Transcriptomic, proteomic, and functional consequences of codon usage bias in human cells during heterologous gene expression

Author:

Picard Marion A. L.1,Leblay Fiona1,Cassan Cécile1,Willemsen Anouk1,Daron Josquin1,Bauffe Frédérique1,Decourcelle Mathilde2,Demange Antonin1,Bravo Ignacio G.1ORCID

Affiliation:

1. French National Center for Scientific Research Laboratory MIVEGEC (CNRS, IRD, University of Montpellier) Montpellier France

2. BioCampus Montpellier (University of Montpellier, CNRS, INSERM) Montpellier France

Abstract

AbstractDifferences in codon frequency between genomes, genes, or positions along a gene, modulate transcription and translation efficiency, leading to phenotypic and functional differences. Here, we present a multiscale analysis of the effects of synonymous codon recoding during heterologous gene expression in human cells, quantifying the phenotypic consequences of codon usage bias at different molecular and cellular levels, with an emphasis on translation elongation. Six synonymous versions of an antibiotic resistance gene were generated, fused to a fluorescent reporter, and independently expressed in HEK293 cells. Multiscale phenotype was analyzed by means of quantitative transcriptome and proteome assessment, as proxies for gene expression; cellular fluorescence, as a proxy for single‐cell level expression; and real‐time cell proliferation in absence or presence of antibiotic, as a proxy for the cell fitness. We show that differences in codon usage bias strongly impact the molecular and cellular phenotype: (i) they result in large differences in mRNA levels and protein levels, leading to differences of over 15 times in translation efficiency; (ii) they introduce unpredicted splicing events; (iii) they lead to reproducible phenotypic heterogeneity; and (iv) they lead to a trade‐off between the benefit of antibiotic resistance and the burden of heterologous expression. In human cells in culture, codon usage bias modulates gene expression by modifying mRNA availability and suitability for translation, leading to differences in protein levels and eventually eliciting functional phenotypic changes.

Funder

H2020 European Research Council

European Commission

Horizon 2020 Framework Programme

Publisher

Wiley

Subject

Molecular Biology,Biochemistry

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