Requirement of the poly(A) tail in coronavirus genome replication.
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3' Untranslated Regions↗
Biomedical subjects
B G Hogue
Publications and source records attributed to B G Hogue.
Identification of nucleocapsid binding sites within coronavirus-defective genomes.
The coronavirus nucleocapsid (N) protein is a major structural component of virions that associates with the genomic RNA to form a helical nucleocapsid. N appears to be a multifunctional protein since data also suggest that the protein may be involved in viral RNA replication and translation. All of these functions presumably involve interactions between N and viral RNAs. As a step toward understanding how N interacts with viral RNAs, we mapped high-efficiency N-binding sites within BCV- and MHV-defective genomes. Both in vivo and in vitro assays were used to study binding of BCV and MHV N proteins to viral and nonviral RNAs. N-viral RNA complexes were detected in bovine coronavirus (BCV)-infected cells and in cells transiently expressing the N protein. Filter binding was used to map N-binding sites within Drep, a BCV-defective genome that is replicated and packaged in the presence of helper virus. One high-efficiency N-binding site was identified between nucleotides 1441 and 1875 at the 3' end of the N ORF within Drep. For comparative purposes N-binding sites were also mapped for the mouse hepatitis coronavirus (MHV)-defective interfering (DI) RNA MIDI-C. Binding efficiencies similar to those for Drep were measured for RNA transcripts of a region encompassing the MHV packaging signal (nts 3949-4524), as well as a region at the 3' end of the MHV N ORF (nts 4837-5197) within MIDI-C. Binding to the full-length MIDI-C transcript (approximately 5500 nts) and to an approximately 1-kb transcript from the gene 1a region (nts 935-1986) of MIDI-C that excluded the packaging signal were both significantly higher than that measured for the smaller transcripts. This is the first identification of N-binding sequences for BCV. It is also the first report to demonstrate that N interacts in vitro with sequences other than the packaging signal and leader within the MHV genome. The data clearly demonstrate that N binds coronavirus RNAs more efficiently than nonviral RNAs. The results have implications with regard to the multifunctional role of N.
Animals↗
Identification of a bovine coronavirus packaging signal.
A region of the bovine coronavirus (BCV) genome that functions as a packaging signal has been cloned. The 291-nucleotide clone shares 72% homology with the region of mouse hepatitis coronavirus (MHV) gene 1b that contains the packaging signal. RNA transcripts were packaged into both BCV and MHV virions when the cloned region was appended to a noncoronavirus RNA. This is the first identification of a BCV packaging signal. The data demonstrate that the BCV genome contains a sequence that is conserved at both the sequence and functional levels, thus broadening our insight into coronavirus packaging.
Animals↗
Host protein interactions with the 3' end of bovine coronavirus RNA and the requirement of the poly(A) tail for coronavirus defective genome replication.
RNA viruses have 5' and 3' untranslated regions (UTRs) that contain specific signals for RNA synthesis. The coronavirus genome is capped at the 5' end and has a 3' UTR that consists of 300 to 500 nucleotides (nt) plus a poly(A) tail. To further our understanding of coronavirus replication, we have begun to examine the involvement of host factors in this process for two group II viruses, bovine coronavirus (BCV) and mouse hepatitis coronavirus (MHV). Specific host protein interactions with the BCV 3' UTR [287 nt plus poly(A) tail] were identified using gel mobility shift assays. Competition with the MHV 3' UTR [301 nt plus poly(A) tail] suggests that the interactions are conserved for the two viruses. Proteins with molecular masses of 99, 95, and 73 kDa were detected in UV cross-linking experiments. Less heavily labeled proteins were also detected in the ranges of 40 to 50 and 30 kDa. The poly(A) tail was required for binding of the 73-kDa protein. Immunoprecipitation of UV-cross-linked proteins identified the 73-kDa protein as the cytoplasmic poly(A)-binding protein (PABP). Replication of the defective genomes BCV Drep and MHV MIDI-C, along with several mutants, was used to determine the importance of the poly(A) tail. Defective genomes with shortened poly(A) tails consisting of 5 or 10 A residues were replicated after transfection into helper virus-infected cells. BCV Drep RNA that lacked a poly(A) tail did not replicate, whereas replication of MHV MIDI-C RNA with a deleted tail was detected after several virus passages. All mutants exhibited delayed kinetics of replication. Detectable extension or addition of the poly(A) tail to the mutants correlated with the appearance of these RNAs in the replication assay. RNAs with shortened poly(A) tails exhibited less in vitro PABP binding, suggesting that decreased interactions with the protein may affect RNA replication. The data strongly indicate that the poly(A) tail is an important cis-acting signal for coronavirus replication.
3' Untranslated Regions↗
Coronavirus envelope glycoprotein assembly complexes.
Protein:protein interactions, and their subcellular localization, play important roles in coronavirus assembly. In this study, we have identified similar envelope glycoprotein complexes that are present in mouse hepatitis coronavirus A59 (MHV-A59) and bovine coronavirus (BCV) infected cells. Complexes consisting of the spike (S) and membrane (M) proteins were identified in cells infected with MHV-A59 or BCV. Kinetic analyses demonstrated that S and M quickly associated after translation, and suggested that both initially interacted in a pre-Golgi site. In addition, the hemagglutinin esterase (HE) was identified as part of a complex with M and S in BCV infected cells. Taken together, our data indicate that similar glycoprotein complexes are present in cells infected with two different coronaviruses, and thus likely represent important prerequisite complexes involved in virus assembly.
Animals↗
Coronavirus nucleocapsid protein. RNA interactions.
The coronavirus nucleocapsid protein (N) is involved in encapsidation and packaging of viral RNA. In this study we investigated the ability of the bovine coronavirus (BCV) N protein to interact with RNA. Histidine-tagged BCV N (his-N) protein was expressed in bacteria. A filter binding assay was established to quantitatively measure the binding efficiency of purified his-N to different RNAs. The results indicate that bacterially expressed N bound both BCV and mouse hepatitis coronavirus (MHV) RNAs. Binding to in vitro generated BCV and MHV RNA transcripts was significantly higher than binding to a non-coronavirus RNA. Similar binding efficiencies were measured for a BCV defective genome, pDrep, and a transcript that contained the MHV packaging signal. Interestingly, the entire MHV DI, pMIDI-C, was bound at a higher efficiency than the packaging signal alone. This is one of the first reports to show that N interacts with the MHV packaging signal.
Animals↗
Protein interactions during coronavirus assembly.
Coronaviruses assemble and obtain their envelope at membranes of the intermediate compartment between the endoplasmic reticulum and Golgi complex. Like other enveloped viruses, coronavirus assembly is presumably dependent on protein localization and protein-protein as well as protein-RNA interactions. We have used the bovine coronavirus (BCV) as a model to study interactions between the viral proteins in virus-infected cells that are important for coronavirus assembly. BCV is a prototype for the coronaviruses that express an additional major structural protein, the hemagglutinin esterase (HE), in addition to the spike (S) glycoprotein, membrane (M) glycoprotein, and nucleocapsid (N) protein. Complexes consisting of the M, S, and HE proteins were detected in virus-infected cells by coimmunoprecipitations. Kinetic analyses demonstrated that S protein and HE each quickly formed a complex with M protein after synthesis, whereas heterocomplexes consisting of all three proteins formed more slowly. The kinetics of HE biosynthesis revealed that the half-life of oligomerization was approximately 30 min, which correlated with the appearance of complexes consisting of M, HE, and S proteins, suggesting that oligomerization and/or conformational changes may be important for the S-M-HE protein complexes to form. Only HE dimers were found associated with the heterocomplexes consisting of all three proteins. S-M-HE protein complexes were detected prior to processing of the oligosaccharide chains on HE, indicating that these protein complexes formed in a premedial Golgi compartment before trimming of sugar chains. Transient coexpressions and double-labeling immunofluorescence demonstrated that HE and S proteins colocalized with M protein. This was further supported by coimmunoprecipitation of specific HE-M and S-M protein complexes from transfected cells, indicating that these proteins can form complexes in the absence of other viral proteins.
Animals↗
Bovine coronavirus nucleocapsid protein processing and assembly.
The coronavirus nucleocapsid protein (N) encapsidates the genomic RNA to form a helical nucleocapsid. The requirements for coronavirus nucleocapsid assembly are being studied. Two forms (approximately 50 kDa and 55 kDa) of the bovine coronavirus (BCV) N protein were detected in infected cells. However, only one form, a 50 kDa species, was detected in extracellular virions. After treatment with calf intestinal alkaline phosphatase (CIAP), the 55 kDa intracellular form increased in mobility to comigrate with the 50 kDa form; whereas, the 50 kDa intracellular species and N from extracellular virions was not sensitive to CIAP treatment. The data indicate that specificity exists with regard to assembly of N into the mature virion. The data suggests that processing of N may take place during assembly of either nucleocapsids or virions and that the processing may be a dephosphorylation event.
Alkaline Phosphatase↗
Deletion mutation in the signal anchor domain activates cleavage of the influenza virus neuraminidase, a type II transmembrane protein.
Influenza virus neuraminidase (NA) is a type II integral membrane protein with a long hydrophobic domain [29 amino acids (aa)] at the N terminus that functions as an uncleaved signal for translocation into the endoplasmic reticulum and anchors the protein in the membrane. The function of the transmembrane domain in intracellular transport was investigated by deletion mutagenesis. Expression of the mutated NA in eukaryotic cells and by in vitro translation in the presence of membranes showed that the deletion of eight amino acids (aa 28 to 35) from the carboxy end of the signal anchor domain resulted in cleavage, probably by the signal peptidase and secretion of NA into the culture medium. The mutant NA (N28-35) was present inside the cell predominantly as dimers, secreted as dimers, and was enzymatically inactive. When translated in vitro in the presence of dog pancreatic microsomal membranes, the N28-35 protein underwent cleavage and did not remain anchored to membranes. Two other deletion mutants in the transmembrane domain, N7-17 and N17-23, were partially cleaved and secreted, whereas two mutants, one (N19-27) lacking nine aa in the central region and the other (N1-14) lacking the first 14aa from the N terminus remained uncleaved and exhibited a phenotype similar to the wild-type NA. We conclude that the longer transmembrane domain (29 aa) may play an important role in determining that type II signal is not cleaved during translocation; however, in addition, adjacent amino acid sequences also provide determinants important in signal cleavage.
Amino Acid Sequence↗
Development and application of an enzyme immunoassay for coronavirus OC43 antibody in acute respiratory illness.
Study of coronavirus OC43 infections has been limited because of the lack of sensitive cell culture systems and serologic assays. To improve this circumstance, we developed an indirect enzyme immunoassay (EIA) to detect serum antibody to OC43. Antigen (100 ng) prepared by polyethylene glycol precipitation provided optimal results without a postcoat procedure. Evaluation of intraplate variation indicated that a > or = 2.5-fold increase in serum titer was significant. Sixteen of 18 (89%) paired serum samples with previously identified, reproducible increases in the level of hemagglutination inhibition (HAI) antibody to OC43 also showed significant increases as detected by EIA. Specificity for the EIA was established with paired sera obtained from persons given influenza immunizations or experiencing a respiratory infection. No rise in antibody titers occurred among 33 persons with documented coronavirus 229E infection. EIA was then performed on each of 419 paired serum samples from ambulatory chronic obstructive pulmonary disease patients and healthy older adults, from asthmatic adults presenting for emergency room treatment, and from persons hospitalized with acute respiratory symptoms. Twenty-three antibody rises to OC43 were detected; only nine of these were detected by the HAI test, and the HAI test did not detect any increases in antibody titers that were not detected by EIA. Nineteen of 25 coronavirus OC43 infections for which a month of infection could be assigned occurred between November and February. Overall, 4.4% of acute respiratory illnesses in the studied populations were associated with a coronavirus OC43 infection.
Acute Disease↗
The 9-kDa hydrophobic protein encoded at the 3' end of the porcine transmissible gastroenteritis coronavirus genome is membrane-associated.
The open reading frame potentially encoding a 78 amino acid, 9101 Da hydrophobic protein (HP) and, mapping at the 3' end of the porcine transmissible gastroenteritis coronavirus (TGEV) genome, was shown to be expressed during virus replication. The cloned HP gene was placed in a plasmid under control of the T7 RNA polymerase promoter and in vitro translation of transcripts generated in vitro yielded a 9.1-kDa protein that was immunoprecipitable with porcine hyperimmune anti-TGEV serum. Antiserum raised in rabbits against a 31 amino acid synthetic polypeptide that represented the central hydrophilic region of HP specifically immunoprecipitated HP from TGEV-infected cells. HP was further shown to become associated with microsomal membranes during synthesis in vitro and was found to be closely associated with the endoplasmic reticulum and cell surface membranes in infected cells. The intracellular location of HP suggests that it may play a role in the membrane association of replication complexes or in virion assembly.
Amino Acid Sequence↗
Synthesis and processing of the influenza virus neuraminidase, a type II transmembrane glycoprotein.
The influenza virus neuraminidase (NA), a type II transmembrane glycoprotein, is expressed at the surface of infected cells and is a major structural component of the virion. The kinetics of biosynthesis of NA, including modification of N-linked sugar chains, association with GRP78-BiP, oligomerization, and transport to the cell surface, were examined in A/WSN/33 influenza-infected BHK cells. Prior to gaining endoglycosidase H (endo H) resistance, NA was found to transiently associate with GRP78-BiP (t1/2 approximately 5 min). The protein was synthesized as a monomer and within 10 min a significant fraction of it was chased into dimers and tetramers with a t1/2 approximately 15 to 20 min before endo H resistance was acquired suggesting that oligomerization took place in the endoplasmic reticulum. WSN NA remained completely endo H sensitive up to 15 min after synthesis, acquired partial resistance to endo H between 15 and 30 min (t1/2 approximately 25 min) after synthesis and exhibited heterogeneity in endo H-resistant forms. NA was first detected at the cell surface 30 min after synthesis, increased to a maximum at 1 hr, after which it decreased, presumably due to incorporation into virions. The results on the biosynthesis of NA, a type II protein for which the three-dimensional structure is known, will be useful in structure/function and virion assembly studies.
Animals↗
Structure and expression of the bovine coronavirus hemagglutinin protein.
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Amino Acid Sequence↗
Expression of the porcine transmissible gastroenteritis coronavirus M protein.
Cloned cDNA encoding the M protein of the porcine transmissible gastroenteritis coronavirus (TGEV) was introduced into a vaccinia virus to examine the function of the amino-terminal signal peptide. The M protein expressed by the recombinant virus was targeted to the Golgi region of infected cells, as is the M protein in cells infected with TGEV. The protein appeared not to undergo processing other than glycosylation. However, the vaccinia-expressed M protein was slightly larger than the protein found in TGEV-infected cells, suggesting that a difference in modification exists between the proteins.
Animals↗
Structure and orientation of expressed bovine coronavirus hemagglutinin-esterase protein.
The sequence of the hemagglutinin-esterase (HE) gene for the Mebus strain of bovine coronavirus was obtained from cDNA clones, and its deduced product is a 47,700-kilodalton apoprotein of 424 amino acids. Expression of the HE protein in vitro in the presence of microsomes revealed N-terminal signal peptide cleavage and C-terminal anchorage but not disulfide-linked dimerization. Dimerization was observed only after expression in vivo, during which HE was also transported to the cell surface.
Amino Acid Sequence↗
Synthesis and processing of the bovine enteric coronavirus haemagglutinin protein.
The haemagglutinin molecule on the bovine enteric coronavirus has been identified as a glycoprotein of 140K composed of disulphide-linked subunits of 65K. In this study, we have shown the subunits to be identical by demonstrating an unambiguous amino-terminal amino acid sequence. The unglycosylated subunit was found to have an Mr of 42.5K and to undergo rapid disulphide linkage and glycosylation. Glycosylation was found to be of the asparagine-linked type and some of the oligosaccharides underwent processing to complex forms. Studies with inhibitors of glycosylation suggested that a processing of the haemagglutinin oligosaccharide takes place on the virion whilst it is in the Golgi apparatus. Each haemagglutinin subunit on the mature virion was estimated to possess six or seven carbohydrate chains of either the high-mannose or hybrid type, and three or four chains of the complex type.
Amino Acid Sequence↗
The amino-terminal signal peptide on the porcine transmissible gastroenteritis coronavirus matrix protein is not an absolute requirement for membrane translocation and glycosylation.
cDNA clones mapping within the first 2601 bases of the 3' end of the porcine transmissible gastroenteritis corona-virus (TGEV) genome were sequenced by the method of Maxam and Gilbert and an open reading frame yielding a protein having properties of the matrix (M or E1) protein was identified. It is positioned at the 5' side of the nucleocapsid (N) gene from which it is separated by an intergenic stretch of 12 bases. The deduced M protein comprises 262 amino acids, has a molecular weight of 29,544, is moderately hydrophobic, and has a net charge of +7 at neutral pH. Thirty-four percent of its amino acid sequence is homologous with the M protein of the bovine coronavirus (BCV), 32% with that of the mouse hepatitis coronavirus (MHV), and 19% with that of the avian infectious bronchitis coronavirus (IBV). Judging from alignment with the BCV, MHV, and IBV M proteins, the amino terminus of the TGEV M protein extends 54 amino acids from the virion envelope which compares with only 28 for BCV, 26 for MHV, and 21 for IBV. Eleven of the sixteen amino-terminal amino acids are hydrophobic and the positions of charged amino acids around this sequence suggest that the first 16 amino acids comprise a potentially cleavable signal peptide for membrane insertion. A similar sequence is not found in the M proteins of BCV, MHV, or IBV. When mRNA from infected cells, or RNA prepared by in vitro transcription of the reconstructed M gene, was translated in vitro in the presence of microsomes, the M protein became translocated and glycosylated. When a protein without the amino-terminal signal peptide was made by translating a truncated version of the M gene transcript, some translocation and glycosylation also occurred suggesting that the amino-terminal signal peptide on the TGEV M protein is not an absolute requirement for membrane translocation. Interestingly, the amino-terminal peptide did not appear to be cleaved during in vitro translation in the presence of microsomes suggesting that a step in virion assembly may be required for proper exposure of the cleavage site to the signal peptidase.
Amino Acid Sequence↗
Temporal regulation of bovine coronavirus RNA synthesis.
The structure and synthesis of bovine coronavirus (BCV)-specific intracellular RNA were studied. A genome-size RNA and seven subgenomic RNAs with molecular weights of approximately 3.3 X 10(6), 3.1 X 10(6), 2.6 X 10(6), 1.1 X 10(6), 1.0 X 10(6), 0.8 X 10(6) and 0.6 X 10(6) were detected. Comparisons of BCV intracellular RNAs with those of mouse hepatitis virus (MHV) demonstrated the presence of an additional RNA for BCV, species 2a, of 3.1 X 10(6) daltons. BCV RNAs contain a nested-set structure similar to that of other coronaviruses. This nested-set structure would suggest that the new RNA has a capacity to encode a protein of approximately 430 amino acids. Kinetic studies demonstrated that the synthesis of subgenomic mRNAs and genomic RNA are differentially regulated. At 4 to 8 h post-infection (p.i.), subgenomic RNAs are synthesized at a maximal rate and represent greater than 90% of the total viral RNA synthesized, whereas genome-size RNA accounts for only 7%. Later in infection, at 70 to 72 h p.i., genome-size RNA is much more abundant and accounts for 88% of total RNA synthesized. Immunoprecipitations of [35S]methionine-pulse-labeled viral proteins demonstrated that viral protein synthesis occurs early in the infection, concurrent with the peak of viral subgenomic RNA synthesis. Western blot analysis suggests that these proteins are stable since the proteins are present at high level as late as 70 to 72 h p.i. The kinetics of production of virus particles coincides with the synthesis of genomic RNA. These studies thus indicate that there is a differential temporal regulation of the synthesis of genomic RNA and subgenomic mRNAs, and that the synthesis of genomic RNA is the rate-limiting step regulating the production of virus particles.
Adenocarcinoma↗