Tombusvirus genome may encode the sixth small protein near its 3' terminus

Abstract

A short open reading frame (ORF), ORF6, potentially encoding a polypeptide (pX) of 32-69 amino acids, was revealed upon computer translation of the 3' terminal regions of tomato bushy stunt, cymbidium ringspot, cucumber necrosis and artichoke mottled crinkle tombusviruses. ORF6 has an initiating AUG codon in a favorable context and is evaluated as expressible, judging the distribution of guanosine residues within the codons. Inspection of the alignment of the four putative products encoded by ORF6 shows statistically significant sequence conservation over 11 SD above the random expectation. Secondary structure predictions based on the Garnier method demonstrate strict conservation of a loop between two beta-strands, thus suggesting functional conservation of pXs. It is suggested that pX is not involved in tombusvirus genome replication and encapsidation in cis.