Analysis of six prophages in Lactococcus lactis IL1403: different genetic structure of temperate and virulent phage populations

Abstract

We report the genetic organisation of six prophages present in the genome of Lactococcus lactis IL1403. The three larger prophages (36-42 kb), belong to the already described P335 group of temperate phages, whereas the three smaller ones (13-15 kb) are most probably satellites relying on helper phage(s) for multiplication. These data give a new insight into the genetic structure of lactococcal phage populations. P335 temperate phages have variable genomes, sharing homology over only 10-33% of their length. In contrast, virulent phages have highly similar genomes sharing homology over >90% of their length. Further analysis of genetic structure in all known groups of phages active on other bacterial hosts such as Escherichia coli, Bacillus subtilis, MYCOBACTERIUM: and Streptococcus thermophilus confirmed the existence of two types of genetic structure related to the phage way of life. This might reflect different intensities of horizontal DNA exchange: low among purely virulent phages and high among temperate phages and their lytic homologues. We suggest that the constraints on genetic exchange among purely virulent phages reflect their optimal genetic organisation, adapted to a more specialised and extreme form of parasitism than temperate/lytic phages.

Figure 1

Structure of all known lactococcal prophage genomes. Genome extremities correspond to attB sites. ORFs are shown as arrows, oriented in the direction of their transcription, with designation below. Arrows with identical colour indicate proteins with >70% sequence identity (plain colour), or 20–70% sequence identity (hatched colour). Colour rectangles in the background indicate DNA regions with >60% sequence identity. A white box indicates IS983. Sequences are taken from van Sinderen et al. (5) (r1t), G.Fitzgerald and D.van Sinderen (personal communication; Tuc2009) and this study (bIL285, bIL286, bIL309, bIL310, bIL311 and bIL312).

Figure 2

DNA sequence conservation among genomes of lactococcal phages. Lactococcal phage groups are indicated. Intra-group and inter-group DNA conservation (>60% sequence identity) are indicated by grey and colour rectangles, respectively. Sequences are taken from Crutz-Le Coq et al. (7; bIL170), Chandry et al. (6; sk1), Schouler et al. (3; bIL67), Lubbers et al. (4; c2), van Sinderen et al. (5; r1t), G.Fitzgerald and D.van Sinderen (personal communication; Tuc2009) and this study (bIL285, bIL286 and bIL309).

Figure 3

DNA sequence conservation among genomes of L.lactis phages of the P335, 936 and c6A groups, and phages active on different bacterial species. Colour rectangles indicate DNA regions with >70% sequence identity (plain colour), or 50–70% sequence identity (hatched colour). Sequences are taken from Schouler et al. (3; bIL67), Crutz-Le Coq et al. (7; bIL170), Lucchini et al. (33; Sfi21) and Kaneko et al. (37; PVL).