De Novo Generation of Defective Interfering-like RNAs in Broad Bean Mottle Bromovirus

Abstract

Broad bean mottle virus (BBMV) is the only member of the bromoviruses that is known to accumulate defective-interfering (DI) RNAs (Romero et al., Virology 194, 576-584, 1993). De novo generation of DI-like RNAs was demonstrated during serial passages of BBMV in broad bean using either DI RNA-free virion RNA preparations or transcribed genomic RNA inocula. As for previously described DI RNAs, all but one of the characterized de novo generated DI-like RNAs were derived by a single in-frame deletion from the RNA2 component. The sole exception was derived by two shorter in-frame deletions from RNA2. The maintenance of an open reading frame by all DI-like RNAs suggests the importance of coding capacity and/or the shortened 2a protein in the accumulation of these RNAs during infection. The deletion junction sites were between nucleotides 1152 and 2366, suggesting that the retained regions are essential for the efficient accumulation of BBMV DI-like RNAs in planta. Short regions of sequence similarity and/or complementarity were revealed at the 5′ and 3′ junction borders. We speculate that these regions can facilitate DI (DI-like) RNA formation. In addition to DI-like RNAs, the full-length nucleotide sequences of RNA2 components of the Type and Morocco strains of BBMV are presented.