Phylogeny of the Major Head and Tail Genes of the Wide-Ranging T4-Type Bacteriophages

Abstract

We examined a number of bacteriophages with T4-type morphology that propagate in different genera of enterobacteria, Aeromonas, Burkholderia, and Vibrio. Most of these phages had a prolate icosahedral head, a contractile tail, and a genome size that was similar to that of T4. A few of them had more elongated heads and larger genomes. All these phages are phylogenetically related, since they each had sequences homologous to the capsid gene (gene 23), tail sheath gene (gene 18), and tail tube gene (gene 19) of T4. On the basis of the sequence comparison of their virion genes, the T4-type phages can be classified into three subgroups with increasing divergence from T4: the T-evens, pseudoT-evens, and schizoT-evens. In general, the phages that infect closely related host species have virion genes that are phylogenetically closer to each other than those of phages that infect distantly related hosts. However, some of the phages appear to be chimeras, indicating that, at least occasionally, some genetic shuffling has occurred between the different T4-type subgroups. The compilation of a number of gene 23 sequences reveals a pattern of conserved motifs separated by sequences that differ in the T4-type subgroups. Such variable patches in the gene 23 sequences may determine the size of the virion head and consequently the viral genome length. This sequence analysis provides molecular evidence that phages related to T4 are widespread in the biosphere and diverged from a common ancestor in acquiring the ability to infect different host bacteria and to occupy new ecological niches.

A conserved genetic module that encodes the major virion components in both the coliphage T4 and the marine cyanophage S-PM2

“…2), 15% larger than the 169 kb of T4 genome. The relative size of S-PM2 and T4 genomes is consistent with what would be predicted, assuming the genome DNA entirely fills the volume available in the head of each phage, but that the density of the packing of the DNA it slightly higher in SPM-2 because of the absence of T4-like nucleotide modifica- tions and glucosylation and͞or because of a reduction in the content of internal proteins within the head (21).…”

“…The oligonucleotides used to PCR amplify a Ϸ550-bp segment of gene (g)23 of S-PM2 were oMZIA1Bis (5Ј-GATATTTGIGGIGTTCAGCCIATGA-3Ј) and oMZIA6 (5Ј-CGCGGTTGATTTCCAGCATGATTTC-3Ј). Their sequences are based on the consensus of the g23 sequences in a number of T4 type phages (21,24,25). The oSPM23.2 (5Ј-AAGACCAT-GAATTGCCTTGAGGTC-3Ј) has a g23 sequence that was obtained from sequencing this PCR fragment.…”

“…The majority of these cyanophages appear to be myoviruses with contractile tail structures similar to the wellknown coliphage T4 (9,11,20). The ubiquity of myoviruses in the marine environment is probably a consequence of a virion design that can be easily adapted to different conditions (21). The myoviruses are physically robust and remarkably versatile, and only minor modifications are required to infect bacteria whose habitats range from the animal gut to the open ocean (21,22).…”

“…The ubiquity of myoviruses in the marine environment is probably a consequence of a virion design that can be easily adapted to different conditions (21). The myoviruses are physically robust and remarkably versatile, and only minor modifications are required to infect bacteria whose habitats range from the animal gut to the open ocean (21,22). S-PM2 is a cyanomyovirus isolated from the English Channel and infecting Synechococcus sp.…”

Illuminating structural proteins in viral “dark matter” with metaproteomics

“…S3) of their total ORFs present within the Inclusive Dataset. The most abundant of these four PCs, CAM_CRCL_625, was a T4-like major capsid protein by consensus annotation of the PC's component ORFs (29) and also by structural modeling (30). Moving in order of decreasing spectral abundance, PCs CAM_CRCL_14716 and TARA_183056 were both functionally and taxonomically unannotated by sequence similarity; however, by structural modeling, both had best fits to a capsid protein of cyanophage Syn5 (31), although the TM score for the latter PC was below the recommended cutoff of 0.5 (28).…”