Human cellular homeostasis buffers trans-acting translational effects of heterologous gene expression with very different codon usage bias

Abstract

The frequency of synonymous codons in protein coding genes is non-random and varies both between species and between genes within species. Whether this codon usage bias (CUBias) reflects underlying neutral mutational processes or is instead shaped by selection remains an open debate, especially regarding the role of selection for enhanced protein production. Variation in CUBias of a gene (be it natural synonymous mutations or biotechnological synonymous recoding) can have an enormous impact on its expression by diverse cis- acting mechanisms. But expression of genes with extreme CUBias can also lead to strong phenotypic effects by altering the overall intracellular translation homeostasis via competition for ribosomal machinery or tRNA depletion. In this study, we expressed at high levels in human cells six different synonymous versions of a gene and used matched transcriptomic and proteomic data to evaluate the impact of CUBias of the heterologous gene on the translation of cellular transcripts. Our experimental design focused specifically on differences during translation elongation. Response to expression of the different synonymous sequences was assessed by various approaches, ranging from analyses performed on a per-gene basis to more integrated approaches of the cell as a whole. We observe that the transcriptome displayed substantial changes as a result of heterologous gene expression by triggering an intense antiviral and inflammatory response, but that changes in the proteomes were very modest. Most importantly we notice that changes in translation efficiency of cellular transcripts were not associated with the direction of the CUBias of the heterologous sequences, thereby providing only limited support for trans- acting effects of synonymous changes. We interpret that, in human cells in culture, changes in CUBias can lead to important cis- acting effects in gene expression, but that cellular homeostasis can buffer the phenotypic impact of overexpression of heterologous genes with extreme CUBias.

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

“…We have focused on the effects of CUBias of our focal shble gene on its own expression and function, i.e ., the so‐called cis ‐effects of CUBias. The global trans ‐effects of CUBias of our focal gene on the expression levels of other cellular genes have been analyzed and described in an accompanying manuscript (Jallet et al, 2021). Our results show that a combination of synonymous changes results in important multilevel variation in gene expression levels and leads to dramatic differences in the cellular phenotype.…”

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

“…In the present manuscript we have analysed the multilevel molecular cis -effects of codon usage preferences on gene expression, and have further explored higher-level integration consequences at the cellular level. The global trans -effects of codon usage preferences of our focal gene on the expression levels of other cellular genes have been analysed and described in an accompanying paper (62). We summarize our observations of these cis -effects in Figure 6, which displays variation in the each of the composition and phenotypic variables monitored for the different genotypes analysed.…”

“…the so-called cis -effects of CUBias. The global trans -effects of CUBias of our focal gene on the expression levels of other cellular genes have been analysed and described in an accompanying manuscript 73 . Our results show that a combination of synonymous changes results in important multilevel variation in gene expression levels and leads to dramatic differences in the cellular phenotype.…”