Analyses of the mRNA transcription processes of Punta Toro phlebovirus (Bunyaviridae)

The time course of the syntheses of Punta Toro (PT) phlebovirus (Bunyaviridae) small (S)-size viral RNA (S vRNA), viral complementary RNA (S vcRNA), and messenger RNA (S mRNA) species has been analyzed using single-stranded DNA probes representing the two S-coded gene products. The data obtained support the conclusion that PT S RNA has an ambisense coding strategy (T. Ihara, H. Akashi, and D. H. L. Bishop, Virology 136, 293-306, 1984) with the viral nucleocapsid protein, N, encoded in a viral-complementary, subgenomic, mRNA species and a putative nonstructural protein, NSs, encoded in a viral-sense, subgenomic, second S mRNA species. In the absence of puromycin (or cycloheximide) full-length S vRNA, S vcRNA, and subgenomic N mRNA and putative NSs mRNA species were identified in PT virus-infected cell extracts. In the presence of inhibitors of protein synthesis (puromycin or cycloheximide) newly synthesized N mRNA species were detected, but not full-length S vcRNA, nor S vRNA, nor the S coded NSs mRNA species. The mRNA species recovered from drug-treated cells have been translated in vitro to synthesize viral N protein. Analyses of the 5' ends of the N and NSs mRNA species have shown them to be heterogeneous in sequence and some 11-18 bases longer than the ends of the genomic RNA species, indicating that they represent nonviral primer sequences like those identified for bunyavirus mRNA species (D. H. L. Bishop, M. E. Gay, and Y. Matsuoka, Nucleic Acids Res. 11, 6409-6418, 1983). The presence of such additional sequences on mRNA derived from representatives of two Bunyaviridae genera appears by these analyses to be a more conserved feature than the S RNA coding arrangement of the respective viruses.     

The M RNA of impatiens necrotic spot Tospovirus (Bunyaviridae) has an ambisense genomic organization.

The nucleotide sequence of Impatiens necrotic spot virus (INSV) M RNA was determined from cDNA clones. The INSV M RNA was 4972 nucleotides in length with two open reading frames (ORFs) in an ambisense genomic organization. The larger ORF near the 3' end of the viral RNA, coding for a protein with a predicted molecular weight of 124.9 kDa, was in the viral complementary sense and produced the G2 and G1 proteins. A smaller ORF in the viral sense was capable of coding for a 34.1-kDa polypeptide, designated the NSm protein. Two subgenomic RNA species were detected in INSV-infected tissue that corresponded to the predicted sizes (3.3 and 1.0 kb) of the G2-G1 and NSm mRNAs. The ORFs were separated by a 478 nucleotide A-U-rich intergenic region similar to the regions found in other viral RNAs with ambisense ORFs. The intergenic region was predicted to form a stable stem-loop structure (-81.2 kcal/mole). The ambisense genomic organization is characteristic of the S RNA for members of the Phlebovirus, Uukuvirus, and Tospovirus genera in the Bunyaviridae family. This is the first report of an ambisense Bunyaviridae M RNA.     

Identification of the N and NSS proteins coded by the ambisense S RNA of Punta Toro phlebovirus using monospecific antisera raised to baculovirus expressed N and NSS proteins

An essentially complete DNA copy of the ambisense S RNA species of Punta Toro (PT) phlebovirus (T. Ihara, H. Akashi, and D.H.L. Bishop, 1984, Virology 136, 293-306) has been inserted in either orientation into Autographa californica nuclear polyhedrosis baculovirus (AcNPV) in lieu of the 5' coding region of the AcNPV polyhedrin gene (G.E. Smith, M.D. Summers, and M.J. Fraser, 1983, Mol. Cell. Biol. 3, 2156-2165). The two types of recombinant viruses were used to infect Spodoptera frugiperda cells and the expressed PT viral proteins characterized. Recombinant AcNPV having the S DNA in one orientation expressed PT virus N protein in amounts estimated to represent some 50% of the infected cell extracts, whereas recombinants with the S DNA in the other orientation expressed the putative PT virus NSS protein in lower quantities. Antisera that were monospecific with respect to each of the two PT proteins virus were raised in mice using the corresponding S. frugiperda infected cell extracts and were employed to identify N and NSS proteins in PT virus-infected Vero cells.     

Complete sequences of the glycoproteins and M RNA of Punta Toro phlebovirus compared to those of Rift Valley fever virus

The complete sequence of Punta Toro virus (Phlebovirus, Bunyaviridae) middle size (M), RNA has been determined. The RNA is 4330 nucleotides long (mol wt 1.46 X 10(6), base composition: 26.7% A, 33.6% U, 18.5% G, 21.2% C) and has 3'- and 5'-terminal sequences that, depending on the arrangement, are complementary for some 15 residues. The viral RNA codes in its viral-complementary sequence for a single primary gene product (the viral glycoprotein precursor) that is comprised of 1313 amino acids (146,376 Da) and is abundant in cysteine residues but has few potential asparagine-linked glycosylation sites. The 5'-noncoding region of the Punta Toro M viral-complementary RNA is short (16 nucleotides); the 3'-noncoding sequence is much longer (372 nucleotides). The latter is rich in short stretches of adenylate residues, like the 3'-noncoding regions of the Punta Toro S mRNA species (T. Ihara, H. Akashi, and D. H. L. Bishop, 1984, Virology 136, 293-306). No other large open reading frame has been identified in either the viral, or viral-complementary, M RNA sequences. Limited amino-terminal sequence analyses of the two viral glycoproteins have indicated the gene order and potential cleavage sites in the glycoprotein precursor. The data suggest the existence of a 30 X 10(3)-Da polypeptide (designated NSM) in the glycoprotein precursor that precedes the G1 protein (i.e., gene product order: NSM-G1-G2). Examination of the sequence of the Punta Toro M gene product reveals the presence of multiple hydrophobic sequences including a 19-amino acid, carboxy-proximal, hydrophobic region (G2). This hydrophobic sequence is followed by a 13-amino acid-terminal sequence rich in charged amino acids. The size and constitution of the carboxy-terminal region is consistent with a transmembranal and anchor function for the glycoprotein in the viral envelope. Other regions of the glycoprotein precursor contain sequences of amino acids with a predominantly hydrophobic character (23, 50, and 20 amino acids in length). Their functions are unknown. The amino terminus of the G1 protein is located near the end of the 23-amino acid-long hydrophobic sequence of the presumptive precursor, the hydrophobic 50-amino acid sequence lies within G1, and the amino terminus of G2 is located in the middle of the 20-amino acid-long hydrophobic sequence.(ABSTRACT TRUNCATED AT 400 WORDS)     

Complete nucleotide sequence of the cucumber necrosis virus genome

The complete nucleotide sequence of the cucumber necrosis virus (CNV) genome has been determined. The genome is 4701 nucleotides in length and contains five long open reading frames (ORF). ORF1 begins at the first AUG codon at the 5' terminus and terminates at an amber codon. The predicted molecular weight of the polyprotein encoded by ORF1 is 33 kilodaltons (kDa). Readthrough of the ORF1 amber codon would yield a protein with a molecular weight of 92 kDa. Comparison of the amino acid sequence of the 92-kDa protein with the putative replicases of carnation mottle virus (CarMV) and barley yellow dwarf virus (BYDV) shows extensive sequence similarity. This suggests that the CNV 92-kDa protein is the viral replicase and, furthermore, suggests a close evolutionary relationship between CNV, CarMV, and BYDV, members of the Tombus-, Carmo-, and Luteovirus groups, respectively. Immediately following the 92-kDa protein is ORF3 which can encode a 40-kDa protein. It is identified as the coat protein based on its similarity in amino acid composition to the previously determined CNV coat protein sequence (J. H. Tremaine, 1972, Virology 48, 582-590) and on its amino acid sequence similarity with the tomato bushy stunt virus coat protein. Two nested ORFs (ORF4 and -5), in different frames, follow the coat protein gene. Although it is not known if both ORFs are expressed, they would encode proteins with predicted molecular weights of 21 and 20 kDa, respectively.     

Analyses of Patois group bunyaviruses: evidence for naturally occurring recombinant bunyaviruses and existence of immune precipitable and nonprecipitable nonvirion proteins induced in bunyavirus-infected cells

Shark River (SR) and Pahayokee (PAH) bunyaviruses (Patois serogroup, Bunyavirus genus, family Bunyaviridae) have almost identical L and S RNA oligonucleotide fingerprints, but M RNA fingerprints that are different, suggesting that the two viruses may represent naturally occurring reassortant viruses. These observations are in agreement with serological studies (B. N. Fields, B. E. Henderson, P. H. Coleman, and T. H. Work, 1969, Amer. J. Epidemiol., 89, 222-226) which have distinguished these two viruses by neutralization of infectivity tests (presumably reflecting differences in M RNA gene products, J. R. Gentsch, E. J. Rozhon, R. A. Klimas, L. H. El Said, R. E. Shope, and D. H. L. Bishop, 1980, Virology102, 190-204), but not by complement fixation tests (which probably relate to the viral N polypeptide coded by the S RNA, J. Gentsch, L. R. Wynne, J. P. Clewley, R. E. Shope, and D. H. L. Bishop, 1977b, J. Virol. 24,893-902). The 3' terminal 11 nucleotides of PAH S RNA (3' (HO)OUCAUCAAAUGA ... 5') are identical in sequence to those of the S RNA species of snowshoe hare (SSH) and La Crosse (LAC) viruses, except for a position 7A residue which is a C residue in the SSH and LAC sequences. The major virion polypeptides of SR and PAH viruses include a nucleocapsid polypeptide (N, 22 x 10(3)) and two glycoproteins (PAH: G1 118 x 10(3), G2, 35 x 10(3); SR: G1 113 x 10(3), G2, 35 x 10(3)). In SR-infected cells several immune precipitable polypeptides have been detected. These include 11-, 54-, 64-, 93-, and 104 x 10(3)-dalton polypeptides. In addition, both SR and PAH viruses induce a 74 x 10(3)-dalton polypeptide (p74) that has not been detected in actinomycin D-treated infected cells, and is not immune precipitated from infected cell extracts.     

Localized conserved regions of the S RNA gene products of bunyaviruses are revealed by sequence analyses of the Simbu serogroup Aino virus

The complete nucleotide sequence has been determined for the S RNA of Aino virus, a member of the Simbu serogroup (Bunyavirus genus, family Bunyaviridae). The S RNA is 850 nucleotides long (2.76 × 10⁵ dallons) and in the viral complementary sequence has a short 5' non-coding region of 34 nucleotides and a more extensive 3' non-coding region of 117 nucleotides. The 3'-5' complementarity of the Aino S RNA is about 25 residues long, depending on the arrangement. The Aino sequence predicts that, like snowshoe hare (SSH) and La Crosse (LAC) bunyaviruses (Bishop D.H.L., et al. (1982) Nucleic Acids Res., 10, 3703–3713; Akashi H. and Bishop D.H.L. (1983) J. Virol. 45, 1155–1158), there are two S coded gene products, a nucleoprotein N, and a non-structural protein, NS_S, that are read from overlapping reading frames in the viral complementary sequence. The Aino N primary gene product is composed of 233 amino acids (26.2 × 10³ daltons) and is 45% homologous in sequence with that of LAC virus. The NS_S protein of Aino virus is composed of 91 amino acids (10.5 × 10³ daltons) and is 35% homologous in sequence with the LAC NS_S protein. Unlike those viruses there are no uridylate tracts longer than 4 residues in the 5' non-coding region of the S viral RNA that could function as a template for polyadenylation of Aino S mRNA species.     

Coding strategy of the S RNA segment of Dugbe virus (Nairovirus; Bunyaviridae)

The S RNA segment of Dugbe (DUG) virus (Nairovirus; Bunyaviridae) was sequenced from three overlapping cDNA clones and by primer extension. The S RNA is 1712 nucleotides in length and contains one large open reading frame (ORF) of 1326 nucleotides coding for a 49.4-kDa protein on viral complementary (vc) RNA. This protein in size corresponds to the DUG nucleocapsid (N) protein (P. Cash, 1985, J. Gen. Virol. 66, 141-148). The 49.4-kDa product was expressed as a fusion protein with beta-galactosidase in Escherichia coli cells and confirmed as DUG N protein by Western blotting with DUG N-specific monoclonal antibody. An additional ORF of 150 nucleotides coding for a possible 5.9-kDa protein is present in the +1 reading frame, 3' to the N protein ORF on vcRNA. DUG S segment mRNA was found to be essentially full length. No evidence was obtained for the existence of a smaller mRNA species that could code for a 5.9-kDa protein. Comparisons of the DUG S RNA sequence and predicted N protein amino acid sequence, with the respective sequences of snowshoe hare, La Crosse (bunyaviruses), Punta Toro, Sandfly fever Sicilian (phleboviruses), and Hantaan (hantavirus) viruses, failed to detect any sequence similarity, although the genomic structure of DUG S RNA is similar to that of the S RNA segment of Hantaan (HTN) virus.     

Characterization of baculovirus-expressed Rift Valley fever virus glycoproteins synthesized in insect cells

A cDNA corresponding to the complete coding region of the M RNA of the M12 mutant of Rift Valley fever virus (RVFV) strain ZH548 (K. Takehara, M-K. Min, J.K. Battles, K. Sugiyama, V.C. Emery, J.M. Dalrymple, and D.H.L. Bishop, Virology, 169, 452-457, 1989) has been inserted into the baculovirus transfer vector pAcYM1. By comparison with the parent RVFV, the M RNA of the M12 mutant has a new small open reading frame (ORF1) upstream of the one that initiates the precursor of the viral glycoproteins (ORF2, gene order: NS(M)-G2-G1). A derivative of the M12 cDNA was prepared from which most of the upstream sequences (including a polyT tract and ORF1) were removed. Other cDNA constructs were made from this derivative, constructs in which most of the G1 sequences were also removed, or most of the NS(M) coding sequences, or all of the NS(M) and most of G2 coding sequences. Each RVFV M cDNA construct was inserted into a pAcYM1 transfer vector and recombinant baculoviruses were produced (RVM1-5). The derived viruses were employed to study the expression and properties of the RVFV glycoproteins in Spodoptera frugiperda insect cells. For each recombinant virus evidence was obtained which indicated that the RVFV glycoproteins were produced and processed in the insect cells. Although four of the recombinants gave low expression levels of the RVFV glycoproteins, for the vector that made only the G1 product, the expression level was significantly higher. Immunofluorescence analyses established that the RVFV glycoproteins were present both at intracellular locations and on the surface of the recombinant baculovirus infected insect cells.     

Vaccinia virus host range genes

A gene encoding an 18-kDa polypeptide (ORF C7L) located in the vaccinia virus HindIII C fragment was shown to be functionally equivalent to previously described host range gene (ORF K1L) spanning the HindIII K/M fragment junction. Either C7L or K1L host range gene is necessary and sufficient by itself to allow replication of vaccinia virus on human cells. Deletion of both C7L and K1L genes from the wild-type vaccinia genome is required to derive a virus deficient for replication on human cells. Further, an ORF encoding a 77-kDa polypeptide derived from cowpox (CP77kDa) and previously shown to allow vaccinia to overcome the restriction for replication on Chinese hamster ovary cells could substitute for the vaccinia host range genes C7L and K1L in permitting replication of the virus on human cells. Additionally, the three unique host range genes C7L, K1L, and CP77kDa were functionally equivalent for vaccinia replication on pig kidney cells, but not on rabbit kidney cells.     

Molecular characterization and detection of plum bark necrosis stem pitting-associated virus

The complete RNA genome of plum bark necrosis stem pitting-associated virus (PBNSPaV) was cloned and sequenced and was determined to be 14, 214 nts long. The genome structure revealed seven major open reading frames (ORFs), and nontranslated regions at the 5' and 3' ends. PBNSPaV represents the simplest genome organization in the genus Ampelovirus, family Closteroviridae. The ORFs 1a and 1b encode, respectively, a large polyprotein with a molecular mass (Mr) of 259.6 kDa containing conserved domains characteristic of a papain-like protease, methyltransferase and helicase (ORF1a) and a 64.1-kDa protein of eight conserved motifs characteristic of viral RNA-dependent RNA polymerase (RdRp) (ORF1b). ORF1b is presumably expressed via a +1 ribosomal frameshift mechanism. ORF2 encodes a small 6.3-kDa hydrophobic protein of unknown function. ORF3 encodes a 57.4-kDa protein, a homologue of the HSP70 family of heat shock proteins. ORF4 encodes a 61.6-kDa protein with unknown function. ORF5 encodes a 35.9-kDa capsid protein (CP). Lastly, ORF6 encodes a 25.2-kDa minor capsid protein (CPm). Phylogenetic analyses performed on sequences of the HSP70h RdRp and CP support classification of the virus in the genus Ampelovirus. A real-time TaqMan RT-PCR assay and a one-step RT-PCR were developed for PBNSPaV detection and compared using three different sample preparation methods.     

Rift Valley fever virus M segment: cellular localization of M segment-encoded proteins

The Phlebovirus Rift Valley fever virus (RVFV), like other members of the Bunyaviridae family, matures intracellularly at the smooth-surfaced vesicles in the Golgi region of infected cells. Here we show that in cultured cells the RVFV glycoproteins G2 and G1 accumulate and are retained at this site. To investigate the parameters governing this subcellular localization, we have engineered portions of the cloned RVFV M segment (which encodes a 14- and a 78-kDa protein, in addition to glycoproteins G2 and G1) into vaccinia virus. Immunofluorescent analysis of cells infected with a vaccinia virus recombinant containing the entire open reading frame of the RVFV M segment revealed Golgi localization for glycoproteins G2, G1, the 78-kDa protein, and Golgi as well as some reticular distribution for the 14-kDa protein. These distributions paralleled those seen in authentic RVFV-infected cells. RVFV-vaccinia virus recombinants possessing progressive deletions within the 152 amino acid preglycoprotein sequence of the M segment were analyzed for possible effects on the cellular distribution of G2 and G1. Removal of the first 130 amino acids of the open reading frame amino-terminal to the mature glycoprotein coding sequences, while abolishing production of the 78- and 14-kDa proteins, did not alter the Golgi location of G2 and G1. The data suggest that Golgi-specific signals reside within the G2 and/or G1 glycoprotein sequences. The use of vaccinia virus recombinants provides a genetically manipulable expression system with which to further investigate the sequences involved in the intracellular localization of these Phlebovirus proteins.     

Rapid detection of important human pathogenic Phleboviruses.

BACKGROUND: Rapid diagnostics are not available for several human pathogens in the genus Phlebovirus of the Bunyaviridae. OBJECTIVES: To develop RT-PCR assays for Sandfly Fever Sicilian virus (SFSV), Sandfly Fever Naples virus (SFNV), Toscana virus (TOSV) and Rift Valley Fever virus (RVFV). STUDY DESIGN: RNA standards were generated and used to test the performance of the assays. RESULTS: A detection limit of 10-100 RNA molecules was determined for the SFSV, TOSV and RVFV assays. The sensitivity of the SFNV assay was not determined. The TOSV and the RVFV assays detected recent isolates from Spain and Africa, respectively. CONCLUSION: The assays should help to improve surveillance of pathogenic Phleboviruses.     

The genome structure of turnip crinkle virus

The nucleotide sequence of turnip crinkle virus (TCV) genomic RNA has been determined from cDNA clones representing most of the genome. Segments were confirmed using dideoxynucleotide sequencing directly from viral RNA, and the 3' terminal sequence was confirmed by chemical sequencing of end-labeled genomic RNA. Three open reading frames (ORFs) have been identified by examination of the deduced amino acid sequences and by comparison with the ORFs found in the genome of carnation mottle virus. ORF 1 initiates near the 5' terminus of the genome and is punctuated by an amber termination codon. Translation of ORF 1 would yield a 28-kDa protein and an 88-kDa read-through product. The read-through domain possesses amino acid sequence similarities with putative viral RNA polymerases. ORFs 2 and 3 encode products of 38 (coat protein) and 8 kDa, respectively, which are expressed from subgenomic mRNAs. The organization of the TCV genome suggests that TCV is closely related to carnation mottle virus and distinct from members classified in other small RNA virus groups, such as the tombus- and sobemoviruses.     

Organization of the middle RNA segment of snowshoe hare Bunyavirus

The genetic organization of the M RNA segment of snowshoe hare (SSH) virus, a member of the Bunyavirus genus of the family Bunyaviridae, has been determined. The middle (M) RNA segment has a single open reading frame (ORF) of 1441 amino acids. We have used amino- and carboxy-terminus sequencing and synthetic peptides to map proteins within the ORF. The order of the proteins translated from the single large open reading frame is G2, NSm, G1. The G2 protein extends from amino acids 14 to 299. The molecule is 286 residues long, with a computed nonglycosylated molecular weight of 31,973 Da. It is preceded by a cleaved 13 amino acid signal sequence. G2 includes a long highly hydrophobic sequence and contains three potential N-linked glycosylation sites. The G1 protein occupies the C-terminal end of the open reading frame from amino acids 474 to 1441 (968 amino acid residues) and has a computed nonglycosylated, molecular weight of 108,981 kDa. It has two potential N-linked glycosylation sites, and a potential transmembrane region followed by a potential cytoplasmic domain at the C-terminal end. If membrane associated it has an orientation of N-terminus outer, C-terminus inner. Limited trypsin digestion removes a 33-kDa fragment from the N-terminal end, leaving a virion-associated truncated G1 molecule (amino acids 762 to 1441) with a single N-linked glycosylation site. Between the G2 and G1 molecules there are 174 amino acids, sufficient to code for 19 kDa of protein. Some antibodies raised against peptides within this region react with proteins of 11 kDa (NSm) and 10 kDa present in infected cell lysates, but the exact relationship of these proteins to the open reading frame remains to be determined.