Genome-Wide Identification of the Alba Gene Family in Plants and Stress-Responsive Expression of the Rice Alba Genes

Architectural proteins play key roles in genome construction and regulate the expression of many genes, albeit the modulation of genome plasticity by these proteins is largely unknown. A critical screening of the architectural proteins in five crop species, viz., Oryza sativa, Zea mays, Sorghum bico...

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Main Authors: Jitendra Kumar Verma, Vijay Wardhan, Deepali Singh, Subhra Chakraborty, Niranjan Chakraborty
Format: Article
Language:English
Published: MDPI AG 2018-03-01
Series:Genes
Subjects:
Online Access:http://www.mdpi.com/2073-4425/9/4/183
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spelling doaj-730fdc7edf104ea8ab57292c7d77b05d2020-11-24T23:04:52ZengMDPI AGGenes2073-44252018-03-019418310.3390/genes9040183genes9040183Genome-Wide Identification of the Alba Gene Family in Plants and Stress-Responsive Expression of the Rice Alba GenesJitendra Kumar Verma0Vijay Wardhan1Deepali Singh2Subhra Chakraborty3Niranjan Chakraborty4National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, IndiaNational Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, IndiaSchool of Biotechnology, Gautam Buddha University, Greater NOIDA, Gautam Budh Nagar, Uttar Pradesh 201308, IndiaNational Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, IndiaNational Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, IndiaArchitectural proteins play key roles in genome construction and regulate the expression of many genes, albeit the modulation of genome plasticity by these proteins is largely unknown. A critical screening of the architectural proteins in five crop species, viz., Oryza sativa, Zea mays, Sorghum bicolor, Cicer arietinum, and Vitis vinifera, and in the model plant Arabidopsis thaliana along with evolutionary relevant species such as Chlamydomonas reinhardtii, Physcomitrella patens, and Amborella trichopoda, revealed 9, 20, 10, 7, 7, 6, 1, 4, and 4 Alba (acetylation lowers binding affinity) genes, respectively. A phylogenetic analysis of the genes and of their counterparts in other plant species indicated evolutionary conservation and diversification. In each group, the structural components of the genes and motifs showed significant conservation. The chromosomal location of the Alba genes of rice (OsAlba), showed an unequal distribution on 8 of its 12 chromosomes. The expression profiles of the OsAlba genes indicated a distinct tissue-specific expression in the seedling, vegetative, and reproductive stages. The quantitative real-time PCR (qRT-PCR) analysis of the OsAlba genes confirmed their stress-inducible expression under multivariate environmental conditions and phytohormone treatments. The evaluation of the regulatory elements in 68 Alba genes from the 9 species studied led to the identification of conserved motifs and overlapping microRNA (miRNA) target sites, suggesting the conservation of their function in related proteins and a divergence in their biological roles across species. The 3D structure and the prediction of putative ligands and their binding sites for OsAlba proteins offered a key insight into the structure–function relationship. These results provide a comprehensive overview of the subtle genetic diversification of the OsAlba genes, which will help in elucidating their functional role in plants.http://www.mdpi.com/2073-4425/9/4/183Alba domainarchitectural proteinsevolutionary relevantphylogenetic relationshipregulatory elementssubcellular localization3D structure
collection DOAJ
language English
format Article
sources DOAJ
author Jitendra Kumar Verma
Vijay Wardhan
Deepali Singh
Subhra Chakraborty
Niranjan Chakraborty
spellingShingle Jitendra Kumar Verma
Vijay Wardhan
Deepali Singh
Subhra Chakraborty
Niranjan Chakraborty
Genome-Wide Identification of the Alba Gene Family in Plants and Stress-Responsive Expression of the Rice Alba Genes
Genes
Alba domain
architectural proteins
evolutionary relevant
phylogenetic relationship
regulatory elements
subcellular localization
3D structure
author_facet Jitendra Kumar Verma
Vijay Wardhan
Deepali Singh
Subhra Chakraborty
Niranjan Chakraborty
author_sort Jitendra Kumar Verma
title Genome-Wide Identification of the Alba Gene Family in Plants and Stress-Responsive Expression of the Rice Alba Genes
title_short Genome-Wide Identification of the Alba Gene Family in Plants and Stress-Responsive Expression of the Rice Alba Genes
title_full Genome-Wide Identification of the Alba Gene Family in Plants and Stress-Responsive Expression of the Rice Alba Genes
title_fullStr Genome-Wide Identification of the Alba Gene Family in Plants and Stress-Responsive Expression of the Rice Alba Genes
title_full_unstemmed Genome-Wide Identification of the Alba Gene Family in Plants and Stress-Responsive Expression of the Rice Alba Genes
title_sort genome-wide identification of the alba gene family in plants and stress-responsive expression of the rice alba genes
publisher MDPI AG
series Genes
issn 2073-4425
publishDate 2018-03-01
description Architectural proteins play key roles in genome construction and regulate the expression of many genes, albeit the modulation of genome plasticity by these proteins is largely unknown. A critical screening of the architectural proteins in five crop species, viz., Oryza sativa, Zea mays, Sorghum bicolor, Cicer arietinum, and Vitis vinifera, and in the model plant Arabidopsis thaliana along with evolutionary relevant species such as Chlamydomonas reinhardtii, Physcomitrella patens, and Amborella trichopoda, revealed 9, 20, 10, 7, 7, 6, 1, 4, and 4 Alba (acetylation lowers binding affinity) genes, respectively. A phylogenetic analysis of the genes and of their counterparts in other plant species indicated evolutionary conservation and diversification. In each group, the structural components of the genes and motifs showed significant conservation. The chromosomal location of the Alba genes of rice (OsAlba), showed an unequal distribution on 8 of its 12 chromosomes. The expression profiles of the OsAlba genes indicated a distinct tissue-specific expression in the seedling, vegetative, and reproductive stages. The quantitative real-time PCR (qRT-PCR) analysis of the OsAlba genes confirmed their stress-inducible expression under multivariate environmental conditions and phytohormone treatments. The evaluation of the regulatory elements in 68 Alba genes from the 9 species studied led to the identification of conserved motifs and overlapping microRNA (miRNA) target sites, suggesting the conservation of their function in related proteins and a divergence in their biological roles across species. The 3D structure and the prediction of putative ligands and their binding sites for OsAlba proteins offered a key insight into the structure–function relationship. These results provide a comprehensive overview of the subtle genetic diversification of the OsAlba genes, which will help in elucidating their functional role in plants.
topic Alba domain
architectural proteins
evolutionary relevant
phylogenetic relationship
regulatory elements
subcellular localization
3D structure
url http://www.mdpi.com/2073-4425/9/4/183
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