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Ren J, Feng L, Guo L, Gou H, Lu S, Mao J. Genome-wide identification and expression analysis of the BURP domain-containing genes in Malus domestica. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1717-1731. [PMID: 38162916 PMCID: PMC10754798 DOI: 10.1007/s12298-023-01393-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 01/03/2024]
Abstract
The conserved BURP-containing proteins are specific to plants and play a crucial role in plant growth, development, and response to abiotic stresses. However, less is known about the systematic characterization of BURP-containing proteins in apple. This study aimed to identify and analyze all BURP-containing genes in the apple genome, as well as to examine their expression patterns through various bioinformatics methods. Eighteen members of BURP-containing genes were identified in apple, six members lacked signal peptides, and the secondary structure was mainly a Random coil of BURP-containing genes. Gene structure and Motif analysis showed that proteins have similar structures and are conserved at the C-terminal. Cis-acting element analysis revealed that the proteins contain phytohormone and stress response elements, and chromosomal localization revealed that the family is unevenly distributed across eight chromosomes, with duplication of fragments leading to the expansion of family proteins. Tissue expression showed that MdPG3 and MdPG4 were expressed in different tissues and different varieties, MdRD2 and MdRD7 were highly expressed in 'M74' fruits and MdRD7 in 'M49' leaves, while MdUSP1 was highly expressed in 'GD' roots. The quantitative real-time PCR analysis showed that the expressions of six and seven genes were significantly up-regulated under NaCl and PEG treatments, respectively, whereas MdRD7 was significantly up-regulated under NaCl and PEG treatment over time. This study offers a comprehensive identification and expression analysis of BURP-containing proteins in apple. The findings provide a theoretical foundation for further exploration of the functions of this protein family. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01393-7.
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Affiliation(s)
- Jiaxuan Ren
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
| | - Li Feng
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
| | - Lili Guo
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
| | - Huimin Gou
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
| | - Shixiong Lu
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
| | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
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Wang W, Zhang Z, Li X. Identification and expression analysis of BURP domain-containing genes in jujube and their involvement in low temperature and drought response. BMC Genomics 2022; 23:692. [PMID: 36203136 PMCID: PMC9541082 DOI: 10.1186/s12864-022-08907-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Background Plant-specific BURP domain-containing genes are involved in plant development and stress responses. However, the role of BURP family in jujube (Ziziphus jujuba Mill.) has not been investigated. Results In this study, 17 BURP genes belonging to four subfamilies were identified in jujube based on homology analysis, gene structures, and conserved motif confirmation. Gene duplication analysis indicated both tandem duplication and segmental duplication had contributed to ZjBURP expansion. The ZjBURPs were extensively expressed in flowers, young fruits, and jujube leaves. Transcriptomic data and qRT-PCR analysis further revealed that ZjBURPs also significantly influence fruit development, and most genes could be induced by low temperature, salinity, and drought stresses. Notably, several BURP genes significantly altered expression in response to low temperature (ZjPG1) and drought stresses (ZjBNM7, ZjBNM8, and ZjBNM9). Conclusions These results provided insights into the possible roles of ZjBURPs in jujube development and stress response. These findings would help selecting candidate ZjBURP genes for cold- and drought-tolerant jujube breeding. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08907-9.
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Affiliation(s)
- Wenzhu Wang
- College of Forestry, Research Center for Jujube Engineering and Technology of State Forestry Administration, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhong Zhang
- College of Forestry, Research Center for Jujube Engineering and Technology of State Forestry Administration, Northwest A&F University, Yangling, 712100, Shaanxi, China.,Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518116, Guangdong, China
| | - Xingang Li
- College of Forestry, Research Center for Jujube Engineering and Technology of State Forestry Administration, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Kavas M, Yıldırım K, Seçgin Z, Abdulla MF, Gökdemir G. Genome-wide identification of the BURP domain-containing genes in Phaseolus vulgaris. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1885-1902. [PMID: 34629769 PMCID: PMC8484419 DOI: 10.1007/s12298-021-01052-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/29/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Plant-specific BURP domain-containing proteins have an essential role in the plant's development and stress responses. Although BURP domain-containing proteins have been identified in several plant species, genome-wide analysis of the BURP gene family has not been investigated in the common bean. In the present study, we identified 11 BURP family members in the common bean (Phaseolus vulgaris) genome with a comprehensive in silico analysis. Pairwise alignment and phylogenetic analyses grouped PvBURP members into four subfamilies [RD-22 like (3), PG1β-like (4), BNM2-like (3), and USP-like (1)] according to their amino acid motifs, protein domains and intron-exon structure. The physical and biochemical characteristics of amino acids, motif and intron-exon structure, and cis-regulatory elements of BURPs members were determined. Promoter regions of BURP members included stress, light, and hormone response-related cis-elements. Therefore, expression profiles of PvBURP genes were identified with in silico tools and qRT-PCR analyses under stress (salt and drought) and hormone treatment (ABA, IAA) in the current study. While significant activity changes were not observed in BURP genes in RNA-seq data sets related to salt stress, it was determined that some BURP genes were expressed differently in those with drought stress. We identified 12 different miRNA, including miRNA395, miRNA156, miRNA169, miRNA171, miRNA319, and miRNA390, targeting the nine PvBURP genes using two different in silico tools based on perfect or near-perfect complementarity to their targets. Here we present the first study to identify and characterize the BURP genes in common bean using whole-genome analysis, and the findings may serve as a reference for future functional research in common bean. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01052-9.
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Affiliation(s)
- Musa Kavas
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Turkey
| | - Kubilay Yıldırım
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Ondokuz Mayıs University, Samsun, Turkey
| | - Zafer Seçgin
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Turkey
| | - Mohamed Farah Abdulla
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Turkey
| | - Gökhan Gökdemir
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Turkey
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4
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Sun H, Wei H, Wang H, Hao P, Gu L, Liu G, Ma L, Su Z, Yu S. Genome-wide identification and expression analysis of the BURP domain-containing genes in Gossypium hirsutum. BMC Genomics 2019; 20:558. [PMID: 31286851 PMCID: PMC6615115 DOI: 10.1186/s12864-019-5948-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 06/30/2019] [Indexed: 11/24/2022] Open
Abstract
Background Many BURP domain-containing proteins, which are unique to plants, have been identified. They performed diverse functions in plant development and the stress response. To date, only a few BURP domain-containing genes have been studied, and no comprehensive analysis of the gene family in cotton has been reported. Results In this study, 18, 17 and 30 putative BURP genes were identified in G. raimondii (D5), G. arboreum (A2) and G. hirsutum (AD1), respectively. These BURP genes were phylogenetically classified into eight subfamilies, which were confirmed by analyses of gene structures, motifs and protein domains. The uneven distribution of BURPs in chromosomes and gene duplication analysis indicated that segmental duplication might be the main driving force of the GhBURP family expansion. Promoter regions of all GhBURPs contained at least one putative stress-related cis-elements. Analysis of transcriptomic data and qRT-PCR showed that GhBURPs showed different expression patterns in different organs, and all of them, especially the members of the RD22-like subfamily, could be induced by different stresses, such as abscisic acid (ABA) and salicylic acid (SA), which indicated that the GhBURPs may performed important functions in cotton’s responses to various abiotic stresses. Conclusions Our study comprehensively analyzed BURP genes in G. hirsutum, providing insight into the functions of GhBURPs in cotton development and adaptation to stresses. Electronic supplementary material The online version of this article (10.1186/s12864-019-5948-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Huiru Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, China.,College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, China
| | - Pengbo Hao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, China.,College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Lijiao Gu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, China
| | - Guoyuan Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, China
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, China
| | - Zhengzheng Su
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, China
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, 455000, China. .,College of Agronomy, Northwest A&F University, Yangling, 712100, China.
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Dinh SN, Kang H. An endoplasmic reticulum-localized Coffea arabica BURP domain-containing protein affects the response of transgenic Arabidopsis plants to diverse abiotic stresses. PLANT CELL REPORTS 2017; 36:1829-1839. [PMID: 28803325 DOI: 10.1007/s00299-017-2197-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/05/2017] [Indexed: 06/07/2023]
Abstract
The Coffea arabica BURP domain-containing gene plays an important role in the response of transgenic Arabidopsis plants to abiotic stresses via regulating the level of diverse proteins. Although the functions of plant-specific BURP domain-containing proteins (BDP) have been determined for a few plants, their roles in the growth, development, and stress responses of most plant species, including coffee plant (Coffea arabica), are largely unknown. In this study, the function of a C. arabica BDP, designated CaBDP1, was investigated in transgenic Arabidopsis plants. The expression of CaBDP1 was highly modulated in coffee plants subjected to drought, cold, salt, or ABA. Confocal analysis of CaBDP1-GFP fusion proteins revealed that CaBDP1 is localized in the endoplasmic reticulum. The ectopic expression of CaBDP1 in Arabidopsis resulted in delayed germination of the transgenic plants under abiotic stress and in the presence of ABA. Cotyledon greening and seedling growth of the transgenic plants were inhibited in the presence of ABA due to the upregulation of ABA signaling-related genes like ABI3, ABI4, and ABI5. Proteome analysis revealed that the levels of several proteins are modulated in CaBDP1-expressing transgenic plants. The results of this study underscore the importance of BURP domain proteins in plant responses to diverse abiotic stresses.
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Affiliation(s)
- Sy Nguyen Dinh
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, Korea
- Institute of Environment and Biotechnology, Taynguyen University, 567 Le Duan Street, Buon Ma Thuot, Daklak Province, Vietnam
| | - Hunseung Kang
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, Korea.
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Drought and exogenous abscisic acid alter hydrogen peroxide accumulation and differentially regulate the expression of two maize RD22-like genes. Sci Rep 2017; 7:8821. [PMID: 28821770 PMCID: PMC5562893 DOI: 10.1038/s41598-017-08976-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/17/2017] [Indexed: 12/20/2022] Open
Abstract
Increased biosynthesis of abscisic acid (ABA) occurs in plants in response to water deficit, which is mediated by changes in the levels of reactive oxygen species such as H2O2. Water deficit and ABA induce expression of some RD22-like proteins. This study aimed to evaluate the effect of water deficit and exogenous ABA (50 µM ABA applied every 24 hours for a total of 72 hours) on H2O2 content in Zea mays (maize) and to characterise genes encoding two putative maize RD22-like proteins (designated ZmRD22A and ZmRD22B). The expression profiles of the two putative maize RD22-like genes in response to water deficit and treatment with ABA were examined in leaves. In silico analyses showed that the maize RD22-like proteins share domain organisation with previously characterized RD22-like proteins. Both water deficit and exogenous ABA resulted in increased H2O2 content in leaves but the increase was more pronounced in response to water deficit than to exogenous ABA. Lignin content was not affected by exogenous ABA, whereas it was decreased by water deficit. Expression of both RD22-like genes was up-regulated by drought but the ZmRD22A gene was not influenced by exogenous ABA, whereas ZmRD22B was highly responsive to exogenous ABA.
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7
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Tang Y, Ou Z, Qiu J, Mi Z. Putative signal peptides of two BURP proteins can direct proteins to their destinations in tobacco cell system. Biotechnol Lett 2014; 36:2343-9. [PMID: 25048229 DOI: 10.1007/s10529-014-1603-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 06/26/2014] [Indexed: 10/25/2022]
Abstract
Plant-specific BURP family proteins have a diverse subcellular localization with different functions. However, only limited studies have investigated the functions of their different domains. In the present study, the role of the N-terminal putative signal peptide in protein subcellular localization was investigated using a tobacco cell system. The results showed that SALI3-2 was present in vacuoles, whereas AtRD22 was directed to the apoplast. The N-terminal putative signal peptides of both proteins were confirmed to be the essential and critical domains for targeting the proteins to their destinations. We also demonstrate that the expression and accumulation of mGFP in tobacco cells was increased when mGFP was fused to the putative signal peptide of SALI3-2. The findings offer the potential application of this short peptide in protein production in plants.
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Affiliation(s)
- Yulin Tang
- College of Life Science, Shenzhen University, Shenzhen, 518060, China,
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Harshavardhan VT, Van Son L, Seiler C, Junker A, Weigelt-Fischer K, Klukas C, Altmann T, Sreenivasulu N, Bäumlein H, Kuhlmann M. AtRD22 and AtUSPL1, members of the plant-specific BURP domain family involved in Arabidopsis thaliana drought tolerance. PLoS One 2014; 9:e110065. [PMID: 25333723 PMCID: PMC4198191 DOI: 10.1371/journal.pone.0110065] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 09/08/2014] [Indexed: 12/11/2022] Open
Abstract
Crop plants are regularly challenged by a range of environmental stresses which typically retard their growth and ultimately compromise economic yield. The stress response involves the reprogramming of approximately 4% of the transcriptome. Here, the behavior of AtRD22 and AtUSPL1, both members of the Arabidopsis thaliana BURP (BNM2, USP, RD22 and polygalacturonase isozyme) domain-containing gene family, has been characterized. Both genes are up-regulated as part of the abscisic acid (ABA) mediated moisture stress response. While AtRD22 transcript was largely restricted to the leaf, that of AtUSPL1 was more prevalent in the root. As the loss of function of either gene increased the plant's moisture stress tolerance, the implication was that their products act to suppress the drought stress response. In addition to the known involvement of AtUSPL1 in seed development, a further role in stress tolerance was demonstrated. Based on transcriptomic data and phenotype we concluded that the enhanced moisture stress tolerance of the two loss-of-function mutants is a consequence of an enhanced basal defense response.
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Affiliation(s)
- Vokkaliga Thammegowda Harshavardhan
- Research Group Abiotic Stress Genomics, Interdisciplinary Center for Crop Plant Research (IZN), Halle (Saale), Germany, and Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, OT Gatersleben, Germany
| | - Le Van Son
- Research Group Gene Regulation, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, OT Gatersleben, Germany
- National Key Laboratory of Gene Technology, Institute of Biotechnology Vietnam, Academy of Science and Technology, Hanoi, Vietnam
| | - Christiane Seiler
- Research Group Abiotic Stress Genomics, Interdisciplinary Center for Crop Plant Research (IZN), Halle (Saale), Germany, and Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, OT Gatersleben, Germany
| | - Astrid Junker
- Research Group Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, OT Gatersleben, Germany
| | - Kathleen Weigelt-Fischer
- Research Group Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, OT Gatersleben, Germany
| | - Christian Klukas
- Research Group Image Analysis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, OT Gatersleben, Germany
| | - Thomas Altmann
- Research Group Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, OT Gatersleben, Germany
| | - Nese Sreenivasulu
- Research Group Abiotic Stress Genomics, Interdisciplinary Center for Crop Plant Research (IZN), Halle (Saale), Germany, and Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, OT Gatersleben, Germany
- Grain Quality and Nutrition Center, International Rice Research Institute (IRRI), Metro Manila, Philippines
| | - Helmut Bäumlein
- Research Group Gene Regulation, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, OT Gatersleben, Germany
| | - Markus Kuhlmann
- Research Group Abiotic Stress Genomics, Interdisciplinary Center for Crop Plant Research (IZN), Halle (Saale), Germany, and Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, OT Gatersleben, Germany
- * E-mail:
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Tang Y, Cao Y, Qiu J, Gao Z, Ou Z, Wang Y, Zheng Y. Expression of a vacuole-localized BURP-domain protein from soybean (SALI3-2) enhances tolerance to cadmium and copper stresses. PLoS One 2014; 9:e98830. [PMID: 24901737 PMCID: PMC4047006 DOI: 10.1371/journal.pone.0098830] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 05/07/2014] [Indexed: 11/19/2022] Open
Abstract
The plant-specific BURP family proteins play diverse roles in plant development and stress responses, but the function mechanism of these proteins is still poorly understood. Proteins in this family are characterized by a highly conserved BURP domain with four conserved Cys-His repeats and two other Cys, indicating that these proteins potentially interacts with metal ions. In this paper, an immobilized metal affinity chromatography (IMAC) assay showed that the soybean BURP protein SALI3-2 could bind soft transition metal ions (Cd(2+), Co(2+), Ni(2+), Zn(2+) and Cu(2+)) but not hard metal ions (Ca(2+) and Mg(2+)) in vitro. A subcellular localization analysis by confocal laser scanning microscopy revealed that the SALI3-2-GFP fusion protein was localized to the vacuoles. Physiological indexes assay showed that Sali3-2-transgenic Arabidopsis thaliana seedlings were more tolerant to Cu(2+) or Cd(2+) stresses than the wild type. An inductively coupled plasma optical emission spectrometry (ICP-OES) analysis illustrated that, compared to the wild type seedlings the Sali3-2-transgenic seedlings accumulated more cadmium or copper in the roots but less in the upper ground tissues when the seedlings were exposed to excessive CuCl2 or CdCl2 stress. Therefore, our findings suggest that the SALI3-2 protein may confer cadmium (Cd(2+)) and copper (Cu(2+)) tolerance to plants by helping plants to sequester Cd(2+) or Cu(2+) in the root and reduce the amount of heavy metals transported to the shoots.
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Affiliation(s)
- Yulin Tang
- Shenzhen Key Laboratory of Microbial and Gene Engineering, College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, People’s Republic of China
| | - Yan Cao
- The Key Laboratory for Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, People’s Republic of China
| | - Jianbin Qiu
- The Key Laboratory for Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, People’s Republic of China
| | - Zhan Gao
- Shenzhen Key Laboratory of Microbial and Gene Engineering, College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, People’s Republic of China
| | - Zhonghua Ou
- Shenzhen Key Laboratory of Microbial and Gene Engineering, College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, People’s Republic of China
| | - Yajing Wang
- Shenzhen Key Laboratory of Microbial and Gene Engineering, College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, People’s Republic of China
| | - Yizhi Zheng
- Shenzhen Key Laboratory of Microbial and Gene Engineering, College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, People’s Republic of China
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Genome-wide analysis of BURP domain-containing genes in Maize and Sorghum. Mol Biol Rep 2010; 38:4553-63. [DOI: 10.1007/s11033-010-0587-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Accepted: 11/20/2010] [Indexed: 11/26/2022]
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Xu H, Li Y, Yan Y, Wang K, Gao Y, Hu Y. Genome-scale identification of soybean BURP domain-containing genes and their expression under stress treatments. BMC PLANT BIOLOGY 2010; 10:197. [PMID: 20836857 PMCID: PMC2956546 DOI: 10.1186/1471-2229-10-197] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2009] [Accepted: 09/13/2010] [Indexed: 05/09/2023]
Abstract
BACKGROUND Multiple proteins containing BURP domain have been identified in many different plant species, but not in any other organisms. To date, the molecular function of the BURP domain is still unknown, and no systematic analysis and expression profiling of the gene family in soybean (Glycine max) has been reported. RESULTS In this study, multiple bioinformatics approaches were employed to identify all the members of BURP family genes in soybean. A total of 23 BURP gene types were identified. These genes had diverse structures and were distributed on chromosome 1, 2, 4, 6, 7, 8, 11, 12, 13, 14, and 18. Phylogenetic analysis suggested that these BURP family genes could be classified into 5 subfamilies, and one of which defines a new subfamily, BURPV. Quantitative real-time PCR (qRT-PCR) analysis of transcript levels showed that 15 of the 23 genes had no expression specificity; 7 of them were specifically expressed in some of the tissues; and one of them was not expressed in any of the tissues or organs studied. The results of stress treatments showed that 17 of the 23 identified BURP family genes responded to at least one of the three stress treatments; 6 of them were not influenced by stress treatments even though a stress related cis-element was identified in the promoter region. No stress related cis-elements were found in promoter region of any BURPV member. However, qRT-PCR results indicated that all members from BURPV responded to at least one of the three stress treatments. More significantly, the members from the RD22-like subfamily showed no tissue-specific expression and they all responded to each of the three stress treatments. CONCLUSIONS We have identified and classified all the BURP domain-containing genes in soybean. Their expression patterns in different tissues and under different stress treatments were detected using qRT-PCR. 15 out of 23 BURP genes in soybean had no tissue-specific expression, while 17 out of them were stress-responsive. The data provided an insight into the evolution of the gene family and suggested that many BURP family genes may be important for plants responding to stress conditions.
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Affiliation(s)
- Hongliang Xu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yaxuan Li
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yueming Yan
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Ke Wang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Ya Gao
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yingkao Hu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
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