Tymoviruses partition selection using overlapping genes to allow their replication genes and their movement protein gene to evolve independently.

Abstract

Viral populations evolve as 'negative selection' removes mutants with harmful changes and 'positive selection' preserves mutants with advantageous changes. How do viruses with small genomes, like tymoviruses, resist mutational changes to their most essential functions, such as replication, but remain evolutionarily flexible enough to acquire new hosts and respond to changes in their environment? Tymoviruses have cytosine-rich genomes and a composition that is notably constant throughout their length, suggesting that their unusual composition is driven by a single process. In contrast, the composition of their proteome, which is rich in leucine, proline and serine, varies more, as one would expect, as its individual proteins are selected for different functions. The main genomic ORF encodes the replication proteins and has been shown to be strongly conserved under negative selection, whereas nearly all positively selected sites occur in the movement protein (MP), which is encoded by a gene that overlaps the 5'-terminal third of the main ORF and is in its +1 reading frame. We found that the MP is an intrinsically disordered protein (IDP) especially rich in proline and serine. Patristic distance comparisons of the ORFs of different tymoviruses showed that their replication proteins differ least, the MPs an intermediate amount and the other IDPs most. The MP exploits the bias towards proline and serine to maintain an intrinsically unstructured state, which is presumably required for its functions, whereas the replication proteins have fewer disorder-promoting amino acids and hence preserve the structure required for their enzymatic functions. Thus, tymoviruses conserve the replication proteins in their main reading frame but use frame-shifting and genetic code redundancy to allow positive selection and evolutionary flexibility of the MP.