Nucleotide sequence of the bean strain of southern bean mosaic virus

Othman, Rofina Yasmin; Hull, Roger

doi:10.1016/s0042-6822(95)80044-1

Cited by 40 publications

(30 citation statements)

References 56 publications

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“…None of the clones sequenced had the terminal 5 sequence of the SeMV RNA. A comparison of the 5 terminal 51 nts of pSM63 with SBMV [19] showed that it was identical from nts 14 to 64 (Fig. 2).…”

Section: Resultsmentioning

confidence: 92%

“…It is 15 and 45 nts longer than SBMV-Ark and SBMV [13,19] genomic RNAs and 47 nts shorter than SCPMV genomic RNA [32]. Four potential overlapping ORFs were identified from the messenger sense strand and no ORFs coding greater than 85 amino acids were identified on the negative sense strand.…”

Section: Resultsmentioning

confidence: 96%

“…Efforts to determine 5 end by 5 RACE (Rapid Amplification of cDNA Ends) and RNA sequencing using primer SeMV1A (Table 1) were not successful. However, RT-PCR on viral RNA template using the primer 5NCS (Table 1) which contained 5 terminal 13 nucleotides of SBMV [19] in addition to 8 nucleotides from 5 terminal sequence derived from pSM63 and SeMV 2A or SeMV 7A (Table 1) gave products of 0.9 kb and 4.2 kb respectively (data not shown). These results suggest that 5 end SeMV genomic RNA may have the same nucleotide sequence as SBMV genomic RNA [19].…”

Section: Resultsmentioning

confidence: 99%

“…3). As suggested by Lee and Anderson [13] it is possible that errors or mutations in the previously published sequence of SBMV [19] would have resulted in the misidentification of the ORFs. The overall nucleotide sequence of SeMV and its deduced amino acid sequence from all the four ORFs is closest to SBMV-Ark (73% identity) followed by SCPMV (59.6%).…”

Section: Resultsmentioning

confidence: 99%

“…Molecular details of the assembly/disassembly of the virus can be obtained by in vitro expression and mutational analysis of the coat protein gene. The complete genome sequence of five distinct sobemoviruses have been determined thus far [10,13,15,18,19,32]. A comparison of these genome sequences has revealed important similarities and differences in their organization and expression [28].…”

Section: Introductionmentioning

confidence: 99%

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Complete nucleotide sequence of Sesbania mosaic virus: a new virus species of the genus Sobemovirus

Lokesh

Gopinath

Satheshkumar

et al. 2001

Archives of Virology

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Summary.The complete nucleotide sequence of the Sesbania mosaic virus (SeMV) genomic RNA was determined by sequencing overlapping cDNA clones. The SeMV genome is 4149 nucleotides in length and encodes four potential overlapping open reading frames (ORFs). Comparison of the nucleotide sequence and the deduced amino acid sequence of the four ORFs of SeMV with that of other sobemoviruses revealed that SeMV was closest to southern bean mosaic virus Arkansas isolate (SBMV-Ark, 73% identity). The 5 non-coding regions of SeMV, SBMV and southern cowpea mosaic virus (SCPMV) are nearly identical. However ORF1 of SeMV which encodes for a putative movement protein of M r 18370 has only 34% identity with SBMV-Ark. ORF 2 encodes a polyprotein containing the serine protease, genome linked viral protein (VPg) and RNA dependent RNA polymerase domains and shows 78% identity with SBMV-Ark. The Nterminal amino acid sequence of VPg was found to be TLPPELSIIEIP, which mapped to the region 326-337 of ORF2 product and the cleavage site between the protease domain and VPg was identified to be E 325 -T 326 . The cleavage site between VPg and RNA dependent RNA polymerase was predicted to be E 445 -T 446 based on the amino acid sequence analysis of the polyprotein from different sobemoviruses. ORF3 is nested within ORF2 in a −1 reading frame. The potential ribosomal frame shift signal and the downstream stem-loop structure found in other sobemoviruses are also conserved in SeMV RNA sequence, indicating that ORF3 might be expressed via −1 frame shifting mechanism. ORF4 encodes the coat protein of SeMV, which shows 76 and 66% identity with SBMV-Ark and SCPMV, respectively. Thus the comparison of the non-coding regions and the ORFs of SeMV with other sobemoviruses clearly revealed that it is not a strain of SBMV. Phylogenetic analysis of six different sobemoviruses, including SeMV, * The nucleotide sequence reported in this paper has been submitted to Genebank sequence database and assigned the accession number AY004291. 210 G. L. Lokesh et al. suggests that recombination event is not frequent in this group and that SeMV is a distinct member of the genus sobemovirus. The analysis also shows sobemoviruses infecting monocotyledons and dicotyledons fall into two distinct clusters.

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Section: Resultsmentioning

confidence: 92%

Section: Resultsmentioning

confidence: 96%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Complete nucleotide sequence of Sesbania mosaic virus: a new virus species of the genus Sobemovirus

Lokesh

Gopinath

Satheshkumar

et al. 2001

Archives of Virology

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Structure of native and expanded sobemoviruses by electron cryo-microscopy and image reconstruction

Opalka

Tihova

Brugidou

et al. 2000

Journal of Molecular Biology

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Mapping and Expression of Southern Bean Mosaic Virus Genomic and Subgenomic RNAs

Hacker

Sivakumaran

1997

Virology

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The coat protein of the cowpea strain of southern bean mosaic sobemovirus (SBMV-C) is translated from a subgenomic RNA (sgRNA) that is synthesized in the virus-infected cell. Like the SBMV-C genomic RNA, the sgRNA has a viral protein (VPg) covalently bound to its 5' end. The mechanism(s) by which ribosomes initiate translation on the SBMV-C RNAs is not known. To begin to characterize the translation of the sgRNA it was first necessary to precisely map its 5' end. Primer extension was used to identify SBMV-C nucleotide (nt) 3241 as the transcription start site. As a control, the 5' end of the genomic RNA was also mapped. Surprisingly, the 5' terminal nt of this RNA was identified as SBMV-C nt 2. The primary structure of the 5' ends of these two RNAs is therefore expected to be VPg-ACAAAA. Precise mapping of the 5' end of the sgRNA of the bean strain of SBMV (SBMV-B) demonstrated that it has these same elements. Translation of coat protein from the SBMV-C sgRNA and p21 from the SBMV-C genomic RNA was compared using a cell-free system. The results of these experiments were consistent with translation of these proteins by a 5' end-dependent scanning mechanism rather than by internal ribosome binding.

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Nucleotide sequence of the bean strain of southern bean mosaic virus

Cited by 40 publications

References 56 publications

Complete nucleotide sequence of Sesbania mosaic virus: a new virus species of the genus Sobemovirus

Complete nucleotide sequence of Sesbania mosaic virus: a new virus species of the genus Sobemovirus

Structure of native and expanded sobemoviruses by electron cryo-microscopy and image reconstruction

Mapping and Expression of Southern Bean Mosaic Virus Genomic and Subgenomic RNAs

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