Molecular Piracy: Redirection of Bacteriophage Capsid Assembly by Mobile Genetic Elements

Horizontal transfer of mobile genetic elements (MGEs) is a key aspect of the evolution of bacterial pathogens. Transduction by bacteriophages is especially important in this process. Bacteriophages—which assemble a machinery for efficient encapsidation and transfer of genetic material—often transfer MGEs and other chromosomal DNA in a more-or-less nonspecific low-frequency process known as generalized transduction. However, some MGEs have evolved highly specific mechanisms to take advantage of bacteriophages for their own propagation and high-frequency transfer while strongly interfering with phage production—“molecular piracy”. These mechanisms include the ability to sense the presence of a phage entering lytic growth, specific recognition and packaging of MGE genomes into phage capsids, and the redirection of the phage assembly pathway to form capsids with a size more appropriate for the size of the MGE. This review focuses on the process of assembly redirection, which has evolved convergently in many different MGEs from across the bacterial universe. The diverse mechanisms that exist suggest that size redirection is an evolutionarily advantageous strategy for many MGEs.

Molecular investigation of two novel bacteriophages of a facultative methylotroph, Raoultella ornithinolytica: first report of Raoultella phages

Bacteria of the genus Raoultella are known to inhabit aquatic environments and can be found in medical samples. The pathogenicity of Raoultella ornithinolytica isolates in human has become increasingly important, and several cases of infections have been reported recently. However, there are no reports of isolation of bacteriophages infecting this bacterium. In this study, two novel phages (ISF3 and ISF6) of a methylotrophic Raoultella strain were isolated from sewage. To characterize the isolated phages, morphological features, protein profiles, restriction digestion patterns, and partial genome sequences were studied. Despite morphological differences, electron microscopy revealed that both phages had an icosahedral capsid connected to a contractile tail, suggesting that ISF3 and ISF6 both belong to the family Myoviridae. Partial nucleotide sequences of the ISF3 genome showed 99% to 100% identity to DNA of Klebsiella pneumonia phages KP15, KP27 and BMBT1; however, the restriction digestion profiles of ISF3 genome digested by EcoRI and EcoRV differed from those of Klebsiella phages KP15 and KP27. A partial sequence alignment showed that ISF6 can be classified as a member of a new viral genus due to its significant differences from other previously identified phages. To the best of our knowledge, this is the first report of the isolation and characterization of the specific Raoultella phages that have potential to be used as new pharmaceuticals against R. ornithinolytica.

Encapsulation of Negatively Charged Cargo in MS2 Viral Capsids

Encapsulation into virus-like particles is an efficient way of loading cargo of interest for delivery applications. Here, we describe the encapsulation of proteins with tags comprising anionic amino acids or DNA and gold nanoparticles with negative surface charges inside MS2 bacteriophage capsids to obtain homogeneous nanoparticles with a diameter of 27 nm.

A novel scalable, robust downstream process for oncolytic rat parvovirus: isoelectric point-based elimination of empty particles

The rodent protoparvovirus H-1PV, with its oncolytic and oncosuppressive properties, is a promising anticancer agent currently under testing in clinical trials. This explains the current demand for a scalable, good manufacturing practice-compatible virus purification process yielding high-grade pure infectious particles and overcoming the limitations of the current system based on density gradient centrifugation. We describe here a scalable process offering high purity and recovery. Taking advantage of the isoelectric point difference between full and empty particles, it eliminates most empty particles. Full particles have a significantly higher cationic charge than empty ones, with an isoelectric point of 5.8–6.2 versus 6.3 (as determined by isoelectric focusing and chromatofocusing). Thanks to this difference, infectious full particles can be separated from empty particles and most protein impurities by Convective interaction media^® diethylaminoethyl (DEAE) anion exchange chromatography: applying unpurified H-1PV to the column in 0.15 M NaCl leaves, the former on the column and the latter in the flow through. The full particles are then recovered by elution with 0.25 M NaCl. The whole large-scale purification process involves filtration, single-step DEAE anion exchange chromatography, buffer exchange by cross-flow filtration, and final formulation in Visipaque/Ringer solution. It results in 98% contaminating protein removal and 96% empty particle elimination. The final infectious particle concentration reaches 3.5E10 plaque forming units (PFU)/ml, with a specific activity of 6.8E11 PFU/mg protein. Overall recovery is over 40%. The newly established method is suitable for use in commercial production.

Genetic Diversity in the Major Capsid L1 Protein of HPV-16 and HPV-18 in the Netherlands

Objectives

Intratypic molecular variants of human papillomavirus (HPV) type-16 and -18 exist. In the Netherlands, a bivalent vaccine, composed of recombinant L1 proteins from HPV-16 and -18, is used to prevent cervical cancer since 2009. Long-term vaccination could lead to changes in HPV-16 and -18 virus population, thereby hampering vaccination strategies. We determined the genetic diversity of the L1 gene in HPV-16 and -18 viral strains circulating in the Netherlands at the start of vaccination in order to understand the baseline genetic diversity in the Dutch population.

Methods

DNA sequences of the L1 gene were determined in HPV-16 (n = 241) and HPV-18 (n = 108) positive anogenital samples collected in 2009 and 2011 among Dutch 16- to 24-year old female and male attendees of the sexually transmitted infection (STI) clinics. Phylogenetic analysis was performed and sequences were compared to reference sequences HPV-16 (AF536179) and HPV-18 (X05015) using BioNumerics 7.1.

Results

For HPV-16, ninety-five single nucleotide polymorphism (SNPs) were identified, twenty–seven (28%) were non-synonymous variations. For HPV-18, seventy-one SNPs were identified, twenty-nine (41%) were non-synonymous. The majority of the non-silent variations were located in sequences encoding alpha helix, beta sheet or surface loops, in particular in the immunodominant FG loop, and may influence the protein secondary structure and immune recognition.

Conclusions

This study provides unique pre-vaccination/baseline data on the genetic L1 diversity of HPV-16 and -18 viruses circulating in the Netherlands among adolescents and young adults.

The Mammalian Cell Cycle Regulates Parvovirus Nuclear Capsid Assembly

It is unknown whether the mammalian cell cycle could impact the assembly of viruses maturing in the nucleus. We addressed this question using MVM, a reference member of the icosahedral ssDNA nuclear parvoviruses, which requires cell proliferation to infect by mechanisms partly understood. Constitutively expressed MVM capsid subunits (VPs) accumulated in the cytoplasm of mouse and human fibroblasts synchronized at G0, G1, and G1/S transition. Upon arrest release, VPs translocated to the nucleus as cells entered S phase, at efficiencies relying on cell origin and arrest method, and immediately assembled into capsids. In synchronously infected cells, the consecutive virus life cycle steps (gene expression, proteins nuclear translocation, capsid assembly, genome replication and encapsidation) proceeded tightly coupled to cell cycle progression from G0/G1 through S into G2 phase. However, a DNA synthesis stress caused by thymidine irreversibly disrupted virus life cycle, as VPs became increasingly retained in the cytoplasm hours post-stress, forming empty capsids in mouse fibroblasts, thereby impairing encapsidation of the nuclear viral DNA replicative intermediates. Synchronously infected cells subjected to density-arrest signals while traversing early S phase also blocked VPs transport, resulting in a similar misplaced cytoplasmic capsid assembly in mouse fibroblasts. In contrast, thymidine and density arrest signals deregulating virus assembly neither perturbed nuclear translocation of the NS1 protein nor viral genome replication occurring under S/G2 cycle arrest. An underlying mechanism of cell cycle control was identified in the nuclear translocation of phosphorylated VPs trimeric assembly intermediates, which accessed a non-conserved route distinct from the importin α2/β1 and transportin pathways. The exquisite cell cycle-dependence of parvovirus nuclear capsid assembly conforms a novel paradigm of time and functional coupling between cellular and virus life cycles. This junction may determine the characteristic parvovirus tropism for proliferative and cancer cells, and its disturbance could critically contribute to persistence in host tissues.

Cellular and viral life cycles are connected through multiple, though poorly understood, mechanisms. Parvoviruses infect humans and a broad spectrum of animals, causing a variety of diseases, but they are also used in experimental cancer therapy and serve as vectors for gene therapy. Parvoviruses can only multiply in proliferating cells providing essential replicative and transcriptional functions. However, it is unknown whether the cell cycle regulatory machinery may also control parvovirus assembly. We found that the nuclear translocation of parvovirus MVM capsid subunits (VPs) was highly dependent on physiological cell cycle regulations in mammalian fibroblasts, including: quiescence, progression through G1/S boundary, DNA synthesis, and cell to cell contacts. VPs nuclear translocation was significantly more sensitive to cell cycle controls than viral genome replication and gene expression. The results support nuclear capsid assembly as the major driving process of parvoviruses biological hallmarks, such as pathogenesis in proliferative tissues and tropism for cancer cells. In addition, disturbing the tight coupling of parvovirus assembly with the cell cycle may determine viral persistence in quiescent and post-mitotic host tissues. These findings may contribute to understand cellular regulations on the assembly of other nuclear eukaryotic viruses, and to develop cell cycle-based avenues for antiviral therapy.

Sequence analysis of the capsid gene during a genotype II.4 dominated norovirus season in one university hospital: identification of possible transmission routes

Norovirus (NoV) is a leading cause of gastroenteritis and genotype II.4 (GII.4) is responsible for the majority of nosocomial NoV infections. Our objective was to examine whether sequencing of the capsid gene might be a useful tool for the hospital outbreak investigation to define possible transmission routes. All NoV positive samples submitted from one university hospital during the 2007/8 season were selected. Genotyping of selected samples by partial polymerase gene sequencing had shown that the majority belonged to the GII.4 variant Den Haag 2006b and had identical polymerase sequences. Sequences of the capsid gene (1412 nucleotides) were obtained from the first available sample from 55 patients. From six immunocompromised patients with persistent infections a second sample was also included. As a control for a point-source outbreak, five samples from a foodborne outbreak caused by the same GII.4 variant were analyzed. Forty-seven of the inpatients (85%) were infected with the GII.4 variant Den Haag 2006b. Phylogenetic analysis of the Den Haag 2006b sequences identified four distinct outbreaks in different departments and a fifth outbreak with possible inter-department spread. In addition, a more heterogeneous cluster with evidence of repeated introductions from the community, but also possible inter-department spread was observed. In all six patients with paired sequences, evidence for in vivo evolution of the virus was found. Capsid gene sequencing showed substantial sequence variation among NoV GII.4 variant Den Haag 2006b strains from one single institution during a nine months' period. This method proved useful to understand the local epidemiology and, when used promptly, has the potential to make infection control measures more targeted.

RNA-binding region of Macrobrachium rosenbergii nodavirus capsid protein

White tail disease (WTD) kills prawn larvae and causes drastic losses to the freshwater prawn (Macrobrachium rosenbergii) industry. The main causative agent of WTD is Macrobrachium rosenbergii nodavirus (MrNV). The N-terminal end of the MrNV capsid protein is very rich in positively charged amino acids and is postulated to interact with RNA molecules. N-terminal and internal deletion mutagenesis revealed that the RNA-binding region is located at positions 20-29, where 80 % of amino acids are positively charged. Substitution of all these positively charged residues with alanine abolished the RNA binding. Mutants without the RNA-binding region still assembled into virus-like particles, suggesting that this region is not a part of the capsid assembly domain. This paper is, to the best of our knowledge, the first to report the specific RNA-binding region of MrNV capsid protein.

Effect of temperature and capsid tail on the packing and ejection of viral DNA

We use a simulation technique based on molecular dynamics and stochastic rotation model to present the effect of temperature and capsid tail on the packaging and ejection processes of semiflexible polymers. We consider two types of solvents, a good solvent, where the polymer is neutral and repulsion interactions among its various sections are favored, and one where the polymer is charged, giving rise to extra electrostatic reaction. For tailless capsids, we find that packing a neutral polymer is slightly slower at higher temperatures whereas its ejection is slightly slower at lower temperatures. We find the same trend for a charged polymer but the effect is noticeably larger. At a high enough temperature, we notice that packing a charged polymer can be stopped. On the other hand, at fixed temperature and regardless whether the polymer is charged, packing is much easier for a capsid with a tail whereas ejection is much slower. The effect of including the tail on the dynamics of a charged polymer, in particular, is rather significant: more packing fraction is facilitated at higher temperatures due to more ordered polymer configuration inside the capsid. In contrast, during ejection the tail traps the last remaining beads for quite some time before allowing full ejection. We interpret these results in terms of entropic and electrostatic forces.

Absence of porcine circovirus type 1 (PCV1) and high prevalence of PCV 2 exposure and infection in swine finisher herds

Porcine circovirus (PCV) appeared in 1974 as an unidentified, innocuous viral inhabitant of cell cultures and pigs. Today PCV1 is a contaminant of some human vaccines, and PCV2 is a major pathogen of swine. PCV1 is reportedly ubiquitous in swine but nonpathogenic. Since the interplay of PCV1 and PCV2 in swine might explain variable disease results and shed light on the potential for human exposure, we analyzed in depth the prevalence of PCV1 and PCV2 infection and exposure in the U.S. finishing swine herd. Over 82% of sera from 185 farms were positive for PCV2 by PCR, whereas only 2.4% were positive for PCV1. More than 80% of PCV2 DNA-positive swine were also positive for anti-PCV2 antibodies. PCV1 was only rarely present. Exposure of swine, and therefore humans via pigs, to PCV1 is negligible. We conclude that PCV2 causes a persistent infection in pigs and that PCV1 is absent or rare in swine.

RNA encapsidation assay

Analysis of viral RNA encapsidation assay provides a rapid means of assaying which of the progeny RNA are competent for packaging into stable mature virions. Generally, a parallel analysis of total RNA and RNA obtained from purified virions is advisable for accurate interpretation of the results. In this, we describe a series of in vivo assays in which viral RNA encapsidation can be verified. These include whole plants inoculated either mechanically or by Agroinfiltration and protoplasts. The encapsidation assay described here is for an extensively studied plant RNA virus, brome mosaic virus, and can be reliably applied to other viral systems as well as with appropriate buffers. In principle, the encapsidation assay requires purification of virions from either symptomatic leaves or transfected plant protoplasts followed by RNA isolation. The procedure involves grinding the infected tissue in an appropriate buffer followed by a low speed centrifugation step to remove the cell debris. The supernatant is then emulsified with an organic solvent such as chloroform to remove chlorophyll and cellular material. After a low seed centrifugation, the supernatant is subjected to high speed centrifugation to concentrate the virus as a pellet. Depending on the purity required, the partially purified virus preparation is further subjected to sucrose density gradient centrifugation. Following purification of virions, encapsidated RNA is isolated using standard phenol-chloroform extraction procedure. An important step in the encapsidation assay is the comparative analysis of total and virion RNA preparations by Northern hybridization. This would allow the investigator to compare the number of progeny RNA components synthesized during replication vs. encapsidation. Northern blots are normally hybridized with radioactively labeled RNA probes (riboprobes) for specific and sensitive detection of desired RNA species.

Symmetry types, systems and their multiplicity in the structure of adenovirus capsid. II. Rotational facet groups of five-, three- and two-fold symmetry axes

The icosahedral adenovirus capsid has three rotational symmetry axes of different types. The six five-fold, ten three-fold and the fifteen two-fold axes have two superficial points each, altogether 62. The axes determine the number and location of the identical rotational facet groups and that during the different rotational phases which other regular facets and with what multiplicity shall be covered by them. The number of rotational facets of the five-, three- and two-fold rotational symmetry axes is 4, 6.66 and 10, respectively. In all the three cases, there are two kinds of possible arrangements of the facets. During the rotation--when the facets of the facet group placed on one by one to the neighbouring identical facet groups--at the five-fold axes, the facets of the rotational facet group get into cover position 12 times with all the 20 regular capsid facets, 20 times at the three-fold axes, and 30 times at the two-fold axes in a way that a different facet combination (facet hit) falls to every facet, and the original symmetry is not disturbed. After all, this means 240, 400 and 600 facet combinations, i.e. multiplicity in case of five-, three- and two-fold symmetry axes respectively, and these numbers correspond with that of the theoretically possible variations. The same results can be calculated by multiplying the number of real rotations of the capsid bringing the body into itself, i.e. the number 60 with the number of facets contributing to the five-, three- and two-fold rotational phases. The other way of the determination of multiplicity takes into account that all the facet groups of the capsid rotate simultaneously during all the rotational phases, and this multiplies the number of multiplicity with the number of the rotational types five-, three- and two-fold which result in one and the same multiplicity number in the case of five-, three- and two-fold symmetry, alike 1200. Perpendicular to the five-fold symmetry axes with the line of intersection drawn horizontally in the middle along the 6 geodetic ribbon like motifs a regular decagonal intersection forms and the capsid can be cut into two equal parts, in which the polypeptides show a 72 degree rotation from each other, but with a proper rotation the polypeptides get into a congruent position, which means 300 or 600 specific facet combinations. The capsid similar to the icosahedron has also 15 virtual mirror planes which divide the capsid into two, identically arranged halves, forming six right angle triangles on each facet, altogether 120 smaller rectangular so-called Mobius-triangles on the surface. In the three-fold symmetry axis of the facets, these triangles in two separate groups of three can be rotated symmetrically with 120 degrees according to the orientation of the polypeptide subunits in a way that the hexon and other polypeptides too nearly cover each other. Consequently, the adenovirus capsid is a symmetrically arranged body in which several various symmetry types and symmetry systems can be found and their structural symmetry elements exist simultaneously and covering each other. The icosahedral symmetry types and systems are valid and functional simultaneously and in parallel with great multiplicity, but the existence of more than 1500 structural elements in several depth levels, their order of location and distribution make the symmetry of the capsid richer and more complex.

Herpes simplex virus type 1 accumulation, envelopment, and exit in growth cones and varicosities in mid-distal regions of axons

The mechanism of anterograde transport of alphaherpesviruses in axons remains controversial. This study examined the transport, assembly, and egress of herpes simplex virus type 1 (HSV-1) in mid- and distal axons of infected explanted human fetal dorsal root ganglia using confocal microscopy and transmission electron microscopy (TEM) at 19, 24, and 48 h postinfection (p.i.). Confocal-microscopy studies showed that although capsid (VP5) and tegument (UL37) proteins were not uniformly present in axons until 24 h p.i., they colocalized with envelope (gG) proteins in axonal varicosities and in growth cones at 24 and 48 h p.i. TEM of longitudinal sections of axons in situ showed enveloped and unenveloped capsids in the axonal varicosities and growth cones, whereas in the midregion of the axons, predominantly unenveloped capsids were observed. Partially enveloped capsids, apparently budding into vesicles, were observed in axonal varicosities and growth cones, but not during viral attachment and entry into axons. Tegument proteins (VP22) were found associated with vesicles in growth cones, either alone or together with envelope (gD) proteins, by transmission immunoelectron microscopy. Extracellular virions were observed adjacent to axonal varicosities and growth cones, with some virions observed in crescent-shaped invaginations of the axonal plasma membrane, suggesting exit at these sites. These findings suggest that varicosities and growth cones are probable sites of HSV-1 envelopment of at least a proportion of virions in the mid- to distal axon. Envelopment probably occurs by budding of capsids into vesicles with associated tegument and envelope proteins. Virions appear to exit from these sites by exocytosis.

Cooperative contribution of gag substitutions to nelfinavir-dependent enhancement of precursor cleavage and replication of human immunodeficiency virus type-1

We previously described a clinical human immunodeficiency virus type-1 (HIV-1) isolate, CL-4, which showed nelfinavir (NFV)-dependent enhancement of replication (Matsuoka-Aizawa, S., Sato, H., Hachiya, A., Tsuchiya, K., Takebe, Y., Gatanaga, H., Kimura, S., Oka, S, 2003. Isolation and molecular characterization of a nelfinavir (NFV)-resistant human immunodeficiency virus type 1 that exhibits NFV-dependent enhancement of replication. J. Virol. 77, 318-327.). To identify the responsible region(s) of HIV-1 proteins for such replication enhancement, we constructed a panel of recombinant HIV-1 clones harboring portions of the Gag and protease of CL-4 and analyzed their replication capabilities and Gag processing patterns. Our data suggested that the substitutions in the matrix and N-terminal half of capsid of CL-4 were indispensable for the NFV-dependent enhancement of replication and that NFV facilitated the cleavage between the matrix and capsid of the Gag precursor harboring these substitutions. The substitutions in C-terminal half of capsid rather decreased the cleavability of Gag precursor and NFV counteracted such negative impact. Efficient replication enhancement with NFV can be observed only in the presence of the substitutions in entire Gag and protease of CL-4.

Species-specific exclusion of APOBEC3G from HIV-1 virions by Vif

The HIV-1 accessory protein Vif (virion infectivity factor) is required for the production of infectious virions by CD4(+) lymphocytes. Vif facilitates particle infectivity by blocking the inhibitory activity of APOBEC3G (CEM15), a virion-encapsidated cellular protein that deaminates minus-strand reverse transcript cytosines to uracils. We report that HIV-1 Vif forms a complex with human APOBEC3G that prevents its virion encapsidation. HIV-1 Vif did not efficiently form a complex with mouse APOBEC3G. Vif dramatically reduced the amount of human APOBEC3G encapsidated in HIV-1 virions but did not prevent encapsidation of mouse or AGM APOBEC3G. As a result, these enzymes are potent inhibitors of wild-type HIV-1 replication. The species-specificity of this interaction may play a role in restricting HIV-1 infection to humans. Together these findings suggest that therapeutic intervention that either induced APOBEC3G or blocked its interaction with Vif could be clinically beneficial.

Preliminary approach to find synthetic peptides from nodavirus capsid potentially protective against sea bass viral encephalopathy and retinopathy

Four synthetic peptides of 15 amino acids (aa), corresponding to sequences of the nodavirus DIEV RNA(2) protein, were chosen to test their potential immunogenicity in sea bass. Two of these included the N or C terminal regions (N-ter or C-ter) and the sequences of the others contained a potential external site (aa 127-140: Lp1 and as 266-279: Lp2). Two heat inactivated strains of nodavirus (HI Sb1 and HI Sb2), were used as positive controls and the carrier (KLH) as a negative control. ELISAs were performed to quantify serum antibodies specific to nodavirus, to peptides, and to the carrier in order to monitor their immunogenicity. All the fish reacted to the peptides C-Ter, Lp1 and Lp2 but only 55% of animals injected with N-ter produced specific antibodies. The proportion of fish that produced antibodies that cross reacted with nodavirus was very different with regard to the antigen injected: HI Sb1=88%; HI Sb2=85%; N-ter=38%; C-ter=27%. Protection against nodavirus was investigated by challenging the fish with a virulent viral suspension. The results showed that heat-inactivated Nodavirus protect fish and the N-ter peptide is a potential protective peptide. This initial approach showed that although vaccinating fish with peptides is possible, the tools and strategies of the research used in this field still need to be adapted to fish.

Epidemiology of Norwalk-like virus infections in cattle in The Netherlands

"Norwalk-like viruses" (NLVs) are the most common cause of acute non-bacterial gastroenteritis in humans. Cattle may be a reservoir of NLVs although never bovine NLVs have been found in humans. To gain more insight into the epidemiology of NLV, infections in cattle in The Netherlands were studied. Individual faecal samples from a large dairy herd and 243 pooled samples from veal calf farms were analysed for NLV by RT-PCR. Calves under 3 months of age in the dairy herd were sampled three to five times with 3-week intervals, whereas dairy cattle were sampled twice with a 2-month interval. In 31.6% (77/243) of the veal calf farm samples and in 4.2% (13/312) of the individual dairy cattle samples NLV was detected. The mean age of virus positive dairy cattle was 2.5 months. The highest numbers of NLV positive veal calf farms in The Netherlands were found in the regions with the highest number of veal calf farms. NLV infected veal calf farms were detected in every month throughout the study period. Cattle appeared to be hosts of NLVs, and virus shedding was weakly associated with diarrhoea. Complete ORF2 sequences were obtained from two calf NLVs and phylogenetic analyses suggested that these strains belong to a distinct cluster (GGIII/2) in between GGI and GGII NLVs of humans. Overall, genetic variation between strains as determined by sequence analysis of the P1/P2 capsid region was limited to 14.6%. Our data shows that NLV is endemic in the cattle population in The Netherlands and genetically distinct from NLVs in humans.