Application of bioinformatics in discrimination of pathogenic and non-pathogenic strains of bacteria

Xanthomonas campestris is considered in the industry due to its xanthan production ability. However, some strains are pathogenic for Brassicaceae plants and can cause significant economic losses. In present bioinformatics study, the genomes of five X. campestris strains including three pathogenic and two non-pathogenic bacteria were retrieved from NCBI database. After genome annotation with RAST, the gene clusters and proteins related to pathogenesis in Xanthomonas were identified by BLASTP and then compared. Gene clusters related to production of two virulence factors, secretion system type II (xps and xcs genes) and xanthan exopolysaccharide (gum genes) were present in all of the strains. Pathogenic strains showed the complete gene cluster associated with virulence factor secretion system type ۳ (hrp genes) but the non-pathogenic strains lacked them. The effector type III profile analysis of the X. campestris strains genomes showed that pathogenic strains have the ability to encode a significant number of effector proteins but there are a few encoding genes for these proteins in the genome of non-pathogenic strains. After the examination of the gene cluster related to production of LPS virulence factor, it was found that the content of this gene cluster was different in pathogenic and non-pathogenic strains. The investigation of the presence of secretory system type III gene cluster and the content analysis of LPS encoding genes can help identifying pathogenic strains of X. campestris. The genome comparison of pathogenic and non-pathogenic strains of a bacterium using bioinformatics analysis leads to the identification and development of gene markers which can be useful and efficient in identifying pathogenic strains as well as early diagnosis of the disease.

Keywords:

Comparative genomics , Xanthomonas campestris , Secretion system type III , Xanthan