Identification of essential genes in the Salmonella phage SPN3US reveals novel insights into giant phage head structure and assembly

Julie A. Thomas, Andrea Denisse Benítez Quintana, Martine A. Bosch, Adriana Coll De Peña, Elizabeth Aguilera, Assitan Coulibaly, Weimin Wu, Michael V. Osier, André O. Hudson, Susan E Weintraub, Lindsay W. Black

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)10284-10298
Number of pages15
JournalJournal of Virology
Volume90
Issue number22
DOIs
StatePublished - 2016

Fingerprint

Salmonella Phages
Essential Genes
bacteriophages
Bacteriophages
Salmonella
Virion
virion
Head
Pseudomonas Phages
Genome
Genes
mutants
Salmonella enterica
genes
Mutant Proteins
DNA-Directed RNA Polymerases
Proteome
essential genes
Pseudomonas aeruginosa
genome

ASJC Scopus subject areas

  • Immunology
  • Virology

Cite this

Thomas, J. A., Quintana, A. D. B., Bosch, M. A., De Peña, A. C., Aguilera, E., Coulibaly, A., ... Black, L. W. (2016). Identification of essential genes in the Salmonella phage SPN3US reveals novel insights into giant phage head structure and assembly. Journal of Virology, 90(22), 10284-10298. https://doi.org/10.1128/JVI.01582-16

Identification of essential genes in the Salmonella phage SPN3US reveals novel insights into giant phage head structure and assembly. / Thomas, Julie A.; Quintana, Andrea Denisse Benítez; Bosch, Martine A.; De Peña, Adriana Coll; Aguilera, Elizabeth; Coulibaly, Assitan; Wu, Weimin; Osier, Michael V.; Hudson, André O.; Weintraub, Susan E; Black, Lindsay W.

In: Journal of Virology, Vol. 90, No. 22, 2016, p. 10284-10298.

Research output: Contribution to journalArticle

Thomas, JA, Quintana, ADB, Bosch, MA, De Peña, AC, Aguilera, E, Coulibaly, A, Wu, W, Osier, MV, Hudson, AO, Weintraub, SE & Black, LW 2016, 'Identification of essential genes in the Salmonella phage SPN3US reveals novel insights into giant phage head structure and assembly', Journal of Virology, vol. 90, no. 22, pp. 10284-10298. https://doi.org/10.1128/JVI.01582-16
Thomas, Julie A. ; Quintana, Andrea Denisse Benítez ; Bosch, Martine A. ; De Peña, Adriana Coll ; Aguilera, Elizabeth ; Coulibaly, Assitan ; Wu, Weimin ; Osier, Michael V. ; Hudson, André O. ; Weintraub, Susan E ; Black, Lindsay W. / Identification of essential genes in the Salmonella phage SPN3US reveals novel insights into giant phage head structure and assembly. In: Journal of Virology. 2016 ; Vol. 90, No. 22. pp. 10284-10298.
@article{f225fbca750647219c3be5f495d55114,
title = "Identification of essential genes in the Salmonella phage SPN3US reveals novel insights into giant phage head structure and assembly",
abstract = "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.",
author = "Thomas, {Julie A.} and Quintana, {Andrea Denisse Ben{\'i}tez} and Bosch, {Martine A.} and {De Pe{\~n}a}, {Adriana Coll} and Elizabeth Aguilera and Assitan Coulibaly and Weimin Wu and Osier, {Michael V.} and Hudson, {Andr{\'e} O.} and Weintraub, {Susan E} and Black, {Lindsay W.}",
year = "2016",
doi = "10.1128/JVI.01582-16",
language = "English (US)",
volume = "90",
pages = "10284--10298",
journal = "Journal of Virology",
issn = "0022-538X",
publisher = "American Society for Microbiology",
number = "22",

}

TY - JOUR

T1 - Identification of essential genes in the Salmonella phage SPN3US reveals novel insights into giant phage head structure and assembly

AU - Thomas, Julie A.

AU - Quintana, Andrea Denisse Benítez

AU - Bosch, Martine A.

AU - De Peña, Adriana Coll

AU - Aguilera, Elizabeth

AU - Coulibaly, Assitan

AU - Wu, Weimin

AU - Osier, Michael V.

AU - Hudson, André O.

AU - Weintraub, Susan E

AU - Black, Lindsay W.

PY - 2016

Y1 - 2016

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84995470800&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84995470800&partnerID=8YFLogxK

U2 - 10.1128/JVI.01582-16

DO - 10.1128/JVI.01582-16

M3 - Article

VL - 90

SP - 10284

EP - 10298

JO - Journal of Virology

JF - Journal of Virology

SN - 0022-538X

IS - 22

ER -