Experimental determination of codon usage-dependent selective pressure on high copy-number genes in Saccharomyces cerevisiae.

Lyne Jossé,Tarun Singh,Tobias Von Der Haar

doi:10.1002/yea.3373

Abstract

One of the central hypotheses in the theory of codon usage evolution is that in highly expressed genes, particular codon usage patterns arise because they facilitate efficient gene expression and are thus selected for in evolution. Here, we use plasmid copy number assays and growth rate measurements to explore details of the relationship between codon usage, gene expression level, and selective pressure in Saccharomyces cerevisiae. We find that when high expression levels are required, optimal codon usage is beneficial and provides a fitness advantage, consistent with evolutionary theory. However, when high expression levels are not required, optimal codon usage is surprisingly and strongly selected against. We show that this selection acts at the level of protein synthesis, and we exclude a number of molecular mechanisms as the source for this negative selective pressure including nutrient and ribosome limitations and proteotoxicity effects. These findings deepen our understanding of the evolution of codon usage bias, as well as the design of recombinant protein expression systems.

Highlights

Because the genetic code uses 64 codons to encode 20 amino acids (Crick, Barnett, Brenner, & Watts-Tobin, 1961), most amino acids can be encoded by multiple synonymous codons
We previously described a dual luciferase reporter system allowing us to assess the effect of codon usage variation on Firefly luciferase expression levels
Genes contained in high copy number plasmids are in principle subject to effects at both levels, but because changing the sequence of such a plasmid is equivalent to changing the sequence of multiple genes simultaneously in the genome, we expect the selective forces acting on this system to be more similar to genomewide selective forces than would be the case in a single copy plasmid

Summary

Introduction

Because the genetic code uses 64 codons to encode 20 amino acids (Crick, Barnett, Brenner, & Watts-Tobin, 1961), most amino acids can be encoded by multiple synonymous codons. Correlations between biased codon usage and a number of other parameters have been detected including cellular tRNA content (Ikemura, 1982), translational efficiency (Sharp & Li, 1986), translational accuracy (Zhou, Weems, & Wilke, 2009), RNA structure (Hartl, Moriyama, & Sawyer, 1994), protein structure (Oresic, Dehn, Korenblum, & Shalloway, 2003), genomic GC content (Comeron, Kreitman, & Aguade, 1999), recombination (Comeron et al, 1999), splicing (Chamary & Hurst, 2005), and gene conversion rates (Galtier, 2003). Translational efficiency has gained experimental support as one causative parameter that can lead to codon usage bias (Carlini & Stephan, 2003; Chu et al, 2014; Hense et al, 2010; Zhou et al, 2013). Since synonymous mutations can have substantial effects on expressed protein levels, selection for high gene expression levels will favour codon usage patterns compatible with such high levels, but will avoid patterns that restrict attainable expression levels. The exact relationship between codon usage, protein expression, other associated parameters and selective pressure are still unclear

Methods

Results

Conclusion