From the gene layout in Figure
2, we propose that rV5 contains four transcriptional units comprising genes
10-1-238-164, 11–26, 27–81, and
82–
163, respectively. Based upon the gene arrangement, we would minimally expect bidirectional transcriptional terminators between genes
26 and
27 and genes
163 and
164, and bidirectional promoters between genes
10 and
11 and
81 and
82, respectively. Of these sites, only the bidirectional terminators were located between genes
26 and
27. In addition, bidirectional promoters were discovered between genes
10 and
11. In total, using stringent selection processes, 33 promoters and 20 rho-independent terminators where discovered in the rV5 genome (Additional file
4: Table S4). All had extensive homology to the consensus
E. coli promoters, with 11 possessing extended -10 regions [
34,
35]. Since these promoters are distributed across the rV5 genome, it suggests that modification of the host holo-RNA polymerase, as observed with coliphage T4 to permit recognition of different promoter classes [
42], might not occur in rV5. To investigate this further, we selected the upstream sequence for late genes (
27‐
66) and resubmitted it to MEME [
43]. Eight copies of a motif (TggTAaAAtA) which is similar to the T4 late promoter consensus sequence (TATAAATA) [
44,
45], were identified (Additional file
4: Table S4). Late transcription in T4-like phages is dependent upon three gene products, namely gp45 (RNA polymerase recruitment), gp33 (co-activator of late transcription) and gp55 (late promoter recognition protein). There are no homologs for these proteins in rV5.
PSI-BLAST analysis of gp11 revealed that it is probably a Srd homolog. These proteins are postulated to act as antisigma factors functioning as decoys for RpoD and RpoS. It is homologous to similar proteins in coliphages T4 (NP_049634), Acinetobacter phage 133 (YP_004300600) and Pseudomonas phage φPto-bp6g (AEO14611). Perhaps this is used as a part of a molecular switch between early and late transcription.