Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation

Abstract

To investigate the possible influence of the local rates of translation on protein folding, 16 consecutive rare (in Escherichia coli) codons in the chloramphenicol acetyltransferase (CAT) gene have been replaced by frequent ones. Site-directed silent mutagenesis reduced the pauses in translation of CAT in E. coli S30 extract cell-free system and led to the acceleration of the overall rate of CAT protein synthesis. At the same time, the silently mutated protein (with unaltered protein sequence) synthesized in the E. coli S30 extract system was shown to possess 20% lower specific activity. The data suggest that kinetics of protein translation can affect the in vivo proteinfolding pathway, leading to increased levels of protein misfolding.z 1999 Federation of European Biochemical Societies.

Kinetic modelling indicates that fast-translating codons can coordinate cotranslational protein folding by avoiding misfolded intermediates

“…These equations provide a means of testing the general idea that slowing translation will monotonically increase the probability that a domain will fold cotranslationally, and conversely that speeding up translation will decrease this probability [2][3][4][5][6] . In this work, we have tested this idea by analysing the dynamic behaviour of these cotranslational folding models, and indeed we have found that there are situations in which other scenarios are possible.…”

“…For example, replacement of rare codons with common codons, which are presumed to be translated more quickly, has been found to decrease the cotranslational folding of a number of proteins 2,6,40 , and an in vivo assay examining heterologous protein expression found that four different proteins exhibited increased cotranslational folding when translation rates were globally decreased using a streptomycin-sensitive Escherichia coli strain 3 . The predictions made in the present study indicate that exceptions can exist, and we hope these results will motivate experimental investigations to search for nascent proteins that exhibit increased cotranslational folding upon an increase in individual codon translation rates.…”

“…As translation and folding can occur concomitantly, codon translation rates can affect the outcome of the folding process. Indeed, this is exactly what happens in certain cases, as the variability in the rates at which individual amino acids are covalently attached to the C-terminus of the elongating nascent polypeptide chain can strongly influence whether a protein cotranslationally folds and attains its functionality, or misfolds [2][3][4][5][6][7] . The evidence to date indicates that slowing down translation tends to increase cotranslational folding, and simple arguments suggest that this inverse relationship may be a general phenomenon 8 .…”

Optimizing within-host viral fitness: infected cell lifespan and virion production rate

“…However, these rates may vary with p. For example, increasing protein translation rates has been shown to increase the probability a protein is misfolded (Komar et al, 1999;Cortazzo et al, 2002). Thus assuming that misfolded proteins are not all destroyed and consequently that some are used by the virus, misfolding can lead to increases in c and reductions in k. If a virus has adapted to reduce the antigenicity of its envelope proteins, misfolded proteins could lead to greater antibody binding to free virus, which would in turn lead to an increase in the virion's average clearance rate c. Similarly, misfolded envelope proteins would be expected to have a lower target cell binding rate, thus directly decreasing k. Finally, misfolded viral proteins involved in post cell-invasion processes, such as reverse transcription, should have lower enzymatic activities and shorter intracellular half-lives (and hence concentrations).…”

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

“…It also suggests that, at least for DC SFVP synthesis in CHO cells, Fluitt and Viljoen's estimated rates may have too great a variance. 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 .…”