Nucleotide sequence and genetic organization of barley stripe mosaic virus RNA-γ

The complete nucleotide sequence of RNA 1 of the tentative furovirus peanut clump virus (PCV) has been determined by characterization of cloned cDNA and by direct RNA sequencing. The sequence is 5897 nucleotides in length and contains three long open reading frames (ORFs). The Y-terminal proximal ORF has the potential to encode a polypeptide of M r 130942 (P131) containing methyltransferase and RNA helicase homologous domains and displaying homology with large nonstrnctural proteins of alpha-like viruses, which are known or thought to be involved in virus replication. The P131 ORF is followed in-frame by a second ORF which is probably expressed by partial readthrough of the UGA termination codon of the P131 ORF to produce a polypeptide of M r 191044 (P191). The readthrough region of P191 contains the characteristic 'core' RNA polymerase motif, indicating that the PCV replicase proteins are expressed as a pair of overlapping proteins as in the tobamoviruses, tobraviruses and the furovirus soil-borne wheat mosaic virus (SBWMV). Sequence comparisons indicate that P 131 and P 191 are most closely related to the replicase proteins of SBWMV and the hordeivirus barley stripe mosaic virus (BSMV) but are only distantly related to the replicase of the furovirus beet necrotic yellow vein virus (BNYVV). The T-terminal proximal ORF can encode a putative polypeptide ofM r 14556 (P15) which displays homology to small cysteine-rich proteins of hordeivirnses and SBWMV. We have corrected four errors in the sequence of PCV RNA 2 published previously by Manohar et al. (Virology 195, 33-41, 1993). One of these changes causes two small ORFs near the 3' terminus of RNA 2 to be fused together to create an ORF for a putative polypeptide ofM r 16 833 (P17) which displays extensive homology with the third protein of the triple gene block of BSMV RNA fl.

Section: Sequence Homologiesmentioning

confidence: 99%

Complete Nucleotide Sequence of Peanut Clump Virus RNA 1 and Relationships With Other Fungus-transmitted Rod-shaped Viruses

Herzog

Guilley

Manohar

et al. 1994

“…Gustafson & Armour, 1986;Gustafson et al, 1987Gustafson et al, , 1989. BSMV RNAs are capped and their 3' non-coding region encompasses an internal polydisperse poly(A) and the 3' tRNA-like structure accepting tyrosine (Agranovsky et al, 1979(Agranovsky et al, , 1981(Agranovsky et al, , 1982Kozlov et al, 1984).…”

Section: Introductionmentioning

confidence: 99%

Poa semilatent virus, a hordeivirus having no internal polydisperse poly(A) in the 3' non-coding region of the RNA genome

Agranovsky

Karasev

Novikov

et al. 1992

RNA from the Hungarian isolate of poa semilatent virus (PSLV) directed in vitro synthesis of 120K, 75K, 25K (coat protein) and 20K polypeptides. In vitro translation of PSLV RNA was blocked by the cap analogue, m7Gpp, thus suggesting that the virus RNA was capped. PSLV RNA could be aminoacylated with [~4C]tyrosine in vitro. The sequence of 1-5 kb from the 3' end of the PSLV RNA y component revealed two open reading frames (ORFs) separated by a uridinerich intergenic region. The putative product of the incomplete 5'-proximal ORF showed a close amino acid sequence similarity with the C-terminal segment of the 7a protein (putative RNA replicase) encoded in the barley stripe mosaic virus (BSMV) RNA 7, and the 20K product of the 3'-proximal ORF was found to be related to the 17K 7b product of BSMV. The sequence of 0-8 kb from the 3' end ofPSLV RNA fl encompassed two (incomplete) overlapping ORFs whose putative products are related to the tic and fld proteins encoded in the similarly arranged ORFs of BSMV RNA ft. Nucleotide sequence homology between the respective parts of the two hordeivirus genomes was restricted to the ORF for 7a, the spacer between the ORFs for ya and yb, and the 3' non-coding region, particularly the 95 nucleotide segment at the 3' end representing a tRNAlike structure. Despite limited sequence conservation beyond this segment, the entire 3' non-coding region of PSLV RNA could be folded in a tight pseudoknotted structure closely resembling that of BSMV RNA. Surprisingly, the 'signature' sequence typical for BSMV RNA, internal polydisperse poly(A) intercalated between the coding part and the 3' tRNA-like structure, was not detected in the PSLV genome. Instead, the virus RNA contained several oligoadenylate stretches spaced by other residues, close to the junction of its coding and 3' non-coding portions.

“…A more detailed analysis of these parts of the proteins is shown in Fig. 3 Herzog et al (1994), Gustafson et al (1987Gustafson et al ( , 1989 and Hamilton et al (1987). Fig.…”

mentioning

confidence: 99%

“…For the other viruses, including BSBV, there seems to be no need for such a gene because their movement functions are apparently encoded in a triple gene block which forms part of their smaller RNAs. Genes for structurally and possibly functionally related proteins with molecular masses of 15-17 kDa are found near the 3h-ends of PCV and TRV RNA 1 and on BSMV RNA (Herzog et al, 1994 ;Hamilton et al, 1987 ;Gustafson et al, 1987), whilst a gene for a possibly similar cysteine-rich protein with a molecular mass of 8 kDa is found near the 3h terminus of RNA 3 of PMTV (Scott et al, 1994). The genome of BSBV apparently lacks such a gene.…”

mentioning

confidence: 99%

Beet soil-borne virus RNA 1: genetic analysis enabled by a starting sequence generated with primers to highly conserved helicase-encoding domains.

Koenig¹,

Loss²

1997

The complete sequence of the 5834 nucleotides of RNA 1 of beet soil-borne furovirus (BSBV, Ahlum isolate) was determined using a PCR product obtained with primers to highly conserved coding regions for helicase-like proteins in RNA 1 of furo-, hordei-and tobraviruses as a starting sequence. Unknown parts of the sequence upstream and downstream of this starting sequence were amplified by means of RT-PCR techniques using combinations of specific and random primers. BSBV RNA 1 contains one large ORF for a readthrough protein with a molecular mass of 204 kDa (204K protein) which is interrupted internally by a UAA stop codon terminating the coding region for a protein of 145 kDa (145K protein). The N-and C-terminal parts of the 145K protein and the readthrough domain of the 204K protein contain methyltransferase, helicase and RNA-dependent RNA polymerase motifs, respectively. Unlike other furoand tobraviruses BSBV contains no further genes on its RNA 1.