A design principle for a single-stranded RNA genome that replicates with less double-strand formation

Usui, Kimihito; Ichihashi, Norikazu; Yomo, Tetsuya

Finally, we examined whether natural viral ssRNA genomes obey the same rule that we developed. We first investigated the predicted secondary structure of the ssRNA genome of bacteriophage Q␤, which has been reported to replicate with a low dsRNA ratio during in vitro replication (38) , and found that the GC number in loops is at the same level as that of mutant m14 and is significantly lower than that of the random sequences of the same size and GC ratio, supporting the idea that the 'less GC number in loop' rule is also valid in this genome (Supplementary Figure S2 and Table S2). To further examine the generality of the rule, we investigated all sequence data of ssRNA viral genomes that have been registered in the NCBI database and analyzed the secondary structures to count the GC numbers in the loops. A plot of the GC number against the genome size revealed that the GC numbers in loops of the ssRNA genomes of bacteria and fungi are specifically localized to a region of <1 GC in the loops ( Figure 8A ), suggesting that the ss-RNA viral genomes of these organisms obey the rule. Next, we applied the same analysis to bacterial and fungal viruses possessing other types of genomes (double-stranded RNA, single-and double-stranded DNA) ( Figure 8B ). The GC numbers in loops of other types of genomes are higher than those of ssRNA genomes, indicating that the rule of less GC number in loops is specific to ssRNA genomes. These results suggest that the rule obtained in the in vitro experiments using artificial RNAs is a general rule that governs natural viral ssRNA genomes of all bacteria and of most fungi presently known.