Identification of related genes in phages phi 80 and P22 whose products are inhibitory for phage growth in Escherichia coli IHF mutants

Henthorn, Karla S.; Friedman, David I.

doi:10.1128/jb.177.11.3185-3190.1995

Cited by 20 publications

(24 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Immediately downstream, gene 79 is homologous to the phage P22 rha (orf201) gene, whose product is detrimental for lytic growth in the absence of host integration host factor function (10,40).…”

Section: Resultsmentioning

confidence: 99%

The Generalized TransducingSalmonellaBacteriophage ES18: Complete Genome Sequence and DNA Packaging Strategy

et al. 2005

View full text Add to dashboard Cite

The generalized transducing double-stranded DNA bacteriophage ES18 has an icosahedral head and a long noncontractile tail, and it infects both rough and smooth Salmonella enterica strains. We report here the complete 46,900-bp genome nucleotide sequence and provide an analysis of the sequence. Its 79 genes and their organization clearly show that ES18 is a member of the lambda-like (lambdoid) phage group; however, it contains a novel set of genes that program assembly of the virion head. Most of its integration-excision, immunity, Nin region, and lysis genes are nearly identical to those of the short-tailed Salmonella phage P22, while other early genes are nearly identical to Escherichia coli phages and HK97, S. enterica phage ST64T, or a Shigella flexneri prophage. Some of the ES18 late genes are novel, while others are most closely related to phages HK97, lambda, or N15. Thus, the ES18 genome is mosaically related to other lambdoid phages, as is typical for all group members. Analysis of virion DNA showed that it is circularly permuted and about 10% terminally redundant and that initiation of DNA packaging series occurs across an approximately 1-kbp region rather than at a precise location on the genome. This supports a model in which ES18 terminase can move substantial distances along the DNA between recognition and cleavage of DNA destined to be packaged. Bioinformatic analysis of large terminase subunits shows that the different functional classes of phage-encoded terminases can usually be predicted from their amino acid sequence.Generalized transducing bacteriophages are valuable members of the arsenal of tools for the genetic study of bacteria. ES18 is a temperate, generalized transducing double-stranded DNA (dsDNA) phage that naturally infects Salmonella enterica serovar Typhimurium (48), as well as some serovar Enteriditis, Dublin, Pullorum, Gallinarum, and Paratyphi B strains (52,76). In addition, it can infect Escherichia coli if it displays the Salmonella surface receptor (47). ES18, which has also been called typing phage A18, was originally isolated in about 1953 after its release from Salmonella sp. strain BA19, in which it apparently resided as a prophage (8,75). It has an estimated genome size of about 46,000 bp (74). It is of technical interest because, unlike the well-characterized Salmonella transducing phage P22, it can infect rough strains that do not produce full-length O-antigen, for which no other transducing phages have been studied (48). Yamamoto (98) showed that ES18 is able to recombine to form viable hybrid phages with both the short-tailed phage P22 and the long-tailed phage Fels-1, both of which are now considered to be lambdoid phages (34). Thus, ES18 was also thought to be a lambdoid phage. This was tentatively confirmed in studies by Schmieger and colleagues (74), which found that the ES18 prophage repressor and lysis regions are very similar to those of the short-tailed phage P22 in both sequence and genome location. It has been reported (without publication of the data) that ...

show abstract

Section: Resultsmentioning

confidence: 99%

The Generalized TransducingSalmonellaBacteriophage ES18: Complete Genome Sequence and DNA Packaging Strategy

et al. 2005

View full text Add to dashboard Cite

show abstract

“…Applying this Tn INsertion Sequencing (INSeq) analysis to DNA prepared from fecal samples collected before, during, and after prophage 1 induction showed a dramatic enrichment for transposons located within a ∼600bp intergenic region positioned between the ORFs encoding the prophage's putative Rha protein (22) and cI repressor at the time of its induction 5-9 d after introduction of the 15-member artificial community (Fig. S9 A and B and SI Results).…”

Section: Nonsimultaneous Detection Of Viruses and Community Rearrangementioning

confidence: 99%

Gnotobiotic mouse model of phage–bacterial host dynamics in the human gut

Reyes

McNulty

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

308

269

View full text Add to dashboard Cite

Bacterial viruses (phages) are the most abundant biological group on Earth and are more genetically diverse than their bacterial prey/ hosts. To characterize their role as agents shaping gut microbial community structure, adult germ-free mice were colonized with a consortium of 15 sequenced human bacterial symbionts, 13 of which harbored one or more predicted prophages. One member, Bacteroides cellulosilyticus WH2, was represented by a library of isogenic transposon mutants that covered 90% of its genes. Once assembled, the community was subjected to a staged phage attack with a pool of live or heat-killed virus-like particles (VLPs) purified from the fecal microbiota of five healthy humans. Shotgun sequencing of DNA from the input pooled VLP preparation plus shotgun sequencing of gut microbiota samples and purified fecal VLPs from the gnotobiotic mice revealed a reproducible nonsimultaneous pattern of attack extending over a 25-d period that involved five phages, none described previously. This system allowed us to (i) correlate increases in specific phages present in the pooled VLPs with reductions in the representation of particular bacterial taxa, (ii) provide evidence that phage resistance occurred because of ecological or epigenetic factors, (iii) track the origin of each of the five phages among the five human donors plus the extent of their genome variation between and within recipient mice, and (iv) establish the dramatic in vivo fitness advantage that a locus within a B. cellulosilyticus prophage confers upon its host. Together, these results provide a defined community-wide view of phage-bacterial host dynamics in the gut.T he human gut is home to tens of trillions of microbial cells representing all three domains of life, although most are bacteria. These organisms collaborate and compete for functional niches and physical locations (habitats). Together, they form a continuously functioning microbial metabolic "organ." The microbial diversity, interpersonal variation, and dynamism of the human gut microbiota make the task of identifying the factors that define community configurations extremely challenging.In some ecosystems, phages maintain high bacterial strain level diversity through lysis of their host strains (constant diversity dynamics model; refs 1, 2). The resulting emptied niche is filled with either an evolved resistant bacterial strain or a taxonomically closely related bacterial species. These dynamics have been observed in open marine environments (1). In contrast, a recent study of 37 healthy adults indicated that a person's fecal microbiota was remarkably stable, with 60% of bacterial strains retained over the course of 5 y (3). Stability followed a power law dynamic that when extrapolated suggests that most strains in an individual's gut community are retained for decades (3). In a metagenomic analysis of virus-like particles (VLPs) purified from the fecal microbiota of healthy adult monozygotic twins and their mothers, sampled over the course of a year, viral community structure exh...

show abstract

“…Finally, in phage 80, a function, rha, presumably modulated by IHF, is also involved in the inhibition of growth in an IHF Ϫ host (18,20,21). The rha gene is located in the late operon of phage 80, preceded by genes Q, S, and R, suggesting that Rha together with IHF may also be involved in the control of late gene expression.…”

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

“…For phage 80, a function (rha) which is inhibitory for growth of this phage in IHF Ϫ cells has been described; it maps in the QSR gene region of 80 and is transcribed from the late pRЈ promoter. The mechanism of action of the Rha protein is unknown (18,20,21).Weisberg and Oberto (28a) used a collection of hybrids between HK022 and lambda, constructed in vivo by recombination between the two genomes, to locate the HK022 determinant for the IHF requirement between the replication, P, and antitermination, Q, genes in the right operon of the phage. Since transcription of this part of the genome starts at the pR promoter, far upstream of the determinant region, this location suggests that the IHF effect does not involve a modulation of transcription from a promoter, in contrast to the situation for Mu and lambda cin-1 mentioned above.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Phage HK022 Roi protein inhibits phage lytic growth in Escherichia coli integration host factor mutants

Clerget

Boccard

1996

J Bacteriol

View full text Add to dashboard Cite

Temperate coliphage HK022 requires integration host factor (IHF) for lytic growth. The determinant responsible for this requirement was identified as a new gene (roi) located between genes P and Q. This gene encodes a DNA-binding protein (Roi) containing a helix-turn-helix motif. We have shown that Roi binds a site within its own gene that is closely linked to an IHF binding site. By gel retardation experiments, we have found that IHF binding stabilizes the interaction of Roi with its gene. We have isolated three independent phage mutants that are able to grow on an IHF ؊ host. They carry different mutations scattered in the roi gene and specifying single amino-acid changes. The interactions of all three Roi mutant proteins with the Roi binding site differed from that of the wild type. Roi displays strong similarities, in its C-terminal half, to two putative DNA-binding proteins of bacteriophage P1: Ant1 and KilA. The mode of action of the Roi protein and the possibility that IHF is modulating the expression and/or the action of Roi are discussed.HK022 is a temperate coliphage, a member of the lambdoid family, to which belong phages lambda, 80, 21, P22, and 434. These phages share a common genetic organization which allows the exchange of information, genes or blocks of genes, among them (6). Some genes are always required for the phage to form plaques, while other genes are not essential for phage development in standard hosts but can play important roles in certain circumstances. These have been called accessory genes (6). Some accessory genes are carried by some of the phages in the family but not by others. It is known that phage lambda can form plaques in a host deficient in the integration host factor (IHF). In contrast, HK022 (8) and 80 (20, 21) do not form plaques in a host deficient in IHF. The basis of the HK022 IHF requirement was unknown and is the subject of this study.IHF is a small DNA-binding protein belonging to the family of prokaryotic histone-like proteins. It has remarkable DNAbinding properties: unlike most histone-like proteins, it binds preferentially to specific sites in DNA, makes most of its sequence-specific contacts in the minor groove of DNA, and is one of the strongest DNA-bending proteins (reviewed in references 22 and 23). In bacteria and their mobile genetic elements, IHF participates in a number of cellular processes such as DNA replication, site-specific recombination, bacteriophage packaging, and the positive and negative control of the expression of certain genes (reviewed in references 9, 10, and 23).Bacteriophages Mu, lambda cin-1, and 80 require IHF for plaque formation. The requirement of IHF for growth of Mu and lambda cin-1 appears to be satisfied by IHF's binding to a single identified site in each phage (14, 15). In both cases, IHF exerts its effect at the transcriptional level by modulating transcription from a promoter. For phage 80, a function (rha) which is inhibitory for growth of this phage in IHF Ϫ cells has been described; it maps in the QSR gene region of 80...

show abstract

Identification of related genes in phages phi 80 and P22 whose products are inhibitory for phage growth in Escherichia coli IHF mutants

Abstract: Bacteriophage grows in both IHF

Cited by 20 publications

References 27 publications

The Generalized TransducingSalmonellaBacteriophage ES18: Complete Genome Sequence and DNA Packaging Strategy

The Generalized TransducingSalmonellaBacteriophage ES18: Complete Genome Sequence and DNA Packaging Strategy

Gnotobiotic mouse model of phage–bacterial host dynamics in the human gut

Phage HK022 Roi protein inhibits phage lytic growth in Escherichia coli integration host factor mutants

Contact Info

Product

Resources

About