Reassessment of the Listeria monocytogenespan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome

BMC Genomics

Research Article

Alexander Goesmann¹  Axel Strittmatter²  Rolf Daniel²  Sukhadeo Barbuddhe³  Carsten Kuenne⁴  Torsten Hain⁴  Mobarak Abu Mraheil⁴  Trinad Chakraborty⁴  André Billion⁴ 

[1] Bioinformatics Resource Facility, Center for Biotechnology, Bielefeld University, D-33549, Bielefeld, Germany;Department of Genomic and Applied Microbiology and Goettingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University Goettingen, Grisebachstrasse 8, D-37077, Goettingen, Germany;ICAR Research Complex for Goa, 403402, Ela, Old Goa, India;Institute of Medical Microbiology, German Centre for Infection Research, Justus-Liebig-University, D-35392, Giessen, Germany;

关键词: Horizontal Gene Transfer;    Amino Acid Identity;    Mobile Genetic Element;    Genomic Island;    Accessory Gene;   

DOI  :  10.1186/1471-2164-14-47

 received in 2012-09-07, accepted in 2012-12-15,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundListeria monocytogenes is an important food-borne pathogen and model organism for host-pathogen interaction, thus representing an invaluable target considering research on the forces governing the evolution of such microbes. The diversity of this species has not been exhaustively explored yet, as previous efforts have focused on analyses of serotypes primarily implicated in human listeriosis. We conducted complete genome sequencing of 11 strains employing 454 GS FLX technology, thereby achieving full coverage of all serotypes including the first complete strains of serotypes 1/2b, 3c, 3b, 4c, 4d, and 4e. These were comparatively analyzed in conjunction with publicly available data and assessed for pathogenicity in the Galleria mellonella insect model.ResultsThe species pan-genome of L. monocytogenes is highly stable but open, suggesting an ability to adapt to new niches by generating or including new genetic information. The majority of gene-scale differences represented by the accessory genome resulted from nine hyper variable hotspots, a similar number of different prophages, three transposons (Tn916, Tn554, IS3-like), and two mobilizable islands. Only a subset of strains showed CRISPR/Cas bacteriophage resistance systems of different subtypes, suggesting a supplementary function in maintenance of chromosomal stability. Multiple phylogenetic branches of the genus Listeria imply long common histories of strains of each lineage as revealed by a SNP-based core genome tree highlighting the impact of small mutations for the evolution of species L. monocytogenes. Frequent loss or truncation of genes described to be vital for virulence or pathogenicity was confirmed as a recurring pattern, especially for strains belonging to lineages III and II. New candidate genes implicated in virulence function were predicted based on functional domains and phylogenetic distribution. A comparative analysis of small regulatory RNA candidates supports observations of a differential distribution of trans-encoded RNA, hinting at a diverse range of adaptations and regulatory impact.ConclusionsThis study determined commonly occurring hyper variable hotspots and mobile elements as primary effectors of quantitative gene-scale evolution of species L. monocytogenes, while gene decay and SNPs seem to represent major factors influencing long-term evolution. The discovery of common and disparately distributed genes considering lineages, serogroups, serotypes and strains of species L. monocytogenes will assist in diagnostic, phylogenetic and functional research, supported by the comparative genomic GECO-LisDB analysis server (http://bioinfo.mikrobio.med.uni-giessen.de/geco2lisdb).

【 授权许可】

Unknown   
© Kuenne et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.