The ribosome in action: Tuning of translational efficiency and protein folding

Abstract

The cellular proteome is shaped by the combined activities of the gene expression and quality control machineries. While transcription plays an undoubtedly important role, in recent years also translation emerged as a key step that defines the composition and quality of the proteome and the functional activity of proteins in the cell. Among the different post-transcriptional control mechanisms, translation initiation and elongation provide multiple checkpoints that can affect translational efficiency. A multitude of specific signals in mRNAs can determine the frequency of translation initiation, choice of the open reading frame, global and local elongation velocities, and the folding of the emerging protein. In addition to specific signatures in the mRNAs, also variations in the global pools of translation components, including ribosomes, tRNAs, mRNAs, and translation factors can alter translational efficiencies. The cellular outcomes of phenomena such as mRNA codon bias are sometimes difficult to understand due to the staggering complexity of covariates that affect codon usage, translation, and protein folding. Here we summarize the experimental evidence on how the ribosome-together with the other components of the translational machinery-can alter translational efficiencies of mRNA at the initiation and elongation stages and how translation velocity affects protein folding. We seek to explain these findings in the context of mechanistic work on the ribosome. The results argue in favour of a new understanding of translation control as a hub that links mRNA homeostasis to production and quality control of proteins in the cell.

Synonymous Codons: Choose Wisely for Expression

“…Translation elongation is a major determinant of the composition of the proteome, affecting the amounts of each protein [1–3], the errors within each protein [4–10], and protein folding [11–16]. During translation elongation, each triplet nucleotide codon (see Glossary) in mRNA is decoded in the A-site of the ribosome by interactions with the anticodon of its cognate tRNA ( aminoacyl or charged tRNA ), resulting in insertion of an amino acid, followed by a precise three base translocation of the mRNA (and tRNA) to maintain the reading frame (illustrated in Figure 1).…”

Quality over quantity: optimizing co-translational protein folding with non-‘optimal’ synonymous codons

“…In general, there is an inverse correlation between codon rarity and translation rate [12,13], and codon usage frequencies have proven useful for predicting total translation time over an entire sequence [1]. However, there are clearly additional factors (including nutrient levels and codon context [14–17]) that affect the rate of translation of a single specific codon, although the relative importance and interplay between these factors is still poorly understood. For these reasons, codon usage frequency is less predictive of translation rate for an individual codon or short region than for an entire coding sequence.…”

“…Beyond synonymous codon usage, a variety of other mRNA and nascent chain sequence features can affect local translation rate [17]. In most cases, however, these mechanisms constrain the amino acid sequence of the encoded nascent chain and as a result represent less versatile tools for tuning the co-translational folding of a desired protein sequence.…”

Exploring ribosome composition and newly synthesized proteins through proteomics and potential biomedical applications

“…2 H 8 valine, 13 C 6 lysine and ( 13 C 6 15 N 2 ) lysine; 5 days to 4 animal generations). SILAC stable-labeled mouse ( 13 C 6 lysine in diet) [19] can be used as a “spike-in” internal standard for experiments with various organ cells/tissues and allowed for study of pathology models and knockout mice [63]. Recently, this approach was used for global protein quantitation of mouse heart tissue [66].…”

“…It was experimentally documented that ribosomes in cooperation with other translational components (tRNA, translational factors, etc. ), can alter translational efficiencies of mRNA at the initiation and elongation steps and that translation velocity affects protein folding [19]. One of the methods applied for identification and characterization of the translatome, polysome profiling [20–21], can analyze mRNAs and determine the translation efficiency based on the number of ribosomes bound.…”