Assignment of reovirus mRNA ribosome binding sites to virion genome segments by nucleotide sequence analyses

Homologous Terminal Sequences in the Double-Stranded RNA Genome Segments of Cytoplasmic Polyhedrosis Virus of the Silkworm Bombyx mori

The 3'-terminal regions (20 to 32 residues) of the genome double-stranded RNA (dsRNA) segments of cytoplasmic polyhedrosis virus were sequenced. The dsRNAs, which were labeled at their 3' termini by incubation with [5'-(32)P]pCp and T4 RNA ligase, were denatured and resolved into the plus and minus strands by agarose-urea gel electrophoresis. Ten single-stranded RNAs thus obtained from the five dsRNA segments IV, V, VIII, IX, and X were sequenced by postlabeling methods. Common 3'-terminal sequences, -GUUAGCC and -UUACU, were found in the plus and minus strands, respectively, of all five dsRNA segments. However, adjacent sequences diverged and were considerably variable. The homologous sequences found in the 3' end may be important recognition signals for viral RNA polymerases and for assembly of the genome segments.

Synthesis of the major inner capsid protein VP6 of the human rotavirus Wa in Escherichia coli

The gene for the major inner capsid protein VP6 of human rotavirus strain Wa has been cloned and placed into a bacterial expression vector under the control of the inducible hybrid trp-lac (tac) promoter. Recombinant VP6 was produced at low levels in a cell-free Escherichia coli transcription-translation system programmed with this expression plasmid. The yield of VP6 synthesized in the extract could be increased several-fold by introduction of point mutations upstream and downstream from the start codon. Upon induction with IPTG, E. coli JM105 cells harboring the mutated expression plasmid produced VP6 as shown by immunoblotting of proteins from bacterial lysates with anti-Wa antiserum. Recombinant VP6 appeared to inhibit the growth of E. coli and did not accumulate in the cells to high levels. Conformational analysis with a monoclonal antibody suggested that bacterially produced VP6 adopted an oligomeric structure characteristic for native VP6.

Molecular cloning and characterization of the genome of wound tumor virus: a tumor-inducing plant reovirus

The double-stranded RNA genome of the tumor-inducing plant pathogen, wound tumor virus, was converted to double-stranded DNA and cloned into plasmid pBR322. Multiple apparent full-length copies of 9 of the 12 wound tumor virus genome segments were identified. The entire sequence of cloned genome segment S12, the smallest of the genome segments, was determined. This genome segment was found to be 851 nucleotides in length and to possess a single long open reading frame that extends 178 codons from the first AUG triplet (residues 35-37): information sufficient to encode a protein of the size estimated for the smallest of the previously identified wound tumor virus primary gene products, Pns 12. Sequence data obtained from analysis of cloned cDNA copies of several genome segments and from direct analysis of the 3' termini of the double-stranded genome RNAs revealed that each wound tumor virus genome segment possesses the common terminal sequences: (+) 5'GGUAUU ... UGAU 3' (-) 3'CCAUAA ... ACUA 5'.

Reovirus type 3 genome segment S4: nucleotide sequence of the gene encoding a major virion surface protein

A full-length cDNA copy of reovirus double-stranded RNA genome segment S4 which codes for a major virion structural polypeptide, sigma 3, has been completely sequenced. The 1,196-nucleotide cDNA contains a single long open reading frame in the plus strand extending 1,095 nucleotides from the 5'-proximal A-T-G to a single stop codon. This corresponds to translation of 92% of the S4 gene. The inferred sigma 3 polypeptide is hydrophilic and consists of 365 amino acids, totalling 41,164 daltons.

Variant dsRNAs associated with transmission-defective isolates of wound tumor virus represent terminally conserved remnants of genome segments

Variant double-stranded RNAs are often associated with the genome of transmission-defective isolates of wound tumor virus. These RNAs are replicated and packaged into virus particles in systemically infected plants and are transcribed in vitro by the virion-associated transcriptase. Direct physical evidence that the variant RNAs are remnants of particular WTV genome segments was provided by molecular hybridization studies. Subsequently, ribonuclease T1 digestion products of 3'-end-labeled genome and remnant RNAs were analyzed by one- and two-dimensional electrophoretic techniques. One-dimensional partial and complete digestion patterns were indistinguishable, indicating that the guanosine positions relative to the 3' terminus of the corresponding strands of a particular genome segment and its remnant RNA are the same for at least 40 nucleotides from each end. Fingerprints of the 3' terminal ribonuclease T1-resistant fragments were identical, showing that the nucleotide composition of the 3' terminal ends of the corresponding strands of a particular genome segment and its remnant RNA are also identical. These results indicate that variant RNAs associated with transmission-defective WTV isolates are formed by deletion of an internal portion (as much as 85%) of genomic RNA segments yielding terminally conserved genomic remnants that are functional with respect to transcription, replication, and packaging.

Nucleotide sequence of reovirus genome segment S3, encoding non-structural protein sigma NS

This report describes the complete nucleotide sequence of human reovirus (Dearing strain) genome segment S3. Previous studies indicated that this RNA encodes the major non-structural viral polypeptide sigma NS, a protein that binds ssRNAs (Huisman & Joklik, Virology 70, 411-424, 1976) and has a poly(C)-dependent poly(G) polymerase activity (Gomatos et al., J. Virol. 39, 115-124, 1981). The genome segment consists of 1,198 nucleotides and possesses an open reading frame that extends 366 codons from the first AUG triplet (residues 28-30). There is no significant sequence homology between the plus strand of genome segment S3 and that of genome segment S2 determined previously (Cashdollar et al., PNAS 79, 7644-7648, 1982). However, S3 RNA has significant dyad symmetry and regions that can potentially hybridize (delta G = -26 KCal/mole) with S2 RNA. From the predicted amino acid sequence a possible secondary structure for sigma NS protein was determined. Structural features of reovirus RNA and sigma NS are discussed in relation to their role(s) in viral genome assembly.

Homologous terminal sequences of the genome double-stranded RNAs of bluetongue virus

The 3'-terminal sequences of the 10 double-stranded RNA genome segments of bluetongue virus (serotypes 10 and 11) were determined. The double-stranded RNAs were 3' labeled with [5'-32P]pCp and resolved into 10 segments by electrophoresis. After denaturation, the two complementary strands of segments 4 through 10 were resolved into fast- and slow-migrating species by polyacrylamide gel electrophoresis, and their 3' end sequences were determined. Complete RNase T1 digestion of the individual 3'-labeled double-stranded RNA segments yielded two labeled oligonucleotides, one of which migrated faster than the other on 20% polyacrylamide-7 M urea gels. Sequence analyses of the two oligonucleotides of segments 4 through 10 confirmed the corresponding RNA sequence data. For RNA segments 1 through 3 the oligonucleotide analyses gave comparable results. The 3'-terminal sequences of the fast-migrating RNA species were HOCAAUUU. . . ; those of the slow-migrating RNA species were HOCAUUCACA. . . . Similar results were obtained for double-stranded RNA from bluetongue virus serotypes 10 and 11. Beyond the common termini, the sequences for each segment varied considerably.

Molecular biology of rotaviruses. V. Terminal structure of viral RNA species

The terminal structure of rotavirus genomic ds RNA and in vitro transcribed mRNA was investigated using S1 nuclease digestion and 3' terminal sequence analysis. S1 nuclease analysis indicated that viral mRNA was not a truncated copy of the genome RNA at its 5' end. The 3' terminal sequence analysis of genomic plus strands and mRNA showed that they were coterminal indicating that in vitro transcribed mRNA is a full length copy of the genomic template. The sequence analysis performed on isolated viral RNA species plus strands revealed a completely conserved 3' terminal octanucleotide 5'-AUGUGACC-3' present in both UK tissue culture adapted bovine rotavirus and a human rotavirus isolate. Sequencing of isolated genomic minus strands again revealed a completely conserved 3' terminal sequence of approximately the same length as that seen for the viral plus strands.

Yeast killer dsRNA plasmids are transcribed in vivo to produce full and partial-length plus-stranded RNAs

In vivo transcripts of the L (4.5 kb) and M (1.9 kb) dsRNA plasmids were examined in type I killers of Saccharomyces cerevisiae. Transcripts for both plasmids include full-length (l,m) and partial-length (la,ma) single-stranded species. Both L-dsRNA transcripts (l,la) have in vitro mRNA activity for L-P1, previously shown to be identical to ScV-P1, the 88,000 dalton major capsid protein of the virus-like particles containing L- and M1-dsRNAs. 1, but not 1a, is bound to poly(U)-sepharose and may be polyadenylated. Other L-dsRNA gene products and their transcripts may exist. For M1-dsRNA, both species (m, ma) have in vitro mRNA activity for M1-P1, the 32,000 dalton pre-protoxin encoded by M1-dsRNA. Both m and ma are bound to poly(U)-Sepharose and ma is probably a 5' terminal fragment of m. A functional model for M1-dsRNA killer plasmid structure is presented.

Molecular cloning of double-stranded RNA virus genomes

Genome double-stranded RNAs isolated from purified human reovirus (serotype 3) and rotavirus (Wa strain) were modified at the 3' termini by addition of oligo(C) approximately 15 with T4 RNA ligase. These RNAs were transcribed into cDNA by oligo(dG)-primed reverse transcriptase and cloned after insertion into pBR322 at the Pst I site. Hybridization of plasmid-transformed Escherichia coli RR1 colonies with 32P-labeled viral genome RNAs demonstrated the presence of DNA clones representative of each of the 10 reovirus RNAs and 10 of the 11 constituent segments of the rotavirus genome. Analyses of the size and terminal nucleotide sequences of insert DNAs indicated that some clones contained a full-length copy of the virus genome segment. The complete nucleotide sequence of rotavirus genome segment 11 double-stranded RNA was obtained by using this procedure. It provides a general method for cloning double-stranded RNAs and also nonpolyadenylylated single-stranded RNAs.

In vitro transcription of defective interfering particles of influenza virus produces polyadenylic acid-containing complementary RNAs

Influenza virus defective interfering (DI) RNAs, which originate from polymerase genes by simple internal deletion, can be transcribed in vitro. These DI RNA transcripts contain covalently linked polyadenylic acid, and their synthesis is dependent on ApG or capped RNAs as primers. Furthermore, like the standard viral RNA transcripts, they are complementary in nature and are slightly smaller in size compared with the corresponding DI RNAs. Hybridization of the specific DI RNA transcripts with the corresponding DI RNA segments and analysis of the duplex RNA by gel electrophoresis indicate that they are not incomplete polymerase gene transcripts, but rather the transcripts of the DI RNAs. Since influenza virus DI RNAs contain both the 5' and the 3' termini and transcribe polyadenylic acid-containing complementary RNAs in vitro the mechanism of interference may differ from that of the 5' DI RNAs of Sendai and vesicular stomatitis viruses.

Structure and function of the reovirus genome

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Separation of the plus and minus strands of cytoplasmic polyhedrosis virus and human reovirus double-stranded genome RNAs by gel electrophoresis

The complementary strands of most of the genome double-stranded RNA segments of insect cytoplasmic polyhedrosis virus (CPV) and human reovirus are separated for the first time by agarose gel electrophoresis in in the presence of 7 M urea. CPV (+) strands and most reovirus (-) strands migrate faster than the corresponding strands of opposite polarity. Glyoxal treatment, which modifies guanine residues and prevents G-C basepairing, results in a loss of strand resolution and concomitantly a significant decrease in electrophoretic mobilities. Reovirus mRNAs synthesized in vitro with ITP substituted for GTP show similar decreased electrophoretic mobilities as the glyoxalated mRNAs. These results clearly indicate that the basis for (+) and (-) strand resolution is the presence of secondary structure formed mainly by G-C(U) base-pairs that are maintained during gel electrophoresis in the presence of 7 M urea. When the plus and minus strands of CPV genomes were separated and compared for protein synthesizing activity, it was found that only the plus strands were able to form stable 80S ribosome-RNA initiation complexes in wheat germ cell-free extracts.

Nucleotide sequence at the termini of the DNA of Bacillus subtilis phage phi 29

Phage phi 29 DNA cannot be phosphorylated with polynucleotide kinase and [gamma-32P]ATP because of the presence of a viral protein covalently linked to the 5' termini. The 5' ends can, however, be made susceptible to phosphorylation by treatment with alkali and alkaline phosphatase. Restriction fragments Hpa II C and Hpa II F, corresponding to the right and left ends of phi 29 DNA, respectively, were labeled at the 5' ends with polynucleotide kinase and [gamma-32P]ATP or at the 3' ends with terminal transferase and [alpha-32P]ATP or [alpha-32P]cordycepin 5'-triphosphate. After a secondary cleavage of the labeled fragments, the sequence of the first 150-180 nucleotides at the termini of phi 29 DNA was determined by the method of Maxam and Gilbert. The ends of phi 29 DNA are flush, and a six-nucleotides-long inverted terminal repetition was found. The functional implications of the sequences determined are discussed.

Proximity of mRNA5'-region and 18S rRNA in eukaryotic initiation complexes

Messenger RNA was covalently linked to 18S ribosomal RNA in eukaryotic 40S and 80S initiation complexes by photoreaction with an RNA cross-linking agent, 4'-substituted psoralen. The sites of interaction of the mRNA capped 5'-region included some 3'-ends of 18S rRNA.