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

Abstract

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.

An attempt to identify recombinants between two sobemoviruses in doubly infected oat plants

“…Based on the phylogenetic analysis of 14 RYMV full-length isolates and 58 capsid protein genes sequences, it has been concluded that RYMV evolved in the absence of recombination events (Chare and Holmes, 2006;Fargette et al, 2004). Similarly, on the basis of the phylogenetic comparison of six sobemovirus genomes, including CfMV, RYMV, Lucerne transient streak virus (LTSV), Sesbania mosaic virus (SeMV), Southern cowpea mosaic virus (SCPMV), and Southern bean mosaic virus (SBMV), it was suggested that recombination is neither frequent nor significant in the sobemovirus group (Lokesh et al, 2001). …”

“Natively Unfolded” VPg Is Essential for Sesbania Mosaic Virus Serine Protease Activity

“…NMR studies on cowpea mosaic virus VPg suggested that it does not have any ordered structure (7). In Sobemoviruses, the size of VPg varies between 9 and 12 kDa (8), and it is 9 kDa in SeMV, consisting of 77 amino acid residues (1). The presence of VPg linked to the 5Ј end of the genomic RNA has been confirmed by determining the N-terminal amino acid sequence of VPg in Southern bean mosaic virus, Cocksfoot mottle virus, and SeMV genomic RNA (1, 9, 10).…”

“…Sesbania mosaic virus (SeMV) 1 belongs to the genus Sobemovirus, which infects Sesbania grandiflora (1). It is an icosahedral virus with T ϭ 3 symmetry, and the capsid is made up of 180 coat protein subunits of molecular mass 29 kDa (2).…”

“…It is an icosahedral virus with T ϭ 3 symmetry, and the capsid is made up of 180 coat protein subunits of molecular mass 29 kDa (2). It is a positive sense RNA virus of genome size 4149 nucleotides having four overlapping open reading frames (1). Open reading frame-2 encodes a polyprotein consisting of N-terminal serine protease (Pro), viral protein genome-linked (VPg), a 10-kDa protein, and C-terminal RNA-dependent RNA polymerase (RdRP) domains (3).…”

“…: 91-80-23601561; Fax: 91-80-23600814; E-mail: bchss@biochem.iisc.ernet.in. 1 The abbreviations used are: SeMV, Sesbania mosaic virus; VPg, viral protein genome-linked; Pro, protease; Ni-NTA, nickel-nitrilotriacetic acid; RdRP, RNA-dependent RNA polymerase; IF, initiation factor.…”