A super-family of transcriptional activators regulates bacteriophage packaging and lysis in Gram-positive bacteria

Abstract

The propagation of bacteriophages and other mobile genetic elements requires exploitation of the phage mechanisms involved in virion assembly and DNA packaging. Here, we identified and characterized four different families of phage-encoded proteins that function as activators required for transcription of the late operons (morphogenetic and lysis genes) in a large group of phages infecting Gram-positive bacteria. These regulators constitute a super-family of proteins, here named late transcriptional regulators (Ltr), which share common structural, biochemical and functional characteristics and are unique to this group of phages. They are all small basic proteins, encoded by genes present at the end of the early gene cluster in their respective phage genomes and expressed under cI repressor control. To control expression of the late operon, the Ltr proteins bind to a DNA repeat region situated upstream of the terS gene, activating its transcription. This involves the C-terminal part of the Ltr proteins, which control specificity for the DNA repeat region. Finally, we show that the Ltr proteins are the only phage-encoded proteins required for the activation of the packaging and lysis modules. In summary, we provide evidence that phage packaging and lysis is a conserved mechanism in Siphoviridae infecting a wide variety of Gram-positive bacteria.

Identification and Analysis of a Novel Group of Bacteriophages Infecting the Lactic Acid Bacterium Streptococcus thermophilus

“…The protein products of the terminal ORFs in the 987 group phages appear to be conserved in 9871 to 9873, with that of 9874 being divergent. A Pfam search using these proteins in phages 9871 to 9873 indicates that they belong to the DUF1492 family, which was recently found to be one of several major groups of "late transcriptional regulators" (ltr) in phages of Gram-positive bacteria (69). Similarly, transcriptional regulation appears to be the primary function of the product of ORF48 9874 , which shows approximately 50% amino acid identity with ArpU family transcriptional regulators of various streptococcal species (69).…”

Staphylococcal pathogenicity island DNA packaging system involving cos -site packaging and phage-encoded HNH endonucleases

“…Examination of the packaging modules of phages ϕ12 and ϕSLT revealed an uncharacterized ORF between the late gene regulator rinA (11,12) and the terminase genes terS and terL (SI Appendix, Fig. S2).…”

“…The products of these ORFs, ϕ12p28 and ϕSLTp37 (98% identity), contain a region of homology to proteins of the widespread HNH family of endonucleases, and we considered the possibility that these proteins are involved in packaging. If they were involved in packaging, they would presumably be coregulated with the terminase genesi.e., activated by the late gene regulator RinA (11,12). Accordingly, we constructed reporter gene fusions with and without rinA and tested them for reporter gene expression.…”

Precisely modulated pathogenicity island interference with late phage gene transcription

“…The sequence of gene 32 showed it to be late transcriptional regulator C, ltrC (11,12), which corresponds to 80α rinA (13). LtrC and RinA are regulatory proteins that activate the transcription of the late phage operon (morphogenetic and lysis genes) ( Fig.…”

“…2A). Five families of these proteins have been described, constituting a superfamily of late transcriptional regulators (Ltr) (11,12). These are essential phage genes (14,15) corresponding to coliphage lambda gene Q.…”