Genome sequence of the lytic bacteriophage P1201 from Corynebacterium glutamicum NCHU 87078: Evolutionary relationships to phages from Corynebacterineae

Abstract

P1201 is a lytic corynephage of Corynebacterium glutamicum NCHU 87078. Its genome consists of a linear double-stranded DNA molecule of 70,579 base pairs, with 3'-protruding cohesive ends of ten nucleotides. We have identified 69 putative open reading frames, including three apparent genes (thymidylate synthase, terminase, and RNR alpha subunit genes) that are interrupted by an intein. Protein-splicing activities of these inteins were demonstrated in Escherichia coli. Three structural proteins including major capsid and major tail proteins were separated by SDS-PAGE and identified by both LC-MS-MS and N-terminal sequence analyses. Bioinformatics analysis indicated that only about 8.7% of its putative gene products shared substantial protein sequence similarity with the lytic corynephage BFK20 from Brevibacterium flavum, the only corynephage whose genome had been sequenced to date, revealing that the P1201 genome is distinct from BFK20. The mosaic-like genome of P1201 indicates extensive horizontal gene transfer among P1201, Gordonia terrae phage GTE5, mycobacteriophages, and several regions of Corynebacterium spp. genomes.

Genome Sequences and Characterization of the Related Gordonia Phages GTE5 and GRU1 and Their Use as Potential Biocontrol Agents

“…DNA helicases are predicted to be encoded by orf60 (GTE5) and orf61 (GRU1). The corresponding ORF protein sequences are closely related to those in the Corynebacterium phage P1201 and contain conserved domains characteristic of helicases (8).…”

“…Furthermore, in silico analysis, N-terminal sequencing, and mass spectroscopy together show that the genes encoding the structural proteins are located within this cluster. For example, the first gene (orf16 in GTE5 and its homologue orf15 in GRU1) is predicted to encode the phage portal protein, on the basis of the characteristic pfam05133 motif and its high sequence similarity to the portal protein of phage P1201 (8). A portal vertex protein encoded by orf43 (GTE5) and orf41 (GRU1) appears to be located outside this module and was identified based on the presence of the conserved PHA02531 domain.…”

“…Genes orf16 to orf20 (GTE5) and orf15 to orf19 (GRU1) are organized into an operon-like structure and appear to include the head morphogenesis genes. The genes orf20 (GTE5) and orf19 (GRU1) appear to encode the main capsid protein, while the putative genes orf17 (GTE5) and orf16 (GRU1) encode a protein sharing high similarity with the predicted head protein in phage P1201 (8).…”

“…The genes orf39 and orf40 in GTE5 and their equivalents in GRU1 (i.e., orf37 and orf38) encode proteins sharing high sequence similarities with a chitinase from Rhodococcus equi and more distantly with a lysis-encoding gene in phage P1201 (8). Since these gene products appear to share identity with a single protein in other systems, perhaps they were once encoded by a single gene in GTE5/GRU1 or, alternatively, fused in other systems.…”

Genome Sequence and Characterization of the Tsukamurella Bacteriophage TPA2

“…Five of these proteins could be identified in the genome of TPA2 with sizes consistent with the proteins identified by Thomas (45). The identities of the remaining structural genes remain unknown, but it is possible that some are components of larger proteins that have undergone posttranslational cleavage (9).…”