The genome, transcriptome, and preliminary proteome of Pseudomonas putida bacteriophage gh-1: A new member of the T7 family of bacterial viruses. Computational analyses of genomes of various bacteriophages and their hosts

The genome of lytic bacteriophage gh-1 infecting the common soil bacterium Pseudomonas putida has been sequenced and analysed. The genome of this phage is linear double-stranded DNA containing 37, 359 bp with 216 bp direct terminal repeats (DTR). Like other members of the T7 group, the gh-1 genome contains regions of high homology to T7 interspersed with non-homologous regions that contain small ORFs of unknown function. The genome shares 31 genes in common with other members of the T7 group, including RNA polymerase, and an additional 12 unique putative genes. A high conservation of the essential genes as well as regulatory elements along the genome of gh-1 confirmed its close relationship to the T7 group of phages.; Transcription of gh-1 genes during P. putida infection was analysed using a custom-made DNA microarray that contained twenty-eight selected gh-1 genes. The microarray analysis revealed an orderly sequence of transcription events, not unlike that previously demonstrated for E. coli phage T7, and allowed an estimation of the relative strength of gh-1 RNA polymerase (RNAP) promoters to be made. gh-1 RNAP promoter immediately preceding the major capsid protein gene produced the highest normalized fluorescent intensity value. Microarray analysis of gh-1 transcription was supplemented with conventional Northern blot analysis to confirm the presence of transcriptional elements assigned previously by bioinformatics analysis.; P. putida mutants resistant to gh-1 were demonstrated to have an altered lipopolysaccharide (LPS) structure, indicating that gh-1, similar to the other members of the T7 group, uses LPS as its cellular receptor. Phylogenetic analyses of selected gh-1proteins pointed to a common origin of the essential reproductive enzymes in the T7 group.; The dinucleotide compositions in genomes of 88 double-stranded bacteriophages and some of their respective hosts were also determined. A definite quantitative parallelism was found in relative dinucleotide abundance (RDA) between temperate phages and their hosts, but not between lytic phages and their hosts.; Overall, lytic phages of the T7 group appear to constitute a different mode of evolution than temperate phages.