Transient ribosomal attenuation coordinates protein synthesis and co-translational folding

Abstract

Clustered codons that pair to low-abundance tRNA isoacceptors can form slow-translating regions in the mRNA and cause transient ribosomal arrest. We report that folding efficiency of the Escherichia coli multidomain protein SufI can be severely perturbed by alterations in ribosome-mediated translational attenuation. Such alterations were achieved by global acceleration of the translation rate with tRNA excess in vitro or by synonymous substitutions to codons with highly abundant tRNAs both in vitro and in vivo. Conversely, the global slow-down of the translation rate modulated by low temperature suppresses the deleterious effect of the altered translational attenuation pattern. We propose that local discontinuous translation temporally separates the translation of segments of the peptide chain and actively coordinates their co-translational folding.

Using mitoribosomal profiling to investigate human mitochondrial translation

“…There are many features that can contribute to the pausing and processivity of the synthetic machinery as it translates its template mRNA and it is becoming apparent that this is not as simple as, or restricted to, the secondary structure of the RNA ahead of the ribosome. Pausing may also be regulated by the abundance of charged tRNA, the number of consecutive codons for the same amino acid 2 , the charge of the newly synthesised peptide, folding and secondary structure of the peptide fragment within the exit tunnel 3, 4 , the influence of non-canonical wobble bases in codon:anticodon pairing 5 or by chemical damage of mRNAs or their degradation such that they lack a stop codon. Transient accumulation of ribosomes can also be observed at sites of translation initiation, whilst ribosomes are localising to particular subcellular locations 6 or during recruitment of chaperones or regulatory factors 7 .…”

Accurate Prediction of Cellular Co-Translational Folding Indicates Proteins can Switch from Post- to Co-Translational Folding

“…More recently, it has been demonstrated that the tertiary folding of protein domains can begin during their synthesis by the ribosome 7,15,19,31 . Translation introduces an additional process that can influence nascent protein folding; hence, the kinetic equations describing protein folding have recently been expanded to account for the impact of codon translation rates 10,26 .…”

“…Experimentalists have found that the introduction of presumably slow-translating synonymous substitutions often increases the extent of co-translational protein folding as reflected by the enzymatic activity 42 or resistance to proteases 31 of nascent proteins. For example, a domain in SufI lost resistance to protease degradation when two rare codons were replaced with common codons, suggesting faster elongation kinetics in the mutant transcript provide that domain insufficient time to co-translationally fold 31 . Similarly, it was found that optimizing codon usage in the N-terminal 164 codons of the Neurospora clock protein frequency (FRQ) was sufficient to decrease its ability to associate with the protein WC-2 by 60% 43 .…”

“…Synonymous codon substitutions can radically alter nascent protein behaviour by modifying the translation-elongation kinetics of a transcript 29,30 and thereby changing the timing and efficiency of co-translational processes. Previously, it was demonstrated that the co-translational folding of a domain in the Escherichia coli protein SufI can be abolished by the introduction of fast-translating synonymous codon substitutions in a normally slow-translating region 31 . In light of this, we sought to determine if synonymous codon substitutions can alter the most fundamental classification of nascent protein folding in yeast in the opposite manner.…”

Charting the dynamics of translation

“…This is not surprising because translation speed is unlikely to be the only selective force acting on codon selection. A number of other genomic parameters including GC-contents (Knight et al, 2001), mRNA folding (Tuller et al, 2011;Bentele et al, 2013), co-translation protein folding (Zhang et al, 2009;Xie et al, 1998;Mukhopadhyay et al, 2007) are also relevant. Moreover, even if translation speed were the only adaptive force, it would be very difficult to maintain a globally optimised genome in the face of continuous mutational pressure.…”