An Experimental and Computational Evolution-Based Method to Study a Mode of Co-evolution of Overlapping Open Reading Frames in the AAV2 Viral Genome

Yasuhiro Kawano, Shane Neeley, Kei Adachi, Hiroyuki Nakai

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Overlapping open reading frames (ORFs) in viral genomes undergo co-evolution; however, how individual amino acids coded by overlapping ORFs are structurally, functionally, and co-evolutionarily constrained remains difficult to address by conventional homologous sequence alignment approaches. We report here a new experimental and computational evolution-based methodology to address this question and report its preliminary application to elucidating a mode of co-evolution of the frame-shifted overlapping ORFs in the adeno-associated virus (AAV) serotype 2 viral genome. These ORFs encode both capsid VP protein and non-structural assembly-activating protein (AAP). To show proof of principle of the new method, we focused on the evolutionarily conserved QVKEVTQ and KSKRSRR motifs, a pair of overlapping heptapeptides in VP and AAP, respectively. In the new method, we first identified a large number of capsid-forming VP3 mutants and functionally competent AAP mutants of these motifs from mutant libraries by experimental directed evolution under no co-evolutionary constraints. We used Illumina sequencing to obtain a large dataset and then statistically assessed the viability of VP and AAP heptapeptide mutants. The obtained heptapeptide information was then integrated into an evolutionary algorithm, with which VP and AAP were co-evolved from random or native nucleotide sequences in silico. As a result, we demonstrate that these two heptapeptide motifs could exhibit high degeneracy if coded by separate nucleotide sequences, and elucidate how overlap-evoked co-evolutionary constraints play a role in making the VP and AAP heptapeptide sequences into the present shape. Specifically, we demonstrate that two valine (V) residues and β-strand propensity in QVKEVTQ are structurally important, the strongly negative and hydrophilic nature of KSKRSRR is functionally important, and overlap-evoked co-evolution imposes strong constraints on serine (S) residues in KSKRSRR, despite high degeneracy of the motifs in the absence of co-evolutionary constraints.

Original languageEnglish (US)
Article numbere66211
JournalPLoS One
Volume8
Issue number6
DOIs
StatePublished - Jun 24 2013

Fingerprint

Viral Genome
coevolution
Open Reading Frames
open reading frames
Genes
genome
mutants
Proteins
proteins
Dependovirus
Amino Acid Motifs
Sequence Alignment
Capsid
Valine
Capsid Proteins
Mutant Proteins
nucleotide sequences
Nucleotides
Sequence Homology
methodology

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

An Experimental and Computational Evolution-Based Method to Study a Mode of Co-evolution of Overlapping Open Reading Frames in the AAV2 Viral Genome. / Kawano, Yasuhiro; Neeley, Shane; Adachi, Kei; Nakai, Hiroyuki.

In: PLoS One, Vol. 8, No. 6, e66211, 24.06.2013.

Research output: Contribution to journalArticle

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