Structural complexity of defective-interfering RNAs of Semliki Forest virus as revealed by analysis of complementary DNA

Söderlund, Hans; Keränen, Sirkka; Lehtovaara, Päivi; Palva, Ilkka; Pettersson, Ralf F.; Kääriäinen, Leevi

doi:10.1093/nar/9.14.3403

Cited by 25 publications

(5 citation statements)

References 33 publications

(37 reference statements)

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“…Oligonucleotide fingerprints of DIssBl (A) and DIssB2 (B) of passage 6, DIssC (C) and DIssD (D) of passage 13, DIssE (E) and DIssF (F) of passage 22, and RNA7 of original MHV-JHM (G) and of passage 13 (H). Arrows indicate the oligonucleotide spots which are not present in MHV-JHM genomic RNA. that several alpha virus DI RNAs contain sequence duplications, triplications, and rearrangements in addition to deletions (5,14,15,23,24,33). Similar structures might be present in MHV-JHM DI RNAs.…”

Section: Discussionmentioning

confidence: 77%

Structure of the intracellular defective viral RNAs of defective interfering particles of mouse hepatitis virus

Makino¹,

Fujioka²,

Fujiwara³

1985

J Virol

111

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The intracellular defective RNAs generated during high-multiplicity serial passages of mouse hepatitis virus JHM strain on DBT cells were examined. Seven novel species of single-stranded polyadenylic acid-containing defective RNAs were identified from passages 3 through 22. The largest of these RNAs, DIssA (molecular weight [mw], 5.2 x 106), is identical to the genomic RNA packaged in the defective interfering particles produced from these cells. Other RNA species, DIssBl (mw, 1.9 x 106 to 1.6 x 106), DIssB2 (mw, 1.6 x 106), DIssC (mw, 2.8 x 106) DIssD (mw, 0.82 x 106), DIssE (mw, 0.78 x 106), and DIssF (mw, 1.3 x 106) were detected at different passage levels. RNase Tl-resistant oligonucleotide fingerprinting demonstrated that all these RNAs were related and had multiple deletions of the genomic sequences. They contained different subsets of the genomic sequences from those of the standard intracellular mRNAs of nondefective mouse hepatitis virus JHM strain. Thus these novel intracellular viral RNAs were identified as defective interfering RNAs of mouse hepatitis virus JHM strain. The synthesis of six of the seven normal mRNA species specific to mouse hepatitis virus JHM strain was completely inhibited when cells were infected with viruses of late-passage levels. However, the synthesis of RNA7 and its product, viral nucleoprotein, was not significantly altered in late passages. The possible mechanism for the generation of defective interfering RNAs was discussed.

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Section: Discussionmentioning

confidence: 77%

Structure of the intracellular defective viral RNAs of defective interfering particles of mouse hepatitis virus

Makino¹,

Fujioka²,

Fujiwara³

1985

J Virol

111

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“…The RNA was transferred to nitrocellulose paper and prehybridized as described by Thomas (24). The filters were incubated with a 32P-labeled cDNA probe prepared from RV 40S RNA as described previously (23). The reaction mixture (100 pI) contained 50 mM Tris-hydrochloride (pH 8.3), 60 mM KCl, 12 mM MgCl2, 1 mM dithiothreitol, 0.8 mM each of dATP, dTTP, and dGTP, 0.1 mM of dCTP, 160 pLCi of [ot-32P]dCTP (400 Ci/mmol; Amersham), 10 p.g (about 2.5 pmol) of RV RNA as template, and 5 ,ug of oligo(dT)12 18 (P-L Biochemicals) as primer.…”

Section: Methodsmentioning

confidence: 99%

Rubella virus 40S genome RNA specifies a 24S subgenomic mRNA that codes for a precursor to structural proteins

Oker‐Blom¹,

Ulmanen²,

Kääriäinen³

et al. 1984

J Virol

111

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We have analyzed the structure of the rubella virus genome RNA and the virus-specific RNA species synthesized in B-Vero cells infected with rubella virus. A single-stranded, capped, and polyadenylated RNA species sedimenting at 40S in a sucrose gradient was released from purified virions treated with sodium dodecyl sulfate. This RNA species migrated with an M, of about 3.8 x 106 in an agarose gel after denaturation with glyoxal and dimethyl sulfoxide. Infected cells labeled with [3H]uridine in the presence of actinomycin D contained, in addition to the 40S RNA, a single-stranded polyadenylated 24S RNA species as shown by sucrose gradient analysis. In a Northern blot analysis, this RNA hybridized to a cDNA probe derived from the 3' portion of the genomic 40S RNA. In vitro translation of the 24S RNA species yielded a 110,000-dalton polypeptide, in addition to some smaller products which were immunoprecipitated with an antiserum prepared against the structural proteins El, E2a, E2b, and C. Since the sum of the molecular weights of the nonglycosylated envelope proteins and the capsid protein has been estimated to be about 116,000 (C. Oker-Blom et al., J. Virol. 46:964-973, 1983), these results suggest that the 24S RNA species represents a subgenomic mRNA coding for a precursor (pllO) to the structural proteins of rubella virus. Thus, the strategy of gene expression of rubella virus appears to be similar to that of the alphaviruses. The molecular biology of rubella virus (RV), the sole member of the genus Rubivirus of the Togaviridae family (18), has been rather poorly characterized (4, 5). This is especially true for the synthesis of virus-specific RNAs, the details of which are largely unknown. We have recently found that purified RV contains one capsid protein, C (Mr =

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“…1) except the 250 nucleotides from the 5' end, which has been determined earlier by primer extension of viral RNA (37) and the 22 5' terminal nucleotides by direct RNA sequencing of the antigenome (42). To avoid cloning artefacts the colinearity of the cDNA clones with 42S RNA was determined with Sl-nuclease (33). The nucleotide sequence of the cDNA clones was determined by the Maxam and Gilbert (28) and Sanger dideoxy (34) methods.…”

Section: Resultsmentioning

confidence: 99%

“…Transformation into E. coli HBIOl was according to Mandel and Higa (31). Small scale plasmid DINA was prepared (32) from colonies which had the correct antibiotic resistance pattern and were then assayed for colinearity with viral 42S RNA using S1-nuclease test (33) and large scale plasmid DNA was prepared as previously described (33). DNA sequencinc The nucleotide sequences of the cDNA clones were determined by Maxam and Gilbert (28) or Sanger dideoxy (34) methods.…”

Section: Methodsmentioning

confidence: 99%

Complete nucleotide sequence of the nonstructural protein genes of Semliki Forest virus

Takkinen

1986

Nucl Acids Res

119

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The nucleotide sequence coding for the nonstructural proteins of Semliki Forest virus has been determined from cDNA clones. The total length of this region is 7381 nucleotides, it contains an open reading frame starting at position 86 and ending at an UAA stop codon at position 7379-7381. This open reading frame codes for a 2431 amino acids long polyprotein, from which the individual nonstructural proteins are formed by proteolytic processing steps, so that nsPl is 537, nsP2 798, nsP3 482 and nsP4 614 amino acids. In the closely related Sindbis and Middelburg viruses there is an opal stop codon (UGA) between the genes for nsP3 and nsP4. Interestingly, no stop codon is found in frame in this region of the Semliki Forest virus 42S RNA. In other aspects the amino acid sequence homology between Sindbis, Middelburg and Semliki Forest virus nonstructural proteins is highly significant.

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Structural complexity of defective-interfering RNAs of Semliki Forest virus as revealed by analysis of complementary DNA

Cited by 25 publications

References 33 publications

Structure of the intracellular defective viral RNAs of defective interfering particles of mouse hepatitis virus

Structure of the intracellular defective viral RNAs of defective interfering particles of mouse hepatitis virus

Rubella virus 40S genome RNA specifies a 24S subgenomic mRNA that codes for a precursor to structural proteins

Complete nucleotide sequence of the nonstructural protein genes of Semliki Forest virus

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