A systematic approach to classify and characterize genomic islands driven by conjugative mobility using protein signatures

Author:

Audrey Bioteau1ORCID,Cellier Nicolas2ORCID,White Frédérique1,Jacques Pierre-Étienne1ORCID,Burrus Vincent1ORCID

Affiliation:

1. Département de biologie, Université de Sherbrooke , Sherbrooke, Québec , Canada

2. CGI IMT Mines Albi , Albi , France

Abstract

Abstract Genomic islands (GIs) play a crucial role in the spread of antibiotic resistance, virulence factors and antiviral defense systems in a broad range of bacterial species. However, the characterization and classification of GIs are challenging due to their relatively small size and considerable genetic diversity. Predicting their intercellular mobility is of utmost importance in the context of the emerging crisis of multidrug resistance. Here, we propose a large-scale classification method to categorize GIs according to their mobility profile and, subsequently, analyze their gene cargo. We based our classification decision scheme on a collection of mobility protein motif definitions available in publicly accessible databases. Our results show that the size distribution of GI classes correlates with their respective structure and complexity. Self-transmissible GIs are usually the largest, except in Bacillota and Actinomycetota, accumulate antibiotic and phage resistance genes, and favour the use of a tyrosine recombinase to insert into a host's replicon. Non-mobilizable GIs tend to use a DDE transposase instead. Finally, although tRNA genes are more frequently targeted as insertion sites by GIs encoding a tyrosine recombinase, most GIs insert in a protein-encoding gene. This study is a stepping stone toward a better characterization of mobile GIs in bacterial genomes and their mechanism of mobility.

Funder

Discovery Grant

Natural Sciences and Engineering Research Council of Canada

Canadian Institutes of Health Research

Université de Sherbrooke

Fonds de recherche du Québec – Nature et technologies

Publisher

Oxford University Press (OUP)

Subject

Genetics

Reference57 articles.

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