A defective RNA associated with bamboo mosaic virus and the possible common mechanisms for RNA recombination in potexviruses

A naturally occurring 1.1 kb RNA was isolated from purified virions of bamb oo mosaic potexvirus isolate S (BaMV-S). This RNA is a defective RNA (D RNA ) derived from a single internal deletion of the BaMV genome. A cDNA clone representing the complete nucleotide sequence of the BaMV-S D RNA was gener ated and its nucleotide sequence was determined. The BaMV D cDNA is 1015 nt s in length [excluding the poly(A) tail] and consists of two regions corres ponding to 867 nts of the 5' terminus and 148 nts of the 3' terminus of the BaMV genomic RNA. BaMV D cDNA contains a single open reading frame (ORF) e ncoding a putative 29.7 kDa protein comprised of a fusion of the first 258 amino acids of BaMV ORF 1 and the last 2 amino acids of coat protein. The c oding capacity of D RNA was verified by in vitro translation of native BaMV -S D RNA and of 1.1 kb RNA transcribed in vitro from the full-length D cDNA . BaMV D RNA can be reproducibly generated by serial passages of BaMV-S in Nicotiana benthamiana and is the first D RNA in the potexvirus group shown to be generated de novo. Alignments of sequences surrounding the 5' and 3' junction borders of reported potexvirus D RNAs reveal a 65.2-84.6% sequence identity, suggesting that common mechanisms for viral RNA recombination ar e involved in the generation of potexvirus D RNAs.