Prophage-like elements present in Mycobacterium genomes

Abstract

Background: Prophages, integral components of many bacterial genomes, play significant roles in cognate host bacteria, such as virulence, toxin biosynthesis and secretion, fitness cost, genomic variations, and evolution. Many prophages and prophage-like elements present in sequenced bacterial genomes, such as Bifidobacteria, Lactococcus and Streptococcus, have been described. However, information for the prophage of Mycobacterium remains poorly defined.

Results: In this study, based on the search of the complete genome database from GenBank, the Whole Genome Shotgun (WGS) databases, and some published literatures, thirty-three prophages were described in detail. Eleven of them were full-length prophages, and others were prophage-like elements. Eleven prophages were firstly revealed. They were phiMAV_1, phiMAV_2, phiMmcs_1, phiMmcs_2, phiMkms_1, phiMkms_2, phiBN42_1, phiBN44_1, phiMCAN_1, phiMycsm_1, and phiW7S_1. Their genomes and gene contents were firstly analyzed. Furthermore, comparative genomics analyses among mycobacterioprophages showed that full-length prophage phi172_2 belonged to mycobacteriophage Cluster A and the phiMmcs_1, phiMkms_1, phiBN44_1, and phiMCAN_1 shared high homology and could be classified into one group.

Conclusions: To our knowledge, this is the first systematic characterization of mycobacterioprophages, their genomic organization and phylogeny. This information will afford more understanding of the biology of Mycobacterium.

Figure 1

The genomic organization of M.avium 104 full-length prophage phiMAV_1. The red arrows represent lysogeny module; the blue arrows represent lysis module; the cyan arrows represent DNA packaging and structural modules; the green arrows represent DNA metabolism module. Numbers means the numbering of gene.

Figure 2

Genomic organization of some defective prophage-like elements among mycobacteria. Numbers means the numbering of gene. The red arrows represent lysogeny module; the blue arrows represent lysis module; the cyan arrows represent DNA packaging and structural modules; the green arrows represent DNA metabolism module.

Figure 3

Comparative genomic analyses of prophage-like sequences. Dot plot matrix calculated for the complete genomes of all prophage-like sequences in Mycobacterium. The top x axis and the left y axis provide a scale in kilobases; and the top x axis identifies the prophage genomes that are compared in the corresponding square. The x and y axes are the identical sequences. The slash means that two DNA fragments are homologous to each other. The backslash means that one DNA fragment is homologous with the reverse sequence of other DNA fragment. The word length used is 12 bp.

Figure 4

Global comparison of phiMmcs_1 (or phiMkms_1), phiBN44_1, and phiMCAN_1. Highly related sequences are shown by the red shadings. The blue shadings means that the DNA fragments are highly homologous to complementary sequence of other fragments.

Figure 5

Phylogeny of prophage integrases. Unrooted phylogenetic relationships are represented using NJTree. Bootstrap values from 1,000 reiterations are shown.