Insertion sequence search in oral pathogens

Objectives: Insertion sequence (IS) elements are the simplest transposable DNA in bacteria and have been major causes of genomic changes, such as insertion, deletion, and inversion. In pathogenic bacteria, IS elements modify the expression and cause the transposition of genes controlling interactions of the pathogen with the host organism. In this study, our aims are to identify IS elements and its genomic structure in complete genomes of oral pathogens.

Methods:

A customized analysis pipeline was implemented to automate the following ordered processes: 1) ISfinder database Blastx against complete genome sequences; 2) Inverted repeats search; 3) Second Blastx against IS elements protein database (ISPEP database); 4) Blastx against nr database; 5) Incorporation of gene annotations in results; 6) Refinements of results. After manual curation, all results are presented on the Oralgen website at http://oralgen.lanl.gov/oralgen/bacteria/analysis/InsertionSequences/

Results: All potential IS elements are listed its genome locus, which show genome regions containing several IS elements and the gene records that fall within such regions. Detailed analysis of IS elements are presented in tabular format with information such as its DNA sequence and open reading frames or potential coding sequences, the sequence of the ends of the element, its nomenclature and classification of IS family.

Conclusion: This study provides detailed analysis of insertion sequence elements in oral pathogens. With the increasing number of sequenced oral bacteria, this website is a valuable resource for characterizing IS elements in oral pathogens and will help us understand the important role of IS elements in DNA transposition and rearrangement in the evolution of host-pathogen interactions.

This work is supported by NIH NIDCR under LANL contract no. Y1-DE-6006-02