Genetic relationships among 527 Gram-negative bacterial plasmids.

Plasmids are mosaic in composition with a maintenance "backbone" as well as "accessory" genes obtained via horizontal gene transfer. This horizontal gene transfer complicates the study of their genetic relationships. We describe a method for relating a large number of Gram-negative (GN) bacterial plasmids based on their genetic sequences. Complete coding gene sequences of 527 GN bacterial plasmids were obtained from NCBI. Initial classification of their genetic relationships was accomplished using a computational approach analogous to hybridization of "mixed-genome microarrays." Because of this similarity, the phrase "virtual hybridization" is used to describe this approach. Protein sequences generated from the gene sequences were randomly chosen to serve as "probes" for the virtual arrays, and virtual hybridization for each GN plasmid was achieved using BLASTp. Each resulting intensity matrix was used to generate a distance matrix from which an initial tree was constructed. Relationships were refined for several clusters by identifying conserved proteins within a cluster. Multiple-sequence alignment was applied to the concatenated conserved proteins, and maximum likelihood was used to generate relationships from the results of the alignment. While it is not possible to prove that the genetic relationships among the 527 GN bacterial plasmids obtained in this study are correct, replication of identical results produced in a separate study for a small group of IncA/C plasmids provides evidence that the approach used can correctly predict genetic relationships. In addition, results obtained for clusters of Borrelia plasmids are consistent with the expected exclusivity for plasmids from this genus. Finally, the 527-plasmid tree was used to study the distribution of four common antibiotic resistance genes.

[1]  Pietro Liò,et al.  Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network , 2008, BMC Bioinformatics.

[2]  M. Couturier,et al.  Identification and classification of bacterial plasmids. , 1988, Microbiological reviews.

[3]  Angela C. M. Luyf,et al.  Compositional discordance between prokaryotic plasmids and host chromosomes , 2006, BMC Genomics.

[4]  Yan Boucher,et al.  Phylogenetic reconstruction and lateral gene transfer. , 2004, Trends in microbiology.

[5]  S. Norris,et al.  Correlation between plasmid content and infectivity in Borrelia burgdorferi. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[6]  S Karlin,et al.  Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. , 2001, Trends in microbiology.

[7]  Shira L. Broschat,et al.  Validation of Mixed-Genome Microarrays as a Method for Genetic Discrimination , 2007, Applied and Environmental Microbiology.

[8]  Fred R. McMorris,et al.  Consensusn-trees , 1981 .

[9]  S. Karlin,et al.  Dinucleotide relative abundance extremes: a genomic signature. , 1995, Trends in genetics : TIG.

[10]  Jacques Ravel,et al.  Comparative Genomics of the IncA/C Multidrug Resistance Plasmid Family , 2009, Journal of bacteriology.

[11]  Eva M. Top,et al.  Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes , 2008, Nucleic acids research.

[12]  Julian Parkhill,et al.  A Novel Linear Plasmid Mediates Flagellar Variation in Salmonella Typhi , 2007, PLoS pathogens.

[13]  W. Martin,et al.  Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. , 2011, Genome research.

[14]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[15]  Eric Bapteste,et al.  Network analyses structure genetic diversity in independent genetic worlds , 2009, Proceedings of the National Academy of Sciences.

[16]  S. Karlin,et al.  Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[17]  C W Hill,et al.  Mosaic structure of plasmids from natural populations of Escherichia coli. , 1996, Genetics.

[18]  Matt Griffin,et al.  IncA/C Plasmid-Mediated Florfenicol Resistance in the Catfish Pathogen Edwardsiella ictaluri , 2008, Antimicrobial Agents and Chemotherapy.

[19]  Christopher M Thomas,et al.  Paradigms of plasmid organization , 2000, Molecular microbiology.

[20]  Jean-Michel Claverie,et al.  The Genome of Borrelia recurrentis, the Agent of Deadly Louse-Borne Relapsing Fever, Is a Degraded Subset of Tick-Borne Borrelia duttonii , 2008, PLoS genetics.

[21]  Shira L. Broschat,et al.  bla CMY-2-Positive IncA/C Plasmids from Escherichia coli and Salmonella enterica Are a Distinct Component of a Larger Lineage of Plasmids , 2009, Antimicrobial Agents and Chemotherapy.

[22]  Christian H. Eggers,et al.  Molecular Evidence for a New Bacteriophage ofBorrelia burgdorferi , 1999, Journal of bacteriology.

[23]  A. D. Gordon.  Consensus supertrees: The synthesis of rooted trees containing overlapping sets of labeled leaves , 1986 .

[24]  T. Besser,et al.  Assessing genetic diversity in plasmids from Escherichia coli and Salmonella enterica using a mixed‐plasmid microarray , 2006, Journal of applied microbiology.