Genome Nucleotide Lengths That Are Divisible by Six Are Not Essential but Enhance Replication of Defective Interfering RNAs of the Paramyxovirus Simian Virus 5

Abstract

For some members of the Paramyxoviridae family of negative strand RNA viruses, efficient genome replication only occurs when the total genome length is a multiple of six (6Nlength, whereNis any integer). To determine if this “rule of six” requirement applied to the replication of the prototype paramyxovirus simian virus 5 (SV5), defective interfering (DI) RNA genomes were generated by sequential undiluted passage of virus in tissue culture. Molecular cloning and nucleotide sequence analysis of 10 RNA genomes revealed a series of copyback DI RNAs with chain lengths between 449 and 1365 bases, but only 4 of the 10 naturally occurring RNA genomes were of 6Nlength. Many of the cloned DI genomes could be grouped into two distinct nested sets, with the members of each set having the same polymerase crossover junctions and extent of terminal complementarity but differing from each other by internal deletions. One of these nested sets of genomes consisted of novel DI RNAs that contained a pentameric stretch of nontemplated adenosine residues inserted precisely at the polymerase crossover junction. A reverse genetics system was established in which SV5 DI genomes were replicatedin vivoentirely by cDNA-derived components. Using this system, two naturally occurring SV5 DI RNAs were examined in a mutational analysis to determine the role of genome length on SV5 RNA replication. The progressive insertion of one to six nucleotides into a 6Nlength DI genome (852 bases) resulted in a reduction in replication for RNAs that contained one to four additional bases (∼35–50% of WT levels), followed by an increase back to WT replication levels for genomes that were altered by five and six base insertions (∼70 and 100% of WT levels, respectively). An insertion of five nucleotides into a second non-6Nlength DI RNA (499 total bases) created a genome length that was a multiple of six (504 bases) and led to a ∼10-fold stimulation of replication over that of the unaltered genome. Together, these results indicate that there was a clear influence of 6Ngenome length on SV5 DI RNA replication, but the stringency of this replication requirement appeared to be less than that found previously for other paramyxoviruses. This work completes the testing of the rule of six replication requirement for representatives of each of the four genera of the Paramyxoviridae family and indicates that the preference for replication of 6Nlength RNA genomes varies between the individual paramyxoviruses.