stage-specific or dependent, as well as abiotic and biotic stress-responsive expressions of them. The common regulation of several MaHsfs by abiotic and biotic stress indicated the possible roles of them in plant stress responses. Taken together, this study extended our understanding of MaHsf gene family and identified some candidate MaHsfs with specific expression profiles, which may be used as potential candidates for genetic breeding in banana.
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Hao Z, Wei M, Gong S, Zhao D, Tao J. Transcriptome and digital gene expression analysis of herbaceous peony (Paeonia lactiflora Pall.) to screen thermo-tolerant related differently expressed genes. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0465-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Tang R, Zhu W, Song X, Lin X, Cai J, Wang M, Yang Q. Genome-Wide Identification and Function Analyses of Heat Shock Transcription Factors in Potato. FRONTIERS IN PLANT SCIENCE 2016; 7:490. [PMID: 27148315 DOI: 10.3389/fpls.2016.00490/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/26/2016] [Indexed: 05/25/2023]
Abstract
Heat shock transcription factors (Hsfs) play vital roles in the regulation of tolerance to various stresses in living organisms. To dissect the mechanisms of the Hsfs in potato adaptation to abiotic stresses, genome and transcriptome analyses of Hsf gene family were investigated in Solanum tuberosum L. Twenty-seven StHsf members were identified by bioinformatics and phylogenetic analyses and were classified into A, B, and C groups according to their structural and phylogenetic features. StHsfs in the same class shared similar gene structures and conserved motifs. The chromosomal location analysis showed that 27 Hsfs were located in 10 of 12 chromosomes (except chromosome 1 and chromosome 5) and that 18 of these genes formed 9 paralogous pairs. Expression profiles of StHsfs in 12 different organs and tissues uncovered distinct spatial expression patterns of these genes and their potential roles in the process of growth and development. Promoter and quantitative real-time polymerase chain reaction (qRT-PCR) detections of StHsfs were conducted and demonstrated that these genes were all responsive to various stresses. StHsf004, StHsf007, StHsf009, StHsf014, and StHsf019 were constitutively expressed under non-stress conditions, and some specific Hsfs became the predominant Hsfs in response to different abiotic stresses, indicating their important and diverse regulatory roles in adverse conditions. A co-expression network between StHsfs and StHsf -co-expressed genes was generated based on the publicly-available potato transcriptomic databases and identified key candidate StHsfs for further functional studies.
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Affiliation(s)
- Ruimin Tang
- Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University Nanjing, China
| | - Wenjiao Zhu
- Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University Nanjing, China
| | - Xiaoyan Song
- Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University Nanjing, China
| | - Xingzhong Lin
- Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University Nanjing, China
| | - Jinghui Cai
- Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University Nanjing, China
| | - Man Wang
- Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University Nanjing, China
| | - Qing Yang
- Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University Nanjing, China
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Nagaraju M, Reddy PS, Kumar SA, Srivastava RK, Kishor PBK, Rao DM. Genome-wide Scanning and Characterization of Sorghum bicolor L. Heat Shock Transcription Factors. Curr Genomics 2016; 16:279-91. [PMID: 27006630 PMCID: PMC4765522 DOI: 10.2174/1389202916666150313230812] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/07/2015] [Accepted: 03/12/2015] [Indexed: 11/22/2022] Open
Abstract
A genome-wide scanning of Sorghum bicolor resulted in the identification of 25 SbHsf
genes. Phylogenetic analysis shows the ortholog genes that are clustered with only rice, representing a
common ancestor. Promoter analysis revealed the identification of different cis-acting elements that
are responsible for abiotic as well as biotic stresses. Hsf domains like DBD, NLS, NES, and AHA
have been analyzed for their sequence similarity and functional characterization. Tissue specific expression
patterns of Hsfs in different tissues like mature embryo, seedling, root, and panicle were studied
using real-time PCR. While Hsfs4 and 22 are highly expressed in panicle, 4 and 9 are expressed in
seedlings. Sorghum plants were exposed to different abiotic stress treatments but no expression of any Hsf was observed
when seedlings were treated with ABA. High level expression of Hsf1 was noticed during high temperature as well as
cold stresses, 4 and 6 during salt and 5, 6, 10, 13, 19, 23 and 25 during drought stress. This comprehensive analysis of
SbHsf genes will provide an insight on how these genes are regulated in different tissues and also under different abiotic
stresses and help to determine the functions of Hsfs during drought and temperature stress tolerance.
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Affiliation(s)
- M Nagaraju
- Department of Genetics, Osmania University, Hyderabad 500 007, India
| | - Palakolanu Sudhakar Reddy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru-502324, Hyderabad, India
| | - S Anil Kumar
- Department of Genetics, Osmania University, Hyderabad 500 007, India
| | - Rakesh K Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru-502324, Hyderabad, India
| | - P B Kavi Kishor
- Department of Genetics, Osmania University, Hyderabad 500 007, India
| | - D Manohar Rao
- Department of Genetics, Osmania University, Hyderabad 500 007, India
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Tang R, Zhu W, Song X, Lin X, Cai J, Wang M, Yang Q. Genome-Wide Identification and Function Analyses of Heat Shock Transcription Factors in Potato. FRONTIERS IN PLANT SCIENCE 2016; 7:490. [PMID: 27148315 PMCID: PMC4836240 DOI: 10.3389/fpls.2016.00490] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/26/2016] [Indexed: 05/18/2023]
Abstract
Heat shock transcription factors (Hsfs) play vital roles in the regulation of tolerance to various stresses in living organisms. To dissect the mechanisms of the Hsfs in potato adaptation to abiotic stresses, genome and transcriptome analyses of Hsf gene family were investigated in Solanum tuberosum L. Twenty-seven StHsf members were identified by bioinformatics and phylogenetic analyses and were classified into A, B, and C groups according to their structural and phylogenetic features. StHsfs in the same class shared similar gene structures and conserved motifs. The chromosomal location analysis showed that 27 Hsfs were located in 10 of 12 chromosomes (except chromosome 1 and chromosome 5) and that 18 of these genes formed 9 paralogous pairs. Expression profiles of StHsfs in 12 different organs and tissues uncovered distinct spatial expression patterns of these genes and their potential roles in the process of growth and development. Promoter and quantitative real-time polymerase chain reaction (qRT-PCR) detections of StHsfs were conducted and demonstrated that these genes were all responsive to various stresses. StHsf004, StHsf007, StHsf009, StHsf014, and StHsf019 were constitutively expressed under non-stress conditions, and some specific Hsfs became the predominant Hsfs in response to different abiotic stresses, indicating their important and diverse regulatory roles in adverse conditions. A co-expression network between StHsfs and StHsf -co-expressed genes was generated based on the publicly-available potato transcriptomic databases and identified key candidate StHsfs for further functional studies.
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Liu ZW, Wu ZJ, Li XH, Huang Y, Li H, Wang YX, Zhuang J. Identification, classification, and expression profiles of heat shock transcription factors in tea plant (Camellia sinensis) under temperature stress. Gene 2015; 576:52-9. [PMID: 26431998 DOI: 10.1016/j.gene.2015.09.076] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 09/21/2015] [Accepted: 09/24/2015] [Indexed: 02/03/2023]
Abstract
In vascular plants, heat shock transcription factors (Hsfs) regulate heat stress response by regulating the expression of heat shock proteins. This study systematically and comprehensively analyzed the Hsf family in tea plant [Camellia sinensis (L.) O. Kuntze]. A total of 16 CsHsfs were identified from the transcriptome database of tea plant and analyzed for their phylogenetic relationships, motifs, and physicochemical characteristics. On the basis of the phylogenetic comparison of tea plant with Arabidopsis thaliana, Populus trichocarpa, Theobroma cacao, and Oryza sativa, the CsHsfs were classified into three classes, namely, A (56.25%), B (37.50%), and C (6.25%). Heat mapping showed that the expression profiles of CsHsf genes under non-stress conditions varied among four tea plant cultivars, namely, 'Yunnanshilixiang', 'Chawansanhao', 'Ruchengmaoyecha', and 'Anjibaicha'. Six CsHsf genes (CsHsfA1a, CsHsfA1b, CsHsfA6, CsHsfB1, CsHsfB2b, and CsHsfC1) were selected from classes A, B, and C to analyze the expression profiles of CsHsf genes through quantitative real-time PCR in 'Yingshuang', 'Anjibaicha', and 'Yunnanshilixiang' under high (38 °C) or low (4 °C) temperature stress. Temperature stress positively or negatively regulated all of the selected CsHsf genes, and the expression levels evidently varied even among CsHsf genes belonging to the same class. This study provided a relatively detailed summary of Hsfs in tea plant and may serve as a reference for further studies on the mechanism of temperature stress regulation by CsHsfs.
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Affiliation(s)
- Zhi-Wei Liu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhi-Jun Wu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xing-Hui Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Huang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yong-Xin Wang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jing Zhuang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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Qiao X, Li M, Li L, Yin H, Wu J, Zhang S. Genome-wide identification and comparative analysis of the heat shock transcription factor family in Chinese white pear (Pyrus bretschneideri) and five other Rosaceae species. BMC PLANT BIOLOGY 2015; 15:12. [PMID: 25604453 PMCID: PMC4310194 DOI: 10.1186/s12870-014-0401-5] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 12/22/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Heat shock transcription factors (Hsfs), which act as important transcriptional regulatory proteins in eukaryotes, play a central role in controlling the expression of heat-responsive genes. At present, the genomes of Chinese white pear ('Dangshansuli') and five other Rosaceae fruit crops have been fully sequenced. However, information about the Hsfs gene family in these Rosaceae species is limited, and the evolutionary history of the Hsfs gene family also remains unresolved. RESULTS In this study, 137 Hsf genes were identified from six Rosaceae species (Pyrus bretschneideri, Malus × domestica, Prunus persica, Fragaria vesca, Prunus mume, and Pyrus communis), 29 of which came from Chinese white pear, designated as PbHsf. Based on the structural characteristics and phylogenetic analysis of these sequences, the Hsf family genes could be classified into three main groups (classes A, B, and C). Segmental and dispersed duplications were the primary forces underlying Hsf gene family expansion in the Rosaceae. Most of the PbHsf duplicated gene pairs were dated back to the recent whole-genome duplication (WGD, 30-45 million years ago (MYA)). Purifying selection also played a critical role in the evolution of Hsf genes. Transcriptome data demonstrated that the expression levels of the PbHsf genes were widely different. Six PbHsf genes were upregulated in fruit under naturally increased temperature. CONCLUSION A comprehensive analysis of Hsf genes was performed in six Rosaceae species, and 137 full length Hsf genes were identified. The results presented here will undoubtedly be useful for better understanding the complexity of the Hsf gene family and will facilitate functional characterization in future studies.
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Affiliation(s)
- Xin Qiao
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Meng Li
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Leiting Li
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Hao Yin
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Juyou Wu
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Shaoling Zhang
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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Hu Y, Han YT, Wei W, Li YJ, Zhang K, Gao YR, Zhao FL, Feng JY. Identification, isolation, and expression analysis of heat shock transcription factors in the diploid woodland strawberry Fragaria vesca. FRONTIERS IN PLANT SCIENCE 2015; 6:736. [PMID: 26442049 PMCID: PMC4569975 DOI: 10.3389/fpls.2015.00736] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/29/2015] [Indexed: 05/03/2023]
Abstract
Heat shock transcription factors (Hsfs) are known to play dominant roles in plant responses to heat, as well as other abiotic or biotic stress stimuli. While the strawberry is an economically important fruit plant, little is known about the Hsf family in the strawberry. To explore the functions of strawberry Hsfs in abiotic and biotic stress responses, this study identified 17 Hsf genes (FvHsfs) in a wild diploid woodland strawberry (Fragaria vesca, 2n = 2x = 14) and isolated 14 of these genes. Phylogenetic analysis divided the strawberry FvHsfs genes into three main groups. The evolutionary and structural analyses revealed that the FvHsf family is conserved. The promoter sequences of the FvHsf genes contain upstream regulatory elements corresponding to different stress stimuli. In addition, 14 FvHsf-GFP fusion proteins showed differential subcellular localization in Arabidopsis mesophyll protoplasts. Furthermore, we examined the expression of the 17 FvHsf genes in wild diploid woodland strawberries under various conditions, including abiotic stresses (heat, cold, drought, and salt), biotic stress (powdery mildew infection), and hormone treatments (abscisic acid, ethephon, methyl jasmonate, and salicylic acid). Fifteen of the seventeen FvHsf genes exhibited distinct changes on the transcriptional level during heat treatment. Of these 15 FvHsfs, 8 FvHsfs also exhibited distinct responses to other stimuli on the transcriptional level, indicating versatile roles in the response to abiotic and biotic stresses. Taken together, the present work may provide the basis for further studies to dissect FvHsf function in response to stress stimuli.
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Affiliation(s)
- Yang Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of AgricultureYangling, Shaanxi, China
| | - Yong-Tao Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, Shaanxi, China
| | - Wei Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of AgricultureYangling, Shaanxi, China
| | - Ya-Juan Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, Shaanxi, China
| | - Kai Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of AgricultureYangling, Shaanxi, China
| | - Yu-Rong Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, Shaanxi, China
| | - Feng-Li Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, Shaanxi, China
| | - Jia-Yue Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of AgricultureYangling, Shaanxi, China
- *Correspondence: Jia-Yue Feng, College of Horticulture, Northwest A&F University, No.3 Taicheng Road, Yangling 712100, Shaanxi, China
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Li PS, Yu TF, He GH, Chen M, Zhou YB, Chai SC, Xu ZS, Ma YZ. Genome-wide analysis of the Hsf family in soybean and functional identification of GmHsf-34 involvement in drought and heat stresses. BMC Genomics 2014; 15:1009. [PMID: 25416131 PMCID: PMC4253008 DOI: 10.1186/1471-2164-15-1009] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 10/08/2014] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND High temperature affects organism growth and metabolic activity. Heat shock transcription factors (Hsfs) are key regulators in heat shock response in eukaryotes and prokaryotes. Under high temperature conditions, Hsfs activate heat shock proteins (Hsps) by combining with heat stress elements (HSEs) in their promoters, leading to defense of heat stress. Since the first plant Hsf gene was identified in tomato, several plant Hsf family genes have been thoroughly characterized. Although soybean (Glycine max), an important oilseed crops, genome sequences have been available, the Hsf family genes in soybean have not been characterized accurately. RESULT We analyzed the Hsf genetic structures and protein function domains using the GSDS, Pfam, SMART, PredictNLS, and NetNES online tools. The genome scanning of dicots (soybean and Arabidopsis) and monocots (rice and maize) revealed that the whole-genome replication occurred twice in soybean evolution. The plant Hsfs were classified into 3 classes and 16 subclasses according to protein structure domains. The A8 and B3 subclasses existed only in dicots and the A9 and C2 occurred only in monocots. Thirty eight soybean Hsfs were systematically identified and grouped into 3 classes and 12 subclasses, and located on 15 soybean chromosomes. The promoter regions of the soybean Hsfs contained cis-elements that likely participate in drought, low temperature, and ABA stress responses. There were large differences among Hsfs based on transcriptional levels under the stress conditions. The transcriptional levels of the A1 and A2 subclass genes were extraordinarily high. In addition, differences in the expression levels occurred for each gene in the different organs and at the different developmental stages. Several genes were chosen to determine their subcellular localizations and functions. The subcellular localization results revealed that GmHsf-04, GmHsf-33, and GmHsf-34 were located in the nucleus. Overexpression of the GmHsf-34 gene improved the tolerances to drought and heat stresses in Arabidopsis plants. CONCLUSIONS This present investigation of the quantity, structural features, expression characteristics, subcellular localizations, and functional roles provides a scientific basis for further research on soybean Hsf functions.
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Affiliation(s)
- Pan-Song Li
- />College of Agronomy, Northwest A & F University, Yangling, 712100 China
- />Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Science, Beijing, 100081 China
| | - Tai-Fei Yu
- />Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Science, Beijing, 100081 China
| | - Guan-Hua He
- />Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Science, Beijing, 100081 China
| | - Ming Chen
- />Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Science, Beijing, 100081 China
| | - Yong-Bin Zhou
- />Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Science, Beijing, 100081 China
| | - Shou-Cheng Chai
- />College of Agronomy, Northwest A & F University, Yangling, 712100 China
| | - Zhao-Shi Xu
- />Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Science, Beijing, 100081 China
| | - You-Zhi Ma
- />Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Science, Beijing, 100081 China
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Heat shock factors in carrot: genome-wide identification, classification, and expression profiles response to abiotic stress. Mol Biol Rep 2014; 42:893-905. [PMID: 25403331 DOI: 10.1007/s11033-014-3826-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/10/2014] [Indexed: 12/16/2022]
Abstract
Heat shock factors (HSFs) play key roles in the response to abiotic stress in eukaryotes. In this study, 35 DcHSFs were identified from carrot (Daucus carota L.) based on the carrot genome database. All 35 DcHSFs were divided into three classes (A, B, and C) according to the structure and phylogenetic relationships of four different plants, namely, Arabidopsis thaliana, Vitis vinifera, Brassica rapa, and Oryza sativa. Comparative analysis of algae, gymnosperms, and angiosperms indicated that the numbers of HSF transcription factors were related to the plant's evolution. The expression profiles of five DcHsf genes (DcHsf 01, DcHsf 02, DcHsf 09, DcHsf 10, and DcHsf 16), which selected from each subfamily (A, B, and C), were detected by quantitative real-time PCR under abiotic stresses (cold, heat, high salinity, and drought) in two carrot cultivars, D. carota L. cvs. Kurodagosun and Junchuanhong. The expression levels of DcHsfs were markedly increased by heat stress, except that of DcHsf 10, which was down regulated. The expression profiles of different DcHsfs in the same class also differed under various stress treatments. The expression profiles of these DcHsfs were also different in tissues of two carrot cultivars. This study is the first to identify and characterize the DcHSF family transcription factors in plants of Apiaceae using whole-genome analysis. The results of this study provide an in-depth understanding of the DcHSF family transcription factors' structure, function, and evolution in carrot.
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Song X, Liu G, Duan W, Liu T, Huang Z, Ren J, Li Y, Hou X. Genome-wide identification, classification and expression analysis of the heat shock transcription factor family in Chinese cabbage. Mol Genet Genomics 2014; 289:541-51. [PMID: 24609322 DOI: 10.1007/s00438-014-0833-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 02/20/2014] [Indexed: 12/20/2022]
Abstract
The Hsf gene family, one of the most important transcription factor families, plays crucial roles in regulating heat resistance. However, a systematic and comprehensive analysis of this gene family has not been reported in Chinese cabbage. Therefore, systematic analysis of the Hsf gene family in Chinese cabbage has profound significance. In this study, 35 BrHsf genes were identified from Chinese cabbage, which could be classified into three groups according to their structural characteristics and phylogenetic comparisons with Arabidopsis and rice. Thirty-three BrHsf genes mapped on chromosomes were further assigned to three subgenomes and eight ancestral karyotypes. Distribution mapping showed that BrHsf genes were non-randomly localized on chromosomes. Chinese cabbage and Arabidopsis shared 22 orthologous gene pairs. The expansion of BrHsf genes mainly resulted from genome triplication. Comparative analysis showed that the most Hsf genes were in Chinese cabbage among the five species analyzed. Interestingly, the number of Hsf genes of heat-resistant plants (Theobroma cacao and Musa acuminata) was fewer than that in Chinese cabbage. The expression patterns of BrHsf genes were different in six tissues, based on RNA-seq. Quantitative real-time-PCR analysis showed that the expression level of BrHsf genes varied under various abiotic stresses. In conclusion, this comprehensive analysis of BrHsf genes will provide rich resources, aiding the determination of Hsfs functions in plant heat resistance. Furthermore, the comparative genomics analysis deepened our understanding of Hsf genes' evolution accompanied by the polyploidy event of Chinese cabbage.
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Affiliation(s)
- Xiaoming Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
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