Genomic and Functional Analyses of Rhodococcus equi Phages ReqiPepy6, ReqiPoco6, ReqiPine5, and ReqiDocB7

Abstract

The isolation and results of genomic and functional analyses of Rhodococcus equi phages ReqiPepy6, ReqiDocB7, ReqiPine5, and ReqiPoco6 (hereafter referred to as Pepy6, DocB7, Pine5, and Poco6, respectively) are reported. Two phages, Pepy6 and Poco6, more than 75% identical, exhibited genome organization and protein sequence likeness to Lactococcus lactis phage 1706 and clostridial prophage elements. An unusually high fraction, 27%, of Pepy6 and Poco6 proteins were predicted to possess at least one transmembrane domain, a value much higher than the average of 8.5% transmembrane domain-containing proteins determined from a data set of 36,324 phage protein entries. Genome organization and protein sequence comparisons place phage Pine5 as the first nonmycobacteriophage member of the large Rosebush cluster. DocB7, which had the broadest host range among the four isolates, was not closely related to any phage or prophage in the database, and only 23 of 105 predicted encoded proteins could be assigned a functional annotation. Because of the relationship of Rhodococcus to Mycobacterium, it was anticipated that these phages should exhibit some of the features characteristic of mycobacteriophages. Traits that were identified as shared by the Rhodococcus phages and mycobacteriophages include the prevalent long-tailed morphology and the presence of genes encoding LysBlike mycolate-hydrolyzing lysis proteins. Application of DocB7 lysates to soils amended with a host strain of R. equi reduced recoverable bacterial CFU, suggesting that phage may be useful in limiting R. equi load in the environment while foals are susceptible to infection.Although the "tailed phage," or members of the virus order Caudovirales, constitute the majority of DNA diversity on the planet, the genomes of only a few hundred are known. Moreover, the genomic data that are available for bacteriophages are extremely unevenly distributed in terms of host species, with two-thirds derived from phages of only eight host genera or closely related bacterial species, including those belonging to the Staphylococcus, Mycobacterium, Pseudomonas, Lactococcus, and Burkholderia genera and the Enterobacteriaceae family (28). Nevertheless, some important themes have emerged from analyzing multiple phages that infect closely related host genera. One theme emerging is that despite rampant lateral gene transfer, there are recognizable "phage types" spanning geography and host taxa. Casjens (11a) was able to group 73 tailed-enterophage genomes into 13 phage types, the members of which were more closely related to each other by a number of criteria than they were to any member of another type. It should be noted that the classic enterophages do not include representatives of all phage types. When groups of phages from other host clades are sequenced, new phages and new phage types are identified. For example, among the sequenced phages of Burkholderia, there are members of the established , Mu, and P2 temperate phage types, as well as entirely new virulent phage types, such a...

Evolutionary Relationships among Actinophages and a Putative Adaptation for Growth in Streptomyces spp

“…Genome similarities between phages infecting different bacterial genera have been seen previously, including the Mu-like phages, P2-like phages, and the lambdoid phages. Furthermore, we note that the Rhodococcus equi phage ReqiPine5 and mycobacteriophage Rosebush (cluster B bacteriophage) share multiple homologous gene pairs located syntenously along their genomes, indicating that these phages are likely to be related (33).…”

Human oral viruses are personal, persistent and gender-consistent

“…Despite not identifying smaller contigs that assembled into contig89 on Day 60 (Figure 3, Panel a), we were able to verify that the full contig was present at this time point (Figure 4). We found many putative open reading frames in contig89 that had synteny with Rhodococcus phage Pepy6 and Poco6 (Summer et al, 2011), which are siphoviruses similar to others found in Lactococcus and Clostridium. These data verify that viral genotypes in the human oral cavity are highly persistent, and that some may persist for at least 60 days.…”

“…We did not perform detailed comparisons of viral genotypes and the bacteria present in each subject because our BLAST-based techniques for characterizing viruses generally are considered insufficient to accurately predict the hosts of each virus. (Summer et al, 2011) are labeled gp054, gp065, gp067, gp068, gp069, gp071, gp072, gp105 and gp106. The location of polymorphisms (when compared with a majority rule consensus from all time points combined) are indicated by orange vertical lines.…”

Prevention of Gordonia and Nocardia Stabilized Foam Formation by Using Bacteriophage GTE7

“…This genome is organized as a circularly permuted double-stranded DNA molecule of 74,431 bp with a GϩC content of 56.8 mol%. At the DNA level, only 6% of the sequence shares similarity with that of the phage ReqiDocB7 genome (20), and the remainder (94%) shares no sequence similarity to any other DNA sequence in GenBank. The GTE7 phage genome has 102 putative open reading frames (ORFs) and one tRNA.…”