Complete Genome Sequence of Erwinia amylovora Bacteriophage vB_EamM_Ea35-70

Yagubi, Abdelbaset; Castle, Alan J.; Kropinski, Andrew M.; Banks, Travis; Svircev, A. M.

doi:10.1128/genomea.00413-14

Cited by 31 publications

(16 citation statements)

References 6 publications

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“…Further searches showed that the 10 proteins encoded by these genes in SPN3US also have homologs in other recently identified ϕKZ-related phages, such as Vibrio phage JM2012 (25) and Erwinia phage Ea35-70 (46), and other giant phages (Table 6), supporting the broader relevance of utilizing a genetic system to study SPN3US. Examples of several proteins well conserved in all myoviruses (major head, sheath, and terminase proteins [47]) are also included in Table 6 to illustrate the intrinsically divergent nature of homologous proteins in these phages.…”

Section: Discussionmentioning

confidence: 52%

Identification of Essential Genes in the Salmonella Phage SPN3US Reveals Novel Insights into Giant Phage Head Structure and Assembly

Thomas

Quintana

Bosch

et al. 2016

J Virol

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Giant tailed bacterial viruses, or phages, such as Pseudomonas aeruginosa phage ϕKZ, have long genomes packaged into large, atypical virions. Many aspects of ϕKZ and related phage biology are poorly understood, mostly due to the fact that the functions of the majority of their proteins are unknown. We hypothesized that the Salmonella enterica phage SPN3US could be a useful model phage to address this gap in knowledge. The 240-kb SPN3US genome shares a core set of 91 genes with ϕKZ and related phages, ∼61 of which are virion genes, consistent with the expectation that virion complexity is an ancient, conserved feature. Nucleotide sequencing of 18 mutants enabled assignment of 13 genes as essential, information which could not have been determined by sequence-based searches for 11 genes. Proteome analyses of two SPN3US virion protein mutants with knockouts in 64 and 241 provided new insight into the composition and assembly of giant phage heads. The 64 mutant analyses revealed all the genetic determinants required for assembly of the SPN3US head and a likely head-tail joining role for gp64, and its homologs in related phages, due to the tailless-particle phenotype produced. Analyses of the mutation in 241, which encodes an RNA polymerase β subunit, revealed that without this subunit, no other subunits are assembled into the head, and enabled identification of a “missing” β′ subunit domain. These findings support SPN3US as an excellent model for giant phage research, laying the groundwork for future analyses of their highly unusual virions, host interactions, and evolution.IMPORTANCE In recent years, there has been a paradigm shift in virology with the realization that extremely large viruses infecting prokaryotes (giant phages) can be found in many environments. A group of phages related to the prototype giant phage ϕKZ are of great interest due to their virions being among the most complex of prokaryotic viruses and their potential for biocontrol and phage therapy applications. Our understanding of the biology of these phages is limited, as a large proportion of their proteins have not been characterized and/or have been deemed putative without any experimental verification. In this study, we analyzed Salmonella phage SPN3US using a combination of genomics, genetics, and proteomics and in doing so revealed new information regarding giant phage head structure and assembly and virion RNA polymerase composition. Our findings demonstrate the suitability of SPN3US as a model phage for the growing group of phages related to ϕKZ.

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Section: Discussionmentioning

confidence: 52%

Identification of Essential Genes in the Salmonella Phage SPN3US Reveals Novel Insights into Giant Phage Head Structure and Assembly

Thomas

Quintana

Bosch

et al. 2016

J Virol

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“…The four jumbo myovirus groups package DNA by headful packaging based on homology of their putative terminase genes to the phiKZ terminase ( 9 ). Three of these genomically permuted myovirus groups were assigned their base pair (bp) 1 by alignment to previously published genomes by use of BLASTN ( 10 ) and Gepard ( 11 ) (Ea35-70 for the Deimos-Minion group [ 12 ], EL [ 13 , 14 ] for the RisingSun group, and SPN3US [ 15 ] for the Caitlin group). vB_EamM_Yoloswag shared very little DNA homology with any other phage; therefore, its bp 1 was assigned to position its putative terminase at the beginning of the genome.…”

Section: Genome Announcementmentioning

confidence: 99%

Genome Sequences of 19 Novel Erwinia amylovora Bacteriophages

et al. 2017

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“…Consequently, more than thirty phages related to ϕKZ infecting a range of hosts including Salmonella (e.g., SPN3US), Erwinia amylovora (e.g., Ea35-70), Cronobacter sakazakii (e.g., CR5) and Vibrio spp. (e.g., JM-2012) have now been isolated with the goal of developing novel phage-based therapeutics (Lee et al, 2011 , 2016 ; Jang et al, 2013 ; Meczker et al, 2014 ; Yagubi et al, 2014 ; Bhunchoth et al, 2016 ; Danis-Wlodarczyk et al, 2016 ). For example, PhiEaH2 is one of two phages in “Erwiphage,” the first marketed bacteriophage-based pesticide against E. amylovora in Hungary (Meczker et al, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

To Be or Not To Be T4: Evidence of a Complex Evolutionary Pathway of Head Structure and Assembly in Giant Salmonella Virus SPN3US

et al. 2017

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Giant Salmonella phage SPN3US has a 240-kb dsDNA genome and a large complex virion composed of many proteins for which the functions of most are undefined. We recently determined that SPN3US shares a core set of genes with related giant phages and sequenced and characterized 18 amber mutants to facilitate its use as a genetic model system. Notably, SPN3US and related giant phages contain a bolus of ejection proteins within their heads, including a multi-subunit virion RNA polymerase (vRNAP), that enter the host cell with the DNA during infection. In this study, we characterized the SPN3US virion using mass spectrometry to gain insight into its head composition and the features that its head shares with those of related giant phages and with T4 phage. SPN3US has only homologs to the T4 proteins critical for prohead shell formation, the portal and major capsid proteins, as well as to the major enzymes essential for head maturation, the prohead protease and large terminase subunit. Eight of ~50 SPN3US head proteins were found to undergo proteolytic processing at a cleavage motif by the prohead protease gp245. Gp245 undergoes auto-cleavage of its C-terminus, suggesting this is a conserved activation and/or maturation feature of related phage proteases. Analyses of essential head gene mutants showed that the five subunits of the vRNAP must be assembled for any subunit to be incorporated into the prohead, although the assembled vRNAP must then undergo subsequent major conformational rearrangements in the DNA packed capsid to allow ejection through the ~30 Å diameter tail tube for transcription from the injected DNA. In addition, ejection protein candidate gp243 was found to play a critical role in head assembly. Our analyses of the vRNAP and gp243 mutants highlighted an unexpected dichotomy in giant phage head maturation: while all analyzed giant phages have a homologous protease that processes major capsid and portal proteins, processing of ejection proteins is not always a stable/defining feature. Our identification in SPN3US, and related phages, of a diverged paralog to the prohead protease further hints toward a complicated evolutionary pathway for giant phage head structure and assembly.

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Complete Genome Sequence of Erwinia amylovora Bacteriophage vB_EamM_Ea35-70

Cited by 31 publications

References 6 publications

Identification of Essential Genes in the Salmonella Phage SPN3US Reveals Novel Insights into Giant Phage Head Structure and Assembly

Identification of Essential Genes in the Salmonella Phage SPN3US Reveals Novel Insights into Giant Phage Head Structure and Assembly

Genome Sequences of 19 Novel Erwinia amylovora Bacteriophages

To Be or Not To Be T4: Evidence of a Complex Evolutionary Pathway of Head Structure and Assembly in Giant Salmonella Virus SPN3US

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