The Molecular Switch of Telomere Phages: High Binding Specificity of the PY54 Cro Lytic Repressor to a Single Operator Site

Abstract

Temperate bacteriophages possess a molecular switch, which regulates the lytic and lysogenic growth. The genomes of the temperate telomere phages N15, PY54 and ϕKO2 harbor a primary immunity region (immB) comprising genes for the prophage repressor, the lytic repressor and a putative antiterminator. The roles of these products are thought to be similar to those of the lambda proteins CI, Cro and Q, respectively. Moreover, the gene order and the location of several operator sites in the prototype telomere phage N15 and in ϕKO2 are also reminiscent of lambda-like phages. By contrast, in silico analyses revealed the presence of only one operator (OR3) in PY54. The purified PY54 Cro protein was used for EMSA studies demonstrating that it exclusively binds to a 16-bp palindromic site (OR3) upstream of the prophage repressor gene. The OR3 operator sequences of PY54 and ϕKO2/N15 only differ by their peripheral base pairs, which are responsible for Cro specificity. PY54 cI and cro transcription is regulated by highly active promoters initiating the synthesis of a homogenious species of leaderless mRNA. The location of the PY54 Cro binding site and of the identified promoters suggests that the lytic repressor suppresses cI transcription but not its own synthesis. The results indicate an unexpected diversity of the growth regulation mechanisms in lambda-related phages.

Two novel temperate bacteriophages co-existing in Aeromonas sp. ARM81 – characterization of their genomes, proteomes and DNA methyltransferases

“…The linear plasmid-like phages, similarly to other temperate viruses, possess genes responsible for switching between the lytic and the lysogenic cycle (Hammerl et al, 2015). Such a control region was found in the FARM81ld phage.…”

The diverse genetic switch of enterobacterial and marine telomere phages

“…1). 3,17 In the enterobacterial telomere phages N15, PY54 and fKO2, immB comprises genes potentially encoding the prophage repressor CI, Cro repressor and transcription antiterminator Q. In some other studies CI of N15 and fKO2 has been named CB but throughout this work it is termed CI.…”

“…In fKO2 3 very similar operator sites exist 1 while PY54 exhibits only 1 site (O R 3) that fits into this scheme. 17 The immB regions of the marine telomere phages also contain a putative prophage repressor gene but the product of this gene is not related to CI of the enterobacterial telomere phages (Table 1). Moreover, a cro-related gene could not be identified in marine telomere phages (Fig.…”

“…The transcription start sites of the mRNAs encoding CI and Cro (N15, fKO2, PY54) 17 and CI and gp44 (VP58.5) were determined by sequencing of RACE products. The experiment was carried out using DNA fragments, which encompassed the intergenic region and partial sequences of the repressor genes.…”

“…3 This protein revealed a high binding specificity for a single operator site (O R 3) on the PY54 genome and did not bind to closely related N15 and fKO2 operator sites. 17 Thus, PY54 Cro apparently suppresses cI transcription but not its own synthesis.…”