1. Correction: Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila
- Author
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Christophe Rusniok, Carmen Buchrieser, Leonor Sánchez-Busó, Julian Parkhill, Sophia David, Timothy G. Harrison, Pekka Marttinen, Simon R. Harris, The Wellcome Trust Sanger Institute [Cambridge], Public Health England [London], Helsinki Institute for Information Technology (HIIT), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Aalto University, Aalto University, Biologie des Bactéries intracellulaires - Biology of Intracellular Bacteria, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), This study was funded by the Wellcome Trust (https://wellcome.ac.uk) grant number 098051 to JP and the Agence Nationale de Research (http://www.agence-nationale-recherche.fr) grant number ANR-10-LABX-62-IBEID to CB., We thank the library-generation, sequencing and informatics teams at the Wellcome Trust Sanger Institute for their assistance. We are also grateful to Jukka Corander for his help with the hierBAPS analysis., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Sánchez-Busó, Leonor [0000-0002-4162-0228], Harris, Simon R [0000-0003-1512-6194], Buchrieser, Carmen [0000-0003-3477-9190], Parkhill, Julian [0000-0002-7069-5958], Apollo - University of Cambridge Repository, Aalto University-University of Helsinki, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Wellcome Trust Sanger Institute, Department of Computer Science, Institut Pasteur Paris, Public Health England, and Aalto-yliopisto
- Subjects
0301 basic medicine ,Lipopolysaccharides ,Cancer Research ,[SDV]Life Sciences [q-bio] ,Cell Membranes ,MESH: Legionnaires' Disease ,Outer membrane proteins ,Pathology and Laboratory Medicine ,MESH: Genome, Bacterial ,Genome ,Legionella pneumophila ,Biochemistry ,MESH: Recombinant Proteins ,Database and Informatics Methods ,[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases ,Medicine and Health Sciences ,Genomic library ,MESH: Phylogeny ,Homologous Recombination ,Genetics (clinical) ,MESH: Evolution, Molecular ,Phylogeny ,Data Management ,Species diversity ,Genetics ,education.field_of_study ,Phylogenetic analysis ,Genomics ,Genomic Databases ,Recombinant Proteins ,Bacterial Pathogens ,Nucleic acids ,Phylogenetics ,Medical Microbiology ,Genomic libraries ,Cellular Structures and Organelles ,Legionnaires' Disease ,Recombination ,Research Article ,Bacterial Outer Membrane Proteins ,Computer and Information Sciences ,lcsh:QH426-470 ,DNA recombination ,030106 microbiology ,Population ,Legionella ,Biology ,Research and Analysis Methods ,Microbiology ,MESH: Homologous Recombination ,Evolution, Molecular ,03 medical and health sciences ,Evolutionary Systematics ,staffpaper ,education ,Molecular Biology ,Gene ,Microbial Pathogens ,Ecology, Evolution, Behavior and Systematics ,Taxonomy ,ta113 ,Evolutionary Biology ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,Biology and life sciences ,Bacteria ,MESH: Bacterial Outer Membrane Proteins ,Organisms ,Proteins ,Membrane Proteins ,Computational Biology ,Correction ,pathogens ,DNA ,Cell Biology ,biology.organism_classification ,Genome Analysis ,MESH: Legionella pneumophila ,lcsh:Genetics ,030104 developmental biology ,Biological Databases ,MESH: Lipopolysaccharides ,Homologous recombination ,Genome, Bacterial - Abstract
Legionella pneumophila is an environmental bacterium and the causative agent of Legionnaires’ disease. Previous genomic studies have shown that recombination accounts for a high proportion (>96%) of diversity within several major disease-associated sequence types (STs) of L. pneumophila. This suggests that recombination represents a potentially important force shaping adaptation and virulence. Despite this, little is known about the biological effects of recombination in L. pneumophila, particularly with regards to homologous recombination (whereby genes are replaced with alternative allelic variants). Using newly available population genomic data, we have disentangled events arising from homologous and non-homologous recombination in six major disease-associated STs of L. pneumophila (subsp. pneumophila), and subsequently performed a detailed characterisation of the dynamics and impact of homologous recombination. We identified genomic “hotspots” of homologous recombination that include regions containing outer membrane proteins, the lipopolysaccharide (LPS) region and Dot/Icm effectors, which provide interesting clues to the selection pressures faced by L. pneumophila. Inference of the origin of the recombined regions showed that isolates have most frequently imported DNA from isolates belonging to their own clade, but also occasionally from other major clades of the same subspecies. This supports the hypothesis that the possibility for horizontal exchange of new adaptations between major clades of the subspecies may have been a critical factor in the recent emergence of several clinically important STs from diverse genomic backgrounds. However, acquisition of recombined regions from another subspecies, L. pneumophila subsp. fraseri, was rarely observed, suggesting the existence of a recombination barrier and/or the possibility of ongoing speciation between the two subspecies. Finally, we suggest that multi-fragment recombination may occur in L. pneumophila, whereby multiple non-contiguous segments that originate from the same molecule of donor DNA are imported into a recipient genome during a single episode of recombination., Author summary Legionella pneumophila is an environmental bacterium that causes Legionnaires’ disease, a serious and potentially fatal pneumonia. Previous studies have shown that members of this species undergo a process called recombination, whereby DNA is imported from another bacterial cell into the recipient genome. The imported DNA can either replace an equivalent segment of the genome (homologous recombination) or can comprise novel genes that are new to the recipient genome (non-homologous recombination). Whilst recombination plays an undoubtedly important role in L. pneumophila evolution, accounting for more than 96% of the diversity observed within some lineages, little is known about its biological impact. In this study, we performed a detailed characterisation of the dynamics and effect of homologous recombination on L. pneumophila evolution in six clinically important lineages of L. pneumophila. We identified “hotspot” regions of the genome in which an excess of homologous recombination events was observed, which provided important clues to the selection pressures faced by L. pneumophila. By determining the donors of the recombined regions, we also revealed that recombination has occurred most frequently between isolates from the same clade, but also occurred between isolates from different major clades. This demonstrates the possibility of new adaptations arising in one lineage and being transferred to another distantly related lineage, which we predict has been an important factor in the emergence of several major disease-causing strains from diverse genomic backgrounds.
- Published
- 2017