Assembly and maturation of the bacteriophage lambda procapsid: gpC is the viral protease

A Lambda-evo (λevo) phage platform for Zika virus EDIII protein display

One of the most significant bacteriophage technologies is phage display, in which heterologous peptides are exhibited on the virion surface. This work describes the display of λ decorative protein Dλ linked to the E protein domain III of Zika virus (Dλ-ZEDIII), to the GFP protein (Dλ-GFP), or to different domain III epitopes of the EZIKV protein (Dλ-TD), exhibited on the surface of an in vitro evolved lambda phage (λevo). This phage harbors a gene D deletion and was subjected to directed evolution using Escherichia coli W3110/pDλ-ZEDIII as background. After 20 days (20 cycles of dilution), the λevo phage developed a ~ 22% genome deletion affecting the non-essential λ b region, rendering a more stable phage that exhibited fusion proteins Dλ-ZEDIII or Dλ-GFP but not Dλ-TD. Despite the λevo system was able to decorate itself with the Dλ-ZEDIII protein, the production of viral particles was ~ 1000-fold lower than the λ wild-type, due to the unexpected Dλ-ZEDIII protein aggregation into bacterial inclusion bodies. Decorated phages (106 PFU (plaque forming units)/100 µl) were inoculated into BALB/c mice, and subsequent dot blot and Western blot immunoassays proved the production of murine antibodies against ZIKV (Zika virus). This multipurpose λevo phage display platform may be used interchangeably with other more soluble peptides, providing better yields. KEY POINTS: • λevo platform for displaying recombinant peptides. • Directed evolution to generate λevo with more efficient decoration. • Antigenic reaction in BALB/c mice by inoculating λevo with recombinant peptides.

Structural morphing in the viral portal vertex of bacteriophage lambda

The portal protein of tailed bacteriophage plays essential roles in various aspects of capsid assembly, motor assembly, genome packaging, connector formation, and infection processes. After DNA packaging is complete, additional proteins are assembled onto the portal to form the connector complex, which is crucial as it bridges the mature head and tail. In this study, we report high-resolution cryo-electron microscopy (cryo-EM) structures of the portal vertex from bacteriophage lambda in both its prohead and mature virion states. Comparison of these structures shows that during head maturation, in addition to capsid expansion, the portal protein undergoes conformational changes to establish interactions with the connector proteins. Additionally, the independently assembled tail undergoes morphological alterations at its proximal end, facilitating its connection to the head-tail joining protein and resulting in the formation of a stable portal-connector-tail complex. The B-DNA molecule spirally glides through the tube, interacting with the nozzle blade region of the middle-ring connector protein. These insights elucidate a mechanism for portal maturation and DNA translocation within the phage lambda system.

IMPORTANCE

The tailed bacteriophages possess a distinct portal vertex that consists of a ring of 12 portal proteins associated with a 5-fold capsid shell. This portal protein is crucial in multiple stages of virus assembly and infection. Our research focused on examining the structures of the portal vertex in both its preliminary prohead state and the fully mature virion state of bacteriophage lambda. By analyzing these structures, we were able to understand how the portal protein undergoes conformational changes during maturation, the mechanism by which it prevents DNA from escaping, and the process of DNA spirally gliding.

Systematic and scalable genome-wide essentiality mapping to identify nonessential genes in phages

Phages are one of the key ecological drivers of microbial community dynamics, function, and evolution. Despite their importance in bacterial ecology and evolutionary processes, phage genes are poorly characterized, hampering their usage in a variety of biotechnological applications. Methods to characterize such genes, even those critical to the phage life cycle, are labor intensive and are generally phage specific. Here, we develop a systematic gene essentiality mapping method scalable to new phage-host combinations that facilitate the identification of nonessential genes. As a proof of concept, we use an arrayed genome-wide CRISPR interference (CRISPRi) assay to map gene essentiality landscape in the canonical coliphages λ and P1. Results from a single panel of CRISPRi probes largely recapitulate the essential gene roster determined from decades of genetic analysis for lambda and provide new insights into essential and nonessential loci in P1. We present evidence of how CRISPRi polarity can lead to false positive gene essentiality assignments and recommend caution towards interpreting CRISPRi data on gene essentiality when applied to less studied phages. Finally, we show that we can engineer phages by inserting DNA barcodes into newly identified inessential regions, which will empower processes of identification, quantification, and tracking of phages in diverse applications.

Assembly and Capsid Expansion Mechanism of Bacteriophage P22 Revealed by High-Resolution Cryo-EM Structures

The formation of many double-stranded DNA viruses, such as herpesviruses and bacteriophages, begins with the scaffolding-protein-mediated assembly of the procapsid. Subsequently, the procapsid undergoes extensive structural rearrangement and expansion to become the mature capsid. Bacteriophage P22 is an established model system used to study virus maturation. Here, we report the cryo-electron microscopy structures of procapsid, empty procapsid, empty mature capsid, and mature capsid of phage P22 at resolutions of 2.6 Å, 3.9 Å, 2.8 Å, and 3.0 Å, respectively. The structure of the procapsid allowed us to build an accurate model of the coat protein gp5 and the C-terminal region of the scaffolding protein gp8. In addition, interactions among the gp5 subunits responsible for procapsid assembly and stabilization were identified. Two C-terminal α-helices of gp8 were observed to interact with the coat protein in the procapsid. The amino acid interactions between gp5 and gp8 in the procapsid were consistent with the results of previous biochemical studies involving mutant proteins. Our structures reveal hydrogen bonds and salt bridges between the gp5 subunits in the procapsid and the conformational changes of the gp5 domains involved in the closure of the local sixfold opening and a thinner capsid shell during capsid maturation.

Characterization of a Primordial Major Capsid-Scaffolding Protein Complex in Icosahedral Virus Shell Assembly

Capsid assembly pathways are strongly conserved in the complex dsDNA viruses, where major capsid proteins (MCP) self-assemble into icosahedral procapsid shells, chaperoned by a scaffolding protein. Without a scaffold, the capsid proteins aggregate and form aberrant structures. This, coupled with the rapid co-polymerization of MCP and scaffolding proteins, has thwarted characterization of the earliest steps in shell assembly. Here we interrogate the structure and biophysical properties of a soluble, assembly-deficient phage lambda major capsid protein, MCP(W308A). The mutant protein is folded, soluble to high concentrations and binds to the scaffolding protein in an apparent SP₂:MCP(W308A)₁ stoichiometry but does not assemble beyond this initiating complex. The MCP(W308A) crystal structure was solved to 2.7 Å revealing the canonical HK97 fold in a "pre-assembly" conformation featuring the conserved N-arm and E-loops folded into the body of the protein. Structural, biophysical and computational analyses suggest that MCP(W308A) is thermodynamically trapped in this pre-assembly conformation precluding self-association interactions required for shell assembly. A model is described wherein dynamic interactions between MCP proteins play an essential role in high fidelity viral shell assembly. Scaffold-chaperoned MCP polymerization is a strongly conserved process in all the large dsDNA viruses and our results provide insight into this primordial complex in solution and have broad biological significance in our understanding of virus assembly mechanisms.

Structures of a large prolate virus capsid in unexpanded and expanded states generate insights into the icosahedral virus assembly

Many icosahedral viruses assemble proteinaceous precursors called proheads or procapsids. Proheads are metastable structures that undergo a profound structural transition known as expansion that transforms an immature unexpanded head into a mature genome-packaging head. Bacteriophage T4 is a model virus, well studied genetically and biochemically, but its structure determination has been challenging because of its large size and unusually prolate-shaped, ∼1,200-Å-long and ∼860-Å-wide capsid. Here, we report the cryogenic electron microscopy (cryo-EM) structures of T4 capsid in both of its major conformational states: unexpanded at a resolution of 5.1 Å and expanded at a resolution of 3.4 Å. These are among the largest structures deposited in Protein Data Bank to date and provide insights into virus assembly, head length determination, and shell expansion. First, the structures illustrate major domain movements and ∼70% additional gain in inner capsid volume, an essential transformation to contain the entire viral genome. Second, intricate intracapsomer interactions involving a unique insertion domain dramatically change, allowing the capsid subunits to rotate and twist while the capsomers remain fastened at quasi-threefold axes. Third, high-affinity binding sites emerge for a capsid decoration protein that clamps adjacent capsomers, imparting extraordinary structural stability. Fourth, subtle conformational changes at capsomers' periphery modulate intercapsomer angles between capsomer planes that control capsid length. Finally, conformational changes were observed at the symmetry-mismatched portal vertex, which might be involved in triggering head expansion. These analyses illustrate how small changes in local capsid subunit interactions lead to profound shifts in viral capsid morphology, stability, and volume.

A Designer Nanoparticle Platform for Controlled Intracellular Delivery of Bioactive Macromolecules: Inhibition of Ubiquitin-Specific Protease 7 in Breast Cancer Cells

Biological therapeutics represent an increasing and critical component of newly approved drugs; however, the inability to deliver biologics intracellularly in a controlled manner remains a major limitation. We have developed a semi-synthetic, tunable phage-like particle (PLP) platform derived from bacteriophage λ. The shell surface can be decorated with small-molecule, biological and synthetic moieties, alone or in combination and in defined ratios. Here, we demonstrate that the platform can be used to deliver biological macromolecules intracellularly and in a controlled manner. Ubiquitin-specific protease 7 (USP7) is a deubiquitinating enzyme that has been widely recognized as an ideal target for the treatment of a variety of cancers. Recently, UbV.7.2, a novel biologic derived from the ubiquitin scaffold, was developed for inhibition of USP7, but issues remain in achieving efficient and controlled intracellular delivery of the biologic. We have shown that decoration of PLPs with trastuzumab (Trz), a HER2-targeted therapeutic used in the treatment of various cancers, results in specific targeting and uptake of Trz-PLPs into HER2-overexpressing breast cancer cells. By simultaneously decorating PLPs with Trz and UbV.7.2, we now show that these particles are also internalized by HER2-positive cells, thus providing a means for intracellular delivery of the biologic in a controlled fashion. Internalized particles retain USP7 inhibition activity of UbV.7.2 and alter the metabolic and proteomic landscapes of these cells. This study demonstrates that the λ "designer nanoparticles" represent a powerful system for the intracellular delivery of biologics in a defined dose.

Structural basis of bacteriophage lambda capsid maturation

Bacteriophage lambda is an excellent model system for studying capsid assembly of double-stranded DNA (dsDNA) bacteriophages, some dsDNA archaeal viruses, and herpesviruses. HK97 fold coat proteins initially assemble into a precursor capsid (procapsid) and subsequent genome packaging triggers morphological expansion of the shell. An auxiliary protein is required to stabilize the expanded capsid structure. To investigate the capsid maturation mechanism, we determined the cryo-electron microscopy structures of the bacteriophage lambda procapsid and mature capsid at 3.88 Å and 3.76 Å resolution, respectively. Besides primarily rigid body movements of common features of the major capsid protein gpE, large-scale structural rearrangements of other domains occur simultaneously. Assembly of intercapsomers within the procapsid is facilitated by layer-stacking effects at 3-fold vertices. Upon conformational expansion of the capsid shell, the missing top layer is fulfilled by cementing the gpD protein against the internal pressure of DNA packaging. Our structures illuminate the assembly mechanisms of dsDNA viruses.

Pseudomonas Phage MD8: Genetic Mosaicism and Challenges of Taxonomic Classification of Lambdoid Bacteriophages

Pseudomonas phage MD8 is a temperate phage isolated from the freshwater lake Baikal. The organisation of the MD8 genome resembles the genomes of lambdoid bacteriophages. However, MD8 gene and protein sequences have little in common with classified representatives of lambda-like phages. Analysis of phage genomes revealed a group of other Pseudomonas phages related to phage MD8 and the genomic layout of MD8-like phages indicated extensive gene exchange involving even the most conservative proteins and leading to a high degree of genomic mosaicism. Multiple horizontal transfers and mosaicism of the genome of MD8, related phages and other λ-like phages raise questions about the principles of taxonomic classification of the representatives of this voluminous phage group. Comparison and analysis of various bioinformatic approaches applied to λ-like phage genomes demonstrated different efficiency and contradictory results in the estimation of genomic similarity and relatedness. However, we were able to make suggestions for the possible origin of the MD8 genome and the basic principles for the taxonomic classification of lambdoid phages. The group comprising 26 MD8-related phages was proposed to classify as two close genera belonging to a big family of λ-like phages.

A Cut above the Rest: Characterization of the Assembly of a Large Viral Icosahedral Capsid

The head of Salmonella virus SPN3US is composed of ~50 different proteins and is unusual because within its packaged genome there is a mass (>40 MDa) of ejection or E proteins that enter the Salmonella cell. The assembly mechanisms of this complex structure are poorly understood. Previous studies showed that eight proteins in the mature SPN3US head had been cleaved by the prohead protease. In this study, we present the characterization of SPN3US prohead protease mutants using transmission electron microscopy and mass spectrometry. In the absence of the prohead protease, SPN3US head formation was severely impeded and proheads accumulated on the Salmonella inner membrane. This impediment is indicative of proteolysis being necessary for the release and subsequent DNA packaging of proheads in the wild-type phage. Proteomic analyses of gp245- proheads that the normal proteolytic processing of head proteins had not occurred. Assays of a recombinant, truncated form of the protease found it was active, leading us to hypothesize that the C-terminal propeptide has a role in targeting the protease into the prohead core. Our findings provide new evidence regarding the essential role of proteolysis for correct head assembly in this remarkable parasite.

Characterization and Genome Analysis of a Novel Marine Alteromonas Phage P24

Although Alteromonas is ubiquitous in the marine environment, very little is known about Alteromonas phages, with only ten, thus far, being isolated and reported on. In this study, a novel double-stranded DNA phage, Alteromonas phage P24, which infects Alteromonas macleodii, was isolated from the coastal waters off Qingdao. Alteromonas phage P24 has a siphoviral morphology, with an icosahedral head, 61 ± 1 nm in diameter, and a tail length of 105 ± 1 nm. Alteromonas phage P24 contains lipids. It has an optimal temperature and pH for growth of 20℃ and 5-7, respectively. A one-step growth curve shows a latent period of 55 min, a rise period of 65 min, and an average burst size of approximately 147 virions per cell. Alteromonas phage P24 has the genome of 46,945 bp with 43.80% GC content and 74 open reading frames (ORFs) without tRNA. The results of the phylogenetic tree, based on the mcp and terL genes, show that Alteromonas phage P24 is closely related to Aeromonas phage phiARM81ld. Meanwhile, phylogenetic analysis based on the whole genome of P24 indicates that it forms a unique viral sub-cluster within Siphoviridae. This study contributes to the understanding of the genomic characteristics and the virus-host interactions of Alteromonas phages.

Molecular Characterization and Comparative Genomic Analysis of vB_PaeP_YA3, a Novel Temperate Bacteriophage of Pseudomonas aeruginosa

It is well known that bacteriophages play crucial roles in many aspects, such as controlling the number and the diversity of bacteria and participating in horizontal gene transfer, which is a key process in the evolution of bacteria. However, so far, the number of temperate bacteriophages is still limited, and their life processes are severely unknown, except for members of the lambdoid family of coliphages. In this study, a novel temperate phage of Pseudomonas aeruginosa, YA3 (vB_PaeP_YA3), was isolated from waste water. The morphology of YA3 suggested that it is a Podoviridae. The YA3 genome is a circular double-stranded DNA of 45,253 bp, with an average G + C content of 57.2%. A total of 65 open reading frames (ORFs) were predicted according to the sequence of YA3’s genome, of which only 32 (49.2%) ORFs were assigned with putative functions and 13 ORFs were confirmed by the structural proteome. Genome and proteome analyses confirmed the lysogenic nature of this phage, which encodes the typical lysogen-related proteins integrase, CI, Cro, and Q protein. The genome of YA3 is most closely related with that of temperate phage vB_PaeP_Tr60_Ab31, whereas the homology coverage is just 48%. There are many critical differences between their genomes, involving promoters, lysis pathways, and regulation patterns. YA3 is capable of stably lysogenizing its host P. aeruginosa PA14, targeting the integration site within the serine tRNA gene (PA14_RS20820), which is similar with phage vB_PaeP_Tr60_Ab31. The phylogenetic analysis is more complicated than we thought. Based on phage terminase large subunit (TerL) and CI proteins, phage YA3 is related with phage lambda, while their genome coverage is extremely low (<1%). Therefore, phage YA3 is a considerably novel lambda-like temperate phage, and a further study of its genome may deepen our understanding of the interaction between lysogenic phages and their bacterial hosts.

Capsids and Portals Influence Each Other's Conformation During Assembly and Maturation

The portal proteins of tailed bacteriophage and Herpesvirus capsids form dodecameric rings that occupy one capsid vertex and are incorporated during the assembly of capsid precursors called procapsids or proheads. Portals are essential and serve as the pore for DNA transit and the site of tail attachment; however, bacteriophage HK97 capsid proteins assemble efficiently without a portal when expressed from plasmids. Following portal co-expression, portals were incorporated into about half of the proheads that were made. In the absence of active capsid maturation protease, uncleaved proheads formed dimers, trimers, and tetramers of proheads during purification, but only if they had portals. These appeared bound to membrane-like fragments by their portals and could be disaggregated by detergents, supporting a role for membranes in their formation and in capsid assembly. The precursors to prohead oligomers were detected in cell extracts. These were able to bind to Octyl-Sepharose and could be released by detergent, while uncleaved proheads without portal or cleaved proheads with portal did not bind. Our results document a discrete change in the HK97 portal's hydrophobicity induced by cleavage of the procapsid shell in which it is embedded. Additionally, we detected an increase in the rate of expansion induced by the presence of a portal complex in cleaved HK97 proheads. These results suggest that portals and capsids influence each other's conformation during assembly. The formation of prohead oligomers also provides a rapid and sensitive assay for identification and analysis of portal incorporation mutants.

Portal Protein: The Orchestrator of Capsid Assembly for the dsDNA Tailed Bacteriophages and Herpesviruses

Tailed, double-stranded DNA bacteriophages provide a well-characterized model system for the study of viral assembly, especially for herpesviruses and adenoviruses. A wealth of genetic, structural, and biochemical work has allowed for the development of assembly models and an understanding of the DNA packaging process. The portal complex is an essential player in all aspects of bacteriophage and herpesvirus assembly. Despite having low sequence similarity, portal structures across bacteriophages share the portal fold and maintain a conserved function. Due to their dynamic role, portal proteins are surprisingly plastic, and their conformations change for each stage of assembly. Because the maturation process is dependent on the portal protein, researchers have been working to validate this protein as a potential antiviral drug target. Here we review recent work on the role of portal complexes in capsid assembly, including DNA packaging, as well as portal ring assembly and incorporation and analysis of portal structures.

Occurrence, integrity and functionality of AcaML1-like viruses infecting extreme acidophiles of the Acidithiobacillus species complex

General knowledge on the diversity and biology of microbial viruses infecting bacterial hosts from extreme acidic environments lags behind most other econiches. In this study, we analyse the AcaML1 virus occurrence in the taxon, its genetic composition and infective behaviour under standard acidic and SOS-inducing conditions to assess its integrity and functionality. Occurrence analysis in sequenced acidithiobacilli showed that AcaML1-like proviruses are confined to the mesothermophiles Acidithiobacillus caldus and Thermithiobacillus tepidarius. Among A. caldus strains and isolates this provirus had a modest prevalence (30%). Comparative genomic analysis revealed a significant conservation with the T. tepidarius AcaML1-like provirus, excepting the tail genes, and a high conservation of the virus across strains of the A. caldus species. Such conservation extends from the modules architecture to the gene level, suggesting that organization and composition of these viruses are preserved for functional reasons. Accordingly, the AcaML1 proviruses were demonstrated to excise from their host genomes under DNA-damaging conditions triggering the SOS-response and to produce DNA-containing VLPs. Despite this fact, under the conditions evaluated (acidic) the VLPs obtained from A. caldus ATCC 51756 could not produce productive infections of a candidate sensitive strain (#6) nor trigger it lysis.

Rescue of maturation off-pathway products in the assembly of Pseudomonas phage φ 6

Many complex viruses use an assembly pathway in which their genome is packaged into an empty procapsid which subsequently matures into its final expanded form. We utilized Pseudomonas phage 6, a well-established virus assembly model, to probe the plasticity of the procapsid maturation pathway. The 6 packaging nucleoside triphosphatase (NTPase), which powers sequential translocation of the three viral genomic single-stranded RNA molecules to the procapsid during capsid maturation, is part of the mature 6 virion but may spontaneously be dissociated from the procapsid shell. We demonstrate that the dissociation of NTPase subunits results in premature capsid expansion, which is detected as a change in the sedimentation velocity and as defects in RNA packaging and transcription activity. However, this dead-end conformation of the procapsids was rescued by the addition of purified NTPase hexamers, which efficiently associated on the NTPase-deficient particles and subsequently drove their contraction to the compact naive conformation. The resulting particles regained their biological and enzymatic activities, directing them into a productive maturation pathway. These observations imply that the maturation pathways of complex viruses may contain reversible steps that allow the rescue of the off-pathway conformation in an overall unidirectional virion assembly pathway. Furthermore, we provide direct experimental evidence that particles which have different physical properties (distinct sedimentation velocities and conformations) display different stages of the genome packaging program and show that the transcriptional activity of the 6 procapsids correlates with the number of associated NTPase subunits.

Insights into bacteriophage T5 structure from analysis of its morphogenesis genes and protein components

Bacteriophage T5 represents a large family of lytic Siphoviridae infecting Gram-negative bacteria. The low-resolution structure of T5 showed the T=13 geometry of the capsid and the unusual trimeric organization of the tail tube, and the assembly pathway of the capsid was established. Although major structural proteins of T5 have been identified in these studies, most of the genes encoding the morphogenesis proteins remained to be identified. Here, we combine a proteomic analysis of T5 particles with a bioinformatic study and electron microscopic immunolocalization to assign function to the genes encoding the structural proteins, the packaging proteins, and other nonstructural components required for T5 assembly. A head maturation protease that likely accounts for the cleavage of the different capsid proteins is identified. Two other proteins involved in capsid maturation add originality to the T5 capsid assembly mechanism: the single head-to-tail joining protein, which closes the T5 capsid after DNA packaging, and the nicking endonuclease responsible for the single-strand interruptions in the T5 genome. We localize most of the tail proteins that were hitherto uncharacterized and provide a detailed description of the tail tip composition. Our findings highlight novel variations of viral assembly strategies and of virion particle architecture. They further recommend T5 for exploring phage structure and assembly and for deciphering conformational rearrangements that accompany DNA transfer from the capsid to the host cytoplasm.

Functional domains of the HK97 capsid maturation protease and the mechanisms of protein encapsidation

Tailed double-stranded DNA bacteriophages and herpesviruses build capsids by co-assembling a major capsid protein with an internal scaffolding protein that then exits from the assembled structure either intact or after digestion in situ by a protease. In bacteriophage HK97, the 102-residue N-terminal delta domain of the major capsid protein is also removed by proteolysis after assembly and appears to perform the scaffolding function. We describe the HK97 protease that carries out these maturation cleavages. Insertion mutations at seven sites in the protease gene produced mutant proteins that assemble into proheads, and those in the N-terminal two-thirds were enzymatically inactive. Plasmid-expressed protease was rapidly cleaved in vivo but was stabilized by co-expression with the delta domain. Purified protease was found to be active during the assembly of proheads in vitro. Heterologous fusions to the intact protease or to C-terminal fragments targeted fusion proteins into proheads. We confirm that the catalytic activity resides in the N-terminal two-thirds of the protease polypeptide and suggest that the C-terminal one-fifth of the protein contains a capsid targeting signal. The implications of this arrangement are compared to capsid targeting systems in other phages, herpesviruses, and encapsulins.

Unraveling the role of the C-terminal helix turn helix of the coat-binding domain of bacteriophage P22 scaffolding protein

Many viruses encode scaffolding and coat proteins that co-assemble to form procapsids, which are transient precursor structures leading to progeny virions. In bacteriophage P22, the association of scaffolding and coat proteins is mediated mainly by ionic interactions. The coat protein-binding domain of scaffolding protein is a helix turn helix structure near the C terminus with a high number of charged surface residues. Residues Arg-293 and Lys-296 are particularly important for coat protein binding. The two helices contact each other through hydrophobic side chains. In this study, substitution of the residues of the interface between the helices, and the residues in the β-turn, by aspartic acid was used examine the importance of the conformation of the domain in coat binding. These replacements strongly affected the ability of the scaffolding protein to interact with coat protein. The severity of the defect in the association of scaffolding protein to coat protein was dependent on location, with substitutions at residues in the turn and helix 2 causing the most significant effects. Substituting aspartic acid for hydrophobic interface residues dramatically perturbs the stability of the structure, but similar substitutions in the turn had much less effect on the integrity of this domain, as determined by circular dichroism. We propose that the binding of scaffolding protein to coat protein is dependent on angle of the β-turn and the orientation of the charged surface on helix 2. Surprisingly, formation of the highly complex procapsid structure depends on a relatively simple interaction.

Thermodynamic characterization of viral procapsid expansion into a functional capsid shell

The assembly of "complex" DNA viruses such as the herpesviruses and many tailed bacteriophages includes a DNA packaging step where the viral genome is inserted into a preformed procapsid shell. Packaging triggers a remarkable capsid expansion transition that results in thinning of the shell and an increase in capsid volume to accept the full-length genome. This transition is considered irreversible; however, here we demonstrate that the phage λ procapsid can be expanded with urea in vitro and that the transition is fully reversible. This provides an unprecedented opportunity to evaluate the thermodynamic features of this fascinating and essential step in virus assembly. We show that urea-triggered expansion is highly cooperative and strongly temperature dependent. Thermodynamic analysis indicates that the free energy of expansion is influenced by magnesium concentration (3-13 kcal/mol in the presence of 0.2-10 mM Mg(2+)) and that significant hydrophobic surface area is exposed in the expanded shell. Conversely, Mg(2+) drives the expanded shell back to the procapsid conformation in a highly cooperative transition that is also temperature dependent and strongly influenced by urea. We demonstrate that the gpD decoration protein adds to the urea-expanded capsid, presumably at hydrophobic patches exposed at the 3-fold axes of the expanded capsid lattice. The decorated capsid is biologically active and sponsors packaging of the viral genome in vitro. The roles of divalent metal and hydrophobic interactions in controlling packaging-triggered expansion of the procapsid shell are discussed in relation to a general mechanism for DNA-triggered procapsid expansion in the complex double-stranded DNA viruses.

Virus maturation

We examine virus maturation of selected nonenveloped and enveloped single-stranded RNA viruses, retroviruses, bacteriophages, and herpesviruses. Processes associated with maturation in the RNA viruses range from subtle (nodaviruses and picornaviruses) to dramatic (tetraviruses and togaviruses). The elaborate assembly and maturation pathway of HIV is discussed in contrast to the less sophisticated but highly efficient processes associated with togaviruses. Bacteriophage assembly and maturation are discussed in general terms, with specific examples chosen for emphasis. Finally the herpesviruses are compared with bacteriophages. The data support divergent evolution of nodaviruses, picornaviruses, and tetraviruses from a common ancestor and divergent evolution of alphaviruses and flaviviruses from a common ancestor. Likewise, bacteriophages and herpesviruses almost certainly share a common ancestor in their evolution. Comparing all the viruses, we conclude that maturation is a convergent process that is required to solve conflicting requirements in biological dynamics and function.

Phage λ--new insights into regulatory circuits

Bacteriophage λ, rediscovered in the early 1950s, has served as a model in molecular biology studies for decades. Although currently more complex organisms and more complicated biological systems can be studied, this phage is still an excellent model to investigate principles of biological processes occurring at the molecular level. In fact, very few other biological models provide possibilities to examine regulations of biological mechanisms as detailed as performed with λ. In this chapter, recent advances in our understanding of mechanisms of bacteriophage λ development are summarized and discussed. Particularly, studies on (i) phage DNA injection, (ii) molecular bases of the lysis-versus-lysogenization decision and the lysogenization process itself, (iii) prophage maintenance and induction, (iv), λ DNA replication, (v) phage-encoded recombination systems, (vi) transcription antitermination, (vii) formation of the virion structure, and (viii) lysis of the host cell, as published during several past years, will be presented.

Bacteriophage protein-protein interactions

Bacteriophages T7, λ, P22, and P2/P4 (from Escherichia coli), as well as ϕ29 (from Bacillus subtilis), are among the best-studied bacterial viruses. This chapter summarizes published protein interaction data of intraviral protein interactions, as well as known phage-host protein interactions of these phages retrieved from the literature. We also review the published results of comprehensive protein interaction analyses of Pneumococcus phages Dp-1 and Cp-1, as well as coliphages λ and T7. For example, the ≈55 proteins encoded by the T7 genome are connected by ≈43 interactions with another ≈15 between the phage and its host. The chapter compiles published interactions for the well-studied phages λ (33 intra-phage/22 phage-host), P22 (38/9), P2/P4 (14/3), and ϕ29 (20/2). We discuss whether different interaction patterns reflect different phage lifestyles or whether they may be artifacts of sampling. Phages that infect the same host can interact with different host target proteins, as exemplified by E. coli phage λ and T7. Despite decades of intensive investigation, only a fraction of these phage interactomes are known. Technical limitations and a lack of depth in many studies explain the gaps in our knowledge. Strategies to complete current interactome maps are described. Although limited space precludes detailed overviews of phage molecular biology, this compilation will allow future studies to put interaction data into the context of phage biology.

The bacteriophage lambda gpNu3 scaffolding protein is an intrinsically disordered and biologically functional procapsid assembly catalyst

Procapsid assembly is a process whereby hundreds of copies of a major capsid protein assemble into an icosahedral protein shell into which the viral genome is packaged. The essential features of procapsid assembly are conserved in both eukaryotic and prokaryotic complex double-stranded DNA viruses. Typically, a portal protein nucleates the co-polymerization of an internal scaffolding protein and the major capsid protein into an icosahedral capsid shell. The scaffolding proteins are essential to procapsid assembly. Here, we describe the solution-based biophysical and functional characterization of the bacteriophage lambda (λ) scaffolding protein gpNu3. The purified protein possesses significant α-helical structure and appears to be partially disordered. Thermally induced denaturation studies indicate that secondary structures are lost in a cooperative, apparent two-state transition (T(m)=40.6±0.3 °C) and that unfolding is, at least in part, reversible. Analysis of the purified protein by size-exclusion chromatography suggests that gpNu3 is highly asymmetric, which contributes to an abnormally large Stokes radius. The size-exclusion chromatography data further indicate that the protein self-associates in a concentration-dependent manner. This was confirmed by analytical ultracentrifugation studies, which reveal a monomer-dimer equilibrium (K(d,app)~50 μM) and an asymmetric protein structure at biologically relevant concentrations. Purified gpNu3 promotes the polymerization of gpE, the λ major capsid protein, into virus-like particles that possess a native-like procapsid morphology. The relevance of this work with respect to procapsid assembly in the complex double-stranded DNA viruses is discussed.

The protein interaction map of bacteriophage lambda

Background

Bacteriophage lambda is a model phage for most other dsDNA phages and has been studied for over 60 years. Although it is probably the best-characterized phage there are still about 20 poorly understood open reading frames in its 48-kb genome. For a complete understanding we need to know all interactions among its proteins. We have manually curated the lambda literature and compiled a total of 33 interactions that have been found among lambda proteins. We set out to find out how many protein-protein interactions remain to be found in this phage.

Results

In order to map lambda's interactions, we have cloned 68 out of 73 lambda open reading frames (the "ORFeome") into Gateway vectors and systematically tested all proteins for interactions using exhaustive array-based yeast two-hybrid screens. These screens identified 97 interactions. We found 16 out of 30 previously published interactions (53%). We have also found at least 18 new plausible interactions among functionally related proteins. All previously found and new interactions are combined into structural and network models of phage lambda.

Conclusions

Phage lambda serves as a benchmark for future studies of protein interactions among phage, viruses in general, or large protein assemblies. We conclude that we could not find all the known interactions because they require chaperones, post-translational modifications, or multiple proteins for their interactions. The lambda protein network connects 12 proteins of unknown function with well characterized proteins, which should shed light on the functional associations of these uncharacterized proteins.

Bacteriophage assembly

Bacteriophages have been a model system to study assembly processes for over half a century. Formation of infectious phage particles involves specific protein-protein and protein-nucleic acid interactions, as well as large conformational changes of assembly precursors. The sequence and molecular mechanisms of phage assembly have been elucidated by a variety of methods. Differences and similarities of assembly processes in several different groups of bacteriophages are discussed in this review. The general principles of phage assembly are applicable to many macromolecular complexes.