Unusual genome complexity in Lactobacillus salivarius JCM1046

Hdl Handle:
http://hdl.handle.net/10147/326186
Title:
Unusual genome complexity in Lactobacillus salivarius JCM1046
Authors:
Raftis, Emma J; Forde, Brian M; Claesson, Marcus J; O’Toole, Paul W
Citation:
Raftis EJ et al. Unusual genome complexity in Lactobacillus salivarius JCM1046. BMC Genomics. 2014 Sep 08;15(1):771
Issue Date:
8-Sep-2014
URI:
http://dx.doi.org/10.1186/1471-2164-15-771; http://hdl.handle.net/10147/326186
Abstract:
Abstract Background Lactobacillus salivarius strains are increasingly being exploited for their probiotic properties in humans and animals. Dissemination of antibiotic resistance genes among species with food or probiotic-association is undesirable and is often mediated by plasmids or integrative and conjugative elements. L. salivarius strains typically have multireplicon genomes including circular megaplasmids that encode strain-specific traits for intestinal survival and probiotic activity. Linear plasmids are less common in lactobacilli and show a very limited distribution in L. salivarius. Here we present experimental evidence that supports an unusually complex multireplicon genome structure in the porcine isolate L. salivarius JCM1046. Results JCM1046 harbours a 1.83 Mb chromosome, and four plasmids which constitute 20% of the genome. In addition to the known 219 kb repA-type megaplasmid pMP1046A, we identified and experimentally validated the topology of three additional replicons, the circular pMP1046B (129 kb), a linear plasmid pLMP1046 (101 kb) and pCTN1046 (33 kb) harbouring a conjugative transposon. pMP1046B harbours both plasmid-associated replication genes and paralogues of chromosomally encoded housekeeping and information-processing related genes, thus qualifying it as a putative chromid. pLMP1046 shares limited sequence homology or gene synteny with other L. salivarius plasmids, and its putative replication-associated protein is homologous to the RepA/E proteins found in the large circular megaplasmids of L. salivarius. Plasmid pCTN1046 harbours a single copy of an integrated conjugative transposon (Tn6224) which appears to be functionally intact and includes the tetracycline resistance gene tetM. Conclusion Experimental validation of sequence assemblies and plasmid topology resolved the complex genome architecture of L. salivarius JCM1046. A high-coverage draft genome sequence would not have elucidated the genome complexity in this strain. Given the expanding use of L. salivarius as a probiotic, it is important to determine the genotypic and phenotypic organization of L. salivarius strains. The identification of Tn6224-like elements in this species has implications for strain selection for probiotic applications.
Item Type:
Article
Language:
en
Keywords:
GENETICS
Local subject classification:
PROBIOTICS; GASTROINTESTINAL TRACT

Full metadata record

DC FieldValue Language
dc.contributor.authorRaftis, Emma Jen_GB
dc.contributor.authorForde, Brian Men_GB
dc.contributor.authorClaesson, Marcus Jen_GB
dc.contributor.authorO’Toole, Paul Wen_GB
dc.date.accessioned2014-09-17T09:22:38Z-
dc.date.available2014-09-17T09:22:38Z-
dc.date.issued2014-09-08-
dc.identifier.citationRaftis EJ et al. Unusual genome complexity in Lactobacillus salivarius JCM1046. BMC Genomics. 2014 Sep 08;15(1):771en_GB
dc.identifier.urihttp://dx.doi.org/10.1186/1471-2164-15-771-
dc.identifier.urihttp://hdl.handle.net/10147/326186-
dc.description.abstractAbstract Background Lactobacillus salivarius strains are increasingly being exploited for their probiotic properties in humans and animals. Dissemination of antibiotic resistance genes among species with food or probiotic-association is undesirable and is often mediated by plasmids or integrative and conjugative elements. L. salivarius strains typically have multireplicon genomes including circular megaplasmids that encode strain-specific traits for intestinal survival and probiotic activity. Linear plasmids are less common in lactobacilli and show a very limited distribution in L. salivarius. Here we present experimental evidence that supports an unusually complex multireplicon genome structure in the porcine isolate L. salivarius JCM1046. Results JCM1046 harbours a 1.83 Mb chromosome, and four plasmids which constitute 20% of the genome. In addition to the known 219 kb repA-type megaplasmid pMP1046A, we identified and experimentally validated the topology of three additional replicons, the circular pMP1046B (129 kb), a linear plasmid pLMP1046 (101 kb) and pCTN1046 (33 kb) harbouring a conjugative transposon. pMP1046B harbours both plasmid-associated replication genes and paralogues of chromosomally encoded housekeeping and information-processing related genes, thus qualifying it as a putative chromid. pLMP1046 shares limited sequence homology or gene synteny with other L. salivarius plasmids, and its putative replication-associated protein is homologous to the RepA/E proteins found in the large circular megaplasmids of L. salivarius. Plasmid pCTN1046 harbours a single copy of an integrated conjugative transposon (Tn6224) which appears to be functionally intact and includes the tetracycline resistance gene tetM. Conclusion Experimental validation of sequence assemblies and plasmid topology resolved the complex genome architecture of L. salivarius JCM1046. A high-coverage draft genome sequence would not have elucidated the genome complexity in this strain. Given the expanding use of L. salivarius as a probiotic, it is important to determine the genotypic and phenotypic organization of L. salivarius strains. The identification of Tn6224-like elements in this species has implications for strain selection for probiotic applications.-
dc.language.isoenen
dc.subjectGENETICSen_GB
dc.subject.otherPROBIOTICSen_GB
dc.subject.otherGASTROINTESTINAL TRACTen_GB
dc.titleUnusual genome complexity in Lactobacillus salivarius JCM1046en_GB
dc.typeArticleen
dc.language.rfc3066en-
dc.rights.holderEmma J Raftis et al.; licensee BioMed Central Ltd.-
dc.description.statusPeer Reviewed-
dc.date.updated2014-09-13T19:03:01Z-
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