Analysis of the complete nucleotide sequence of the group IV RNA coliphage SP

Abstract

We report the nucleotide sequence of the Group IV RNA bacteriophage SP. The entire sequence is 4276 nucleotides long. Four cistrons have been identified by comparison with the related Group III phage Q beta. The maturation protein contains 449 amino acids, the coat protein contains 131 amino acids, the read-through protein contains 330 amino acids and the replicase beta-subunit contains 575 amino acids. SP is 59 nucleotides longer than Q beta. We have analyzed both sequence and structural conservation between SP and Q beta and shown that the sequences for the coat and central region of the replicase are strongly conserved between the two genomes. We also show that the S and M replicase binding sites of Q beta are strongly conserved in SP. Interestingly, the base composition of SP and Q beta differ significantly from one another, and most of the differences can be accounted for by a strong preponderance of U in the third position of each codon of Q beta relative to SP. We also compare conserved hairpins associated with potential coat protein and replicase binding sites.

Both yeast W double-stranded RNA and its single-stranded form 20S RNA are linear

“…L-A dsRNA, another dsRNA present in most yeast strains, has been shown to have either a paired C or an unpaired A at its 3' ends (23,24). The sequence of W (+) strand 3' end thus could be ...CC-OH or ... CCA-OH, quite similar to the 3' end terminal sequences found in other (+) strand or double-stranded RNA viruses, such as the RNA Coliphage's (...CCCA-OH) (25,26), or to the tRNA 3' ends (...CCA-OH). We also found the same terminal composition in T dsRNA (another dsRNA present in the same host S. cerevisiae (10)); about 85-90% of both T 3' ends were C and only a minor 10-15% were A (Luis M. Esteban and R. Esteban, unpublished results), consistent with close relationship between T and W (27).…”

A cryptic lysis gene near the start of the Qβ replicase gene in the +1 frame

“…This speculation is consistent with that of Bollback & Huelsenbeck (2001) who proposed that the ancestral RNA phage genome was small and had its lysis gene located around its coat protein and replicase genes. However, it is contrary to the ‘deletion hypothesis’ (Furuse 1987), in which the ancestral RNA phage resembled group B‐IV phages, such as SP phage, which have large genomes and their lysis function mediated by their A2 gene (Inokuchi et al . 1988; Priano et al .…”

Viral escape from antisense RNA

“…These two substitutions were retained in all selection II isolates except IIA, which reverted to Wt sequence at 224. The sequence of Wt differed from the published sequence at positions 30 (U not C) and 208 (A not G) (GenBank X07489; Inokuchi et al, 1988). Except for positions 224 and 236, substitutions resulting from antisense selection are either in non-coding regions (34, 36 and 39) or do not change the inferred amino acid sequence of a protein.…”