Survey and characterization of casposon elements in bacterial and archeal genomes

Abstract

Mobile genetic elements (MGEs) are biological elements capable of inserting their genetic content into the chromosome of a host cell. The importance of MGEs in the biology of prokaryortic and eukaryotic organisms has been gaining increasing recognition. A novel group of self-synthesizing elements, the casposons, has been recently described. The elucidation of the ancestral position of their Cas1 endonuclease in the phylogeny of this family of proteins suggests that these elements played a fundamental role in the development of the adaptive immunity of prokaryotes and in the origin of the CRISPR-Cas system. Our group has recently developed two bioinformatics tools: TABAJARA, for the design and rational construction of profile HMMs, and e-Finder, a program that uses such models for the detection of multigenic elements in assembled genomes. This project aims to construct specific profile HMMs of the casposon-derived Cas1 and PolB proteins with TABAJARA program and use them for a large survey of these elements in the PATRIC database of genomes using the e-Finder program. The elements will be characterized in regard to their structure, functions and evolutionary relationships. Our group already has a collaboration with Dr. Mart Krupovic (Pasteur Institute, Paris), the discoverer of these mobile elements, and a proof-of-principle has already demonstrated the viability of our strategy. A better knowledge of the diversity of casposons may reveal new important aspects in the evolution and diversity of these elements, their role in the origin of CRISPRs and the development of adaptive immunity of prokaryotes.