Complete nucleotide sequence, molecular analysis and genome structure of bacteriophage A118 of Listeria monocytogenes: implications for phage evolution

A118 is a temperate phage isolated from Listeria monocytogenes, In this stu dy, we report the entire nucleotide sequence and structural analysis of its 40 834 bp DNA. Electron microscopic and enzymatic analyses revealed that t he A118 genome is a linear, circularly permuted, terminally redundant colle ction of double-stranded DNA molecules. No evidence for cohesive ends or fo r a terminase recognition (pac) site could be obtained, suggesting that A11 8 viral DNA is packaged via a headful mechanism. Partial denaturation mappi ng of DNA cross-linked to the tail shaft indicated that DNA packaging proce eds from left to right with respect to the arbitrary genomic map and the di rection of genes necessary for lytic development. Seventy-two open reading frames (ORFs) were identified on the A118 genome, which are apparently orga nized in a life cycle-specific manner into at least three major transcripti onal units, N-terminal amino acid sequencing, bioinformatic analyses and fu nctional characterizations enabled the assignment of possible functions to 26 ORFs, which included DNA packaging proteins, morphopoetic proteins, lysi s components, lysogeny control-associated functions and proteins necessary for DNA recombination, modification and replication. Comparative analysis o f the A118 genome structure with other bacteriophages revealed local, but s ometimes extensive, similarities to a number of phages spanning a broader p hylogenetic range of various low G+C host bacteria, which implies relativel y recent exchange of genes or genetic modules, We have also identified the A118 attachment site attP and the corresponding attB in Listeria monocytoge nes, and show that site-specific integration of the A118 prophage by the A1 18 integrase occurs into a host gene homologous to comK of Bacillus subtili s, an autoregulatory gene specifying the major competence transcription fac tor.