Nonoptimal codon usage influences protein structure in intrinsically disordered regions

Mian Zhou, Tao Wang, Jingjing Fu, Guanghua Xiao, Yi Liu

Research output: Contribution to journalArticle

32 Citations (Scopus)

Abstract

Summary: Synonymous codons are not used with equal frequencies in most genomes. Codon usage has been proposed to play a role in regulating translation kinetics and co-translational protein folding. The relationship between codon usage and protein structures and the in vivo role of codon usage in eukaryotic protein folding is not clear. Here, we show that there is a strong codon usage bias in the filamentous fungus Neurospora. Importantly, we found genome-wide correlations between codon choices and predicted protein secondary structures: Nonoptimal codons are preferentially used in intrinsically disordered regions, and more optimal codons are used in structured domains. The functional importance of such correlations in vivo was confirmed by structure-based codon manipulation of codons in the Neurospora circadian clock gene frequency (frq). The codon optimization of the predicted disordered, but not well-structured regions of FRQ impairs clock function and altered FRQ structures. Furthermore, the correlations between codon usage and protein disorder tendency are conserved in other eukaryotes. Together, these results suggest that codon choices and protein structures co-evolve to ensure proper protein folding in eukaryotic organisms.

Original languageEnglish (US)
Pages (from-to)974-987
Number of pages14
JournalMolecular Microbiology
Volume97
Issue number5
DOIs
StatePublished - Sep 1 2015

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Codon
Proteins
Protein Folding
Neurospora
Genome
Secondary Protein Structure
Circadian Clocks
Eukaryota
Gene Frequency
Fungi

ASJC Scopus subject areas

  • Molecular Biology
  • Microbiology

Cite this

Nonoptimal codon usage influences protein structure in intrinsically disordered regions. / Zhou, Mian; Wang, Tao; Fu, Jingjing; Xiao, Guanghua; Liu, Yi.

In: Molecular Microbiology, Vol. 97, No. 5, 01.09.2015, p. 974-987.

Research output: Contribution to journalArticle

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