Foot-and-mouth disease virus RNA. Presence of 3'-terminal polyriboadenylic acid and absence of amino acid binding ability

Genomic comparison of foot-and-mouth disease virus R strain and its chick-passaged attenuated strain

The present study examined the genomic differences between foot-and-mouth disease virus (FMDV) R strain and its attenuated, chick-passaged (R(304)) strain. Eleven pairs of primers were used to amplify the complete genome of FMDV R and R(304) by RT-PCR. Each fragment was cloned into pMD18-T vector and sequenced. Nucleotide analyses showed that the genome encoding regions of R and R(304) strains open reading frame (ORF) were both 6966 nucleotides (nt) in length, encoding 2322 amino acids. One hundred and ten nucleotides or 32 amino acids were found to be mutated most frequently were in the 3A gene. The next highest rates of mutation were observed in the LP and 1D genes. No mutations were found in either the 2A or 2C genes. The length of 5'IRES region and 3'UTR were 450 nt and 94 nt, respectively. The 5'IRES region and 3'UTR had only 4 nt and 3 nt mutation, respectively after attenuation. The R(304) poly(A) tail length of 18 nt, while that of the R strain was 30 nt. This result demonstrated the primary genomic changes of a FMDV and its attenuated strain, which has important implications in understanding the molecular epidemiology and functional genomics of FMDV.

IRES-driven translation is stimulated separately by the FMDV 3'-NCR and poly(A) sequences

The 3' end region of foot-and-mouth disease virus (FMDV) consists of two distinct elements, a 90 nt untranslated region (3'-NCR) and a poly(A) tract. Removal of either the poly(A) tract or both the 3'-NCR and the poly(A) tract abrogated infectivity in susceptible cells in the context of a full-length cDNA clone. We have addressed the question of whether the impairment of RNA infectivity is related to defects at the translation level using a double approach. First, compared to the full-length viral RNA, removal of the 3' sequences reduced the efficiency of translation in vitro. Secondly, a stimulatory effect of the 3' end sequences on IRES-dependent translation was found in vivo using bicistronic constructs. RNAs carrying the FMDV 3' end sequences linked to the second cistron showed a significant stimulation of IRES-dependent translation, whereas cap-dependent translation was not affected. Remarkably, IRES-dependent stimulation exerted by the poly(A) tract or the 3'-NCR seems to be the result of two separate events, as the 3'-NCR alone enhanced IRES activity on its own. Under conditions of FMDV Lb protease-induced translation shut-off, the stimulation of IRES activity reached values above 6-fold in living cells. A northern blot analysis indicated that IRES stimulation was not the consequence of a change in the stability of the bicistronic RNA produced in transfected cells. Analysis of the RNA-binding proteins interacting with a mixture of 3' end and IRES probes showed an additive pattern. Altogether, our results strongly suggest that individual signals in the viral 3' end ensure stimulation of FMDV translation.

Molecular cloning of foot and mouth disease virus genome and nucleotide sequences in the structural protein genes

Foot and mouth disease virus (FMDV), of the family Picornaviridae, consists of a single-stranded RNA (approximately 8,000 nucleotides), the translation of which is initiated on the 3' side of a 150-nucleotide poly(C) tract and yields a single polyprotein which is processed by host cell proteases into four primary products (Fig. 1). One or more virus-specified proteases further cleave these into the final products, the capsid proteins (VP1-4) being derived from the precursor p88 (for review see ref. 5). There are seven serotypes of the virus and as it has been shown that the immunizing activity of FMDV particles is associated primarily with VP1 (refs 6, 7), it seems likely that antigenic variation in FMDV is a result of changes in the structure of this protein. To further our understanding of this variation and as a first step in the possible development of FMDV vaccines from genetically manipulated microorganisms, we report here the construction and analysis of recombinant plasmids containing cDNA copies of the RNA. Comparison of the deduced amino acid sequence with the known polypeptide sequences shows that the NH2-termini of VP2 and VP3 are conserved between the A and O serotypes whereas that of VP1 (the immunizing antigen) varies by as much as 42% between serotypes.

Nucleotide sequence heterogeneity of the RNA from a natural population of foot-and-mouth-disease virus

The genomic RNA from isolates of foot-and-mouth-disease virus (FMDV) of serological types O or C obtained during epizootic outbreaks have been analysed by two-dimensional gel electrophoresis of the T1 RNase-generated oligonucleotides (T1 fingerprinting). Among virus isolates that are closely related serologically, 4-12 oligonucleotide changes were detected constitute the genome, the variations affect 0.7%-2.2% positions in FMDV RNA. Higher nucleotide-sequence divergence exists between the genomic RNAs from serologically unrelated viruses, while a 100-fold lower RNA sequence heterogeneity has been detected by analysis of individual clones derived from one viral isolate. Oligonucleotide mapping indicates that the variant oligonucleotides are scattered throughout the FMDV genome. We suggest that extensive genetic variability at many RNA sites is the basis for the antigenic diversity of FMDV.

A low molecular weight nuclear RNA from HeLa cells inhibits exogenous messenger RNA-dependent protein synthesis

A low molecular weight RNA of nuclear origin from adenovirus-infected HeLa cells inhibited rabbit reticulocyte polyribosomal RNA-dependent cell-free protein synthesis by reducing th formation of 80 S ribosome from 40 S-mRNA complex and 60 S subunits. This inhibitor did not hybridize with intact or HindIII-digested fragments of the viral DNA. Therefore it appears to be a 5.5 S RNA of cellular origin, which binds significantly with authentic IF-M2B from rabbit reticulocytes. In all these characteristics the inhibitor appears identical to a similar 5.5 S inhibitor RNA from non-infected HeLa cells.

Isolation of a foot-and-mouth disease polyuridylic acid polymerase and its inhibition by antibody

A template-dependent polyuridylic acid [poly(U)] polymerase has been isolated from BHK cells infected with foot-and-mouth disease virus (FMDV). Enzyme activity in a 20,000 x g supernatant of a cytoplasmic extract was concentrated by precipitation with 30 to 50% saturated ammonium sulfate. The poly(U) polymerase was freed of membranes by sodium dodecyl sulfate and 1,1,2-trichlorotrifluoroethane extraction, and RNA was removed by precipitation with 2 M LiCl. The solubilized poly(U) polymerase required polyadenylic acid as template complexed to an oligouridylic acid primer and Mg2+ for activity, but was inhibited by Mn2+. Antisera from animals infected with FMDV had previously been shown to inhibit the activity of FMDV RNA replicase complexed to the endogenous RNA template. The same antisera also inhibited the activity of poly(U) polymerase. Antisera depleted of antibody by absorption with the virus infection-associated antigen of FMDV no longer inhibited replicase and polymerase activities. The evidence suggests that FMDV RNA replicase, poly(U) polymerase, and the virus infection-associated antigen share a common protein.

Sequence of 129 nucleotides at the 3'-terminus of encephalomyocarditis virus RNA

The sequence of 129 nucleotides next to the poly(A) tail of encephalomyocarditis virus RNA has been determined by rapid gel sequencing of cDNA synthesized with DNA polymerase I or reverse transcriptase and a phasing primer, [5'-32P]p(dT)8dC. The sequence is in accord with (a) the pyrimidine tracts which were mapped in blocks along the cDNA, (B) the sequences of seven characteristic T1 RNase oligonucleotides in the RNA transcribed from the cDNA with RNA polymerase, and (c) a limited amount of sequence deduced by partial spleen phosphodiesterase digestion and depurination of endonuclease IV oligonucleotides. The 3' end shows little secondary structure on its own. Ten nonsense codons block all three reading frames such that at least 26 nucleotides do not code for protein. The possible function of a homology A-A-U-A-A-A with other polyadenylated RNAs is discussed.