Characterization of the Lysogeny DNA Module from the TemperateStreptococcus thermophilusBacteriophage φSfi21

Abstract

Phage phi Sfi21, the only temperate Streptococcus thermophilus phage from our phage collection, showed extensive DNA homology with virulent phages from lytic group I. Southern blot hybridizations demonstrated that the phi Sfi21-specific DNA was clustered in an approximately 6.6-kb-long region, the putative lysogeny module. Sequence analysis and database research identified an integrase within this module; orf 203 with homology to an anonymous orf 258 from the temperate lactococcal phage BK5-T; orf 127 and orf 122 with weak homology to the N- and C-terminal parts, respectively, of the cl-like repressor from lactococcal phages Tuc2009 and BK5-T; orf 75 with homology to a repressor protein from lambdoid phage 434 and an anti-repressor ant with homology to phage P1. The molecular arrangement of the predicted orfs in phage phi Sfi21 was very similar to that of the lactococcal phage BK5-T. The transition from phi Sfi21-specific DNA into DNA shared with virulent phages was abrupt and flanked at one side by notable DNA repeats. Sequence analysis identified a holin protein to the left of the lysogeny module. A site-specific deletion of 2.4 kb, which reproducibly transformed phi Sfi21 into a lytic phage, was localized in the lysogeny module. It was flanked at both sides by conspicuous DNA repeats. One repeat region reflected the DNA around the attP site, while the other reflected the putative genetic switch region between repressor and anti-repressor genes. S. thermophilus host Sfi1 transformed with a plasmid containing int and orf 203 showed resistance to superinfection by heterologous phages, but not by the homologous phi Sfi21. Part of the int gene could be deleted without loss of this activity, while a deletion in orf 203 resulted in loss of the phage resistance. We speculate on the possibility of a bipartite immunity system for the control of lysogeny in phi Sfi21.

Prophage Genomics

“…Given the presence of this gene family in several kinds of elements, it becomes problematic to use integrase as a prophage signature. In our own experience with one specific class of temperate phages (Siphoviridae), reasonably conserved phage proteins are the integrase (32), the portal protein, the terminase (52), and the tail tape measure protein. A further complication is that the current NCBI phage database is small (at the time of writing, it contained 136 complete phage genomes) and is dominated by a single phage group, Siphoviridae (1, 136) (contributing 53 complete genomes, followed by 18 Inoviridae, 17 Podoviridae, and 13 Myoviridae genomes).…”

“…In the lysogenic state, only two Sfi21 genome regions were transcribed from the otherwise transcriptionally silent prophage (209). One transcript com- (34) to the superinfection exclusion (sie) genes located directly upstream of the phage integrase (32). The cloned cI repressor protected a cell against superinfection with temperate phages (34), while the cloned sie gene conferred protection against many virulent phages (32).…”

Characterization and Expression Analysis of Staphylococcus aureus Pathogenicity Island 3

“…This has led to the supposition that this gene was acquired by S. aureus through horizontal transfer from D. nodosus during co-colonization or infection of sheep (5) because the D. nodosus vap genes appear to reside on an integrated bacteriophage (25,26). The predicted product of sapi3_18 is 75% similar over 58 amino acids to a putative cro-like repressor of Streptococcus thermophilus bacteriophage Sfi21 (27,28). Even stronger homology is seen between the predicted product of sapi3_19 and the cI-like repressor of S. thermophilus phage Sfi21 (27, 28) (84% similarity over 67 amino acids) and Lactobacillus casei phage A2 repressor (29) (80% similarity over 76 amino acids).…”

Genomic Organization and Molecular Analysis of Virulent Bacteriophage 2972 Infecting an Exopolysaccharide-Producing Streptococcus thermophilus Strain

“…Six complete genome sequences of S. thermophilus phages are currently available. They include the cos-type phages DT1 (66), Sfi19 (42), Sfi21 (12), and 7201 (62), as well as the pac-type phages O1205 (61) and Sfi11 (39,40). DT1, Sfi19, and Sfi11 are virulent phages, while the others are temperate.…”