DNA structure at the plasmid origin-of-Transfer indicates its potential transfer range
Artikel i vetenskaplig tidskrift, 2018

Horizontal gene transfer via plasmid conjugation enables antimicrobial resistance (AMR) to spread among bacteria and is a major health concern. The range of potential transfer hosts of a particular conjugative plasmid is characterised by its mobility (MOB) group, which is currently determined based on the amino acid sequence of the plasmid-encoded relaxase. To facilitate prediction of plasmid MOB groups, we have developed a bioinformatic procedure based on analysis of the origin-of-Transfer (oriT), a merely 230 bp long non-coding plasmid DNA region that is the enzymatic substrate for the relaxase. By computationally interpreting conformational and physicochemical properties of the oriT region, which facilitate relaxase-oriT recognition and initiation of nicking, MOB groups can be resolved with over 99% accuracy. We have shown that oriT structural properties are highly conserved and can be used to discriminate among MOB groups more efficiently than the oriT nucleotide sequence. The procedure for prediction of MOB groups and potential transfer range of plasmids was implemented using published data and is available at http://dnatools.eu/MOB/plasmid.HTML.

Författare

Jan Zrimec

Institute of Metagenomics and Microbial Technologies (IMMT)

Chalmers, Biologi och bioteknik, Systembiologi

University of Primorska

Aleš Lapanje

Institut Jozef Stefan

Saratov State University

Institute of Metagenomics and Microbial Technologies (IMMT)

Scientific Reports

2045-2322 (ISSN)

Vol. 8 1820

Ämneskategorier

Mikrobiologi

Bioinformatik (beräkningsbiologi)

Bioinformatik och systembiologi

DOI

10.1038/s41598-018-20157-y