Genome-wide identification and expression profiling of two-component system (TCS) genes in Brassica oleracea in response to shade stress.

Autor:	Sadaqat M; Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan., Umer B; Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan., Attia KA; Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia., Abdelkhalik AF; Biotechnology School, Nile University, Giza, Egypt.; Rice Biotechnology Lab, Rice Research and Training Center, Field Crops Research Institute, ARC, Kafrelshikh, Egypt., Azeem F; Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan., Javed MR; Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan., Fatima K; Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan., Zameer R; Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan., Nadeem M; Wheat Research Institute, Ayub Agriculture Research Institute, Faisalabad, Pakistan., Tanveer MH; Wheat Research Institute, Ayub Agriculture Research Institute, Faisalabad, Pakistan., Sun S; Department of Biotechnology, Chonnam National University, Yesosu Campus, Yesosu Si, Republic of Korea., Ercisli S; Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Türkiye.; HGF Agro, Ata Teknokent, Erzurum, Türkiye., Nawaz MA; Advanced Engineering School (Agrobiotek), Tomsk State University, Tomsk, Russia.; Center for Research in the Field of Materials and Technologies, Tomsk State University, Tomsk, Russia.
Jazyk:	angličtina
Zdroj:	Frontiers in genetics [Front Genet] 2023 May 30; Vol. 14, pp. 1142544. Date of Electronic Publication: 2023 May 30 (Print Publication: 2023).
DOI:	10.3389/fgene.2023.1142544
Abstrakt:	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. Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2023 Sadaqat, Umer, Attia, Abdelkhalik, Azeem, Javed, Fatima, Zameer, Nadeem, Tanveer, Sun, Ercisli and Nawaz.)
Databáze:	MEDLINE
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