The Footprint of Genome Architecture in the Largest Genome Expansion in RNA Viruses

• DOI: 10.1371/journal.ppat.1003500
• Publication Date: 2013-07-18T22:51:46Z
• Authors: Chris Lauber; Jelle J. Goeman; Maria del Carmen ...; Phan Thi Nga; Eric J. Snijder; Kouichi Morita; Alexander E. Gorb...
• Keywords: ORFS; RNA virus; Genome size; Genomic Organization

The small size of RNA virus genomes (2-to-32 kb) has been attributed to high mutation rates during replication, which is thought lack proof-reading. This paradigm being revisited owing the discovery a 3'-to-5' exoribonuclease (ExoN) in nidoviruses, monophyletic group positive-stranded viruses with conserved genome architecture. ExoN, homolog canonical DNA proof-reading enzymes, exclusively encoded by nidoviruses larger than 20 kb. All other known non-segmented have smaller genomes. Here we use evolutionary analyses show that two- three-fold expansion nidovirus was accompanied large number replacements proteins at scale comparable Tree Life. To unravel common patterns such genetically diverse viruses, established relation between genomic regions sequence alignment-free manner. We exploited conservation architecture partition each into five non-overlapping regions: 5' untranslated region (UTR), open reading frame (ORF) 1a, ORF1b, 3'ORFs (encompassing 3'-proximal ORFs), and 3' UTR. Each analyzed for its contribution change under different models. non-linear model statistically outperformed linear one captured >92% data variation. Accordingly, were concluded reached points on an trajectory dominated consecutive increases ORF1a, 3'ORFs. Our findings indicate unidirectional hierarchical these regions, are distinguished their expression mechanism. In contrast, cooperate bi-directionally functional level life cycle, they predominantly control expression, dissemination, respectively. Collectively, our suggest associated region-specific division labor leave footprint may limit size.