Plasmids are vectors for redundant chromosomal genes in the Bacillus cereus group.

Jinshui Zheng,Lifang Ruan,Daohong Jiang,Donghai Peng,Ming Sun,Ziyu Guan,Shiyun Cao

doi:10.1186/s12864-014-1206-5

Abstract

BackgroundProkaryotic plasmids have played significant roles in the evolution of bacterial genomes and have a great impact on the metabolic functions of the host cell. Many bacterial strains contain multiple plasmids, but the relationships between bacterial plasmids and chromosomes are unclear. We focused on plasmids from the Bacillus cereus group because most strains contain several plasmids.ResultsWe collected the genome sequences of 104 plasmids and 20 chromosomes from B. cereus group strains, and we studied the relationships between plasmids and chromosomes by focusing on the pan-genomes of these plasmids and chromosomes. In terms of basic features (base composition and codon usage), the genes on plasmids were more similar to the chromosomal variable genes (distributed genes and unique genes) than to the chromosomal core genes. Although all the functional categories of the chromosomal genes were exhibited by the plasmid genes, the proportions of each category differed between these two gene sets. The 598 gene families shared between chromosomes and plasmids displayed a uniform distribution between the two groups. A phylogenetic analysis of the shared genes, including the chromosomal core gene set, indicated that gene exchange events between plasmids and chromosomes occurred frequently during the evolutionary histories of the strains and species in this group. Moreover, the shared genes between plasmids and chromosomes usually had different promoter and terminator sequences, suggesting that they are regulated by different elements at the transcriptional level.ConclusionsWe speculate that for the entire B. cereus group, adaptive genes are preserved on both plasmids and chromosomes; however, in a single cell, homologous genes on plasmids and the chromosome are controlled by different regulators to reduce the burden of maintaining redundant genes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-014-1206-5) contains supplementary material, which is available to authorized users.

Highlights

Prokaryotic plasmids have played significant roles in the evolution of bacterial genomes and have a great impact on the metabolic functions of the host cell
Plasmids of the B. cereus group share dynamic gene pools with chromosomes We focused on pan-genomic plasmids and chromosomes to study the relationships between plasmids and chromosomes
A codon usage analysis with CAI indicated that the plasmid genes showed no difference from the chromosomal variable genes but were significantly different from the chromosomal core genes (P < 2.2 × 10−16, Mann–Whitney test) (Figure 1B)

Summary

Introduction

Prokaryotic plasmids have played significant roles in the evolution of bacterial genomes and have a great impact on the metabolic functions of the host cell. Horizontal gene transfer (HGT) plays an important role in bacterial evolution by providing foreign genetic material for gene exchange between prokaryotes [1]. One of the most important contributors to HGT is plasmids, which can be transferred between cells as vectors for genes and can provide a basis for genomic rearrangements via homologous recombination [2]. In this process, events in which genes are gained and/or lost force bacterial genomes to evolve. Plasmids have been studied for different purposes by many researchers These studies have mainly focused on the intrinsic characteristics and accessory functions of plasmids. By analyzing the plasmids of genus Acinetobacter, the same research group found that most of these plasmids lack

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