Upadhyay AK, Sowdhamini R. Genome-Wide Analysis of Domain-Swap Predicted Products in the Genome of Anti-Stress Medicinal Plant:
Ocimum tenuiflorum.
Bioinform Biol Insights 2019;
13:1177932218821362. [PMID:
30692846 PMCID:
PMC6335655 DOI:
10.1177/1177932218821362]
[Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/08/2018] [Indexed: 11/18/2022] Open
Abstract
Computational approaches to high-throughput data are gaining importance because
of explosion of sequences in the post-genomic era. This explosion of sequence
data creates a huge gap among the domains of sequence structure and function,
since the experimental techniques to determine the structure and function are
very expensive, time taking, and laborious in nature. Therefore, there is an
urgent need to emphasize on the development of computational approaches in the
field of biological systems. Engagement of proteins in quaternary arrangements,
such as domain swapping, might be relevant for higher compatibility of such
genes at stress conditions. In this study, the capacity to engage in domain
swapping was predicted from mere sequence information in the whole genome of
holy Basil (Ocimum tenuiflorum), which is well known to be an
anti-stress agent. Approximately, one-fourth of the proteins of O
tenuiflorum are predicted to undergo three-dimensional (3D)-domain
swapping. Furthermore, function annotation was carried out on all the predicted
domain-swap sequences from the O tenuiflorum and
Arabidopsis thaliana for their distribution in different
Pfam protein families and gene ontology (GO) terms. These domain-swapped protein
sequences are associated with many Pfam protein families with a wide range of GO
annotation terms. A comparative analysis of domain-swap-predicted sequences in
O tenuiflorum with gene products in A
thaliana reveals that around 26% (2522 sequences) are close
homologues across the 2 genomes. Functional annotation of predicted
domain-swapped sequences infers that predicted domain-swap sequences are
involved in diverse molecular functions, such as in gene regulation of abiotic
stress conditions and adaptation to different environmental niches. Finally, the
positively predicted sequences of A thaliana and O
tenuiflorum were also examined for their presence in stress
regulome, as recorded in our STIFDB database, to check the involvement of these
proteins in different abiotic stresses.
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