In silico functional prediction of hypothetical proteins from the core genome of Corynebacterium pseudotuberculosis biovar ovis

PeerJ

article

Carlos Leonardo Araújo¹  Iago Blanco¹  Luciana Souza¹  Sandeep Tiwari²  Lino César Pereira¹  Preetam Ghosh³  Vasco Azevedo²  Artur Silva¹  Adriana Folador¹ 

[1] Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará;Institute of Biological Sciences, Federal University of Minas Gerais;Department of Computer Science, Virginia Commonwealth University

关键词: Hypothetical proteins;    Functional annotation;    Corynebacterium pseudotuberculosis;    Caseous lymphadenitis;   

DOI  :  10.7717/peerj.9643

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Corynebacterium pseudotuberculosis is a pathogen of veterinary relevance diseases, being divided into two biovars: equi and ovis; causing ulcerative lymphangitis and caseous lymphadenitis, respectively. The isolation and sequencing of C. pseudotuberculosis biovar ovis strains in the Northern and Northeastern regions of Brazil exhibited the emergence of this pathogen, which causes economic losses to small ruminant producers, and condemnation of carcasses and skins of animals. Through the pan-genomic approach, it is possible to determine and analyze genes that are shared by all strains of a species—the core genome. However, many of these genes do not have any predicted function, being characterized as hypothetical proteins (HP). In this study, we considered 32 C. pseudotuberculosis biovar ovis genomes for the pan-genomic analysis, where were identified 172 HP present in a core genome composed by 1255 genes. We are able to functionally annotate 80 sequences previously characterized as HP through the identification of structural features as conserved domains and families. Furthermore, we analyzed the physicochemical properties, subcellular localization and molecular function. Additionally, through RNA-seq data, we investigated the differential gene expression of the annotated HP. Genes inserted in pathogenicity islands had their virulence potential evaluated. Also, we have analyzed the existence of functional associations for their products based on protein–protein interaction networks, and perform the structural prediction of three targets. Due to the integration of different strategies, this study can underlie deeper in vitro researches in the characterization of these HP and the search for new solutions for combat this pathogen.

【 授权许可】

CC BY