A rare codon-based translational program of cell proliferation

Abstract

Background The speed of translation elongation is primarily determined by the abundance of tRNAs. Thus, the codon usage influences the rate with which individual mRNAs are translated. As the nature of tRNA pools and modifications can vary across biological conditions, codon elongation rates may also vary, leading to fluctuations in the protein production from individual mRNAs. Although it has been observed that functionally related mRNAs exhibit similar codon usage, presumably to provide an effective way to coordinate expression of multiple proteins, experimental evidence for codon-mediated translation efficiency modulation of functionally related mRNAs in specific conditions is scarce and the associated mechanisms are still debated. Results Here, we reveal that mRNAs whose expression increases during cell proliferation are enriched in rare codons, poorly adapted to tRNA pools. Ribosome occupancy profiling and proteomics measurements show that upon increased cell proliferation, transcripts enriched in rare codons undergo a higher translation boost than transcripts with common codons. Re-coding of a fluorescent reporter with rare codons increased protein output by ~ 30% relative to a reporter re-coded with common codons. Although the translation capacity of proliferating cells was higher compared to resting cells, we did not find evidence for the regulation of individual tRNAs. Among the models that were proposed so far to account for codon-mediated translational regulation upon changing conditions, the one that seems most consistent with our data involves a global upregulation of ready-to-translate tRNAs, which we show can lead to a higher increase in the elongation velocity at rare codons compared to common codons. Conclusions We propose that the alleviation of translation bottlenecks in rapidly dividing cells enables preferential upregulation of pro-proliferation proteins, encoded by mRNAs that are enriched in rare codons.

Prevention of dsRNA‐induced interferon signaling by AGO1x is linked to breast cancer cell proliferation

“…The method is based on the incorporation of L-HPG, an amino acid analog of methionine containing an alkyne moiety, and Alexa Fluor 594 azide. The seeding of MDA-MB-231 cells and incubation of HPG in the medium were performed exactly as done earlier in the laboratory (Guimaraes et al, 2020). HeLa cells, in a slight modification from MDA-MB-231 cells, were incubated with HPG for a 30-min duration as per manufacturer's protocol.…”

Adaptation of codon and amino acid use for translational functions in highly expressed cricket genes

“…In some organisms, however, the correspondence between optimal codon use in highly expressed genes and the matching tRNA abundance has been weak [ 23 ], or not observed for some codons [ 91 , 92 ], which has been interpreted as limited/absent support for adaptation of tRNA abundance and optimal codon use in certain systems [ 23 , 92 ]. However, growing evidence suggests that there is a complex supply-demand relationship between codons and tRNAs that may affect multiple aspects of translation [ 45 – 47 , 93 ], such that a universal connection between optimal codons and matching tRNA gene copy numbers may not always be expected even under a selection model [ 20 , 45 , 47 ]. For instance, some optimal codons may obligately require wobble tRNAs (no direct matching tRNAs) [ 20 ], which act to allow slow translation [ 51 , 52 ], and thus a positive relationship between codon use in highly expressed genes and high tRNA abundance would not be expected for those codons.…”

Differential regulation of mRNA fate by the human Ccr4-Not complex is driven by CDS composition and mRNA localisation

“…The distinct transcript pools present in proliferation and differentiation have been shown to have opposing synonymous codon usage signatures (76–78). mRNAs enriched for AU-ending codons are abundant in proliferation, whereas it is the mRNAs that contain more GC-ending codons that are abundant in differentiation (77,78). Having observed a clear distinction in how GC-ending and AU-ending codons impact Ccr4-Not-mediated regulation of an mRNA’s stability (Fig.…”

“…Recent studies in human cells have also found AU-ending codons to be destabilising (81,123), whereas another study has found GC-ending codons to be destabilising (94). It is of note that this differential regulation may change with cellular context as it has been demonstrated that mRNAs preferentially involved in proliferation (enriched for AU-ending codons) and differentiation (enriched for GC-ending codons) have distinct codon usage and the tRNA pool available is altered to reflect this (77,78,124). Thus, the inconsistency in whether it is the AU-ending or GC-ending synonymous codons that are classified as destabilising in the literature could be explained by conditional differences.…”