Proteins of bacteriophage phi6

Sinclair, Jacqueline F.; Tzagoloff, Alexander; Levine, D.; Mindich, Leonard

doi:10.1128/jvi.16.3.685-695.1975

Cited by 97 publications

(63 citation statements)

References 19 publications

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“…It is rarer for nonstructural genes that are not on the exterior of the virion to be a host range determinant, but there are examples of this in avian influenza virus (PB2) (46,47) and in picornaviruses (48,49). While P5 plays a role in both 6 entry and egress (50)(51)(52), P12 is solely associated with egress from cells (forming membranes from the host cytoplasmic membrane around completed nucleocapsids) and is not detected in 6 virions (28,53). P12 was a hot spot of change in entropy for 6-WT, and 10 of the 13 clones that did not have a mutation in P3 had one of five nonsynonymous mutations in P12, which strongly suggests that this nonstructural protein has a role in host range expansion to P. syringae pv.…”

Section: Discussionmentioning

confidence: 99%

Existing Host Range Mutations Constrain Further Emergence of RNA Viruses

Zhao

Seth-Pasricha

Stemate

et al. 2019

J Virol

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RNA viruses are capable of rapid host shifting, typically due to a point mutation that confers expanded host range. As additional point mutations are necessary for further expansions, epistasis among host range mutations can potentially affect the mutational neighborhood and frequency of niche expansion. We mapped the mutational neighborhood of host range expansion using three genotypes of the double-stranded RNA (dsRNA) bacteriophage 6 (wild type and two isogenic host range mutants) on the novel host Pseudomonas syringae pv. atrofaciens. Both Sanger sequencing of 50 P. syringae pv. atrofaciens mutant clones for each genotype and population Illumina sequencing revealed the same high-frequency mutations allowing infection of P. syringae pv. atrofaciens. Wild-type 6 had at least nine different ways of mutating to enter the novel host, eight of which are in p3 (host attachment protein gene), and 13/50 clones had unchanged p3 genes. However, the two isogenic mutants had dramatically restricted neighborhoods: only one or two mutations, all in p3. Deep sequencing revealed that wild-type clones without mutations in p3 likely had changes in p12 (morphogenic protein), a region that was not polymorphic for the two isogenic host range mutants. Sanger sequencing confirmed that 10/13 of the wild-type 6 clones had nonsynonymous mutations in p12, and 2 others had point mutations in p9 and p5. None of these genes had previously been associated with host range expansion in 6. We demonstrate, for the first time, epistatic constraint in an RNA virus due to host range mutations themselves, which has implications for models of serial host range expansion. IMPORTANCE RNA viruses mutate rapidly and frequently expand their host ranges to infect novel hosts, leading to serial host shifts. Using an RNA bacteriophage model system (Pseudomonas phage 6), we studied the impact of preexisting host range mutations on another host range expansion. Results from both clonal Sanger and Illumina sequencing show that extant host range mutations dramatically narrow the neighborhood of potential host range mutations compared to that of wild-type 6. This research suggests that serial host-shifting viruses may follow a small number of molecular paths to enter additional novel hosts. We also identified new genes involved in 6 host range expansion, expanding our knowledge of this important model system in experimental evolution. KEYWORDS entropy, epistasis, host range mutations, RNA virus E merging and reemerging viruses that shift host to infect new species pose significant economic and health costs to humans, animals, plants, and our ecosystems (1-3). While ecological exposure is an essential part of emergence on a novel host (2), spillover infection of the novel host typically requires a host range mutation, the genetic component of host range expansion (4). These exaptive host range mutations Citation Zhao L, Seth-Pasricha M, Stemate D, Crespo-Bellido A, Gagnon J, Draghi J, Duffy S. 2019. Existing host range mutations constrain further emergence of RNA...

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Section: Discussionmentioning

confidence: 99%

Existing Host Range Mutations Constrain Further Emergence of RNA Viruses

Zhao

Seth-Pasricha

Stemate

et al. 2019

J Virol

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“…P5 plays a role in both phi6 entry and egress: copies of this muralytic enzyme underneath the lipid coat bore through the cell wall to allow phi6 to re-envelop itself with the host's cytoplasmic membrane, and it is used to lyse host cells after sufficient replication (56)(57)(58). P12, however, is solely associated with egress from cells (forming membranes from the host cytoplasmic membrane around completed nucleocapsids) and is not detected in phi6 virions (35,59). P12 was a hotspot of change in entropy for phi6-WT and 10 of the 13 clones that did not have a mutation in P3 had one of five nonsynonymous mutations in P12, which strongly suggests that this non-structural protein has a role in host range expansion to PA.…”

Section: Specific Mutations Found In Our Studymentioning

confidence: 99%

Existing host range mutations constrain further emergence of RNA viruses

Zhao

Seth-Pasricha

Stemate

et al. 2018

Preprint

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RNA viruses are capable of rapid host shifting, typically due to a point mutation that confers expanded host range. As additional point mutations are necessary for further expansions, epistasis among host range mutations can potentially affect the mutational neighborhood and frequency of niche expansion. We mapped the mutational neighborhood of host range expansion using three genotypes of the dsRNA bacteriophage phi6 (wildtype and two isogenic host range mutants) on the novel host Pseudomonas syringae pv. atrofaciens (PA). Sanger sequencing of fifty PA mutant clones for each genotype and population Illumina sequencing both revealed the same high frequency mutations allowing infection of PA. Wildtype phi6 had at least nine different ways of mutating to enter the novel host, eight of which are in p3 (host attachment protein gene), and 13/50 clones had unchanged p3 genes. However, the two isogenic mutants had dramatically restricted neighborhoods: only one or two mutations, all in p3. Deep sequencing revealed that wildtype clones without mutations in p3 likely had changes in p12 (morphogenic protein), a region that was not polymorphic for the two isogenic host range mutants. Sanger sequencing confirmed that 10/13 of the wildtype phi6 clones had nonsynonymous mutations in p12 and two others had point mutations in p9 and p5 -none of these genes had previously been associated with host range expansion in phi6. We demonstrate, for the first time, epistatic constraint in an RNA virus due to host range mutations themselves, which has implications for models of serial host range expansion. ImportanceRNA viruses mutate rapidly and frequently expand their host ranges to infect novel hosts, leading to serial host shifts. Using an RNA bacteriophage model system (Pseudomonas phage phi6), we studied the impact of pre-existing host range mutations on another host range expansion. Results from both clonal Sanger and Illumina sequencing show extant host range mutations dramatically narrow the neighborhood of potential host range mutations compared to wildtype phi6. This research suggests that serial host shifting viruses may follow a small number of molecular paths to enter additional novel hosts. We also identified . CC-BY-NC 4.0

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“…A candidate for such a system comes from the bacteriophage φ6. Unlike most bacteriophages, φ6 contains a proteinaceous nucleocapsid surrounded by an envelope containing lipids and several membrane proteins 14,15 . During its normal life cycle, φ6 infects the bacterium Pseudomonas phaseolicola 16 via a membrane fusion event 17 , and thus the membrane is a crucial part of an infectious viral particle.…”

Section: Introduction: (~620/750 Words No Sub-headings)mentioning

confidence: 99%

Synthetic lipid-containing scaffolds enhance production by co-localizing enzymes

Myhrvold

2016

Preprint

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~150 words)Subcellular organization is critical for isolating, concentrating, and protecting biological activities.Natural subcellular organization is often achieved using co-localization of proteins on scaffold molecules, thereby enhancing metabolic fluxes and enabling co-regulation. Synthetic scaffolds extend these benefits to new biological processes, and are typically constructed from proteins or nucleic acids. To expand the range of available building materials, we use a minimal set of components from the lipidencapsulated bacteriophage φ6 to form synthetic lipid-containing scaffolds (SLSs) in E. coli. Analysis of diffusive behavior by tracking particles in live cells indicates that SLSs are >20 nm in diameter; furthermore, density measurements demonstrate that SLSs contain a mixture of lipids and proteins. The fluorescent proteins mCitrine and mCerulean can be co-localized to SLSs. To test for effects on enzymatic production, we localized two enzymes involved in indigo biosynthesis to SLSs. We observed a scaffold-dependent increase in indigo production, showing that SLSs can enhance metabolic reactions.

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Proteins of bacteriophage phi6

Abstract: We investigated the protein composition of the lipid-containing bacteriophage 06. We also studied the synthesis of phage-specific proteins in the host bacterium Pseudomonas phaseolicola HB1OY. The virion was found to contain 10 proteins of the following molecular weights: P1,

Cited by 97 publications

References 19 publications

Existing Host Range Mutations Constrain Further Emergence of RNA Viruses

Existing Host Range Mutations Constrain Further Emergence of RNA Viruses

Existing host range mutations constrain further emergence of RNA viruses

Synthetic lipid-containing scaffolds enhance production by co-localizing enzymes

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