Morphogenesis of bacteriophage phi 6: a presumptive viral membrane precursor

Application of artificial scaffold systems in microbial metabolic engineering

In nature, metabolic pathways are often organized into complex structures such as multienzyme complexes, enzyme molecular scaffolds, or reaction microcompartments. These structures help facilitate multi-step metabolic reactions. However, engineered metabolic pathways in microbial cell factories do not possess inherent metabolic regulatory mechanisms, which can result in metabolic imbalance. Taking inspiration from nature, scientists have successfully developed synthetic scaffolds to enhance the performance of engineered metabolic pathways in microbial cell factories. By recruiting enzymes, synthetic scaffolds facilitate the formation of multi-enzyme complexes, leading to the modulation of enzyme spatial distribution, increased enzyme activity, and a reduction in the loss of intermediate products and the toxicity associated with harmful intermediates within cells. In recent years, scaffolds based on proteins, nucleic acids, and various organelles have been developed and employed to facilitate multiple metabolic pathways. Despite varying degrees of success, synthetic scaffolds still encounter numerous challenges. The objective of this review is to provide a comprehensive introduction to these synthetic scaffolds and discuss their latest research advancements and challenges.

Structural Studies of Bacteriophage Φ6 and Its Transformations during Its Life Cycle

From the first isolation of the cystovirus bacteriophage Φ6 from Pseudomonas syringae 50 years ago, we have progressed to a better understanding of the structure and transformations of many parts of the virion. The three-layered virion, encapsulating the tripartite double-stranded RNA (dsRNA) genome, breaches the cell envelope upon infection, generates its own transcripts, and coopts the bacterial machinery to produce its proteins. The generation of a new virion starts with a procapsid with a contracted shape, followed by the packaging of single-stranded RNA segments with concurrent expansion of the capsid, and finally replication to reconstitute the dsRNA genome. The outer two layers are then added, and the fully formed virion released by cell lysis. Most of the procapsid structure, composed of the proteins P1, P2, P4, and P7 is now known, as well as its transformations to the mature, packaged nucleocapsid. The outer two layers are less well-studied. One additional study investigated the binding of the host protein YajQ to the infecting nucleocapsid, where it enhances the transcription of the large RNA segment that codes for the capsid proteins. Finally, I relate the structural aspects of bacteriophage Φ6 to those of other dsRNA viruses, noting the similarities and differences.

Discovery and Classification of the φ6 Bacteriophage: An Historical Review

The year 2023 marks the fiftieth anniversary of the discovery of the bacteriophage φ6. The review provides a look back on the initial discovery and classification of the lipid-containing and segmented double-stranded RNA (dsRNA) genome-containing bacteriophage-the first identified cystovirus. The historical discussion describes, for the most part, the first 10 years of the research employing contemporary mutation techniques, biochemical, and structural analysis to describe the basic outline of the virus replication mechanisms and structure. The physical nature of φ6 was initially controversial as it was the first bacteriophage found that contained segmented dsRNA, resulting in a series of early publications that defined the unusual genomic quality. The technology and methods utilized in the initial research (crude by current standards) meant that the first studies were quite time-consuming, hence the lengthy period covered by this review. Yet when the data were accepted, the relationship to the reoviruses was apparent, launching great interest in cystoviruses, research that continues to this day.

Heterologous RNA Recombination in the Cystoviruses φ6 and φ8: A Mechanism of Viral Variation and Genome Repair

Recombination and mutation of viral genomes represent major mechanisms for viral evolution and, in many cases, moderate pathogenicity. Segmented genome viruses frequently undergo reassortment of the genome via multiple infection of host organisms, with influenza and reoviruses being well-known examples. Specifically, major genomic shifts mediated by reassortment are responsible for radical changes in the influenza antigenic determinants that can result in pandemics requiring rapid preventative responses by vaccine modifications. In contrast, smaller mutational changes brought about by the error-prone viral RNA polymerases that, for the most part, lack a replication base mispairing editing function produce small mutational changes in the RNA genome during replication. Referring again to the influenza example, the accumulated mutations-known as drift-require yearly vaccine updating and rapid worldwide distribution of each new formulation. Coronaviruses with a large positive-sense RNA genome have long been known to undergo intramolecular recombination likely mediated by copy choice of the RNA template by the viral RNA polymerase in addition to the polymerase-based mutations. The current SARS-CoV-2 origin debate underscores the importance of understanding the plasticity of viral genomes, particularly the mechanisms responsible for intramolecular recombination. This review describes the use of the cystovirus bacteriophage as an experimental model for recombination studies in a controlled manner, resulting in the development of a model for intramolecular RNA genome alterations. The review relates the sequence of experimental studies from the laboratory of Leonard Mindich, PhD at the Public Health Research Institute-then in New York City-and covers a period of approximately 12 years. Hence, this is a historical scientific review of research that has the greatest relevance to current studies of emerging RNA virus pathogens.

Microbial production of lipid-protein vesicles using enveloped bacteriophage phi6

Background

Cystoviruses have a phospholipid envelope around their nucleocapsid. Such a feature is unique among bacterial viruses (i.e., bacteriophages) and the mechanisms of virion envelopment within a bacterial host are largely unknown. The cystovirus Pseudomonas phage phi6 has an envelope that harbors five viral membrane proteins and phospholipids derived from the cytoplasmic membrane of its Gram-negative host. The phi6 major envelope protein P9 and the non-structural protein P12 are essential for the envelopment of its virions. Co-expression of P9 and P12 in a Pseudomonas host results in the formation of intracellular vesicles that are potential intermediates in the phi6 virion assembly pathway. This study evaluated the minimum requirements for the formation of phi6-specific vesicles and the possibility to localize P9-tagged heterologous proteins into such structures in Escherichia coli.

Results

Using transmission electron microscopy, we detected membranous structures in the cytoplasm of E. coli cells expressing P9. The density of the P9-specific membrane fraction was lower (approximately 1.13 g/cm³ in sucrose) than the densities of the bacterial cytoplasmic and outer membrane fractions. A P9-GFP fusion protein was used to study the targeting of heterologous proteins into P9 vesicles. Production of the GFP-tagged P9 vesicles required P12, which protected the fusion protein against proteolytic cleavage. Isolated vesicles contained predominantly P9-GFP, suggesting selective incorporation of P9-tagged fusion proteins into the vesicles.

Conclusions

Our results demonstrate that the phi6 major envelope protein P9 can trigger formation of cytoplasmic membrane structures in E. coli in the absence of any other viral protein. Intracellular membrane structures are rare in bacteria, thus making them ideal chasses for cell-based vesicle production. The possibility to locate heterologous proteins into the P9-lipid vesicles facilitates the production of vesicular structures with novel properties. Such products have potential use in biotechnology and biomedicine.

Electronic supplementary material

The online version of this article (10.1186/s12934-019-1079-z) contains supplementary material, which is available to authorized users.

Controlled Disassembly and Purification of Functional Viral Subassemblies Using Asymmetrical Flow Field-Flow Fractionation (AF4)

Viruses protect their genomes by enclosing them into protein capsids that sometimes contain lipid bilayers that either reside above or below the protein layer. Controlled dissociation of virions provides important information on virion composition, interactions, and stoichiometry of virion components, as well as their possible role in virus life cycles. Dissociation of viruses can be achieved by using various chemicals, enzymatic treatments, and incubation conditions. Asymmetrical flow field-flow fractionation (AF4) is a gentle method where the separation is based on size. Here, we applied AF4 for controlled dissociation of enveloped bacteriophage φ6. Our results indicate that AF4 can be used to assay the efficiency of the dissociation process and to purify functional subviral particles.

RNA Phage Biology in a Metagenomic Era

The number of novel bacteriophage sequences has expanded significantly as a result of many metagenomic studies of phage populations in diverse environments. Most of these novel sequences bear little or no homology to existing databases (referred to as the "viral dark matter"). Also, these sequences are primarily derived from DNA-encoded bacteriophages (phages) with few RNA phages included. Despite the rapid advancements in high-throughput sequencing, few studies enrich for RNA viruses, i.e., target viral rather than cellular fraction and/or RNA rather than DNA via a reverse transcriptase step, in an attempt to capture the RNA viruses present in a microbial communities. It is timely to compile existing and relevant information about RNA phages to provide an insight into many of their important biological features, which should aid in sequence-based discovery and in their subsequent annotation. Without comprehensive studies, the biological significance of RNA phages has been largely ignored. Future bacteriophage studies should be adapted to ensure they are properly represented in phageomic studies.

Evaluation of Phi6 Persistence and Suitability as an Enveloped Virus Surrogate

Recent outbreaks involving enveloped viruses, such as Ebola virus, have raised questions regarding the persistence of enveloped viruses in the water environment. Efforts have been made to find enveloped virus surrogates due to challenges investigating viruses that require biosafety-level 3 or 4 handling. In this study, the enveloped bacteriophage Phi6 was evaluated as a surrogate for enveloped waterborne viruses. The persistence of Phi6 was tested in aqueous conditions chosen based on previously published viral persistence studies. Our results demonstrated that the predicted T₉₀ (time for 90% inactivation) of Phi6 under the 12 evaluated conditions varied from 24 min to 117 days depending on temperature, biological activity, and aqueous media composition. Phi6 persistence was then compared with persistence values from other enveloped viruses reported in the literature. The apparent suitability of Phi6 as an enveloped virus surrogate was dependent on the temperature and composition of the media tested. Of evaluated viruses, 33%, including all conditions considered, had T₉₀ values greater than the 95% confidence interval for Phi6. Ultimately, these results highlight the variability of enveloped virus persistence in the environment and the value of working with the virus of interest for environmental persistence studies.

Double-stranded RNA virus outer shell assembly by bona fide domain-swapping

Correct outer protein shell assembly is a prerequisite for virion infectivity in many multi-shelled dsRNA viruses. In the prototypic dsRNA bacteriophage φ6, the assembly reaction is promoted by calcium ions but its biomechanics remain poorly understood. Here, we describe the near-atomic resolution structure of the φ6 double-shelled particle. The outer T=13 shell protein P8 consists of two alpha-helical domains joined by a linker, which allows the trimer to adopt either a closed or an open conformation. The trimers in an open conformation swap domains with each other. Our observations allow us to propose a mechanistic model for calcium concentration regulated outer shell assembly. Furthermore, the structure provides a prime exemplar of bona fide domain-swapping. This leads us to extend the theory of domain-swapping from the level of monomeric subunits and multimers to closed spherical shells, and to hypothesize a mechanism by which closed protein shells may arise in evolution.

Double-shelled bacteriophage φ6 is a well-studied model system used to understand assembly of dsRNA viruses. Here the authors report a near-atomic resolution cryo-EM structure of φ6 and propose a model for the structural transitions occurring in the outer shell during genome packaging.

Synthetic Lipid-Containing Scaffolds Enhance Production by Colocalizing Enzymes

Subcellular organization is critical for isolating, concentrating, and protecting biological activities. Natural subcellular organization is often achieved using colocalization of proteins on scaffold molecules, thereby enhancing metabolic fluxes and enabling coregulation. 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 lipid-encapsulated bacteriophage ϕ6 to form synthetic lipid-containing scaffolds (SLSs) in E. coli. Analysis of diffusive behavior by particle tracking 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 colocalized 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 the production of a commercially relevant metabolite.

Comparison of lipid-containing bacterial and archaeal viruses

Lipid-containing bacteriophages were discovered late and considered to be rare. After further phage isolations and the establishment of the domain Archaea, several new prokaryotic viruses with lipids were observed. Consequently, the presence of lipids in prokaryotic viruses is reasonably common. The wealth of information about how prokaryotic viruses use their lipids comes from a few well-studied model viruses (PM2, PRD1, and ϕ6). These bacteriophages derive their lipid membranes selectively from the host during the virion assembly process which, in the case of PM2 and PRD1, culminates in the formation of protein capsid with an inner membrane, and for ϕ6 an outer envelope. Several inner membrane-containing viruses have been described for archaea, and their lipid acquisition models are reminiscent to those of PM2 and PRD1. Unselective acquisition of lipids has been observed for bacterial mycoplasmaviruses and archaeal pleolipoviruses, which resemble each other by size, morphology, and life style. In addition to these shared morphotypes of bacterial and archaeal viruses, archaea are infected by viruses with unique morphotypes, such as lemon-shaped, helical, and globular ones. It appears that structurally related viruses may or may not have a lipid component in the virion, suggesting that the significance of viral lipids might be to provide viruses extended means to interact with the host cell.

Frequency and fitness consequences of bacteriophage φ6 host range mutations

Viruses readily mutate and gain the ability to infect novel hosts, but few data are available regarding the number of possible host range-expanding mutations allowing infection of any given novel host, and the fitness consequences of these mutations on original and novel hosts. To gain insight into the process of host range expansion, we isolated and sequenced 69 independent mutants of the dsRNA bacteriophage Φ6 able to infect the novel host, Pseudomonas pseudoalcaligenes. In total, we found at least 17 unique suites of mutations among these 69 mutants. We assayed fitness for 13 of 17 mutant genotypes on P. pseudoalcaligenes and the standard laboratory host, P. phaseolicola. Mutants exhibited significantly lower fitnesses on P. pseudoalcaligenes compared to P. phaseolicola. Furthermore, 12 of the 13 assayed mutants showed reduced fitness on P. phaseolicola compared to wildtype Φ6, confirming the prevalence of antagonistic pleiotropy during host range expansion. Further experiments revealed that the mechanistic basis of these fitness differences was likely variation in host attachment ability. In addition, using computational protein modeling, we show that host-range expanding mutations occurred in hotspots on the surface of the phage's host attachment protein opposite a putative hydrophobic anchoring domain.

Evolutionary genomics of host-use in bifurcating demes of RNA virus phi-6

BACKGROUND

Viruses are exceedingly diverse in their evolved strategies to manipulate hosts for viral replication. However, despite these differences, most virus populations will occasionally experience two commonly-encountered challenges: growth in variable host environments, and growth under fluctuating population sizes. We used the segmented RNA bacteriophage ϕ6 as a model for studying the evolutionary genomics of virus adaptation in the face of host switches and parametrically varying population sizes. To do so, we created a bifurcating deme structure that reflected lineage splitting in natural populations, allowing us to test whether phylogenetic algorithms could accurately resolve this 'known phylogeny'. The resulting tree yielded 32 clones at the tips and internal nodes; these strains were fully sequenced and measured for phenotypic changes in selected traits (fitness on original and novel hosts).

RESULTS

We observed that RNA segment size was negatively correlated with the extent of molecular change in the imposed treatments; molecular substitutions tended to cluster on the Small and Medium RNA chromosomes of the virus, and not on the Large segment. Our study yielded a very large molecular and phenotypic dataset, fostering possible inferences on genotype-phenotype associations. Using further experimental evolution, we confirmed an inference on the unanticipated role of an allelic switch in a viral assembly protein, which governed viral performance across host environments.

CONCLUSIONS

Our study demonstrated that varying complexities can be simultaneously incorporated into experimental evolution, to examine the combined effects of population size, and adaptation in novel environments. The imposed bifurcating structure revealed that some methods for phylogenetic reconstruction failed to resolve the true phylogeny, owing to a paucity of molecular substitutions separating the RNA viruses that evolved in our study.

Bacteriophage ϕ6 nucleocapsid surface protein 8 interacts with virus-specific membrane vesicles containing major envelope protein 9

Enveloped double-stranded RNA (dsRNA) bacterial virus Pseudomonas phage ϕ6 has been developed into an advanced assembly system where purified virion proteins and genome segments self-assemble into infectious viral particles, inferring the assembly pathway. The most intriguing step is the membrane assembly occurring inside the bacterial cell. Here, we demonstrate that the middle virion shell, made of protein 8, associates with the expanded viral core particle and the virus-specific membrane vesicle.

Toroidal surface complexes of bacteriophage ϕ12 are responsible for host-cell attachment

Cryo-electron tomography and subtomogram averaging are utilized to determine that the bacteriophage ϕ12, a member of the Cystoviridae family, contains surface complexes that are toroidal in shape, are composed of six globular domains with six-fold symmetry, and have a discrete density connecting them to the virus membrane-envelope surface. The lack of this kind of spike in a reassortant of ϕ12 demonstrates that the gene for the hexameric spike is located in ϕ12's medium length genome segment, likely to the P3 open reading frames which are the proteins involved in viral-host cell attachment. Based on this and on protein mass estimates derived from the obtained averaged structure, it is suggested that each of the globular domains is most likely composed of a total of four copies of P3a and/or P3c proteins. Our findings may have implications in the study of the evolution of the cystovirus species in regard to their host specificity.

The origin of phospholipids of the enveloped bacteriophage phi6

The phospholipid class and molecular species compositions of bacteriophage phi6 and its host Pseudomonas syringae were determined quantitatively using TLC and liquid-chromatography/electrospray ionization mass-spectrometry. In addition, the fatty acid compositions of the phospholipids were analyzed by gas-chromatography/mass-spectrometry. The phage contained significantly more phosphatidylglycerol (PG) and less phosphatidylethanolamine (PE) than the host cytoplasmic (CM) and outer (OM) membranes. In addition, the phospholipid molecular species composition of the viral membrane differed from those of the host membranes, but resembled that of CM more than OM as shown by principal component analysis (PCA). The membrane of phi6 contained more 34:1 and 34:2, and less 32:1 PE and PG molecular species than the host CM or OM. Also, phi6 contained negligible amounts of saturated phospholipid molecular species. These data provide the first biochemical evidence suggesting that phi6 obtains its lipids from the CM. This process is not unselective, but certain phospholipid species are preferentially incorporated in the phage membrane. Common factors leading to similar enrichment of PG in every membrane-containing bacterial virus system studied so far (phi6, PM2, PRD1, PR4, Bam35) are discussed.

Self-assembly of double-stranded RNA bacteriophages

Double-stranded RNA viruses infecting bacterial hosts belong to the Cystoviridae family. Bacteriophage phi6 is one of the best characterized dsRNA viruses and shares structural as well as functional similarities with other well-studied eukaryotic dsRNA viruses (e.g. L-A, rotavirus, bluetongue virus, and reovirus). The assembly pathway of the enveloped, triple-layered phi6 virion has been well documented and can be divided into four distinct steps which are (1) procapsid formation, (2) genome encapsidation and replication, (3) nucleocapsid surface shell assembly, and (4) envelope formation. In this review, we focus primarily on the procapsid and nucleocapsid assembly for which in vitro systems have been established. The in vitro assembly systems have been instrumental in revealing assembly intermediates and conformational changes that are common to phi6 and phi8, two cystoviruses with negligible sequence homology. Two viral enzymes, the packaging NTPase (P4) and the RNA-dependent RNA polymerase (P2), were found essential for the nucleation step. The nucleation complex contains one or more tetramers of the major procapsid protein (P1) and is further stabilized by protein P4. Interaction of P1 and P4 during assembly is accompanied by an additional folding of their respective polypeptide chains. The in vitro assembled procapsids were shown to selectively package and replicate the genomic ssRNA. Furthermore, in vitro assembly of infectious nucleocapsids has been achieved in the case of phi6. The in vitro studies indicate that the nucleocapsid coat protein (P8) assembles around the polymerase complex in a template-assisted manner. Implications for the assembly of other dsRNA viruses are also presented.

Plasmid-directed assembly of the lipid-containing membrane of bacteriophage phi 6

The nucleocapsid of bacteriophage phi 6 is enveloped within a lipid-containing membrane. The membrane is composed of proteins P3, P6, P9, P10, and P13 and phospholipids. The relationship between membrane protein P9 and morphogenetic protein P12 was studied in the absence of phage infection. cDNA copies of genes 9 and 12 were expressed on plasmids in Pseudomonas syringae pv. phaseolicola. Immunoblotting demonstrated the presence of protein P9 in strains carrying both gene 9 and gene 12 but not in strains with gene 9 alone. In the absence of P12, P9 was found to be unstable. Simultaneous synthesis of proteins P9 and P12 led to the formation of a low-density P9 particle having a buoyant density similar to that of precursor structures composed of phospholipid and proteins isolated from phi 6-infected cells. These results are consistent with results of previous genetic experiments suggesting that P9 and P12 are necessary and sufficient for the formation of the phi 6 envelope. Extensions of P9 at the C terminus do not impair particle formation; however, N-terminal extensions or C-terminal deletions that extend into the hydrophobic region of P9 do impair particle formation.

Generation of infectious nucleocapsids by in vitro assembly of the shell protein on to the polymerase complex of the dsRNA bacteriophage phi 6

A method for the in vitro uncoating of the phi 6 nucleocapsid (NC) was developed. The resulting particle, designated as the NC core, containing the genomic double-stranded (ds) RNA segments and the proteins P1, P2, P4 and P7, was not infectious but had a highly enhanced in vitro transcriptase activity compared to that of the intact NC. The NC shell protein P8 was purified by immunoaffinity chromatography, and it was shown to self-assemble to shell-like structures upon addition of calcium ions. The conditions for the self-assembly of the shell were optimized. Shell reassembly on to the NC cores restored the infectivity but resulted in a decrease of transcriptase activity. No reassembly of the shell on to RNA-less cores (procapsids) produced from a cDNA construction in Escherichia coli was observed. Our results suggest that the intracellular uncoating of the NC is the event activating the phi 6 dsRNA transcriptase and that the NC shell is necessary for infectivity, probably for the passage of the NC through the host cytoplasmic membrane. Packaging of the dsRNA segments into the procapsid appears to be a prerequisite for NC shell assembly.

The structure of bacteriophage phi 6: protease digestion of phi 6 virions

Proteolysis experiments with phi 6 virions show that the adsorption protein, P3, is digested by both trypsin and chymotrypsin. In addition, chymotrypsin also removes P6, a protein thought to be the anchor for P3 in the phi 6 membrane.

Characterization of phi 6 mutants that are temperature sensitive in the morphogenetic protein P12

P12 is a morphogenetic protein necessary for the envelopment of the bacteriophage phi 6 nucleocapsid with the viral membrane. Gene 12 is located along with three other genes on the smallest chromosome of the virion. ts mutants in P12 were obtained by first characterizing the isoelectric focusing behavior of phi 6 proteins and then screening ts mutants of phi 6 that had previously been assigned to chromosome C for changes in the behavior of P12. In this manner, three independently isolated mutants were identified and were found to have morphogenetic consequences at restrictive temperatures similar to gene 12 nonsense mutants in nonsuppressor cells in that only unenveloped nucleocapsids were formed. When infected cells were labeled at restrictive temperature, 27 degrees, and then shifted to 21 degrees, normal phage particles were formed; however, the hydrophobic membrane proteins in the particles were not labeled, indicating that functional P12 must be present at the time of synthesis of the membrane proteins for them to assemble into virions or that the defective P12 leads the membrane proteins into a nonfunctional pathway.