Nucleotide Sequence of Tomato Black Ring Virus RNA-1

Abstract

SUMMARYThe sequence of the 7356 nucleotide [excluding the 3' poly(A)] RNA-1 of tomato black ring virus (TBRV) was determined from overlapping cDNA clones. A putative initiation codon at nucleotide 26l was considered to be the start of an open reading frame which terminates at a UAG codon at position 7053. The predicted translation product is a protein of 2264 amino acids with an Mr of 253 680 (254K). Comparison of the amino acid sequence of this 254K protein with other viral proteins revealed three regions, each having about 60~ homology with a region of the three cowpea mosaic virus (CPMV) proteins (58K, 24K, 87K) which are thought to be involved in replication of the CPMV RNAs. The same regions show similarities, although less extended, with proteins 2C, 3C and 3D of picornaviruses. From these results we suggest that the genome organization of TBRV is similar to that of comoviruses and picornaviruses.

The Complete Nucleotide Sequence of Plum Pox Virus RNA

“…70 to 90 nucleotides upstream of the poly(A) tail in TVMV, TEV, PeMV and PPV-NAT may also represent a polyadenylation signal as demonstrated for yeasts, where this region is located 30 to 40 nucleotides in front of the poly(A) tail (Zaret & Sherman, 1982). This sequence was also found in the 3' non-coding region of tomato black ring virus RNA-1 (Greif et al, 1988) and RNA-2 (Meyer et al, 1986), and CPMV (van Wezenbeek et al, 1983;Lomonossoff & Shanks, 1983); these viruses also contain plus-sense, monocistronic polyadenylated RNAs.…”

Nucleotide sequence of Hungarian grapevine chrome mosaic nepovirus RNA1

“…An additional protein might be encoded at the N-terminus of the polyprotein in nepoviruses because this region is conserved between TBRV and GCMV but has no CPMV counterpart. The existence of this hypothetical protein has already been suspected in TBRV (13) and the homology profile presented in figure 5, as well as the conservation of its presumed cleavage site, provide additional evidence for its existence.…”

“…6-C): the threonine is changed into a serine, also a polar residue, and, more strikingly, the histidine supposed to be part of the substrate binding pocket in that type of proteases [for a review see (44)] is replaced by a leucine in GCMV. The histidine/leucine substitution in the active site of a viral cysteine protease has also been reported in the case of the only other nepovirus so far sequenced, TBRV (13). The last block of homology concerns the polymerase region where a large domain, extending from residues 1450 to 1850, is highly homologous with both TBRV and CPMV (Fig.…”

“…Those similarities made some authors regard GCMV as a strain of TBRV (8) although others considered them to be two distinct viruses (10). Sequencing of the TBRV genome has recently been achieved (11,12,13) and its genetic organization was found to be very similar to that of the comovirus cowpea mosaic virus (CPMV) (15,16).…”

Nucleotide sequence of tomato ringspot virus RNA-2

“…The 5' non-coding region of TomRSV RNA-2 was analysed and compared to the corresponding regions of the two RNA components of TBRV (Meyer et al, 1986;Greif et al, 1988) and GCMV Le Gall et al, 1989), RNA-2 of GFLV (Serghini et al, 1990) and the B and M components of the comovirus CPMV (Lomonossoff & Shanks, 1983;van Wezenbeek et al, 1983). It has been reported previously that TBRV, GCMV, GFLV and CPMV share a conserved UGAAAAAU sequence downstream from the 5' terminus (Serghini et al, 1990).…”