Digestion pattern of reovirus outer capsid protein sigma3 determined by mass spectrometry

Reovirus genomic diversity confers plasticity for protease utility during adaptation to intracellular uncoating

IMPORTANCE

Reoviruses infect many mammals and are widely studied as a model system for enteric viruses. However, most of our reovirus knowledge comes from laboratory strains maintained on immortalized L929 cells. Herein, we asked whether naturally circulating reoviruses possess the same genetic and phenotypic characteristics as laboratory strains. Naturally circulating reoviruses obtained from sewage were extremely diverse genetically. Moreover, sewage reoviruses exhibited poor fitness on L929 cells and relied heavily on gut proteases for viral uncoating and productive infection compared to laboratory strains. We then examined how naturally circulating reoviruses might adapt to cell culture conditions. Within three passages, virus isolates from the parental sewage population were selected, displaying improved fitness and intracellular uncoating in L929 cells. Remarkably, selected progeny clones were present at 0.01% of the parental population. Altogether, using reovirus as a model, our study demonstrates how the high genetic diversity of naturally circulating viruses results in rapid adaptation to new environments.

A Single Point Mutation, Asn16→Lys, Dictates the Temperature-Sensitivity of the Reovirus tsG453 Mutant

Studies of conditionally lethal mutants can help delineate the structure-function relationships of biomolecules. Temperature-sensitive (ts) mammalian reovirus (MRV) mutants were isolated and characterized many years ago. Two of the most well-defined MRV ts mutants are tsC447, which contains mutations in the S2 gene encoding viral core protein σ2, and tsG453, which contains mutations in the S4 gene encoding major outer-capsid protein σ3. Because many MRV ts mutants, including both tsC447 and tsG453, encode multiple amino acid substitutions, the specific amino acid substitutions responsible for the ts phenotype are unknown. We used reverse genetics to recover recombinant reoviruses containing the single amino acid polymorphisms present in ts mutants tsC447 and tsG453 and assessed the recombinant viruses for temperature-sensitivity by efficiency-of-plating assays. Of the three amino acid substitutions in the tsG453 S4 gene, Asn₁₆-Lys was solely responsible for the tsG453ts phenotype. Additionally, the mutant tsC447 Ala₁₈₈-Val mutation did not induce a temperature-sensitive phenotype. This study is the first to employ reverse genetics to identify the dominant amino acid substitutions responsible for the tsC447 and tsG453 mutations and relate these substitutions to respective phenotypes. Further studies of other MRV ts mutants are warranted to define the sequence polymorphisms responsible for temperature sensitivity.

Single Amino Acid Differences between Closely Related Reovirus T3D Lab Strains Alter Oncolytic Potency In Vitro and In Vivo

Little is known about how genetic variations in viruses affect their success as therapeutic agents. The type 3 Dearing strain of Mammalian orthoreovirus (T3D) is undergoing clinical trials as an oncolytic virotherapy. Worldwide, studies on reovirus oncolysis use T3D stocks propagated in different laboratories. Here, we report that genetic diversification among T3D stocks from various sources extensively impacts oncolytic activity. The T3D strain from the Patrick Lee laboratory strain (TD3^PL) showed significantly stronger oncolytic activities in a murine model of melanoma than the strain from the Terence Dermody laboratory (T3D^TD). Overall in vitro replication and cytolytic properties of T3D laboratory strains were assessed by measuring virus plaque size on a panel of human and mouse tumor cells, and results were found to correlate with in vivo oncolytic potency in a melanoma model. T3D^PL produced larger plaques than T3D^TD and than the T3D strain from the ATCC (T3D^ATCC) and from the Kevin Coombs laboratory (T3D^KC). Reassortant and reverse genetics analyses were used to decipher key genes and polymorphisms that govern enhanced plaque size of T3D^PL Five single amino acid changes in the S4, M1, and L3 genome segments of reovirus were each partially correlated with plaque size and when combined were able to fully account for differences between T3D^PL and T3D^TD Moreover, polymorphisms were discovered in T3D^TD that promoted virus replication and spread in tumors, and a new T3D^PL/T3D^TD hybrid was generated with enhanced plaque size compared to that of T3D^PL Altogether, single amino acid changes acquired during laboratory virus propagation can have a large impact on reovirus therapeutic potency and warrant consideration as possible confounding variables between studies.IMPORTANCE The reovirus serotype 3 Dearing (T3D) strain is in clinical trials for cancer therapy. We find that closely related laboratory strains of T3D exhibit large differences in their abilities to replicate in cancer cells in vitro, which correlates with oncolytic activity in a in a murine model of melanoma. The study reveals that five single amino acid changes among three reovirus genes strongly impact reovirus therapeutic potency. In general, the findings suggest that attention should be given to genomic divergence of virus strains during research and optimization for cancer therapy.

Polymorphisms in the Most Oncolytic Reovirus Strain Confer Enhanced Cell Attachment, Transcription, and Single-Step Replication Kinetics

Reovirus serotype 3 Dearing (T3D) replicates preferentially in transformed cells and is in clinical trials as a cancer therapy. Laboratory strains of T3D, however, exhibit differences in plaque size on cancer cells and differences in oncolytic activity in vivo This study aimed to determine why the most oncolytic T3D reovirus lab strain, the Patrick Lee laboratory strain (T3D^PL), replicates more efficiently in cancer cells than other commonly used laboratory strains, the Kevin Coombs laboratory strain (T3D^KC) and Terence Dermody laboratory (T3D^TD) strain. In single-step growth curves, T3D^PL titers increased at higher rates and produced ∼9-fold higher burst size. Furthermore, the number of reovirus antigen-positive cells increased more rapidly for T3D^PL than for T3D^TD In conclusion, the most oncolytic T3D^PL possesses replication advantages in a single round of infection. Two specific mechanisms for enhanced infection by T3D^PL were identified. First, T3D^PL exhibited higher cell attachment, which was attributed to a higher proportion of virus particles with insufficient (≤3) σ1 cell attachment proteins. Second, T3D^PL transcribed RNA at rates superior to those of the less oncolytic T3D strains, which is attributed to polymorphisms in M1-encoding μ2 protein, as confirmed in an in vitro transcription assay, and which thus demonstrates that T3D^PL has an inherent transcription advantage that is cell type independent. Accordingly, T3D^PL established rapid onset of viral RNA and protein synthesis, leading to more rapid kinetics of progeny virus production, larger virus burst size, and higher levels of cell death. Together, these results emphasize the importance of paying close attention to genomic divergence between virus laboratory strains and, mechanistically, reveal the importance of the rapid onset of infection for reovirus oncolysis.IMPORTANCE Reovirus serotype 3 Dearing (T3D) is in clinical trials for cancer therapy. Recently, it was discovered that highly related laboratory strains of T3D exhibit large differences in their abilities to replicate in cancer cells in vitro, which correlates with oncolytic activity in a murine model of melanoma. The current study reveals two mechanisms for the enhanced efficiency of T3D^PL in cancer cells. Due to polymorphisms in two viral genes, within the first round of reovirus infection, T3D^PL binds to cells more efficiency and more rapidly produces viral RNAs; this increased rate of infection relative to that of the less oncolytic strains gives T3D^PL a strong inherent advantage that culminates in higher virus production, more cell death, and higher virus spread.

From touchdown to transcription: the reovirus cell entry pathway

Mammalian orthoreoviruses (reoviruses) are prototype members of the Reoviridae family of nonenveloped viruses. Reoviruses contain ten double-stranded RNA gene segments enclosed in two concentric protein shells, outer capsid and core. These viruses serve as a versatile experimental system for studies of virus cell entry, innate immunity, and organ-specific disease. Reoviruses engage cells by binding to cell-surface carbohydrates and the immunoglobulin superfamily member, junctional adhesion molecule-A (JAM-A). JAM-A is a homodimer formed by extensive contacts between its N-terminal immunoglobulin-like domains. Reovirus attachment protein σ1 disrupts the JAM-A dimer, engaging a single JAM-A molecule by virtually the same interface used for JAM-A homodimerization. Following attachment to JAM-A and carbohydrate, reovirus internalization is promoted by β1 integrins, most likely via clathrin-dependent endocytosis. In the endocytic compartment, reovirus outer-capsid protein σ3 is removed by cathepsin proteases, which exposes the viral membrane-penetration protein, μ1. Proteolytic processing and conformational rearrangements of μ1 mediate endosomal membrane rupture and delivery of transcriptionally active reovirus core particles into the host cell cytoplasm. These events also allow the φ cleavage fragment of μ1 to escape into the cytoplasm where it activates NF-κB and elicits apoptosis. This review will focus on mechanisms of reovirus cell entry and activation of innate immune response signaling pathways.

Susceptibility of mantle cell lymphomas to reovirus oncolysis

Mantle cell lymphoma (MCL) an incurable B-cell, non-Hodgkin lymphoma (NHL) urgently requires new treatments. We assessed reovirus mediated oncolysis in a panel of human MCL cell lines. In vitro, we found the cytopathic effect of reovirus infection ranged from high to very limited and correlated with levels of Ras activation. In vivo, a single reovirus injection intra-tumorally resulted in complete regression of both the injected and the contra-lateral tumor in a subcutaneous bi-tumor model, in one out of three cell lines tested. Reovirus treatment of MCL seems feasible but will need to be guided by the presence of molecular determinants of reovirus susceptibility.

Conformational changes accompany activation of reovirus RNA-dependent RNA transcription

Many critical biologic processes involve dynamic interactions between proteins and nucleic acids. Such dynamic processes are often difficult to delineate by conventional static methods. For example, while a variety of nucleic acid polymerase structures have been determined at atomic resolution, the details of how some multi-protein transcriptase complexes actively produce mRNA, as well as conformational changes associated with activation of such complexes, remain poorly understood. The mammalian reovirus innermost capsid (core) manifests all enzymatic activities necessary to produce mRNA from each of the 10 encased double-stranded RNA genes. We used rapid freezing and electron cryo-microscopy to trap and visualize transcriptionally active reovirus core particles and compared them to inactive core images. Rod-like density centered within actively transcribing core spike channels was attributed to exiting nascent mRNA. Comparative radial density plots of active and inactive core particles identified several structural changes in both internal and external regions of the icosahedral core capsid. Inactive and transcriptionally active cores were partially digested with trypsin and identities of initial tryptic peptides determined by mass spectrometry. Differentially-digested peptides, which also suggest transcription-associated conformational changes, were placed within the known three-dimensional structures of major core proteins.

Genetic characterization of a new mammalian reovirus, type 2 Winnipeg (T2W)

We previously described isolation of a potentially new reovirus strain from the central nervous system of an 8-week-old female infant with a history of active varicella, oral thrush, hypoalbuminemia, intermittent fevers, diarrhea and feeding intolerance [Hermann et al., Ped. Inf. Dis J. 23, 373 (2004)]. This reovirus strain was tentatively identified as a member of the serotype 2 group by virus neutralization and RNA-gel electrophoresis studies and has been named type 2 Winnipeg (T2W). For this study we determined the nucleotide sequences of the T2W S1, S2, S3 and S4 genome segments to allow molecular comparison with other reoviruses. Comparative segment alignments of T2W S1 gene sequence with other reovirus S1 sequences showed T2W belongs to reovirus serotype 2. T2W S1 is most similar to the S1 genes of reovirus strains T2/Human/Netherlands/1,984 and T2/Human/Netherlands/1,973 with nucleotide identity >93%. The T2W S2 gene showed highest identity to reovirus T1 Lang S2 (approximately 75%). The T2W S3 gene showed highest identity to the S3 gene of T3/Human/Netherlands/1,983 (approximately 74%), and the T2W S4 gene showed highest identity to the T2 Jones S4 gene (approximately 73%). Pairwise protein comparisons between T2W sigma proteins and all available reovirus sigma proteins ranged from <21% identity for the sigma1 comparisons to more than 95% identity for sigma2 comparisons. The predicted T2W sigma1, sigma2 and sigma3 protein sequences were confirmed by mass spectrometry.

Reovirus mu1 structural rearrangements that mediate membrane penetration

Membrane penetration by nonenveloped reoviruses is mediated by the outer-capsid protein, mu1 (76 kDa). Previous evidence has suggested that an autolytic cleavage in mu1 allows the release of its N-terminally myristoylated peptide, mu1N (4 kDa), which probably then interacts with the target-cell membrane. A substantial rearrangement of the remaining portion of mu1, mu1C (72 kDa), must also have occurred for mu1N to be released, and some regions in mu1C may make additional contacts with the membrane. We describe here a particle-free system to study conformational rearrangements of mu1. We show that removal of the protector protein sigma3 is not sufficient to trigger rearrangement of free mu1 trimer and that free mu1 trimer undergoes conformational changes similar to those of particle-associated mu1 when induced by similar conditions. The mu1 rearrangements require separation of the mu1 trimer head domains but not the mu1N/C autocleavage. We have also obtained a relatively homogeneous form of the structurally rearranged mu1 (mu1*) in solution. It is an elongated monomer and retains substantial alpha-helix content. We have identified a protease-resistant approximately 23-kDa fragment of mu1*, which contains the largely alpha-helical regions designated domains I and II in the conformation of mu1 prior to rearrangement. We propose that the mu1 conformational changes preceding membrane penetration or disruption during cell entry involve (i) separation of the beta-barrel head domains in the mu1 trimer, (ii) autolytic cleavage at the mu1N/C junction, associated with partial unfolding of mu1C and release of mu1N, and (iii) refolding of the N-terminal helical domains of mu1C, with which mu1N was previously complexed, accompanied by dissociation of the mu1 trimer.

Sequences of avian reovirus M1, M2 and M3 genes and predicted structure/function of the encoded mu proteins

We report the first sequence analysis of the entire complement of M-class genome segments of an avian reovirus (ARV). We analyzed the M1, M2 and M3 genome segment sequences, and sequences of the corresponding muA, muB and muNS proteins, of two virus strains, ARV138 and ARV176. The ARV M1 genes were 2,283 nucleotides in length and predicted to encode muA proteins of 732 residues. Alignment of the homologous mammalian reovirus (MRV) mu2 and ARV muA proteins revealed a relatively low overall amino acid identity ( approximately 30%), although several highly conserved regions were identified that may contribute to conserved structural and/or functional properties of this minor core protein (i.e. the MRV mu2 protein is an NTPase and a putative RNA-dependent RNA polymerase cofactor). The ARV M2 genes were 2158 nucleotides in length, encoding predicted muB major outer capsid proteins of 676 amino acids, more than 30 amino acids shorter than the homologous MRV mu1 proteins. In spite of the difference in size, the ARV/MRV muB/mu1 proteins were more conserved than any of the homologous proteins encoded by other M- or S-class genome segments, exhibiting percent amino acid identities of approximately 45%. The conserved regions included the residues involved in the maturation- and entry- specific proteolytic cleavages that occur in the MRV mu1 protein. Notably missing was a region recently implicated in MRV mu1 stabilization and in forming "hub and spokes" complexes in the MRV outer capsid. The ARV M3 genes were 1996 nucleotides in length and predicted to encode a muNS non-structural protein of 635 amino acids, significantly shorter than the homologous MRV muNS protein, which is attributed to several substantial deletions in the aligned ARV muNS proteins. Alignments of the ARV and MRV muNS proteins revealed a low overall amino acid identity ( approximately 25%), although several regions were relatively conserved.

High-resolution mass spectrometric mapping of reovirus digestion

Reovirus is an enteric virus built from eight structural proteins that form a double-layered capsid. During virus entry into cells the reovirus outermost capsid layer (composed of proteins sigma3 and mu1C) is proteolytically processed to generate first an infectious subviral particle (ISVP), then the transcriptionally active core particle. Previous studies have demonstrated that protein sigma3, the outermost protein in the viral capsid, is removed from virus particles extremely rapidly. Other studies, using the detergent tetradecyl sulfate (14SO4) in combination with the protease chymotrypsin, have shown that mu1C cleavage is not necessary for infectious viral processing. We have recently used mass spectrometry to characterize the cascade of sigma3 proteolysis in intact reovirus serotype 1 Lang (T1L) virions (Mendez et al., Virology 2003; 311: 289-304). In the present study, we use high-resolution mass spectrometry to characterize the cascade of outer capsid digestion of both T1L and the other commonly used reovirus strain (serotype 3 Dearing [T3D]), with the protease trypsin, both in the presence and absence of 14SO4. These studies indicate that digestion kinetics and specificities are determined both by virus type and by presence or absence of detergent. Presence of detergent accelerated digestion of both outer capsid proteins. In contrast to chymotrypsin digestion, which segregated sigma3 digestion from mu1 digestion, both proteins were rapidly digested by trypsin in the presence of detergent.

Features of reovirus outer capsid protein mu1 revealed by electron cryomicroscopy and image reconstruction of the virion at 7.0 Angstrom resolution

Reovirus is a useful model for addressing the molecular basis of membrane penetration by one of the larger nonenveloped animal viruses. We now report the structure of the reovirus virion at approximately 7.0 A resolution as obtained by electron cryomicroscopy and three-dimensional image reconstruction. Several features of the myristoylated outer capsid protein mu1, not seen in a previous X-ray crystal structure of the mu1-sigma3 heterohexamer, are evident in the virion. These features appear to be important for stabilizing the outer capsid, regulating the conformational changes in mu1 that accompany perforation of target membranes, and contributing directly to membrane penetration during cell entry.

Putative autocleavage of outer capsid protein micro1, allowing release of myristoylated peptide micro1N during particle uncoating, is critical for cell entry by reovirus

Several nonenveloped animal viruses possess an autolytic capsid protein that is cleaved as a maturation step during assembly to yield infectious virions. The 76-kDa major outer capsid protein micro1 of mammalian orthoreoviruses (reoviruses) is also thought to be autocatalytically cleaved, yielding the virion-associated fragments micro1N (4 kDa; myristoylated) and micro1C (72 kDa). In this study, we found that micro1 cleavage to yield micro1N and micro1C was not required for outer capsid assembly but contributed greatly to the infectivity of the assembled particles. Recoated particles containing mutant, cleavage-defective micro1 (asparagine --> alanine substitution at amino acid 42) were competent for attachment; processing by exogenous proteases; structural changes in the outer capsid, including micro1 conformational change and sigma1 release; and transcriptase activation but failed to mediate membrane permeabilization either in vitro (no hemolysis) or in vivo (no coentry of the ribonucleotoxin alpha-sarcin). In addition, after these particles were allowed to enter cells, the delta region of micro1 continued to colocalize with viral core proteins in punctate structures, indicating that both elements remained bound together in particles and/or trapped within the same subcellular compartments, consistent with a defect in membrane penetration. If membrane penetration activity was supplied in trans by a coinfecting genome-deficient particle, the recoated particles with cleavage-defective micro1 displayed much higher levels of infectivity. These findings led us to propose a new uncoating intermediate, at which particles are trapped in the absence of micro1N/micro1C cleavage. We additionally showed that this cleavage allowed the myristoylated, N-terminal micro1N fragment to be released from reovirus particles during entry-related uncoating, analogous to the myristoylated, N-terminal VP4 fragment of picornavirus capsid proteins. The results thus suggest that hydrophobic peptide release following capsid protein autocleavage is part of a general mechanism of membrane penetration shared by several diverse nonenveloped animal viruses.

Mass spectrometric characterization of proteins from the SARS virus: a preliminary report

A new coronavirus has been implicated as the causative agent of severe acute respiratory syndrome (SARS). We have used convalescent sera from several SARS patients to detect proteins in the culture supernatants from cells exposed to lavage another SARS patient. The most prominent protein in the supernatant was identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a approximately 46-kDa species. This was found to be a novel nucleocapsid protein that matched almost exactly one predicted by an open reading frame in the recently published nucleotide sequence of the same virus isolate (>96% coverage). A second viral protein corresponding to the predicted approximately 139-kDa spike glycoprotein has also been examined by MALDI-TOF MS (42% coverage). After peptide N-glycosidase F digestion, 12 glycosylation sites in this protein were confirmed. The sugars attached to four of the sites were also identified. These results suggest that the nucleocapsid protein is a major immunogen that may be useful for early diagnostics, and that the spike glycoprotein may present a particularly attractive target for prophylactic intervention in combating SARS.