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R H Symons

Publications and source records attributed to R H Symons.

At least 73 records · Page 4Linked to original sources
PubMed1984

Nucleotide sequence of cucumber-mosaic-virus RNA 2 reveals a translation product significantly homologous to corresponding proteins of other viruses.

The nucleotide sequence of the 3035 residues of RNA 2 (Mr 1.03 X 10(6) ) of the Q strain of cucumber mosaic virus (CMV) was determined by sequencing M13 clones of the RNA 2 cDNA and by dideoxy sequencing using primers prepared either from M13 clones or by chemical synthesis. A single long open reading frame starts at the second AUG from the 5' end of RNA 2 and encodes 839 amino acids (Mr 94333). This frame has flanking regions of 92 nucleotides at the 5' terminus and 423 nucleotides at the 3' terminus. Computer analysis of the nucleotide sequence showed that CMV RNA 2 has a significant homology with RNA 2 of brome mosaic virus (BMV) and alfalfa mosaic virus (AMV) and also with a region for tobacco mosaic virus (TMV) RNA encoding the read-through part of the 183-kDa protein. About 400 amino acids in the central region of the CMV RNA 2 translation product have a striking homology with the corresponding proteins encoded by BMV and AMV and with the read-through part of the TMV 183-kDa protein. Hydrophobicity plots of CMV and BMV RNA translation products also had apparent similarities. It is concluded that CMV is related to BMV, AMV and TMV in order of increasing evolutionary divergence.

Amino Acid Sequence↗
PubMed1983

Satellite RNA of cucumber mosaic virus forms a secondary structure with partial 3'-terminal homology to genomal RNAs.

Sat-RNA is one of several replicating satellite RNAs which have been isolated from RNA encapsidated in cucumber mosaic virus (CMV) and which are totally dependent on CMV for replication. The 336 residue sequence of Sat-RNA obtained using the dideoxynucleotide chain termination and partial enzymic digestion procedures shows only a few short stretches (up to 11 residues) of sequence homology with one of the three CMV genomal RNAs so far sequenced. Sat-RNA has 88% sequence homology with another, previously sequenced, satellite RNA of CMV, CARNA 5. Analysis of partial digests of 5'- or 3' -32P-Sat-RNA with nuclease S1 or RNase T1 under non-denaturing conditions showed that only about 10% of the residues in Sat-RNA were cleaved. Further data on base-paired segments of Sat-RNA were obtained using digestion with RNase T1 followed by electrophoretic fractionation of the resulting fragments under both non-denaturing and denaturing conditions. On the basis of this data, a complete secondary structure model is proposed for Sat-RNA with 52% of its residues involved in base pairs. A prominent hairpin at the 3'-terminus of Sat-RNA shows considerable sequence and structural homology with parts of the 3'-terminal tRNA-like structure of the CMV genomal RNAs.

Base Composition↗
PubMed1982

Comparative sequence and structure of viroid-like RNAs of two plant viruses.

A newly discovered group of spherical plant viruses contains a bipartite genome consisting of a single-strand linear RNA molecule (RNA 1, Mr 1.5 x 10(6) ), and a single-strand, covalently closed circular viroid-like RNA molecule (RNA 2, Mr approximately 125,000). The nucleotide sequences of the RNA 2 of two of these, velvet tobacco mottle virus and solanum nodiflorum mottle virus, have been determined. RNA 2 of solanum nodiflorum mottle virus consists of 377 residues whereas that of velvet tobacco mottle virus consists of two approximately equimolar species, one of 366 residues and the other, with a single nucleotide deletion, of 365 residues. There is 92-95% sequence homology between the RNA 2 species of the two viruses. The predicted secondary structures possess extensive intramolecular base pairing to give rod-like structures similar to those of viroids. The structural similarities between the RNAs 2 of velvet tobacco mottle virus and solanum nodiflorum mottle virus and viroids may reflect functional similarities.

Base Sequence↗
PubMed1982

Cucumber mosaic virus RNA 3. Determination of the nucleotide sequence provides the amino acid sequences of protein 3A and viral coat protein.

The complete sequence of the 2193 residues of RNA 3 (Mr 746000) of cucumber mosaic virus (Q strain) was determined by a combination of chemical and enzymic sequencing techniques utilizing cloned DNA fragments. The nucleotide sequence of RNA 3 also gave the complete sequence of 1027 residues of RNA 4 (Mr 349000), which codes for the viral coat protein and is derived from the 3' end; there are 53 untranslated nucleotides at the 5' end of RNA 4. The nucleotide sequence provided the amino acid sequences of the two proteins coded for by RNA 3: the 5'-terminal 3A protein with 333 amino acids (Mr 36700) and the 3'-terminal viral coat protein with 236 amino acids (Mr 26200). These two coding regions are in the same reading frame, are separated by an intercistronic region of 123 nucleotides and are flanked by two untranslated regions of 94 nucleotides at the 5' terminus and of 263 nucleotides at the 3' terminus. Secondary structure models are postulated for parts of the RNA 3 sequence. These are considered to be important in the control of the translation and replication of RNA 3 and in the processing of RNA 3 to give RNA 4.

Amino Acid Sequence↗
PubMed1981

Avocado sunblotch viroid: primary sequence and proposed secondary structure.

The sequence of the 247 nucleotide residues of the single strand circular RNA of avocado sunblotch viroid (ASBV) was determined using partial enzymic cleavage methods on overlapping viroid fragments obtained by partial ribonuclease digestion followed by 32p-labelling in vitro at their 5'-ends. ASBV is much smaller than potato spindle tuber viroid (PSTV; 359 residues) and chrysanthemum stunt viroid (CSV; 356 residues). A secondary structure model for ASBV is proposed and contains 67% of its residues base paired. In contrast to the extensive (69%) sequence homology of CSV with PSTV, only 18% of the ASBV sequence is homologous to PSTV and CSV. There are eight potential polypeptide translation products with chain lengths from 4 to 63 amino acid residues coded for by the plus (infectious) strand and four potential translation products (2 to 60 residues) coded for by the minus strand. An improved method is described for the synthesis of gamma-32p-ATP of high specific activity.

Base Sequence↗
PubMed1981

Chrysanthemum stunt viroid: primary sequence and secondary structure.

The sequence of the 356 nucleotide residues of chrysanthemum stunt viroid (CSV) has been determined. Overlapping linear viroid fragments were obtained by partial ribonuclease digestion, radiolabelled in vitro at their 5'-ends, and sequenced using partial enzymic cleavage methods. Of the CSV sequence, 69% is contained in the published sequence of potato spindle tuber viroid (PSTV). Differences in the primary sequence of CSV and PSTV suggest that neither the positive nor putative negative strands of these two viroids code for functional polypeptide products. However, the two viroids can form similar secondary structures, implicating a role for viroid structure in replication.

Base Sequence↗
PubMed1980

Cleavage of DNA.RNA hybrids by type II restriction enzymes.

The action of a number of restriction enzymes on DNA.RNA hybrids has been examined using hybrids synthesised with RNAs of cucumber mosaic virus as templates. The enzymes EcoRI, HindII, SalI, MspI, HhaI, AluI, TaqI and HaeIII cleaved the DNA strand of the hybrids (and possible also the RNA strand) into specific fragments. For four of these enzymes, HhaI, AluI, TaqI and HaeIII, comparison of the restriction fragments produced with the known sequences of the viral RNAs confirmed that they were recognising and cleaving the DNA strand of the hybrids at their correct recognition sequences. It is likely that the ability to utilise DNA.RNA hybrids as substrates is a general property of Type II restriction enzymes.

DNA Restriction Enzymes↗
PubMed1979

Extensive sequence homology at the 3'-termini of the four RNAs of cucumber mosaic virus.

The sequences of 270 residues from the 3'-termini of the four RNAs of cucumber mosaic virus have been determined by copying the in vitro polyadenylated RNAs with reverse transcriptase using d(pT8G) as primer and the 2',3'-dideoxynucleoside 5'-triphosphates as specific chain terminators. The terminal sequences of RNAs 3 and 4 were identical; this was expected since hybridization data has shown that the sequence of RNA 4 was present at the 3'-end of RNA 3 (Gould and Symons (1978) Eur. J. Biochem. 91, 269-278). The first 138 residues of RNAs 1 and 2 were identical to those of RNAs 3 and 4 except for one residue in RNA 1 and three residues in RNA 2. From residue 139 to 270 from the 3'-terminus, RNAs 1 and 2 showed, relative to RNAs 3 and 4, a non-homologous region of 33 residues, a homologous region of 40 residues, a partially homologous region of 14 residues which probably extended to about residue 300. There were 11 residues different between RNAs 1 and 2.

Base Composition↗
PubMed1978

Alfalfa mosaic virus RNA. Determination of the sequence homology between the four RNA species and a comparison with the four RNA species of cucumber mosaic virus.

The method of Taylor et al. [Taylor, J. M., Illmensee, R & Summers, J. (1976) Biochim. Biophys. Acta, 442, 324--330 and Gould and Symons (1977) Nucleic Acids Res. 4, 3787--3802] has been used to transcribe complementary DNA probes from the four major RNAs of alfalfa mosaic virus (AMV). Analysis of the kinetics of hybridization of these probes in homologous and heterologous complementary DNA . RNA hybridization reactions has shown that the sequence of the smallest RNA (RNA 4), which contains the coat protein gene, is present within RNA 3 and located at the 3' end of this RNA species. RNAs 1 and 2 are unique RNA molecules with little or no sequence homology between them or RNAs 3 and 4. This latter observation contrasts with the situation that occurs in cucumber mosaic virus (CMV) as CMV RNAs 1--4 were shown to have a common nucleotide stretch of 200 bases at their 3' termini; the location of RNA 4 within RNA 3 of CMV was also shown to be at the 3' end of this RNA species.

Avian Myeloblastosis Virus↗