Predicting plasmid promiscuity based on genomic signature

Haruo Suzuki, Hirokazu Yano, Celeste J. Brown, Eva M. Top

Research output: Contribution to journalArticle

66 Citations (Scopus)

Abstract

Despite the important contribution of self-transmissible plasmids to bacterial evolution, little is understood about the range of hosts in which these plasmids have evolved. Our goal was to infer this so-called evolutionary host range. The nucleotide composition, or genomic signature, of plasmids is often similar to that of the chromosome of their current host, suggesting that plasmids acquire their hosts' signature over time. Therefore, we examined whether the evolutionary host range of plasmids could be inferred by comparing their trinucleotide composition to that of all completely sequenced bacterial chromosomes. The diversity of candidate hosts was determined using taxonomic classification and genetic distance. The method was first tested using plasmids from six incompatibility (Inc) groups whose host ranges are generally thought to be narrow (IncF, IncH, and IncI) or broad (IncN, IncP, and IncW) and then applied to other plasmid groups. The evolutionary host range was found to be broad for IncP plasmids, narrow for IncF and IncI plasmids, and intermediate for IncH and IncN plasmids, which corresponds with their known host range. The IncW plasmids as well as several plasmids from the IncA/C, IncP, IncQ, IncU, and PromA groups have signatures that were not similar to any of the chromosomal signatures, raising the hypothesis that these plasmids have not been ameliorated in any host due to their promiscuous nature. The inferred evolutionary host range of IncA/C, IncP-9, and IncL/M plasmids requires further investigation. In this era of high-throughput sequencing, this genomic signature method is a useful tool for predicting the host range of novel mobile elements.

Original languageEnglish
Pages (from-to)6045-6055
Number of pages11
JournalJournal of Bacteriology
Volume192
Issue number22
DOIs
Publication statusPublished - 2010 Nov
Externally publishedYes

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Plasmids
Host Specificity
Bacterial Chromosomes
Nucleotides
Chromosomes

ASJC Scopus subject areas

  • Microbiology
  • Molecular Biology

Cite this

Predicting plasmid promiscuity based on genomic signature. / Suzuki, Haruo; Yano, Hirokazu; Brown, Celeste J.; Top, Eva M.

In: Journal of Bacteriology, Vol. 192, No. 22, 11.2010, p. 6045-6055.

Research output: Contribution to journalArticle

Suzuki, Haruo ; Yano, Hirokazu ; Brown, Celeste J. ; Top, Eva M. / Predicting plasmid promiscuity based on genomic signature. In: Journal of Bacteriology. 2010 ; Vol. 192, No. 22. pp. 6045-6055.
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