Abstract
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.
Highlights
Plants encounter multiple abiotic and biotic stresses in a complex environment, which hamper their growth and development [1]
We investigated the contribution of Alba proteins harbouring an Alba domain (Pfam PF01918)
The amino acid sequences were examined for the presence of the Alba domain using the NCBI Conserved Domain Database (CDD) [28]
Summary
Plants encounter multiple abiotic and biotic stresses in a complex environment, which hamper their growth and development [1]. Genes 2018, 9, 183 affinity) superfamily of proteins has received global attention immediately after the Alba proteins were identified from archaea as sequence-independent DNA-binding proteins [4,5,6]. The members of this superfamily are diversely found in archaea and eukaryotes as small, basic, dimeric nucleic acid-binding proteins [7,8,9,10,11]. The functional diversity among Alba proteins encompasses transcriptional and translational regulation, genome packaging and organization, development and differentiation, and RNA metabolism [2,8,11,14]. The biological roles of Alba proteins are poorly understood because of their multiple paralogs, posttranslational modifications, differential binding affinity, and functional crosstalk
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