Comparative Omics-Based Identification and Expression Analysis of a Two-Component System in <i>Vigna radiata</i> in Drought Stress
Two-component system (TCS) genes regulate a wide range of biological activities in prokaryotes and eukaryotes, including plants. TCS plays an important role in cellular responses to external stimuli, such as biotic and abiotic factors. In plants, this system supports cell division, leaf senescence,...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-03-01
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| Series: | Agronomy |
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| Online Access: | https://www.mdpi.com/2073-4395/13/4/989 |
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| author | Muhammad Amin Afzal Farrukh Azeem Shumaila Afzal Naila Afzal Muhammad Rizwan Hyojin Seo Asad Ali Shah Muhammad Amjad Nawaz |
| author_facet | Muhammad Amin Afzal Farrukh Azeem Shumaila Afzal Naila Afzal Muhammad Rizwan Hyojin Seo Asad Ali Shah Muhammad Amjad Nawaz |
| author_sort | Muhammad Amin Afzal |
| collection | DOAJ |
| description | Two-component system (TCS) genes regulate a wide range of biological activities in prokaryotes and eukaryotes, including plants. TCS plays an important role in cellular responses to external stimuli, such as biotic and abiotic factors. In plants, this system supports cell division, leaf senescence, stress response, chloroplast division, and nutrient signaling. There are three kinds of proteins responsible for the appropriate functioning of the TCS system: histidine kinases (HKs), histidine phosphotransfer proteins (HPs), and response regulators (RRs). The results of the current study revealed that <i>Vigna radiata</i> has 54 genes encoding potential TCS proteins, which were divided into three subgroups: 18 HKs, 9 HPs (seven true and two pseudos), and 27 RRs (8 type-A, 8 type-B, 3 type-C, and 8 PRRS). The anticipated TCS genes were widely dispersed across all eleven chromosomes and had family-specific intron/exon structures. After investigating TCS genes in a variety of plant species, we determined that <i>Vigna</i> HK (L)s, HPs, and RRs have closer evolutionary relationships with other legume genes. Gene duplication, including segmental and tandem types, is the most frequent source of gene family expansion. Multiple stress-related cis-elements were predicted in the promoter sequences of the VrTCS genes. RNA-seq data analysis demonstrated that VrTCS genes were expressed in clusters of upregulated and downregulated groups in response to drought stress. Moreover, these clusters were differentially expressed as early or late responses to drought stress. Real-time qPCR showed that <i>VrHK2</i>, <i>VrHK3</i>, <i>VrPHYE</i>, <i>VrHP4.1</i>, <i>VrRR5.2</i>, and <i>VrRR10</i> genes were upregulated, while <i>VrRR3</i> and <i>VrHP6.1</i> genes were downregulated in response to drought stress. The current study highlights the architecture of <i>V. radiata</i> TCS and provides a robust framework for subsequent functional evaluation. |
| first_indexed | 2024-03-11T05:20:23Z |
| format | Article |
| id | doaj.art-e86ab4ad5d5741b5a0c9876e77d81d32 |
| institution | Directory Open Access Journal |
| issn | 2073-4395 |
| language | English |
| last_indexed | 2024-03-11T05:20:23Z |
| publishDate | 2023-03-01 |
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| record_format | Article |
| series | Agronomy |
| spelling | doaj.art-e86ab4ad5d5741b5a0c9876e77d81d322023-11-17T17:55:59ZengMDPI AGAgronomy2073-43952023-03-0113498910.3390/agronomy13040989Comparative Omics-Based Identification and Expression Analysis of a Two-Component System in <i>Vigna radiata</i> in Drought StressMuhammad Amin Afzal0Farrukh Azeem1Shumaila Afzal2Naila Afzal3Muhammad Rizwan4Hyojin Seo5Asad Ali Shah6Muhammad Amjad Nawaz7Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, PakistanDepartment of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, PakistanDepartment of Microbiology, University of Agricultural, Faisalabad 38000, PakistanDepartment of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, PakistanDepartment of Environmental Sciences, Government College University, Faisalabad 38000, PakistanKorean Soybean Research Institute, 950 Worasan-ro, Jinju 52840, Republic of KoreaDepartment of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, PakistanAdvanced Engineering School (Agrobiotek), Tomsk State University, Lenin Ave, 36, 63050 Tomsk, RussiaTwo-component system (TCS) genes regulate a wide range of biological activities in prokaryotes and eukaryotes, including plants. TCS plays an important role in cellular responses to external stimuli, such as biotic and abiotic factors. In plants, this system supports cell division, leaf senescence, stress response, chloroplast division, and nutrient signaling. There are three kinds of proteins responsible for the appropriate functioning of the TCS system: histidine kinases (HKs), histidine phosphotransfer proteins (HPs), and response regulators (RRs). The results of the current study revealed that <i>Vigna radiata</i> has 54 genes encoding potential TCS proteins, which were divided into three subgroups: 18 HKs, 9 HPs (seven true and two pseudos), and 27 RRs (8 type-A, 8 type-B, 3 type-C, and 8 PRRS). The anticipated TCS genes were widely dispersed across all eleven chromosomes and had family-specific intron/exon structures. After investigating TCS genes in a variety of plant species, we determined that <i>Vigna</i> HK (L)s, HPs, and RRs have closer evolutionary relationships with other legume genes. Gene duplication, including segmental and tandem types, is the most frequent source of gene family expansion. Multiple stress-related cis-elements were predicted in the promoter sequences of the VrTCS genes. RNA-seq data analysis demonstrated that VrTCS genes were expressed in clusters of upregulated and downregulated groups in response to drought stress. Moreover, these clusters were differentially expressed as early or late responses to drought stress. Real-time qPCR showed that <i>VrHK2</i>, <i>VrHK3</i>, <i>VrPHYE</i>, <i>VrHP4.1</i>, <i>VrRR5.2</i>, and <i>VrRR10</i> genes were upregulated, while <i>VrRR3</i> and <i>VrHP6.1</i> genes were downregulated in response to drought stress. The current study highlights the architecture of <i>V. radiata</i> TCS and provides a robust framework for subsequent functional evaluation.https://www.mdpi.com/2073-4395/13/4/989TCSsignalingHKsRRsHPsPPI |
| spellingShingle | Muhammad Amin Afzal Farrukh Azeem Shumaila Afzal Naila Afzal Muhammad Rizwan Hyojin Seo Asad Ali Shah Muhammad Amjad Nawaz Comparative Omics-Based Identification and Expression Analysis of a Two-Component System in <i>Vigna radiata</i> in Drought Stress Agronomy TCS signaling HKs RRs HPs PPI |
| title | Comparative Omics-Based Identification and Expression Analysis of a Two-Component System in <i>Vigna radiata</i> in Drought Stress |
| title_full | Comparative Omics-Based Identification and Expression Analysis of a Two-Component System in <i>Vigna radiata</i> in Drought Stress |
| title_fullStr | Comparative Omics-Based Identification and Expression Analysis of a Two-Component System in <i>Vigna radiata</i> in Drought Stress |
| title_full_unstemmed | Comparative Omics-Based Identification and Expression Analysis of a Two-Component System in <i>Vigna radiata</i> in Drought Stress |
| title_short | Comparative Omics-Based Identification and Expression Analysis of a Two-Component System in <i>Vigna radiata</i> in Drought Stress |
| title_sort | comparative omics based identification and expression analysis of a two component system in i vigna radiata i in drought stress |
| topic | TCS signaling HKs RRs HPs PPI |
| url | https://www.mdpi.com/2073-4395/13/4/989 |
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