Interspecific adaptation by binary choice at de novo polyomavirus T antigen site through accelerated codon-constrained Val-Ala toggling within an intrinsically disordered region.

Abstract

It is common knowledge that conserved residues evolve slowly. We challenge generality of this central tenet of molecular biology by describing the fast evolution of a conserved nucleotide position that is located in the overlap of two open reading frames (ORFs) of polyomaviruses. The de novo ORF is expressed through either the ALTO protein or the Middle T antigen (MT/ALTO), while the ancestral ORF encodes the N-terminal domain of helicase-containing Large T (LT) antigen. In the latter domain the conserved Cys codon of the LXCXE pRB-binding motif constrains codon evolution in the overlapping MT/ALTO ORF to a binary choice between Val and Ala codons, termed here as codon-constrained Val-Ala (COCO-VA) toggling. We found the rate of COCO-VA toggling to approach the speciation rate and to be significantly accelerated compared to the baseline rate of chance substitution in a large monophyletic lineage including all viruses encoding MT/ALTO and three others. Importantly, the COCO-VA site is located in a short linear motif (SLiM) of an intrinsically disordered region, a typical characteristic of adaptive responders. These findings provide evidence that the COCO-VA toggling is under positive selection in many polyomaviruses, implying its critical role in interspecific adaptation, which is unprecedented for conserved residues.

• Authors: Chris Lauber, Siamaque Kazem, Alexander A Kravchenko, Mariet C W Feltkamp, Alexander E Gorbalenya
• Journal: Nucleic acids research (Nucleic Acids Res) Vol. 43 Issue 10 Pg. 4800-13 (May 26 2015) ISSN: 1362-4962 [Electronic] England
• PMID: 25904630 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Chemical References

• Antigens, Polyomavirus Transforming
• Codon
• Intrinsically Disordered Proteins
• Valine
• Alanine

Topics

• Adaptation, Biological
• Alanine (genetics)
• Antigens, Polyomavirus Transforming (genetics)
• Codon
• Evolution, Molecular
• Intrinsically Disordered Proteins (genetics)
• Open Reading Frames
• Phylogeny
• Polyomavirus (classification, genetics)
• Valine (genetics)