Landscape of ROD9 Island: Functional annotations and biological network of hypothetical proteins in Salmonella enterica

Nikita Soni; Sunil Kumar Swain; Ravi Kant; Aditya Singh; Rahul Ravichandran; Suresh K Verma; Pritam Kumar Panda; Mrutyunjay Suar

doi:10.1016/j.compbiolchem.2019.107110

Landscape of ROD9 Island: Functional annotations and biological network of hypothetical proteins in Salmonella enterica

Comput Biol Chem. 2019 Dec:83:107110. doi: 10.1016/j.compbiolchem.2019.107110. Epub 2019 Aug 16.

Authors

Nikita Soni¹, Sunil Kumar Swain², Ravi Kant³, Aditya Singh¹, Rahul Ravichandran⁴, Suresh K Verma⁵, Pritam Kumar Panda⁶, Mrutyunjay Suar⁷

Affiliations

¹ School of Biotechnology and Bioinformatics, D. Y. Patil (Deemed to be University), Navi Mumbai, India.
² School of Biotechnology, KIIT University, Bhubaneswar, India.
³ University of Delhi, New Delhi, India.
⁴ School of Chemical and Biotechnology, SASTRA University, Tamil Nadu, India.
⁵ Institute of Environmental Medicine (IMM), C6, Molecular Toxicology, Karolinska Institutet, Sweden.
⁶ Division of Pediatric Hematology and Oncology, University Medical Center, University of Freiburg, Germany. Electronic address: pritam.panda@physics.uu.se.
⁷ School of Biotechnology, KIIT University, Bhubaneswar, India. Electronic address: musar@kiitbiotech.ac.in.

PMID: 31445418
DOI: 10.1016/j.compbiolchem.2019.107110

Abstract

Salmonella, an Enterobacteria is a therapeutically important pathogen for the host. The advancement of genome sequencing of S. enterica serovar Enteritidis have identified a distinct ROD9 pathogenic island, imparting virulence. The occurrence of 17 ROD9 hypothetical proteins, necessitates subsequent bioinformatics approach for structural and functional aspects of protein-protein relations or networks in different pathogenic phenotypes express. A collective analysis using predictive bioinformatics tools that includes NCBI-BLASTp and BLAST2GO annotated the motif patterns and functional significance. The VFDB identified 10 virulence proteins at both genomic and metagenomic level. Phylogenetic analysis revealed a divergent and convergent relationship between 17 ROD9 and 41 SP-1 proteins. Here, combining a comprehensive approach from sequence based, motif recognitions, domain identification, virulence ability to structural modelling provides a precise function to ROD9 proteins biological network, for which no experimental information is available.

Keywords: Biological network; GO annotations; Molecular docking; ROD9; SEN1005; Text mining; Virulence.

MeSH terms

Bacterial Proteins / analysis*
Bacterial Proteins / genetics
Bacterial Proteins / metabolism
Databases, Protein
Molecular Sequence Annotation*
Phenotype
Salmonella enterica / chemistry*
Salmonella enterica / metabolism

Substances

Bacterial Proteins