The genome sequence of Escherichia coli tailed phage D6 and the diversity of Enterobacteriales circular plasmid prophages

Gilcrease, Eddie B.; Casjens, Sherwood

doi:10.1016/j.virol.2017.12.019

Cited by 42 publications

(71 citation statements)

References 90 publications

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“…In addition, contrary to some previous statements, phage genomes rarely contain antibiotic resistance genes, and if antibioresistance transfer can be sometimes attributed to phages, it is more likely due to generalized transduction rather than lysogeny (Enault et al ., ). Nevertheless, a new category of self transferable plasmid‐phages could change this view as some of them carry ATB resistance genes (SSU5 super‐cluster) (Gilcrease and Casjens, ).…”

Section: Resultsmentioning

confidence: 99%

Prophages in Salmonella enterica: a driving force in reshaping the genome and physiology of their bacterial host?

Wahl

Battesti

Ansaldi

2018

Molecular Microbiology

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Thanks to the exponentially increasing number of publicly available bacterial genome sequences, one can now estimate the important contribution of integrated viral sequences to the diversity of bacterial genomes. Indeed, temperate bacteriophages are able to stably integrate the genome of their host through site-specific recombination and transmit vertically to the host siblings. Lysogenic conversion has been long acknowledged to provide additional functions to the host, and particularly to bacterial pathogen genomes where prophages contribute important virulence factors. This review aims particularly at highlighting the current knowledge and questions about lysogeny in Salmonella genomes where functional prophages are abundant, and where genetic interactions between host and prophages are of particular importance for human health considerations.

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Section: Resultsmentioning

confidence: 99%

Prophages in Salmonella enterica: a driving force in reshaping the genome and physiology of their bacterial host?

Wahl

Battesti

Ansaldi

2018

Molecular Microbiology

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“…Brucella phage BiBPO1 is capable of integrating in the genomes of a broad range of hosts by targeting conserved integration sites in tRNA genes [62]. An alternative temperate lifestyle is to circumvent integration altogether by maintaining the genome as a plasmid [63], as was observed in the temperate broad-host-range Ochrobactrum phage POI1126 [64]. Interestingly, the widespread crAssphage does not encode an integrase protein and has never been found integrated in any bacterial genome, but it does have two proteins with putative plasmid replication domains in its genome [65,66].…”

Section: Aspects Of Host Range After Entry Into the Host Cellmentioning

confidence: 99%

Molecular and Evolutionary Determinants of Bacteriophage Host Range

Jonge

Nóbrega

Brouns

et al. 2019

Trends in Microbiology

321

248

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The host range of a bacteriophage is the taxonomic diversity of hosts it can successfully infect. Host range, one of the central traits to understand in phages, is determined by a range of molecular interactions between phage and host throughout the infection cycle. While many well studied model phages seem to exhibit a narrow host range, recent ecological and metagenomics studies indicate that phages may have specificities that range from narrow to broad. There is a growing body of studies on the molecular mechanisms that enable phages to infect multiple hosts. These mechanisms, and their evolution, are of considerable importance to understanding phage ecology and the various clinical, industrial, and biotechnological applications of phage. Here we review knowledge of the molecular mechanisms that determine host range, provide a framework defining broad host range in an evolutionary context, and highlight areas for additional research.

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“…Similar dot plots with members of the other small virulent Enterobacteriales phage clusters not shown in Fig. 4 (16,17) showed little or no similarity, with the following single exception. Members of the MSW-3-like Myoviridae cluster (15) also have divergently transcribed putative early gene clusters where the DNA polymerase, helicase, and primase genes have locations that parallel those of the 9NA-like phages, and a high-resolution dot plot between these two clusters shows an approximately 9-kbp very weak diagonal line where these genes have sequence similarities (Fig.…”

Section: Resultsmentioning

confidence: 86%

DNA Packaging and Genomics of theSalmonella9NA-Like Phages

Zeng

Gilcrease

Hendrix

et al. 2019

J Virol

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We present the genome sequences of Salmonella enterica tailed phages Sasha, Sergei, and Solent. These phages, along with Salmonella phages 9NA, FSL_SP-062, and FSL_SP-069 and the more distantly related Proteus phage PmiS-Isfahan, have similarly sized genomes of between 52 and 57 kbp in length that are largely syntenic. Their genomes also show substantial genome mosaicism relative to one another, which is common within tailed phage clusters. Their gene content ranges from 80 to 99 predicted genes, of which 40 are common to all seven and form the core genome, which includes all identifiable virion assembly and DNA replication genes. The total number of gene types (pangenome) in the seven phages is 176, and 59 of these are unique to individual phages. Their core genomes are much more closely related to one another than to the genome of any other known phage, and they comprise a well-defined cluster within the family Siphoviridae. To begin to characterize this group of phages in more experimental detail, we identified the genes that encode the major virion proteins and examined the DNA packaging of the prototypic member, phage 9NA. We show that it uses a pac site-directed headful packaging mechanism that results in virion chromosomes that are circularly permuted and about 13% terminally redundant. We also show that its packaging series initiates with double-stranded DNA cleavages that are scattered across a 170-bp region and that its headful measuring device has a precision of ±1.8%. IMPORTANCE The 9NA-like phages are clearly highly related to each other but are not closely related to any other known phage type. This work describes the genomes of three new 9NA-like phages and the results of experimental analysis of the proteome of the 9NA virion and DNA packaging into the 9NA phage head. There is increasing interest in the biology of phages because of their potential for use as antibacterial agents and for their ecological roles in bacterial communities. 9NA-like phages that infect two bacterial genera have been identified to date, and related phages infecting additional Gram-negative bacterial hosts are likely to be found in the future. This work provides a foundation for the study of these phages, which will facilitate their study and potential use.

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The genome sequence of Escherichia coli tailed phage D6 and the diversity of Enterobacteriales circular plasmid prophages

Cited by 42 publications

References 90 publications

Prophages in Salmonella enterica: a driving force in reshaping the genome and physiology of their bacterial host?

Prophages in Salmonella enterica: a driving force in reshaping the genome and physiology of their bacterial host?

Molecular and Evolutionary Determinants of Bacteriophage Host Range

DNA Packaging and Genomics of theSalmonella9NA-Like Phages

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