1
|
Hui W, Wu H, Zheng H, Wang K, Yang T, Fan J, Wu J, Wang J, Al Mutairi AA, Yang H, Yang C, Cui B, Loake GJ, Gong W. Genome-wide characterization of RR gene family members in Zanthoxylum armatum and the subsequent functional characterization of the C-type RR. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108943. [PMID: 39032447 DOI: 10.1016/j.plaphy.2024.108943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 07/10/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
Response Regulators (RRs) are crucial regulators in plant development and stress responses, comprising A-type, B-type, C-type, and pseudo-RR subfamilies. However, previous studies have often focused on specific subfamilies, which restricts our understanding of the complete RR gene family. In this study, we conducted a comprehensive analysis of 63 RR members from Zanthoxylum armatum, using phylogenetic relationships, motif composition, cis-acting elements, gene duplication and collinearity analyses. Segmental repeats among ZaRR genes enhanced the various environmental adaptabilities of Z. armatum, and the B-type ZaRR exhibited significant collinearity with the RRs in P. trichocarpa and C. sinensis. Cis-element analysis indicated ZaRRs play a significant role in abiotic stress and phytohormone pathways, particularly in light, drought, cold, abscisic acid (ABA) and salicylic acid (SA) responses. Abundant Ethylene Response Factor (ERF) and reproduction-associated binding sites in ZaRR promoters suggested their roles in stress and reproductive processes. A-type ZaRRs were implicated in plant vegetative and reproductive growth, whereas B-type ZaRRs contributed to both growth and stress responses. C-type ZaRRs were associated with plant reproductive growth, whereas pseudo-RRs may function in plant stress responses, such as water logging, cold, and response to ethylene (ETH), SA, and jasmonic acid (JA). Ectopic expression of ZaRR24, a C-type RR, inhibits growth, induces early flowering, and shortens fruit length in Arabidopsis. ZaRR24 overexpression also affected the expression of A- and B-type RRs, as well as floral meristem and organ identity genes. These findings establish a solid and comprehensive foundation for RR gene research in Z. armatum, and provide a platform for investigating signal transduction in other woody plants.
Collapse
Affiliation(s)
- Wenkai Hui
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Han Wu
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hao Zheng
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Kai Wang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ting Yang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiangtao Fan
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiaojiao Wu
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jingyan Wang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Ahmed A Al Mutairi
- Biology Department, College of Science, Jouf University, Sakaka, 41412, Saudi Arabia
| | - Hua Yang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chunlin Yang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Beimi Cui
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK.
| | - Gary J Loake
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK.
| | - Wei Gong
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China.
| |
Collapse
|
2
|
Sadaqat M, Fatima K, Azeem F, Shaheen T, Rahman MU, Ali T, Al-Megrin WAI, Tahir Ul Qamar M. Computational analysis and expression profiling of two-component system (TCS) gene family members in mango ( Mangifera indica) indicated their roles in stress response. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP24055. [PMID: 38870341 DOI: 10.1071/fp24055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/19/2024] [Indexed: 06/15/2024]
Abstract
The two-component system (TCS) gene family is among the most important signal transduction families in plants and is involved in the regulation of various abiotic stresses, cell growth and division. To understand the role of TCS genes in mango (Mangifera indica ), a comprehensive analysis of TCS gene family was carried out in mango leading to identification of 65 MiTCS genes. Phylogenetic analysis divided MiTCSs into three groups (histidine kinases, histidine-containing phosphotransfer proteins, and response regulators) and 11 subgroups. One tandem duplication and 23 pairs of segmental duplicates were found within the MiTCSs . Promoter analysis revealed that MiTCSs contain a large number of cis -elements associated with environmental stresses, hormone response, light signalling, and plant development. Gene ontology analysis showed their involvement in various biological processes and molecular functions, particularly signal transduction. Protein-protein interaction analysis showed that MiTCS proteins interacted with each other. The expression pattern in various tissues and under many stresses (drought, cold, and disease) showed that expression levels varied among various genes in different conditions. MiTCSs 3D structure predictions showed structural conservation among members of the same groups. This information can be further used to develop improved cultivars and will serve as a foundation for gaining more functional insights into the TCS gene family.
Collapse
Affiliation(s)
- Muhammad Sadaqat
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Kinza Fatima
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Farrukh Azeem
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Tayyaba Shaheen
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Mahmood-Ur- Rahman
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Tehreem Ali
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Wafa Abdullah I Al-Megrin
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Muhammad Tahir Ul Qamar
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| |
Collapse
|
3
|
Liu H, Liu N, Peng C, Huang J, Hua W, Fu Z, Liu J. Two-Component System Genes in Brassica napus: Identification, Analysis, and Expression Patterns in Response to Abiotic and Biotic Stresses. Int J Mol Sci 2023; 24:17308. [PMID: 38139141 PMCID: PMC10743665 DOI: 10.3390/ijms242417308] [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: 10/31/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
The two-component system (TCS), consisting of histidine kinases (HKs), histidine phosphotransfer proteins (HPs) and response regulators (RRs) in eukaryotes, plays pivotal roles in regulating plant growth, development, and responses to environment stimuli. However, the TCS genes were poorly characterized in rapeseed, which is an important tetraploid crop in Brassicaceae. In this work, a total of 182 BnaTCS genes were identified, including 43 HKs, 16 HPs, and 123 RRs, which was more than that in other crops due to segmental duplications during the process of polyploidization. It was significantly different in genetic diversity between the three subfamilies, and some members showed substantial genetic differentiation among the three rapeseed ecotypes. Several hormone- and stress-responsive cis-elements were identified in the putative promoter regions of BnaTCS genes. Furthermore, the expression of BnaTCS genes under abiotic stresses, exogenous phytohormone, and biotic stresses was analyzed, and numerous candidate stress-responsive genes were screened out. Meanwhile, using a natural population with 505 B. napus accessions, we explored the genetic effects of BnaTCS genes on salt tolerance by association mapping analysis and detected some significant association SNPs/genes. The result will help to further understand the functions of TCS genes in the developmental and stress tolerance improvement in B. napus.
Collapse
Affiliation(s)
- Hongfang Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (H.L.)
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (H.L.)
| | - Chen Peng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (H.L.)
| | - Jiaquan Huang
- School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 570208, China
| | - Wei Hua
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (H.L.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhengwei Fu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (H.L.)
| | - Jing Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (H.L.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| |
Collapse
|
4
|
Kasapoglu AG, Ilhan E, Aydin M, Yigider E, Inal B, Buyuk I, Taspinar MS, Ciltas A, Agar G. Characterization of Two-Component System gene ( TCS) in melatonin-treated common bean under salt and drought stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1733-1754. [PMID: 38162914 PMCID: PMC10754802 DOI: 10.1007/s12298-023-01406-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/21/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
The two-component system (TCS) generally consists of three elements, namely the histidine kinase (HK), response regulator (RR), and histidine phosphotransfer (HP) gene families. This study aimed to assess the expression of TCS genes in P. vulgaris leaf tissue under salt and drought stress and perform a genome-wide analysis of TCS gene family members using bioinformatics methods. This study identified 67 PvTCS genes, including 10 PvHP, 38 PvRR, and 19 PvHK, in the bean genome. PvHK2 had the maximum number of amino acids with 1261, whilst PvHP8 had the lowest number with 87. In addition, their theoretical isoelectric points were between 4.56 (PvHP8) and 9.15 (PvPRR10). The majority of PvTCS genes are unstable. Phylogenetic analysis of TCS genes in A. thaliana, G. max, and bean found that PvTCS genes had close phylogenetic relationships with the genes of other plants. Segmental and tandem duplicate gene pairs were detected among the TCS genes and TCS genes have been subjected to purifying selection pressure in the evolutionary process. Furthermore, the TCS gene family, which has an important role in abiotic stress and hormonal responses in plants, was characterized for the first time in beans, and its expression of TCS genes in bean leaves under salt and drought stress was established using RNAseq and qRT-PCR analyses. The findings of this study will aid future functional and genomic studies by providing essential information about the members of the TCS gene family in beans. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01406-5.
Collapse
Affiliation(s)
- Ayse Gul Kasapoglu
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, 25050 Erzurum, Turkey
| | - Emre Ilhan
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, 25050 Erzurum, Turkey
| | - Murat Aydin
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ataturk University, 25050 Erzurum, Turkey
| | - Esma Yigider
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ataturk University, 25050 Erzurum, Turkey
| | - Behcet Inal
- Department of Agricultural Biotechnology, Faculty of Agriculture, Siirt University, 56100 Siirt, Turkey
| | - Ilker Buyuk
- Department of Biology, Faculty of Science, Ankara University, 06100 Ankara, Turkey
| | - Mahmut Sinan Taspinar
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ataturk University, 25050 Erzurum, Turkey
| | - Abdulkadir Ciltas
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ataturk University, 25050 Erzurum, Turkey
| | - Guleray Agar
- Department of Biology, Faculty of Science, Ataturk University, 25050 Erzurum, Turkey
| |
Collapse
|
5
|
Zhao L, Wang Y, Cui R, Cui Y, Lu X, Chen X, Wang J, Wang D, Yin Z, Wang S, Peng F, Guo L, Chen C, Ye W. Analysis of the histidine kinase gene family and the role of GhHK8 in response to drought tolerance in cotton. PHYSIOLOGIA PLANTARUM 2023; 175:e14022. [PMID: 37882310 DOI: 10.1111/ppl.14022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/27/2023] [Accepted: 08/29/2023] [Indexed: 10/27/2023]
Abstract
As an important member of the two-component system (TCS), histidine kinases (HKs) play important roles in various plant developmental processes and signal transduction in response to a wide range of biotic and abiotic stresses. So far, the HK gene family has not been investigated in Gossypium. In this study, a total of 177 HK gene family members were identified in cotton. They were further divided into seven groups, and the protein characteristics, genetic relationship, gene structure, chromosome location, collinearity, and cis-elements identification were comprehensively analyzed. Whole genome duplication (WGD) / segmental duplication may be the reason why the number of HK genes doubled in tetraploid Gossypium species. Expression analysis revealed that most cotton HK genes were mainly expressed in the reproductive organs and the fiber at initial stage. Gene expression analysis revealed that HK family genes are involved in cotton abiotic stress, especially drought stress and salt stress. In addition, gene interaction networks showed that HKs were involved in the regulation of cotton abiotic stress, especially drought stress. VIGS experiments have shown that GhHK8 is a negative regulatory factor in response to drought stress. Our systematic analysis provided insights into the characteristics of the HK genes in cotton and laid a foundation for further exploring their potential in drought stress resistance in cotton.
Collapse
Affiliation(s)
- Lanjie Zhao
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| | - Yongbo Wang
- Hunan Institute of Cotton Science, Changde, China
| | - Ruifeng Cui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| | - Yupeng Cui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| | - Xuke Lu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| | - Xiugui Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| | - Junjuan Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| | - Delong Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| | - Zujun Yin
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| | - Shuai Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| | - Fanjia Peng
- Hunan Institute of Cotton Science, Changde, China
| | - Lixue Guo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| | - Chao Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| | - Wuwei Ye
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization/National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Anyang, Henan, China
| |
Collapse
|
6
|
Cruz-Bautista R, Ruíz-Villafán B, Romero-Rodríguez A, Rodríguez-Sanoja R, Sánchez S. Trends in the two-component system's role in the synthesis of antibiotics by Streptomyces. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12623-z. [PMID: 37341754 DOI: 10.1007/s00253-023-12623-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 06/22/2023]
Abstract
Despite the advances in understanding the regulatory networks for secondary metabolite production in Streptomyces, the participation of the two-component systems (TCS) in this process still requires better characterization. These sensing systems and their responses to environmental stimuli have been described by evaluating mutant strains with techniques that allow in-depth regulatory responses. However, defining the stimulus that triggers their activation is still a task. The transmembrane nature of the sensor kinases and the high content of GC in the streptomycetes represent significant challenges in their study. In some examples, adding elements to the assay medium has determined the respective ligand. However, a complete TCS description and characterization requires specific amounts of the involved proteins that are most difficult to obtain. The availability of enough sensor histidine kinase concentrations could facilitate the identification of the ligand-protein interaction, and besides would allow the establishment of its phosphorylation mechanisms and determine their tridimensional structure. Similarly, the advances in the development of bioinformatics tools and novel experimental techniques also promise to accelerate the TCSs description and provide knowledge on their participation in the regulation processes of secondary metabolite formation. This review aims to summarize the recent advances in the study of TCSs involved in antibiotic biosynthesis and to discuss alternatives to continue their characterization. KEY POINTS: • TCSs are the environmental signal transducers more abundant in nature. • The Streptomyces have some of the highest number of TCSs found in bacteria. • The study of signal transduction between SHKs and RRs domains is a big challenge.
Collapse
Affiliation(s)
- Rodrigo Cruz-Bautista
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico.
| | - Beatriz Ruíz-Villafán
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico
| | - Alba Romero-Rodríguez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico
| | - Romina Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, 04510, Mexico City, Mexico.
| |
Collapse
|
7
|
Sadaqat M, Umer B, Attia KA, Abdelkhalik AF, Azeem F, Javed MR, Fatima K, Zameer R, Nadeem M, Tanveer MH, Sun S, Ercisli S, Nawaz MA. Genome-wide identification and expression profiling of two-component system (TCS) genes in Brassica oleracea in response to shade stress. Front Genet 2023; 14:1142544. [PMID: 37323660 PMCID: PMC10267837 DOI: 10.3389/fgene.2023.1142544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/26/2023] [Indexed: 06/17/2023] Open
Abstract
The Two-component system (TCS) consists of Histidine kinases (HKs), Phosphotransfers (HPs), and response regulator (RR) proteins. It has an important role in signal transduction to respond to a wide variety of abiotic stresses and hence in plant development. Brassica oleracea (cabbage) is a leafy vegetable, which is used for food and medicinal purposes. Although this system was identified in several plants, it had not been identified in Brassica oleracea yet. This genome-wide study identified 80 BoTCS genes consisting of 21 HKs, 8 HPs, 39 RRs, and 12 PRRs. This classification was done based on conserved domains and motif structure. Phylogenetic relationships of BoTCS genes with Arabidopsis thaliana, Oryza sativa, Glycine max, and Cicer arietinum showed conservation in TCS genes. Gene structure analysis revealed that each subfamily had conserved introns and exons. Both tandem and segmental duplication led to the expansion of this gene family. Almost all of the HPs and RRs were expanded through segmental duplication. Chromosomal analysis showed that BoTCS genes were dispersed across all nine chromosomes. The promoter regions of these genes were found to contain a variety of cis-regulatory elements. The 3D structure prediction of proteins also confirmed the conservation of structure within subfamilies. MicroRNAs (miRNAs) involved in the regulation of BoTCSs were also predicted and their regulatory roles were also evaluated. Moreover, BoTCSs were docked with abscisic acid to evaluate their binding. RNA-seq-based expression analysis and validation by qRT-PCR showed significant variation of expression for BoPHYs, BoERS1.1, BoERS2.1, BoERS2.2, BoRR10.2, and BoRR7.1 suggesting their importance in stress response. These genes showing unique expression can be further used in manipulating the plant's genome to make the plant more resistant the environmental stresses which will ultimately help in the increase of plant's yield. More specifically, these genes have altered expression in shade stress which clearly indicates their importance in biological functions. These findings are important for future functional characterization of TCS genes in generating stress-responsive cultivars.
Collapse
Affiliation(s)
- Muhammad Sadaqat
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Basit Umer
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Kotb A. Attia
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Amr F. Abdelkhalik
- Biotechnology School, Nile University, Giza, Egypt
- Rice Biotechnology Lab, Rice Research and Training Center, Field Crops Research Institute, ARC, Kafrelshikh, Egypt
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Muhammad Rizwan Javed
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Kinza Fatima
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Roshan Zameer
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Majid Nadeem
- Wheat Research Institute, Ayub Agriculture Research Institute, Faisalabad, Pakistan
| | | | - Sangmi Sun
- Department of Biotechnology, Chonnam National University, Yesosu Campus, Yesosu Si, Republic of Korea
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Türkiye
- HGF Agro, Ata Teknokent, Erzurum, Türkiye
| | - Muhammad Amjad Nawaz
- Advanced Engineering School (Agrobiotek), Tomsk State University, Tomsk, Russia
- Center for Research in the Field of Materials and Technologies, Tomsk State University, Tomsk, Russia
| |
Collapse
|
8
|
Shang C, Ye T, Zhou Q, Chen P, Li X, Li W, Chen S, Hu Z, Zhang W. Genome-Wide Identification and Bioinformatics Analyses of Host Defense Peptides Snakin/GASA in Mangrove Plants. Genes (Basel) 2023; 14:genes14040923. [PMID: 37107683 PMCID: PMC10137857 DOI: 10.3390/genes14040923] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/03/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Host defense peptides (HDPs) are components of plant defensive barriers that resist microbial infection. Members of the Snakin/GASA protein family in plants have functions of regulating plant growth, defense, and bacteriostasis. Most mangrove plants grow in coastal zones. In order to survive in harsh environments, mangrove plants have evolved complex adaptations against microbes. In this study, Snakin/GASA family members were identified and analyzed in the genomes of three mangrove species. Twenty-seven, thirteen, and nine candidate Snakin/GASA family members were found in Avicennia marina, Kandelia obovata, and Aegiceras corniculatum, respectively. These Snakin/GASA family members were identified and categorized into three subfamilies via phylogenetic analysis. The genes coding for the Snakin/GASA family members were unevenly distributed on chromosomes. Collinearity and conservative motif analyses showed that the Snakin/GASA family members in K. obovata and A. corniculatum underwent multiple gene duplication events. Snakin/GASA family member expression in normal leaves and leaves infected with pathogenic microorganisms of the three mangrove species was verified using real-time quantitative polymerase chain reaction. The expression of KoGASA3 and 4, AcGASA5 and 10, and AmGASA1, 4, 5, 15, 18, and 23 increased after microbial infection. This study provides a research basis for the verification of HDPs from mangrove plants and suggests directions for the development and utilization of marine biological antimicrobial peptides.
Collapse
Affiliation(s)
- Chenjing Shang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Ting Ye
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Qiao Zhou
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Pengyu Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Xiangyu Li
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Wenyi Li
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Si Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Zhangli Hu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Wei Zhang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| |
Collapse
|
9
|
Rasool A, Azeem F, Ur-Rahman M, Rizwan M, Hussnain Siddique M, Bay DH, Binothman N, Al Kashgry NAT, Qari SH. Omics-assisted characterization of two-component system genes from Gossypium Raimondii in response to salinity and molecular interaction with abscisic acid. FRONTIERS IN PLANT SCIENCE 2023; 14:1138048. [PMID: 37063177 PMCID: PMC10102465 DOI: 10.3389/fpls.2023.1138048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
The two-component system (TCS) genes are involved in a wide range of physiological processes in prokaryotes and eukaryotes. In plants, the TCS elements help in a variety of functions, including cell proliferation, response to abiotic and biotic stresses, leaf senescence, nutritional signaling, and division of chloroplasts. Three different kinds of proteins make up the TCS system in plants. These are known as HKs (histidine kinases), HPs (histidine phosphotransfer), and RRs (response regulators). We investigated the genome of Gossypium raimondii and discovered a total of 59 GrTCS candidates, which include 23 members of the HK family, 8 members of the HP family, and 28 members of the RR family. RR candidates are further classified as type-A (6 members), type-B (11 members), type-C (2 members), and pseudo-RRs (9 members). The GrTCS genes were analyzed in comparison with the TCS components of other plant species such as Arabidopsis thaliana, Cicer arietinum, Sorghum bicolor, Glycine max, and Oryza sativa. This analysis revealed both conservation and changes in their structures. We identified 5 pairs of GrTCS syntenic homologs in the G. raimondii genome. All 59 TCS genes in G. raimondii are located on all thirteen chromosomes. The GrTCS promoter regions have several cis-regulatory elements, which function as switches and respond to a wide variety of abiotic stresses. RNA-seq and real-time qPCR analysis showed that the majority of GrTCS genes are differentially regulated in response to salt and cold stress. 3D structures of GrTCS proteins were predicted to reveal the specific function. GrTCSs were docked with abscisic acid to assess their binding interactions. This research establishes the groundwork for future functional studies of TCS elements in G. raimondii, which will further focus on stress resistance and overall development.
Collapse
Affiliation(s)
- Asima Rasool
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Mahmood Ur-Rahman
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Rizwan
- Department of Environmental Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Hussnain Siddique
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Daniyah Habiballah Bay
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Najat Binothman
- Department of Chemistry, College of Sciences & Arts, King Abdulaziz University, Rabigh, Saudi Arabia
| | | | - Sameer H. Qari
- Department of Biology, A1-Jumum University College, Umm A1-Qura University, Makkah, Saudi Arabia
| |
Collapse
|
10
|
Liu H, Chen R, Li H, Lin J, Wang Y, Han M, Wang T, Wang H, Chen Q, Chen F, Chu P, Liang C, Ren C, Zhang Y, Yang F, Sheng Y, Wei J, Wu X, Yu G. Genome-wide identification and expression analysis of SlRR genes in response to abiotic stress in tomato. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:322-333. [PMID: 36457231 DOI: 10.1111/plb.13494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 11/15/2022] [Indexed: 06/17/2023]
Abstract
The cytokinin two-component signal transduction system (TCS) is involved in many biological processes, including hormone signal transduction and plant growth regulation. Although cytokinin TCS has been well characterized in Arabidopsis thaliana, its role in tomato remains elusive. In this study, we characterized the diversity and function of response regulator (RR) genes, a critical component of TCS, in tomato. In total, we identified 31 RR genes in the tomato genome. These SlRR genes were classified into three subgroups (type-A, type-B and type-C). Various stress-responsive cis-elements were present in the tomato RR gene promoters. Their expression responses under pesticide treatment were evaluated by transcriptome analysis. Their expression under heat, cold, ABA, salinity and NaHCO3 treatments was further investigated by qRT-PCR and complemented with the available transcription data under these treatments. Specifically, SlRR13 expression was significantly upregulated under salinity, drought, cold and pesticide stress and was downregulated under ABA treatment. SlRR23 expression was induced under salt treatment, while the transcription level of SlRR1 was increased under cold and decreased under salt stress. We also found that GATA transcription factors played a significant role in the regulation of SlRR genes. Based on our results, tomato SlRR genes are involved in responses to abiotic stress in tomato and could be implemented in molecular breeding approaches to increase resistance of tomato to environmental stresses.
Collapse
Affiliation(s)
- H Liu
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - R Chen
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - H Li
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - J Lin
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - Y Wang
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - M Han
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - T Wang
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - H Wang
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - Q Chen
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - F Chen
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - P Chu
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - C Liang
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - C Ren
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - Y Zhang
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - F Yang
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - Y Sheng
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - J Wei
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - X Wu
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - G Yu
- Heilongjiang Bayi Agricultural University, Daqing, China
| |
Collapse
|
11
|
Huo R, Zhao Y, Liu T, Xu M, Wang X, Xu P, Dai S, Cui X, Han Y, Liu Z, Li Z. Genome-wide identification and expression analysis of two-component system genes in sweet potato ( Ipomoea batatas L.). FRONTIERS IN PLANT SCIENCE 2023; 13:1091620. [PMID: 36714734 PMCID: PMC9878860 DOI: 10.3389/fpls.2022.1091620] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Two-component system (TCS), which comprises histidine kinases (HKs), histidine phosphotransfer proteins (HPs), and response regulators (RRs), plays essential roles in regulating plant growth, development, and response to various environmental stimuli. TCS genes have been comprehensively identified in various plants, while studies on the genome-wide identification and analysis of TCS in sweet potato were still not reported. Therefore, in this study, a total of 90 TCS members consisting of 20 HK(L)s, 11 HPs, and 59 RRs were identified in the genome of Ipomoea batatas. Furthermore, their gene structures, conserved domains, and phylogenetic relationships were analyzed in detail. Additionally, the gene expression profiles in various organs were analyzed, and response patterns to adverse environmental stresses were investigated. The results showed that these 90 TCS genes were mapped on 15 chromosomes with a notably uneven distribution, and the expansion of TCS genes in sweet potato was attributed to both segmental and tandem duplications. The majority of the TCS genes showed distinct organ-specific expression profiles, especially in three types of roots (stem roots, fibrous roots, tuberous roots). Moreover, most of the TCS genes were either induced or suppressed upon treatment with abiotic stresses (drought, salinity, cold, heat) and exogenous phytohormone abscisic acid (ABA). In addition, the yeast-two hybrid system was used to reveal the HK-HP-RR protein-protein interactions. IbHP1, IbHP2, IbHP4, and IbHP5 could interact with three HKs (IbHK1a, IbHK1b, and IbHK5), and also interact with majority of the type-B RRs (IbRR20-IbRR28), while no interaction affinity was detected for IbHP3. Our systematic analyses could provide insights into the characterization of the TCS genes, and further the development of functional studies in sweet potato.
Collapse
Affiliation(s)
- Ruxue Huo
- Jiangsu Key Laboratory of Phylogeny and Comparative Genomics, School of Life Sciences, Institute of Integrative Plant Biology, Jiangsu Normal University, Xuzhou, China
- College of Agriculture and Forestry Science, Linyi University, Linyi, China
| | - Yanshu Zhao
- College of Agriculture and Forestry Science, Linyi University, Linyi, China
| | - Tianxu Liu
- College of Agriculture and Forestry Science, Linyi University, Linyi, China
| | - Meng Xu
- College of Agriculture and Forestry Science, Linyi University, Linyi, China
| | - Xiaohua Wang
- College of Agriculture and Forestry Science, Linyi University, Linyi, China
| | - Ping Xu
- College of Agriculture and Forestry Science, Linyi University, Linyi, China
| | - Shengjie Dai
- College of Agriculture and Forestry Science, Linyi University, Linyi, China
| | - Xiaoyu Cui
- College of Agriculture and Forestry Science, Linyi University, Linyi, China
| | - Yonghua Han
- Jiangsu Key Laboratory of Phylogeny and Comparative Genomics, School of Life Sciences, Institute of Integrative Plant Biology, Jiangsu Normal University, Xuzhou, China
| | - Zhenning Liu
- College of Agriculture and Forestry Science, Linyi University, Linyi, China
| | - Zongyun Li
- Jiangsu Key Laboratory of Phylogeny and Comparative Genomics, School of Life Sciences, Institute of Integrative Plant Biology, Jiangsu Normal University, Xuzhou, China
| |
Collapse
|
12
|
Asati R, Tripathi MK, Tiwari S, Yadav RK, Tripathi N. Molecular Breeding and Drought Tolerance in Chickpea. LIFE (BASEL, SWITZERLAND) 2022; 12:life12111846. [PMID: 36430981 PMCID: PMC9698494 DOI: 10.3390/life12111846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/05/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]
Abstract
Cicer arietinum L. is the third greatest widely planted imperative pulse crop worldwide, and it belongs to the Leguminosae family. Drought is the utmost common abiotic factor on plants, distressing their water status and limiting their growth and development. Chickpea genotypes have the natural ability to fight drought stress using certain strategies viz., escape, avoidance and tolerance. Assorted breeding methods, including hybridization, mutation, and marker-aided breeding, genome sequencing along with omics approaches, could be used to improve the chickpea germplasm lines(s) against drought stress. Root features, for instance depth and root biomass, have been recognized as the greatest beneficial morphological factors for managing terminal drought tolerance in the chickpea. Marker-aided selection, for example, is a genomics-assisted breeding (GAB) strategy that can considerably increase crop breeding accuracy and competence. These breeding technologies, notably marker-assisted breeding, omics, and plant physiology knowledge, underlined the importance of chickpea breeding and can be used in future crop improvement programmes to generate drought-tolerant cultivars(s).
Collapse
Affiliation(s)
- Ruchi Asati
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Manoj Kumar Tripathi
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Correspondence: (M.K.T.); (N.T.)
| | - Sushma Tiwari
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Rakesh Kumar Yadav
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Niraj Tripathi
- Directorate of Research Services, Jawaharlal Nehru Agricultural University, Jabalpur 482004, India
- Correspondence: (M.K.T.); (N.T.)
| |
Collapse
|
13
|
Liu L, Ma X, Bilal M, Wei L, Tang S, Luo H, Zhao Y, Wang Z, Duan X. Toxicity and inhibition mechanism of gallic acid on physiology and fermentation performance of Escherichia coli. BIORESOUR BIOPROCESS 2022; 9:76. [PMID: 38647760 PMCID: PMC10992115 DOI: 10.1186/s40643-022-00564-w] [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: 04/23/2022] [Accepted: 07/10/2022] [Indexed: 11/10/2022] Open
Abstract
Gallic acid is a natural phenolic acid that has a stress inhibition effect on Escherichia coli. This study by integrates fermentation characteristics and transcriptional analyses to elucidate the physiological mechanism of E. coli 3110 response to gallic acid. Compared with the control (without stress), the cell growth was severely retarded, and irregular cell morphology appeared in the case of high levels of gallic acid stress. The glucose consumption of E. coli was reduced successively with the increase of gallic acid content in the fermentation medium. After 20 h of gallic acid stress, cofactor levels (ATP, NAD+ and NADH) of E. coli 3110 were similarly decreased, indicating a more potent inhibitory effect of gallic acid on E. coli. The transcriptional analysis revealed that gallic acid altered the gene expression profiles related to five notable differentially regulated pathways. The genes related to the two-component system were up-regulated, while the genes associated with ABC-transporter, energy metabolism, carbon metabolism, and fatty acid biosynthesis were down-regulated. This is the first report to comprehensively assess the toxicity of gallic acid on E. coli. This study has implications for the efficient production of phenolic compounds by E. coli and provides new ideas for the study of microbial tolerance to environmental stress and the identification of associated tolerance targets.
Collapse
Affiliation(s)
- Lina Liu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China.
| | - Xiaolong Ma
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Linlin Wei
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Shijie Tang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Hongzhen Luo
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Yuping Zhao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Zhaoyu Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Xuguo Duan
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| |
Collapse
|
14
|
Safder I, Shao G, Sheng Z, Hu P, Tang S. Genome-wide identification studies - A primer to explore new genes in plant species. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:9-22. [PMID: 34558163 DOI: 10.1111/plb.13340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
Genome data have accumulated rapidly in recent years, doubling roughly after every 6 months due to the influx of next-generation sequencing technologies. A plethora of plant genomes are available in comprehensive public databases. This easy access to data provides an opportunity to explore genome datasets and recruit new genes in various plant species not possible a decade ago. In the past few years, many gene families have been published using these public datasets. These genome-wide studies identify and characterize gene members, gene structures, evolutionary relationships, expression patterns, protein interactions and gene ontologies, and predict putative gene functions using various computational tools. Such studies provide meaningful information and an initial framework for further functional elucidation. This review provides a concise layout of approaches used in these gene family studies and demonstrates an outline for employing various plant genome datasets in future studies.
Collapse
Affiliation(s)
- I Safder
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| | - G Shao
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| | - Z Sheng
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| | - P Hu
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| | - S Tang
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| |
Collapse
|
15
|
Zameer R, Sadaqat M, Fatima K, Fiaz S, Rasul S, Zafar H, Qayyum A, Nashat N, Raza A, Shah AN, Batool R, Azeem F, Sun S, Chung G. Two-Component System Genes in Sorghum bicolor: Genome-Wide Identification and Expression Profiling in Response to Environmental Stresses. Front Genet 2021; 12:794305. [PMID: 34899869 PMCID: PMC8655132 DOI: 10.3389/fgene.2021.794305] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/08/2021] [Indexed: 12/31/2022] Open
Abstract
The two-component signal transduction system (TCS) acts in a variety of physiological processes in lower organisms and has emerged as a key signaling system in both prokaryotes and eukaryotes, including plants. TCS genes assist plants in processes such as stress resistance, cell division, nutrition signaling, leaf senescence, and chloroplast division. In plants, this system is composed of three types of proteins: response regulators (RRs), histidine kinases (HKs), and histidine phosphotransfer proteins (HPs). We aimed to study the Sorghum bicolor genome and identified 37 SbTCS genes consisting of 13 HKs, 5 HPs, and 19 RRs (3 type-A RRs, 7 type-B RRs, 2 type-C RRs, and 7 pseudo-RRs). The structural and phylogenetic comparison of the SbTCS members with their counterparts in Arabidopsis thaliana, Oryza sativa, Cicer arietinum, and Glycine max showed group-specific conservations and variations. Expansion of the gene family members is mostly a result of gene duplication, of both the tandem and segmental types. HKs and RRs were observed to be originated from segmental duplication, while some HPs originated from tandem duplication. The nuclear genome of S. bicolor contain 10 chromosomes and these SbTCS genes are randomly distributed on all the chromosomes. The promoter sequences of the SbTCS genes contain several abiotic stress-related cis-elements. RNA-seq and qRT-PCR-based expression analysis demonstrated most of the TCS genes were responsive to drought and salt stresses in leaves, which suggest their role in leaf development. This study lays a foundation for further functional study of TCS genes for stress tolerance and developmental improvement in S. bicolor.
Collapse
Affiliation(s)
- Roshan Zameer
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Sadaqat
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Kinza Fatima
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Sumaira Rasul
- Institute of Molecular Biology and Bio-Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Hadeqa Zafar
- Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Abdul Qayyum
- Department of Agronomy, The University of Haripur, Haripur, Pakistan
| | - Naima Nashat
- Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan
| | - Ali Raza
- Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Riffat Batool
- Department of Botany, GC Women University, Faisalabad, Pakistan
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Sangmi Sun
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
| |
Collapse
|
16
|
Yang X, Guo T, Li J, Chen Z, Guo B, An X. Genome-wide analysis of the MYB-related transcription factor family and associated responses to abiotic stressors in Populus. Int J Biol Macromol 2021; 191:359-376. [PMID: 34534587 DOI: 10.1016/j.ijbiomac.2021.09.042] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 09/08/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
MYB proteins are one of the most abundant transcription factor families in the plant kingdom. Evidence has increasingly revealed that MYB-related proteins function in diverse plant biological processes. However, little is known about the genome-wide characterization and functions of MYB-related proteins in Populus, an important model and commercial tree species. In this study, 152 PtrMYBRs were identified and unevenly located on 19 Populus chromosomes. A phylogenetic analysis divided them into six major subgroups, supported by conserved gene organization, consensus motifs, and protein domain architecture. Promoter assessment and gene ontology classification results indicated that the MYB-related family is likely involved in plant development and responses to various environmental stressors. The Populus MYB-related family members showed various expression patterns in different tissues and stress conditions, implying their crucial roles in the development and stress responses in Populus. Co-expression analyses revealed that Populus MYB-related genes might participate in the regulation of antioxidant defense system and various signaling pathways in response to stress. The three-dimensional structures of different subgroup of Populus MYB-related proteins further provided functional information at the proteomic level. These findings provide valuable information for a prospective functional dissection of MYB-related proteins and genetic improvement of Populus.
Collapse
Affiliation(s)
- Xiaoyu Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Ting Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Juan Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China
| | - Zhong Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Bin Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Shanxi Academy of Forest Sciences, Taiyuan, Shanxi 030012, China
| | - Xinmin An
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| |
Collapse
|
17
|
Abdullah, Faraji S, Mehmood F, Malik HMT, Ahmed I, Heidari P, Poczai P. The GASA Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome Wide Identification and Expression Analysis. AGRONOMY 2021; 11:1425. [DOI: 10.3390/agronomy11071425] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The gibberellic acid-stimulated Arabidopsis (GASA/GAST) gene family is widely distributed in plants and involved in various physiological and biological processes. These genes also provide resistance to abiotic and biotic stresses, including antimicrobial, antiviral, and antifungal. We are interested in characterizing the GASA gene family and determining its role in various physiological and biological process in Theobroma cacao. Here, we report 17 tcGASA genes distributed on six chromosomes in T. cacao. The gene structure, promoter region, protein structure and biochemical properties, expression, and phylogenetics of all tcGASAs were analyzed. Phylogenetic analyses divided tcGASA proteins into five groups. Among 17 tcGASA genes, nine segmentally duplicating genes were identified which formed four pairs and cluster together in phylogenetic tree. Differential expression analyses revealed that most of the tcGASA genes showed elevated expression in the seeds (cacao food), implying their role in seed development. The differential expression of tcGASAs was recorded between the tolerant and susceptible cultivars of cacao, which indicating their possible role as fungal resistant. Our findings provide new insight into the function, evolution, and regulatory system of the GASA family genes in T.cacao and may suggest new target genes for development of fungi-resistant cacao varieties in breeding programs.
Collapse
|
18
|
Wu S, Yu K, Li L, Wang L, Liang W. Enhancement of exopolysaccharides production and reactive oxygen species level of Nostoc flagelliforme in response to dehydration. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:34300-34308. [PMID: 33646551 DOI: 10.1007/s11356-021-13051-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/16/2021] [Indexed: 06/12/2023]
Abstract
Nostoc flagelliforme is a remarkable drought-resistant terrestrial cyanobacterium whose exopolysaccharides (EPS) have been found to exert important physiological and ecological functions, and the EPS are known to improve soil physicochemical properties. In this study, we used physiological and molecular methods to investigate the influences of three moisture loss levels on EPS production and the antioxidant system in N. flagelliforme. The aim was to reveal the EPS production mechanism involved in the gene differential expression and antioxidant system of N. flagelliforme in response to drought. Our results showed that EPS contents increased by 13% and 22% after 6-h and 48-h dehydration (6HAD and 48HAD) compared with 4-h rehydration (4HAR), respectively. The same trends were also detected for most EPS synthesis genes, especially glycosyltransferases. Furthermore, the intracellular reactive oxygen species (ROS) levels in N. flagelliforme were generally higher at 6HAD and 48HAD than at 4HAR. Superoxide dismutase (SOD) and peroxidase (POD) activities were restricted in N. flagelliforme under 6HAD and 48HAD compared with 4HAR, but the opposite result was found in catalase (CAT) activity. These results provide a new foundation for understanding the mechanism of EPS accumulation in N. flagelliforme in response to drought.
Collapse
Affiliation(s)
- Shijie Wu
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
- School of Life Sciences, Ningxia University, Yinchuan, 750021, China
| | - Kaiqiang Yu
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
- School of Life Sciences, Ningxia University, Yinchuan, 750021, China
| | - Long Li
- College of Physical Education, Ningxia Normal University, Guyuan, 756000, China
| | - Lingxia Wang
- School of Life Sciences, Ningxia University, Yinchuan, 750021, China
| | - Wenyu Liang
- School of Life Sciences, Ningxia University, Yinchuan, 750021, China.
| |
Collapse
|
19
|
Hoang XLT, Prerostova S, Thu NBA, Thao NP, Vankova R, Tran LSP. Histidine Kinases: Diverse Functions in Plant Development and Responses to Environmental Conditions. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:297-323. [PMID: 34143645 DOI: 10.1146/annurev-arplant-080720-093057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The two-component system (TCS), which is one of the most evolutionarily conserved signaling pathway systems, has been known to regulate multiple biological activities and environmental responses in plants. Significant progress has been made in characterizing the biological functions of the TCS components, including signal receptor histidine kinase (HK) proteins, signal transducer histidine-containing phosphotransfer proteins, and effector response regulator proteins. In this review, our scope is focused on the diverse structure, subcellular localization, and interactions of the HK proteins, as well as their signaling functions during development and environmental responses across different plant species. Based on data collected from scientific studies, knowledge about acting mechanisms and regulatory roles of HK proteins is presented. This comprehensive summary ofthe HK-related network provides a panorama of sophisticated modulating activities of HK members and gaps in understanding these activities, as well as the basis for developing biotechnological strategies to enhance the quality of crop plants.
Collapse
Affiliation(s)
- Xuan Lan Thi Hoang
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Ho Chi Minh City 700000, Vietnam; , ,
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Sylva Prerostova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, 165 02 Prague 6, Czech Republic; ,
| | - Nguyen Binh Anh Thu
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Ho Chi Minh City 700000, Vietnam; , ,
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Nguyen Phuong Thao
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Ho Chi Minh City 700000, Vietnam; , ,
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Radomira Vankova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, 165 02 Prague 6, Czech Republic; ,
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas 79409, USA;
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| |
Collapse
|
20
|
Chuong NN, Hoang XLT, Nghia DHT, Nguyen NC, Thao DTT, Tran TB, Ngoc TTM, Thu NBA, Nguyen QT, Thao NP. Ectopic expression of GmHP08 enhances resistance of transgenic Arabidopsis toward drought stress. PLANT CELL REPORTS 2021; 40:819-834. [PMID: 33725150 DOI: 10.1007/s00299-021-02677-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Ectopic expression of Glycine max two-component system member GmHP08 in Arabidopsis enhanced drought tolerance of transgenic plants, possibly via ABA-dependent pathways. Phosphorelay by two-component system (TCS) is a signal transduction mechanism which has been evolutionarily conserved in both prokaryotic and eukaryotic organisms. Previous studies have provided lines of evidence on the involvement of TCS genes in plant perception and responses to environmental stimuli. In this research, drought-associated functions of GmHP08, a TCS member from soybean (Glycine max L.), were investigated via its ectopic expression in Arabidopsis system. Results from the drought survival assay showed that GmHP08-transgenic plants exhibited higher survival rates compared with their wild-type (WT) counterparts, indicating better drought resistance of the former group. Analyses revealed that the transgenic plants outperformed the WT in various regards, i.e. capability of water retention, prevention of hydrogen peroxide accumulation and enhancement of antioxidant enzymatic activities under water-deficit conditions. Additionally, the expression of stress-marker genes, especially antioxidant enzyme-encoding genes, in the transgenic plants were found greater than that of the WT plants. In contrary, the expression of SAG13 gene, one of the senescence-associated genes, and of several abscisic acid (ABA)-related genes was repressed. Data from this study also revealed that the ectopic expression lines at germination and early seedling development stages were hypersensitive to exogenous ABA treatment. Taken together, our results demonstrated that GmHP08 could play an important role in mediating plant response to drought, possibly via an ABA-dependent manner.
Collapse
Affiliation(s)
- Nguyen Nguyen Chuong
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Quarter 6, Linh Trung Ward, Thu Duc, Ho Chi Minh, 700000, Vietnam
- Vietnam National University, Linh Trung Ward, Thu Duc, Ho Chi Minh, 700000, Vietnam
| | - Xuan Lan Thi Hoang
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Quarter 6, Linh Trung Ward, Thu Duc, Ho Chi Minh, 700000, Vietnam
- Vietnam National University, Linh Trung Ward, Thu Duc, Ho Chi Minh, 700000, Vietnam
| | - Duong Hoang Trong Nghia
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Quarter 6, Linh Trung Ward, Thu Duc, Ho Chi Minh, 700000, Vietnam
- Vietnam National University, Linh Trung Ward, Thu Duc, Ho Chi Minh, 700000, Vietnam
| | - Nguyen Cao Nguyen
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Quarter 6, Linh Trung Ward, Thu Duc, Ho Chi Minh, 700000, Vietnam
- Vietnam National University, Linh Trung Ward, Thu Duc, Ho Chi Minh, 700000, Vietnam
| | - Dau Thi Thanh Thao
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Quarter 6, Linh Trung Ward, Thu Duc, Ho Chi Minh, 700000, Vietnam
- Vietnam National University, Linh Trung Ward, Thu Duc, Ho Chi Minh, 700000, Vietnam
| | - Tram Bao Tran
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Quarter 6, Linh Trung Ward, Thu Duc, Ho Chi Minh, 700000, Vietnam
- Vietnam National University, Linh Trung Ward, Thu Duc, Ho Chi Minh, 700000, Vietnam
| | - Tran Thi My Ngoc
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Quarter 6, Linh Trung Ward, Thu Duc, Ho Chi Minh, 700000, Vietnam
- Vietnam National University, Linh Trung Ward, Thu Duc, Ho Chi Minh, 700000, Vietnam
| | - Nguyen Binh Anh Thu
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Quarter 6, Linh Trung Ward, Thu Duc, Ho Chi Minh, 700000, Vietnam
- Vietnam National University, Linh Trung Ward, Thu Duc, Ho Chi Minh, 700000, Vietnam
| | - Quang Thien Nguyen
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Quarter 6, Linh Trung Ward, Thu Duc, Ho Chi Minh, 700000, Vietnam
- Vietnam National University, Linh Trung Ward, Thu Duc, Ho Chi Minh, 700000, Vietnam
| | - Nguyen Phuong Thao
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Quarter 6, Linh Trung Ward, Thu Duc, Ho Chi Minh, 700000, Vietnam.
- Vietnam National University, Linh Trung Ward, Thu Duc, Ho Chi Minh, 700000, Vietnam.
| |
Collapse
|
21
|
Abdullah, Faraji S, Mehmood F, Malik HMT, Ahmed I, Heidari P, Poczai P. The GASA Gene Family in Theobroma cacao: Genome wide Identification and Expression Analysis.. [DOI: 10.1101/2021.01.27.425041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
AbstractThe gibberellic acid-stimulated Arabidopsis (GASA/GAST) gene family is widely distributed in plants. The role of the GASA gene family has been reported previously in various physiological and biological processes, such as cell division, root and seed development, stem growth, and fruit ripening. These genes also provide resistance to abiotic and biotic stresses including antimicrobial, antiviral, and antifungal. Here, we report 17 tcGASA genes in Theobroma cacao L. distributed on six chromosomes. The gene structure, promoter-region sequences, protein structure, and biochemical properties, expression, and phylogenetics of all tcGASAs were analyzed. Phylogenetic analyses divided tcGASA proteins into five groups. The nine segmentally duplicating genes form four pairs and cluster together in phylogenetic tree. Purifying selection pressure was recorded on tcGASA, including duplicated genes. Several stress/hormone-responsive cis-regulatory elements were also recognized in the promoter region of tcGASAs. Differential expression analyses revealed that most of the tcGASA genes showed elevated expression in the seeds (cacao food), implying their role in seed development. The black rod disease of genus Phytophthora caused up to 20–25% loss (700,000 metric tons) in world cacao production. The role of tcGASA genes in conferring fungal resistance was also explored based on RNAseq data against Phytophthora megakarya. The differential expression of tcGASA genes was recorded between the tolerant and susceptible cultivars of cacao plants, which were inoculated with the fungus for 24h and 72h. This differential expression indicating possible role of tcGASA genes to fungal resistant in cacao. Our findings provide new insight into the function, evolution, and regulatory system of the GASA family genes in T. cacao and provide new target genes for development of fungi-resistant cacao varieties in breeding programs.
Collapse
|
22
|
Nghia DHT, Chuong NN, Hoang XLT, Nguyen NC, Tu NHC, Huy NVG, Ha BTT, Nam TNH, Thu NBA, Tran LSP, Thao NP. Heterologous Expression of a Soybean Gene RR34 Conferred Improved Drought Resistance of Transgenic Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2020; 9:E494. [PMID: 32290594 PMCID: PMC7238260 DOI: 10.3390/plants9040494] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 12/19/2022]
Abstract
Two-component systems (TCSs) have been identified as participants in mediating plant response to water deficit. Nevertheless, insights of their contribution to plant drought responses and associated regulatory mechanisms remain limited. Herein, a soybean response regulator (RR) gene RR34, which is the potential drought-responsive downstream member of a TCS, was ectopically expressed in the model plant Arabidopsis for the analysis of its biological roles in drought stress response. Results from the survival test revealed outstanding recovery ratios of 52%-53% in the examined transgenic lines compared with 28% of the wild-type plants. Additionally, remarkedly lower water loss rates in detached leaves as well as enhanced antioxidant enzyme activities of catalase and superoxide dismutase were observed in the transgenic group. Further transcriptional analysis of a subset of drought-responsive genes demonstrated higher expression in GmRR34-transgenic plants upon exposure to drought, including abscisic acid (ABA)-related genes NCED3, OST1, ABI5, and RAB18. These ectopic expression lines also displayed hypersensitivity to ABA treatment at germination and post-germination stages. Collectively, these findings indicated the ABA-associated mode of action of GmRR34 in conferring better plant performance under the adverse drought conditions.
Collapse
Affiliation(s)
- Duong Hoang Trong Nghia
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Ho Chi Minh City 700000, Vietnam; (D.H.T.N.); (N.N.C.); (X.L.T.H.); (N.C.N.); (N.H.C.T.); (N.V.G.H.); (B.T.T.H.); (T.N.H.N.); (N.B.A.T.)
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Nguyen Nguyen Chuong
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Ho Chi Minh City 700000, Vietnam; (D.H.T.N.); (N.N.C.); (X.L.T.H.); (N.C.N.); (N.H.C.T.); (N.V.G.H.); (B.T.T.H.); (T.N.H.N.); (N.B.A.T.)
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Xuan Lan Thi Hoang
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Ho Chi Minh City 700000, Vietnam; (D.H.T.N.); (N.N.C.); (X.L.T.H.); (N.C.N.); (N.H.C.T.); (N.V.G.H.); (B.T.T.H.); (T.N.H.N.); (N.B.A.T.)
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Nguyen Cao Nguyen
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Ho Chi Minh City 700000, Vietnam; (D.H.T.N.); (N.N.C.); (X.L.T.H.); (N.C.N.); (N.H.C.T.); (N.V.G.H.); (B.T.T.H.); (T.N.H.N.); (N.B.A.T.)
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Nguyen Huu Cam Tu
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Ho Chi Minh City 700000, Vietnam; (D.H.T.N.); (N.N.C.); (X.L.T.H.); (N.C.N.); (N.H.C.T.); (N.V.G.H.); (B.T.T.H.); (T.N.H.N.); (N.B.A.T.)
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Nguyen Van Gia Huy
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Ho Chi Minh City 700000, Vietnam; (D.H.T.N.); (N.N.C.); (X.L.T.H.); (N.C.N.); (N.H.C.T.); (N.V.G.H.); (B.T.T.H.); (T.N.H.N.); (N.B.A.T.)
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Bui Thi Thanh Ha
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Ho Chi Minh City 700000, Vietnam; (D.H.T.N.); (N.N.C.); (X.L.T.H.); (N.C.N.); (N.H.C.T.); (N.V.G.H.); (B.T.T.H.); (T.N.H.N.); (N.B.A.T.)
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Thai Nguyen Hoang Nam
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Ho Chi Minh City 700000, Vietnam; (D.H.T.N.); (N.N.C.); (X.L.T.H.); (N.C.N.); (N.H.C.T.); (N.V.G.H.); (B.T.T.H.); (T.N.H.N.); (N.B.A.T.)
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Nguyen Binh Anh Thu
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Ho Chi Minh City 700000, Vietnam; (D.H.T.N.); (N.N.C.); (X.L.T.H.); (N.C.N.); (N.H.C.T.); (N.V.G.H.); (B.T.T.H.); (T.N.H.N.); (N.B.A.T.)
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang 550000, Vietnam;
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Nguyen Phuong Thao
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Ho Chi Minh City 700000, Vietnam; (D.H.T.N.); (N.N.C.); (X.L.T.H.); (N.C.N.); (N.H.C.T.); (N.V.G.H.); (B.T.T.H.); (T.N.H.N.); (N.B.A.T.)
- Vietnam National University, Ho Chi Minh City 700000, Vietnam
| |
Collapse
|
23
|
Tan L, Ijaz U, Salih H, Cheng Z, Ni Win Htet N, Ge Y, Azeem F. Genome-Wide Identification and Comparative Analysis of MYB Transcription Factor Family in Musa acuminata and Musa balbisiana. PLANTS 2020; 9:plants9040413. [PMID: 32230872 PMCID: PMC7238746 DOI: 10.3390/plants9040413] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/19/2020] [Accepted: 03/21/2020] [Indexed: 11/16/2022]
Abstract
MYB transcription factors (TFs) make up one of the most important TF families in plants. These proteins play crucial roles in processes related to development, metabolism, and stimulus-response; however, very few studies have been reported for the characterization of MYB TFs from banana. The current study identified 305 and 251 MYB genes from Musa acuminata and Musa balbisiana, respectively. Comprehensive details of MYBs are reported in terms of gene structure, protein domain, chromosomal localization, phylogeny, and expression patterns. Based on the exon-intron arrangement, these genes were classified into 12 gene models. Phylogenetic analysis of MYBs involving both species of banana, Oryza sativa, and Arabidopsis thaliana distributed these genes into 27 subfamilies. This highlighted not only the conservation, but also the gain/loss of MYBs in banana. Such genes are important candidates for future functional investigations. The MYB genes in both species exhibited a random distribution on chromosomes with variable densities. Estimation of gene duplication events revealed that segmental duplications represented the major factor behind MYB gene family expansion in banana. Expression profiles of MYB genes were also explored for their potential involvement in acetylene response or development. Collectively, the current comprehensive analysis of MYB genes in both species of banana will facilitate future functional studies.
Collapse
Affiliation(s)
- Lin Tan
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS)-Hainan Key Laboratory of Banana Genetic Improvement, Haikou 571101, Hainan, China; (L.T.); (H.S.); (Z.C.); (N.N.W.H.); (Y.G.)
| | - Usman Ijaz
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan;
| | - Haron Salih
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS)-Hainan Key Laboratory of Banana Genetic Improvement, Haikou 571101, Hainan, China; (L.T.); (H.S.); (Z.C.); (N.N.W.H.); (Y.G.)
| | - Zhihao Cheng
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS)-Hainan Key Laboratory of Banana Genetic Improvement, Haikou 571101, Hainan, China; (L.T.); (H.S.); (Z.C.); (N.N.W.H.); (Y.G.)
| | - Nwe Ni Win Htet
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS)-Hainan Key Laboratory of Banana Genetic Improvement, Haikou 571101, Hainan, China; (L.T.); (H.S.); (Z.C.); (N.N.W.H.); (Y.G.)
| | - Yu Ge
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS)-Hainan Key Laboratory of Banana Genetic Improvement, Haikou 571101, Hainan, China; (L.T.); (H.S.); (Z.C.); (N.N.W.H.); (Y.G.)
| | - Farrukh Azeem
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS)-Hainan Key Laboratory of Banana Genetic Improvement, Haikou 571101, Hainan, China; (L.T.); (H.S.); (Z.C.); (N.N.W.H.); (Y.G.)
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan;
- Correspondence:
| |
Collapse
|