21 Contemporary RNA Genomes

Abstract

So, naturalists observe, a flea

hath smaller fleas that on him prey;

And these have smaller fleas to bite ’em

And so proceed ad infinitum,

Thus every poet [viral evolutionist] in his kind,

Is bit by him that comes behind.

Jonathan Swift 1667–1745

The exclusive existence of RNA genomes is part of the central postulate of the RNA world, a hypothetical pre-DNA and pre-encoded-protein period in early evolution. In contrast, natural extant RNA genomes are almost exclusively composed of infectious RNA agents, viruses, sub-viruses, and some derivatives. The latter comprise a few degenerate viruses that are known in plants and fungi (one in Saccharomyces cerevisiae, L-A, is well characterized) and a “carrier” state entity for some viruses in which the viral RNA is maintained in the cytoplasm for several generations (see Onodera et al. 1992), The known RNA genomes that are not associated with a capsid-like structure, and that are not apparently infectious, are few in number and small in size. For example, a 2800-nucleotide linear single-stranded RNA and a deletion derivative replicate in maize mitochondria and are transmitted with the mitochondria. The RNAs are free in the sense of not being sequestered in nucleocapsids (Zhang and Brown 1993). Detailed characterization of such “RNA plasmids” is clearly worthwhile, but they do not affect the generality of the statement about modern RNA genomes being essentially confined to infectious agents.

All modern RNA genomes rely on the cellular translation apparatus and other components specified by DNA genomes and are very far...