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Genome-wide identification of the Alba gene family in plants and stress-responsive expression of the rice Alba genes

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Title Genome-wide identification of the Alba gene family in plants and stress-responsive expression of the rice Alba genes
 
Creator Verma, Jitendra Kumar
Wardhan, Vijay
Singh, Deepali
Chakraborty, Subhra
Chakraborty, Niranjan
 
Subject Alba domain
architectural proteins
evolutionary relevant
phylogenetic relationship
regulatory elements
subcellular localization
3D structure
 
Description Accepted date: 29 January 2018
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.
This work was financially supported by the Department of Biotechnology (DBT) [BT/184/NE/TBP/2011 and BT/PR12919/AGR/02/676/2009], Ministry of Science and Technology, Govt. of India. The authors also thank DST for providing a predoctoral fellowship [SERB(EMR/2015/001870)] to J.K.V. and the Council of Scientific & Industrial Research (CSIR), Govt. of India, for providing a postdoctoral fellowship [38(1385)/13/EMR-II] to V.W. We appreciate Jasbeer Singh for the illustrations and graphical representation in the manuscript.
 
Date 2018-04-03T09:40:51Z
2018-04-03T09:40:51Z
2018
 
Type Article
 
Identifier Genes, 9(4): 183
2073-4425
http://223.31.159.10:8080/jspui/handle/123456789/848
http://www.mdpi.com/2073-4425/9/4/183
10.3390/genes9040183
 
Language en_US
 
Format application/pdf
 
Publisher MDPI AG