An exploration of ambigrammatic sequences in narnaviruses

Joseph L. DeRisi,Hanna Retallack,David Yllanes,Amy Kistler,Greg Huber,Michael Wilkinson

doi:10.1038/s41598-019-54181-3

Abstract

Narnaviruses have been described as positive-sense RNA viruses with a remarkably simple genome of ~3 kb, encoding only a highly conserved RNA-dependent RNA polymerase (RdRp). Many narnaviruses, however, are ‘ambigrammatic’ and harbour an additional uninterrupted open reading frame (ORF) covering almost the entire length of the reverse complement strand. No function has been described for this ORF, yet the absence of stops is conserved across diverse narnaviruses, and in every case the codons in the reverse ORF and the RdRp are aligned. The >3 kb ORF overlap on opposite strands, unprecedented among RNA viruses, motivates an exploration of the constraints imposed or alleviated by the codon alignment. Here, we show that only when the codon frames are aligned can all stop codons be eliminated from the reverse strand by synonymous single-nucleotide substitutions in the RdRp gene, suggesting a mechanism for de novo gene creation within a strongly conserved amino-acid sequence. It will be fascinating to explore what implications this coding strategy has for other aspects of narnavirus biology. Beyond narnaviruses, our rapidly expanding catalogue of viral diversity may yet reveal additional examples of this broadly-extensible principle for ambigrammatic-sequence development.

Highlights

Narnaviruses have been described as positive-sense RNA viruses with a remarkably simple genome of ~3 kb, encoding only a highly conserved RNA-dependent RNA polymerase (RdRp)
We refer to these examples, with large reverse open reading frame features, as ambigrammatic narnaviruses, where the adjective is derived from ambigram, a set of letters with two, orientation-dependent readings[16]
Including both ambigrammatic and non-ambigrammatic narnaviruses to generate a null distribution of lengths of open reading frame (ORF) that may overlap the RdRp, we find that the expected probability of a long sequence without a stop codon is well approximated by an exponential distribution, and that the expected probability of an ORF with the observed length is negligible (Fig. 4)

Summary

Introduction

Narnaviruses have been described as positive-sense RNA viruses with a remarkably simple genome of ~3 kb, encoding only a highly conserved RNA-dependent RNA polymerase (RdRp). A remarkable feature of some narnaviruses is the existence of an additional large open reading frame (ORF), defined as a region devoid of stop codons, which spans nearly the full length of the reverse complement sequence of the virus genome. We refer to these examples, with large reverse open reading frame (rORF) features, as ambigrammatic narnaviruses, where the adjective is derived from ambigram, a set of letters with two, orientation-dependent readings[16]. The two alternative forward reading frames, though not directly relevant for experimental observations in narnaviruses, are discussed for completeness

Methods

Results

Conclusion