Bovine Coronavirus Nonstructural Protein 1 (p28) Is an RNA Binding Protein That Binds Terminal Genomic cis-Replication Elements

Nonstructural protein 1 (nsp1), a 28-kDa protein in the bovine coronavirus (BCoV) and closely related mouse hepatitis coronavirus, is the first protein cleaved from the open reading frame 1 (ORF 1) polyprotein product of genome translation. Recently, a 30-nucleotide (nt) cis-replication stem-loop VI (SLVI) has been mapped at nt 101 to 130 within a 288-nt 5′-terminal segment of the 738-nt nsp1 cistron in a BCoV defective interfering (DI) RNA. Since a similar nsp1 coding region appears in all characterized groups 1 and 2 coronavirus DI RNAs and must be translated in cis for BCoV DI RNA replication, we hypothesized that nsp1 might regulate ORF 1 expression by binding this intra-nsp1 cistronic element. Here, we (i) establish by mutation analysis that the 72-nt intracistronic SLV immediately upstream of SLVI is also a DI RNA cis-replication signal, (ii) show by gel shift and UV-cross-linking analyses that cellular proteins of ∼60 and 100 kDa, but not viral proteins, bind SLV and SLVI, (SLV-VI) and (iii) demonstrate by gel shift analysis that nsp1 purified from Escherichia coli does not bind SLV-VI but does bind three 5′ untranslated region (UTR)- and one 3′ UTR-located cis-replication SLs. Notably, nsp1 specifically binds SLIII and its flanking sequences in the 5′ UTR with ∼2.5 μM affinity. Additionally, under conditions enabling expression of nsp1 from DI RNA-encoded subgenomic mRNA, DI RNA levels were greatly reduced, but there was only a slight transient reduction in viral RNA levels. These results together indicate that nsp1 is an RNA-binding protein that may function to regulate viral genome translation or replication but not by binding SLV-VI within its own coding region.Coronaviruses (CoVs) (59) cause primarily respiratory and gastroenteric diseases in birds and mammals (35, 71). In humans, they most commonly cause mild upper respiratory disease, but the recently discovered human CoVs (HCoVs), HCoV-NL63 (65), HCoV-HKU1 (73), and severe acute respiratory syndrome (SARS)-CoV (40) cause serious diseases in the upper and lower respiratory tracts. The SARS-CoV causes pneumonia with an accompanying high (∼10%) mortality rate (69). The ∼30-kb positive-strand CoV genome, the largest known among RNA viruses, is 5′ capped and 3′ polyadenylated and replicates in the cytoplasm (41). As with other characterized cytoplasmically replicating positive-strand RNA viruses (3), translation of the CoV genome is an early step in replication, and terminally located cis-acting RNA signals regulate translation and direct genome replication (41). How these happen mechanistically in CoVs is only beginning to be understood.In the highly studied group 2 mouse hepatitis coronavirus model (MHV A59 strain) and its close relative the bovine CoV (BCoV Mebus strain), five higher-order cis-replication signals have been identified in the 5′ and 3′ untranslated regions (UTRs). These include two in the 5′ UTR required for BCoV defective interfering (DI) RNA replication (Fig. ​(Fig.1A)1A) described as stem-loop III (SLIII) (50) and SLIV (51). Recently, the SLI region in BCoV (15) has been reanalyzed along with the homologous region in MHV and is now described as comprising SL1 and SL2 (Fig. ​(Fig.1A),1A), of which SL2 has been shown to be a cis-replication structure in the context of the MHV genome (38). In the 3′ UTR, two higher-order cis-replication structures have been identified that function in both DI RNA and the MHV genome. These are a 5′-proximal bulged SL and adjacent pseudoknot that potentially act together as a unit (23, 27, 28, 72) and a 3′-proximal octamer-associated bulged SL (39, 76) (Fig. ​(Fig.1A).1A). In addition, the 5′-terminal 65-nucleotide (nt) leader and the 3′-terminal poly(A) tail have been shown to be cis-replication signals for BCoV DI RNA (15, 60).Open in a separate windowFIG. 1.RNA structures in the BCoV genome tested for nsp1 binding. (A) BCoV 5′-terminal and 3′-terminal cis-acting RNA SL structures and flanking sequences identified for BCoV DI RNA replication. Regions of the genome are identified and SL cis-replication elements are identified schematically. Open boxes at nt 100 and 211 identify AUG start codons for the short upstream ORF and ORF 1, respectively. A closed box at nt 124 identifies the UAG stop codon for the short upstream ORF. Shown below the SL structures are the RNA segments used as ³²P-labeled probes in the gel shift assays. BSL-PK, bulged SL-pseudoknot; 8mer-BSL, octamer-associated bulged SL. (B) Gel shift assays for probes when used with purified nsp1. Protein-RNA complexes identifying a shifted probe are labeled C.In CoVs, the 5′-proximal open reading frame (ORF) of ∼20 kb (called ORF 1) comprising the 5′ two-thirds of the genome is translated to overlapping polyproteins of ∼500 and ∼700 kDa, named pp1a and pp1ab (41). pp1ab is formed by a −1 ribosomal frameshift event at the ORF1a-ORF1b junction during translation (41). pp1a and pp1ab are proteolytically processed into potentially 16 nonstructural protein (nsp) end products or partial end products that are proposed to function together as the replicase (24). ORF 1a encodes nsps 1 to 11 which include papain-like proteases (nsp3), a 3C-like main protease (nsp5), membrane-anchoring proteins (nsps 4 and 6), a potential primase (nsp8), and RNA-binding proteins (nsp 7/nsp 8 complex and nsps 9 and 10) of imprecisely understood function (19, 20, 24, 25, 29, 43, 49, 77). ORF 1b encodes nsps 12 to 16 which function as an RNA-dependent RNA polymerase, a helicase, an exonuclease, an endonuclease, and a 2′-O-methyltransferase, respectively (6, 17, 24, 44). 3′ Proximal genomic ORFs encoding structural and accessory proteins are translated from a 3′-nested set of subgenomic mRNAs (sgmRNAs) (41).The N-terminal ORF 1a protein, nsp1, in the case of BCoV and MHV is also named p28 to identify the cleaved 28-kDa product (18). The precise role of nsp1 in virus replication has not been determined, but it is known that a sequence encoding an N-proximal nsp1 region in MHV (nt 255 to 369 in the 738-nt coding sequence) cannot be deleted from the genome without loss of productive infection (10). nsp1 also directly binds nsp7 and nsp10 (11) and by confocal microscopy is found associated with the membranous replication complex (10, 66) and virus assembly sites (11). The amino acid sequence of nsp1 is poorly conserved among CoVs, indicating that it may be a protein that interacts with cellular components (1, 58). In the absence of other viral proteins, MHV nsp1 induces general host mRNA degradation (79) and cell cycle arrest (16). The SARS-CoV nsp1 homolog, a 20-kDa protein, has been reported to cause mRNA degradation (30, 45), inhibition of host protein synthesis (30, 45, 70), inhibition of interferon signaling (70, 79), and cytokine dysregulation in lung cells (36).In this study, we examine the RNA-binding properties of BCoV nsp1 with the hypothesis that it is a potential regulator of translation or replication through its binding of SLVI mapping within its coding region. The rationale for this hypothesis stems from five observations. (i) In the BCoV DI RNA, the 5′-terminal one-third (approximately) of the nsp1 cistron and the entire nucleocapsid (N) protein cistron together comprise the single contiguous ORF in the DI RNA, and most of both coding regions appear required for DI RNA replication (15). (ii) The partial nsp1 cistron in the DI RNA must be translated in cis for DI RNA replication in helper virus-infected cells (12, 14). (iii) A similar part of the nsp1 cistron is found in the genome of all characterized naturally occurring group 1 and 2 CoV DI RNAs described to date (7, 8). (iv) A cis-acting SL named SLVI is found within the partial nsp1 cistron in the BCoV DI RNA (12). (v) Translation, which involves a 5′→3′ transit of ribosomes, and negative-strand synthesis, which involves a 3′→5′ transit of the RNA-dependent RNA polymerase, cannot simultaneously occur on the same molecule with a single ORF (4, 31). Thus, to enable genome replication an inhibition of translation at least early in infection for cytoplasmically replicating positive-strand RNA viruses is required (4, 5, 22, 32). Mechanisms of translation inhibition have been described for the Qβ viral genome, wherein the viral replicase autoregulates translation by binding an intracistronic cis-replication element (32), and for the polio virus genome, wherein genome circularization inhibits the early translation step (5, 22). Therefore, since nsp1 is synthesized early and also contains an intracistronic cis-replication element, we postulated that it is autoregulatory with RNA binding properties.Here, we do the following: (i) demonstrate by mutagenesis analysis that the 72-nt SLV, mapping immediately upstream of SLVI and within the partial nsp1 cistron, is also a cis-acting DI RNA replication element; (ii) show by gel shift and UV cross-linking analyses that there is likely no binding of an intracellular viral protein to SLV and SLVI (SLV-VI), but there is binding of unidentified cellular proteins of ∼60 and 100 kDa; and (iii) show by gel shift analysis that recombinant nsp1 purified from Escherichia coli does not bind SLV-VI but does bind SLs I to IV in the 5′ UTR and also the 3′-terminal bulged SL in the 3′ UTR, suggesting a possible regulatory role at these sites. Notably, specific binding with ∼2.5 μM affinity of nsp1 to SLIII and its flanking regions in the 5′ UTR was observed. Additionally, we show that, under conditions that would express nsp1 from a DI RNA-encoded sgmRNA, DI RNA levels are greatly reduced; viral RNA species levels, however, are reduced only slightly, and this reduction is transient. These results together indicate that nsp1 is an RNA-binding protein that may function as a regulator of viral translation or replication but not through its binding of cis-acting SLs V and VI within its own cistron.     

Role of N-Linked Glycosylation of the 5-HT2A Receptor in JC Virus Infection

JC virus (JCV) is a human polyomavirus and the causative agent of the fatal demyelinating disease progressive multifocal leukoencephalopathy (PML). JCV infection of host cells is dependent on interactions with cell surface asparagine (N)-linked sialic acids and the serotonin 5-hydroxytryptamine_2A receptor (5-HT_2AR). The 5-HT_2AR contains five potential N-linked glycosylation sites on the extracellular N terminus. Glycosylation of other serotonin receptors is essential for expression, ligand binding, and receptor function. Also, glycosylation of cellular receptors has been reported to be important for JCV infection. Therefore, we hypothesized that the 5-HT_2AR N-linked glycosylation sites are required for JCV infection. Treatment of 5-HT_2AR-expressing cells with tunicamycin, an inhibitor of N-linked glycosylation, reduced JCV infection. Individual mutation of each of the five N-linked glycosylation sites did not affect the capacity of 5-HT_2AR to support JCV infection and did not alter the cell surface expression of the receptor. However, mutation of all five N-linked glycosylation sites simultaneously reduced the capacity of 5-HT_2AR to support infection and altered the cell surface expression. Similarly, tunicamycin treatment reduced the cell surface expression of 5-HT_2AR. Mutation of all five N-linked glycosylation sites or tunicamycin treatment of cells expressing wild-type 5-HT_2AR resulted in an altered electrophoretic mobility profile of the receptor. Treatment of cells with PNGase F, to remove N-linked oligosaccharides from the cell surface, did not affect JCV infection in 5-HT_2AR-expressing cells. These data affirm the importance of 5-HT_2AR as a JCV receptor and demonstrate that the sialic acid component of the receptor is not directly linked to 5-HT_2AR.The initial interaction between virus and host occurs via molecular interactions of viral attachment proteins and receptors on host cells. Therefore, receptor recognition is a critical host cell determinant and may play a key regulatory role in viral pathogenesis. The polyomavirus JC virus (JCV) is a ubiquitous human pathogen (21, 25, 32) that is initially subclinical yet establishes a persistent infection in the kidney (11). In immunosuppressed individuals JCV can become reactivated, leading to infection in the central nervous system (CNS) (13-15, 20), where the virus specifically targets glial cells, including astrocytes and the myelin-producing cells, oligodendrocytes (40, 48). JCV infection and cytolytic destruction of oligodendroglia cause the fatal disease progressive multifocal leukoencephalopathy (PML) (1, 22). The most common cause of PML is associated with human immunodeficiency virus (HIV) and AIDS (10, 23). However, in recent years PML has been reported in patients receiving immunosuppressive therapies for autoimmune diseases such as Crohn''s disease (44), multiple sclerosis (MS) (24, 26, 28, 47), systemic lupus erythematosus (5, 33), and rheumatoid arthritis (5, 19, 37). The prognosis of PML is bleak, as the disease progresses rapidly and usually proves fatal within 1 year of the onset of symptoms. While current treatment options for PML are limited (23), recent studies suggest that mirtazapine, a serotonin receptor antagonist, may be capable of slowing the progression of PML (6, 27, 45, 46).JCV has a nonenveloped, icosahedral capsid that encapsidates a circular double-stranded DNA (dsDNA) genome (39). JCV attachment to cells is mediated by an N-linked glycoprotein with either α(2,3)- or α(2,6)-linked sialic acid (16, 31), suggesting that N-linked glycosylation of cellular receptors is important for JCV infection. N-linked glycosylation is a posttranslational process by which oligosaccharides are added to asparagine residues, and this modification is important for protein processing, folding, expression, and function (43). Previous studies from our laboratory revealed that the JCV also requires the serotonin 5-hydroxytryptamine_2A receptor (5-HT_2AR) to mediate JCV infection (18, 35, 38), while others report that JCV infection can occur in the absence of 5-HT_2AR (7, 8). 5-HT_2AR is a seven-transmembrane-spanning G-protein-coupled receptor that belongs to a large family of 5-HT serotonin receptors. 5-HT_2AR is abundantly expressed on cells in the brain (4), including glial cells (3), and in the kidney (4), which parallels the sites of JCV infection. N-linked glycosylation plays a key regulatory role in the function of serotonin receptors. Mutation of N-linked glycosylation sites in human 5-HT_3AR and 5-HT_5AR results in decreased expression at the plasma membrane, which is critical for receptor function (17, 34). N-linked glycosylation of murine 5-HT_3AR regulates plasma membrane targeting, ligand binding, Ca²⁺ flux, and receptor trafficking (36), suggesting that glycosylation is essential for expression and function of serotonin receptors.While previous studies have concluded that JCV utilizes an N-linked glycoprotein with α(2,3)-linked sialic acid (31) or α(2,6)-linked sialic acid (16) and 5-HT_2AR (18) to initiate infection in host cells, the mechanism(s) by which JCV engages its cellular receptors and the importance of receptor glycosylation remain unclear. 5-HT_2AR contains potential asparagine (N)-linked glycosylation sites, five of which are predicted to be expressed in the extracellular amino-terminal region, where they could be accessible to the virus (2). The goal of this study was to determine whether potential N-linked glycosylation sites expressed in 5-HT_2AR are required for JCV infection. We found that N-linked glycosylation of 5-HT_2AR is important for receptor expression but not necessary for JCV infection.     

Nuclear Magnetic Resonance Structure of the Nucleic Acid-Binding Domain of Severe Acute Respiratory Syndrome Coronavirus Nonstructural Protein 3

The nuclear magnetic resonance (NMR) structure of a globular domain of residues 1071 to 1178 within the previously annotated nucleic acid-binding region (NAB) of severe acute respiratory syndrome coronavirus nonstructural protein 3 (nsp3) has been determined, and N- and C-terminally adjoining polypeptide segments of 37 and 25 residues, respectively, have been shown to form flexibly extended linkers to the preceding globular domain and to the following, as yet uncharacterized domain. This extension of the structural coverage of nsp3 was obtained from NMR studies with an nsp3 construct comprising residues 1066 to 1181 [nsp3(1066-1181)] and the constructs nsp3(1066-1203) and nsp3(1035-1181). A search of the protein structure database indicates that the globular domain of the NAB represents a new fold, with a parallel four-strand β-sheet holding two α-helices of three and four turns that are oriented antiparallel to the β-strands. Two antiparallel two-strand β-sheets and two 3₁₀-helices are anchored against the surface of this barrel-like molecular core. Chemical shift changes upon the addition of single-stranded RNAs (ssRNAs) identified a group of residues that form a positively charged patch on the protein surface as the binding site responsible for the previously reported affinity for nucleic acids. This binding site is similar to the ssRNA-binding site of the sterile alpha motif domain of the Saccharomyces cerevisiae Vts1p protein, although the two proteins do not share a common globular fold.The coronavirus replication cycle begins with the translation of the 29-kb positive-strand genomic RNA to produce two large polyprotein species (pp1a and pp1ab), which are subsequently cleaved to produce 15 or possibly 16 nonstructural proteins (nsp''s) (11). Among these, nsp3 is the largest nsp and also the largest coronavirus protein. nsp3 is a glycosylated (16, 22), multidomain (36, 51), integral membrane protein (38). All known coronaviruses encode a homologue of severe acute respiratory syndrome coronavirus (SARS-CoV) nsp3, and sequence analysis suggests that at least some functions of nsp3 may be found in all members of the order Nidovirales (11). Hallmarks of the coronavirus nsp3 proteins include one or two papain-like proteinase domains (3, 12, 16, 31, 56, 62), one to three histone H2A-like macrodomains which may bind RNA or RNA-like substrates (5, 9, 48, 54, 55), and a carboxyl-terminal Y domain of unknown function (13). An extensive bioinformatics analysis of the coronavirus replicase proteins by Snijder et al. (51) provided detailed annotations of the then-recently sequenced SARS-CoV genome (35, 47), including the identification of a domain unique to SARS-CoV and the prediction of the ADP-ribose-1″-phosphatase (ADRP) activity of the X domain (since shown to be one of the macrodomains).Only limited information is so far available regarding the ways in which the functions of nsp3 are involved in the coronavirus replication cycle. Some functions of nsp3 appear to be directed toward protein; e.g., the nsp3 proteinase domain cleaves the amino-terminal two or three nsp''s from the polyprotein and has deubiquitinating activity (4, 6, 14, 30, 53, 60). Most homologues of the most conserved macrodomain of nsp3 appear to possess ADRP activity (9, 34, 41-43, 48, 59) and may act on protein-conjugated poly(ADP-ribose); however, this function appears to be dispensable for replication (10, 42) and may not be conserved in all coronaviruses (41). The potential involvement of nsp3 in RNA replication is suggested by the presence of several RNA-binding domains (5, 36, 49, 54, 55). nsp3 has been identified in convoluted membrane structures that are also associated with other replicase proteins and that have been shown to be involved in viral RNA synthesis (16, 24, 52), and nsp3 papain-like proteinase activity is essential for replication (14, 62). Other conserved structural features of nsp3 include two ubiquitin-like domains (UB1 and UB2) (45, 49). We have also recently reported that nsp3 is a structural protein, since it was identified as a minor component of purified SARS-CoV preparations, although it is not known whether nsp3 is directly involved in virogenesis or is incidentally incorporated due to protein-protein or protein-RNA interactions (36).A nucleic acid-binding region (NAB) is located within the polypeptide segment of residues 1035 to 1203 of nsp3. The NAB is expected to be located in the cytoplasm, along with the papain-like protease, ADRP, a region unique to SARS-CoV (the SARS-CoV unique domain [SUD]), and nsp3a, since both the N and C termini of nsp3 were shown previously to be cytoplasmic (38). Two hydrophobic segments are membrane spanning (38), and the NAB is located roughly 200 residues in the N-terminal direction from the first membrane-spanning segment. This paper presents the next step in the structural coverage of nsp3, with the determination of the NAB structure. The structural studies included nuclear magnetic resonance (NMR) characterization of two constructs, an nsp3 construct comprising residues 1035 to 1181 [nsp3(1035-1181)] and nsp3(1066-1203), and complete NMR structure determination for the construct nsp3(1066-1181) (see Fig. ​Fig.8).8). The structural data were then used as a platform from which to investigate the nature of the previously reported single-stranded RNA (ssRNA)-binding activity of the NAB (36). Since no three-dimensional (3D) structures for the corresponding domains in other group II coronaviruses are known and since the SARS-CoV NAB has only very-low-level sequence identity to other proteins, such data could not readily be derived from comparisons with structurally and functionally characterized homologues.Open in a separate windowFIG. 8.Sequence alignment of the polypeptide segment nsp3(1066-1181) that forms the globular domain of the SARS-CoV NAB with homologues from other group II coronaviruses. Protein multiple-sequence alignment was performed using ClustalW2 and included sequences from SARS-CoV Tor2 (accession no. {"type":"entrez-protein","attrs":{"text":"AAP41036","term_id":"30795144","term_text":"AAP41036"}}AAP41036) and representatives of three protein clusters corresponding to three group II coronavirus lineages identified by a BLAST search: bat coronavirus HKU5-5 (BtCoV-HKU5-5; accession no. {"type":"entrez-protein","attrs":{"text":"ABN10901","term_id":"124389468","term_text":"ABN10901"}}ABN10901), BtCoV-HKU9-1 (accession no. {"type":"entrez-protein","attrs":{"text":"P0C6T6","term_id":"190360129","term_text":"P0C6T6"}}P0C6T6), and human coronavirus HKU1-N16 (HCoV-HKU1-N16; accession no. {"type":"entrez-protein","attrs":{"text":"ABD75496","term_id":"89515407","term_text":"ABD75496"}}ABD75496). Above the sequences, the positions in full-length SARS-CoV nsp3, the locations of the regular secondary structures in the presently solved NMR structure of the SARS-CoV NAB globular domain, and the residue numbering in this domain are indicated. Amino acids are colored according to conservation and biochemical properties, following ClustalW conventions. Residues implicated in interactions with ssRNA are marked with inverted black triangles. In the present context, the key features are that there is only one position with conservation of K or R (red) and that there are extended sequences with conservation of hydrophobic residues (blue) (see the text).     

The Spike Protein of Murine Coronavirus Regulates Viral Genome Transport from the Cell Surface to the Endoplasmic Reticulum during Infection

We observed that the nonfusogenic mouse hepatitis virus (MHV) strain MHV-2 reached a titer of ∼2 log₁₀ higher than that of the fusogenic strain A59 in astrocytoma DBT cells. To determine whether the spike protein is responsible for the difference, a recombinant virus, Penn-98-1, that contains the A59 genome with a spike from MHV-2 was used to infect DBT cells. Results showed that Penn-98-1 behaved like MHV-2, thus establishing a role for the spike protein in viral growth. The inverse correlation between viral fusogenicity and growth was further established in four different cell types and with a fusogenic mutant, the S757R mutant, derived from isogenic Penn-98-1. While both A59 and Penn-98-1 entered cells at similar levels, viral RNA and protein syntheses were significantly delayed for A59. Interestingly, when the genomic RNAs were delivered directly into the cells via transfection, the levels of gene expression for these viruses were similar. Furthermore, cell fractionation experiments revealed that significantly more genomic RNAs for the nonfusogenic MHVs were detected in the endoplasmic reticulum (ER) within the first 2 h after infection than for the fusogenic MHVs. Pretreatment of Penn-98-1 with trypsin reversed its properties in syncytium formation, virus production, and genome transport to the ER. These findings identified a novel role for the spike protein in regulating the uncoating and delivery of the viral genome to the ER after internalization.Murine coronavirus mouse hepatitis virus (MHV) is a member of the family Coronaviridae. It is an enveloped, positive-strand-RNA virus. The viral envelope contains three or four structural proteins, depending on the virus strain (21). The spike (S) protein is a glycoprotein with a molecular mass of approximately 180 kDa. For some MHV strains, such as JHM and A59, the S protein is cleaved by a furin-like proteinase into two subunits, the amino-terminal S1 and the carboxyl-terminal S2. The S1 subunit is thought to form the globular head of the spike and is responsible for the initial attachment of the virus to the receptor on the cell surface. The S2 subunit, which forms the stalk portion of the spike and which anchors the S protein to the viral envelope, facilitates the fusion between the viral envelope and the cell membrane and cell-cell fusion (4, 7, 20, 25, 39). In contrast, the S protein of some other MHV strains, such as MHV-2, does not undergo cleavage and usually does not cause cell-cell fusion (15, 34). It appears that the cleavability of the MHV S protein is associated usually, though not always, with its fusogenicity (10, 36). It has been suggested that the fusogenicity of the S protein may determine the route of virus entry, i.e., via direct fusion with plasma membranes or following endocytosis (11, 34), although the mechanism for virus-induced cell-cell fusion may differ from that for virus-cell fusion during entry (8). The S protein also elicits the induction of neutralizing antibodies and cell-mediated immunity in infected hosts (3). It is therefore an important determinant for viral infectivity, pathogenicity, and virulence (2, 5, 31, 38). The hemagglutinin-esterase (HE) protein is present only in certain MHV strains (22, 42) and may play a role in viral pathogenesis (44, 45). The small envelope (E) protein and the membrane (M) protein play a key role in virus assembly (40). The nucleocapsid (N) protein is a phosphoprotein of approximately 50 kDa and is associated with the RNA genome to form the nucleocapsid inside the envelope (21, 37).Infection of host cells by MHV is mediated through the interaction between the S protein and the cellular receptors that are members of the carcinoembryonic antigen (CEA) family of the immunoglobulin superfamily (9). This interaction then triggers fusion between the viral envelope and the plasma membrane or the endosomal membrane, the latter of which follows receptor-mediated endocytosis, thus allowing the nucleocapsid to deliver into the cytoplasm. Direct entry from the plasma membrane appears to be the predominant route for most MHV strains (19, 28), although entry by some mutant MHVs, such as OBLV60 and MHV-2, is low pH dependent, i.e., via endocytosis (11, 34). However, nothing is known about how the genomic RNA is transported to the rough endoplasmic reticulum (ER) for translation. Once on the ER, the viral genomic RNA is translated into a polymerase polyprotein from the 5′-end two open reading frames (two-thirds of the genome) via ribosomal frameshifting. The polymerase polyproteins in turn synthesize genomic and multiple species of subgenomic mRNAs. These mRNAs are then translated into nonstructural and structural proteins, the latter of which are essential for generation of progeny viruses.MHV can infect rodents, causing hepatitis, enteritis, nephritis, and central nervous system diseases. In the mouse central nervous system, some MHV strains, such as JHM and A59, are neurovirulent, causing acute encephalitis and chronic demyelination (1, 13), while others, such as MHV-2, exhibit extremely low neurovirulence, causing only meningitis without apparent encephalitis and demyelination (6, 16, 41). Extensive mutagenesis studies in combination with targeted RNA recombination have identified that the S protein is the major determinant of MHV pathogenicity in animals, although other viral genes also appear to modulate viral pathogenicity (17, 32). For example, the recombinant MHV Penn-98-1, which contains the S protein of MHV-2 in an A59 genome background, causes acute meningoencephalitis similar to that caused by A59 but does not cause demyelination similar to that observed for MHV-2 (6). It has also been shown that the amounts of antigen staining and necrosis in the liver correlate with the viral titer, which is determined largely by the S protein (29). However, how the S protein affects viral titer in cell culture and in animals is not known.In the present study, we initially observed that the levels of production of infectious viruses in an astrocytoma DBT cell line were markedly different among three MHV strains. Using the recombinant MHV Penn-98-1 and its isogenic S757R mutant, we further established that the S protein is responsible for the observed difference. The difference in virus production between A59 and Penn-98-1 was detected as early as 4 to 6 h postinfection (p.i.) and likely occurred during the early stages of the virus life cycle but after virus internalization. Interestingly, when the genomic RNAs were delivered directly into the cells via transfection, the levels of gene expression for these viruses were similar. Furthermore, cell fractionation experiments revealed that significantly more genomic RNAs for nonfusogenic MHVs were delivered to the ER within the first 2 h after infection than for fusogenic MHVs. These results demonstrate that the spike protein of MHV can regulate the intracellular transport of the viral genome to the ER following internalization. To our knowledge, this is the first study identifying a role for a coronavirus S protein in genome delivery in addition to its well-established role in receptor binding and virus-cell and cell-cell fusions during infection.     

Genetic,Structural, and Antigenic Analyses of Glycan Diversity in the O-Linked Protein Glycosylation Systems of Human Neisseria Species

Bacterial capsular polysaccharides and lipopolysaccharides are well-established ligands of innate and adaptive immune effectors and often exhibit structural and antigenic variability. Although many surface-localized glycoproteins have been identified in bacterial pathogens and symbionts, it not clear if and how selection impacts associated glycoform structure. Here, a systematic approach was devised to correlate gene repertoire with protein-associated glycoform structure in Neisseria species important to human health and disease. By manipulating the protein glycosylation (pgl) gene content and assessing the glycan structure by mass spectrometry and reactivity with monoclonal antibodies, it was established that protein-associated glycans are antigenically variable and that at least nine distinct glycoforms can be expressed in vitro. These studies also revealed that in addition to Neisseria gonorrhoeae strain N400, one other gonococcal strain and isolates of Neisseria meningitidis and Neisseria lactamica exhibit broad-spectrum O-linked protein glycosylation. Although a strong correlation between pgl gene content, glycoform expression, and serological profile was observed, there were significant exceptions, particularly with regard to levels of microheterogeneity. This work provides a technological platform for molecular serotyping of neisserial protein glycans and for elucidating pgl gene evolution.It is now well established that protein glycosylation based on both N- and O-linked modifications occurs in bacterial species. In N-linked systems exemplified by the system in Campylobacter jejuni, large numbers of proteins that are translocated to the periplasm are glycosylated based on the presence of sequon elements and asparagine-targeting oligosaccharyltransferases related to those that operate in eukaryotes (21, 36, 69, 73). Two O-linked systems associated with covalent modification of type IV pilin subunits in pathogenic Neisseria species and in selected strains of Pseudomonas aeruginosa have been particularly well characterized (2, 16, 46-48, 54). The latter systems are remarkably similar to the N-linked system characterized in C. jejuni in that oligosaccharides are synthesized cytoplasmically as lipid-linked precursors that are then flipped into the periplasm. Protein-targeting oligosaccharyltransferases structurally related to the WaaL family of O-antigen ligases then transfer the oligosaccharides to protein substrates (2, 18, 49). The similarities between these N- and O-linked systems are perhaps best illustrated by genetic and functional interactions between components of the C. jejuni oligosaccharide biosynthetic machinery and elements of the neisserial pilin glycosylation pathway (2, 18). In contrast, the mechanisms operating in other bacterial O-linked systems are not completely understood yet, and there appears to be considerable diversity in the mechanisms of oligosaccharide synthesis, transfer of the glycan to the protein, and the cellular compartment in which glycan addition takes place. Prime examples of this diversity include the glycosylation of major subunits of S-layers (53), flagella (40), and type IV pili, as well as nonpilus adhesins, such as autotransporters (7, 51) and a family of serine-rich proteins identified in Gram-positive species (72). Recently, the pilin glycosylation system in the Gram-negative species Neisseria gonorrhoeae (the etiological agent of gonorrhea) was shown to be a general O-linked system in which a large set of structurally distinct periplasmic proteins undergo glycosylation (64). Likewise, a general O-linked glycosylation system targeting periplasmic and surface-exposed proteins has been documented in Bacteroides fragilis (19). In addition, an increasing number of lipoproteins in Mycobacterium tuberculosis have been found to be O glycosylated, and current evidence suggests that a single glycosylation pathway operates with these proteins (50).The large number of bacterial protein glycosylation systems strongly suggests that these systems are advantageous and affect fitness. In fact, mutants with mutations in the general glycosylation systems of C. jejuni and B. fragilis are defective in mucosal colonization, although the fundamental basis for the observations is unclear (19, 23). In some cases, defects in protein stability and trafficking have been documented. Examples of the latter have been reported for the Aida and Ag43 autotransporter adhesins of Escherichia coli and the serine-rich Fap1 streptococcal adhesin (11, 35, 72). In these cases, the glycosylation status appears to influence protein integrity along with intracellular or membrane trafficking events.Glycosylation may also influence protein structure and function or activity at the extracellular level. In the context of host-symbiont and host-pathogen interactions, bacterial cell surface polysaccharides and glycolipid glycans are well-established targets of both innate and adaptive immune responses (13, 61). However, the potential influence of protein-linked carbohydrate on immune recognition and signaling is only beginning to be investigated. Given the well-established effect of conjugating protein to carbohydrate on glycan-related immunogenicity, glycoproteins could be predicted to promote a robust T-cell-dependent antibody response directed toward glycan epitopes. In line with this, immunization of mice with O-glycosylated type IV pilin from P. aeruginosa strain 1244 (which bears a single repeat unit of the O antigen, the dominant component of its lipopolysaccharide) resulted in protection against challenge with immunological specificity for the O-polysaccharide (27). In addition, structural heterogeneity of carbohydrate modifications has been shown to affect the serospecificity of Campylobacter flagellins (41). With regard to innate immunity, the N-linked protein glycans of C. jejuni have been shown to influence interleukin-6 production by human dendritic cells via interaction with the macrophage galactose-type lectin (MGL) (62). Also, flagellin glycosylation of the phytopathogenic bacteria Pseudomonas syringae pv. glycinea and P. syringae pv. tomato appears to play an important role in hypersensitive cell death in nonhost plants and in host cell recognition (56, 57). Similarly, the flagellin glycosylation status in P. aeruginosa influences proinflammatory responses in human cell cultures (63).Studies of O-linked flagellar glycosylation in P. aeruginosa, C. jejuni, and a number of Gram-positive species have revealed considerable variability in genomic glycosylation islands (40). In addition to differences in gene content, some genes localized in these loci are subject to phase (on-off) variation involving slipped-strand mispairing events. Similar findings have been obtained for the O-linked glycosylation system in N. gonorrhoeae and a related system in Neisseria meningitidis (2, 4, 29, 48). These observations strongly suggest that protein-associated glycans are positively selected. However, attempts to elucidate the evolutionary processes impacting these systems are complicated by difficulties in connecting genotype with phenotype. For example, predicting enzymatic activities of components involved in glycan biosynthesis based on the sequence alone is notoriously difficult. Therefore, glycosylation-related functions are characterized best by using purified components in in vitro assays. Moreover, despite recent advances in mass spectrometric (MS) and nuclear magnetic resonance (NMR) technologies, glycoprotein structural analysis is still arduous, particularly when proteins are expressed at low levels. Thus, current methodologies are not optimized for studies of large numbers of strains and mutants.The broad-spectrum O-linked protein glycosylation system of N. gonorrhoeae is particularly well characterized with regard to the genetics of oligosaccharide biosynthesis, modification, and transfer to protein via the PglO/PglL oligosaccharyltransferase. As shown using strain N400, combined genetic and MS analyses, including interspecies complementation, have revealed that this system (designated the pgl [protein glycosylation] system) is remarkably similar to the N-linked system of C. jejuni with respect to the use of a peptide-proximal 2,4-diacetamido-2,4,6-trideoxyhexose (DATDH) sugar and related biosynthetic pathways for generating lipid-linked glycan substrates (2, 18, 39). The lipid-linked DATDH sugar can be further converted successively into hexose (Hex)-DATDH disaccharide and Hex-Hex-DATDH trisaccharide forms by the PglA and PglE glycosyltransferases, respectively (2). The hexoses in both the di- and trisaccharide forms can also undergo O acetylation by the PglI enzyme (2, 70). As pglA, pglE, and pglI are each predicted to be subject to phase variation in some backgrounds, strains have the potential to express five distinct glycoforms (2, 4, 29, 48, 70). A similar system operates in N. meningitidis strain c311, although to date only pilin and the AniA nitrite reductase proteins have been shown to be glycosylated (37). Pioneering analyses of pilin from this strain identified a trisaccharide with a terminal alpha-1-4-linked digalactose moiety attached to DATDH (54). Interestingly, nearly one-half of N. meningitidis isolates are reported to have a unique allele of pglB designated pglB2 associated with synthesis of a proximal glyceramido-acetamido trideoxyhexose (GATDH) rather than DATDH (10). In addition, some strains of both N. gonorrhoeae and N. meningitidis have been reported to contain additional genes predicted to encode glycosyltransferases linked to the core locus that includes the pglF, pglB, pglC, and pglD genes (32, 48). Thus, it appears that the number of protein-associated glycans may be far greater than currently perceived. The genus Neisseria also includes a number of related species that colonize humans, including Neisseria lactamica, which is closely related to N. gonorrhoeae and N. meningitidis but is rarely associated with disease (24), as well as other, more divergent commensal species. An examination of recently available genome sequences of these nonpathogenic species revealed that they contain open reading frames (ORFs) whose products share high levels of amino acid identity with many of the protein glycosylation components found in N. gonorrhoeae and N. meningitidis and with many of the N. gonorrhoeae proteins targeted for glycosylation. However, protein glycosylation has not been documented in any of these species yet.Here, we developed a systematic approach for elucidating intra- and interstrain glycan diversity and its genetic basis in neisserial O-linked glycans by employing serotyping, mass spectrometric analyses, and genetically defined recombinant backgrounds. We then used these tools to demonstrate that protein-associated glycans are antigenically variable and that isolates of N. meningitidis and N. lactamica also exhibit broad-spectrum O-linked protein glycosylation.     

Cultivation of Fastidious Bacteria by Viability Staining and Micromanipulation in a Soil Substrate Membrane System

Soil substrate membrane systems allow for microcultivation of fastidious soil bacteria as mixed microbial communities. We isolated established microcolonies from these membranes by using fluorescence viability staining and micromanipulation. This approach facilitated the recovery of diverse, novel isolates, including the recalcitrant bacterium Leifsonia xyli, a plant pathogen that has never been isolated outside the host.The majority of bacterial species have never been recovered in the laboratory (1, 14, 19, 24). In the last decade, novel cultivation approaches have successfully been used to recover “unculturables” from a diverse range of divisions (23, 25, 29). Most strategies have targeted marine environments (4, 23, 25, 32), but soil offers the potential for the investigation of vast numbers of undescribed species (20, 29). Rapid advances have been made toward culturing soil bacteria by reformulating and diluting traditional media, extending incubation times, and using alternative gelling agents (8, 21, 29).The soil substrate membrane system (SSMS) is a diffusion chamber approach that uses extracts from the soil of interest as the growth substrate, thereby mimicking the environment under investigation (12). The SSMS enriches for slow-growing oligophiles, a proportion of which are subsequently capable of growing on complex media (23, 25, 27, 30, 32). However, the SSMS results in mixed microbial communities, with the consequent difficulty in isolation of individual microcolonies for further characterization (10).Micromanipulation has been widely used for the isolation of specific cell morphotypes for downstream applications in molecular diagnostics or proteomics (5, 15). This simple technology offers the opportunity to select established microcolonies of a specific morphotype from the SSMS when combined with fluorescence visualization (3, 11). Here, we have combined the SSMS, fluorescence viability staining, and advanced micromanipulation for targeted isolation of viable, microcolony-forming soil bacteria.