Systematic Detection of Amino Acid Substitutions in Proteomes Reveals Mechanistic Basis of Ribosome Errors and Selection for Translation Fidelity

Abstract

Highlights d A new methodology to detect and quantify most translation errors in proteomes d Most amino acid substitutions result from mis-pairing between codons and anti-codons d Proteins' error rates are reduced at conserved and highly expressed proteins d Translation speed is negatively correlated with error rates

Reshaping of the Arabidopsis thaliana proteome landscape and co-regulation of proteins in development and immunity

“…The authors of the latter study define exchanges as near cognate errors (NeCE) when two of the three bases between error bearing origin and destination codon match and as non-cognate error (NoCE) when there is no such match between possible error bearing origin and destination codons. Interestingly, 5 of the 8 substitutions we found to be abundant in Arabidopsis (Asn->Met, Ala->Asp, Pro->Glu, Asp->Asn, Glu->Gln) were also abundant in yeast but not E.coli, and three (Ala->Asp, Asp->Asn, Glu->Gln) were NeCEs suggesting conserved patterns of translational error in eukaryotes, a possible method of generating random phenotype variants in genetically identical organisms (Mordret et al, 2019).…”

“…Next to the prevalence of known artificial and biologically occurring modifications, amino 814 acid substitutions were found to be common. Such exchanges are generally caused by815 ribosome infidelity, have a number of biological implications and have been reported 816 previously in human cell lines(Chick et al, 2015), human tissue (Bagwan et al, 2018)817 and in E.coli and yeast in detail(Mordret et al, 2019). The authors of the latter study 818 define exchanges as near cognate errors (NeCE) when two of the three bases between 819 error bearing origin and destination codon match and as non-cognate error (NoCE) 820 when there is no such match between possible error bearing origin and destination 821 codons.…”

“…The authors of the latter study 818 define exchanges as near cognate errors (NeCE) when two of the three bases between 819 error bearing origin and destination codon match and as non-cognate error (NoCE) 820 when there is no such match between possible error bearing origin and destination 821 codons. Interestingly, 5 of the 8 substitutions we found to be abundant in Arabidopsis 822 (Asn->Met, Ala->Asp, Pro->Glu, Asp->Asn, Glu->Gln) were also abundant in yeast but 823 not E.coli, and three (Ala->Asp, Asp->Asn, Glu->Gln) were NeCEs suggesting 824 conserved patterns of translational error in eukaryotes, a possible method of generating 825 random phenotype variants in genetically identical organisms(Mordret et al, 2019).826This phenomenon may also highlight the limitations of searching protein databases 827 derived from reference genomes with proteomics data.828Root and Seed Proteomes829The root is a highly specialized, plastic tissue that confers structural stability to the 830 above ground portion of the plant and is responsible for the uptake of nutrients and 831 water from the soil. Thus it exudes a number of metabolites, peptides and proteins that832 allow it to interact with the rhizobiome.…”

Dynamic changes in tRNA modifications and abundance during T-cell activation

“…It is possible to speculate that ribosomal frameshifting might enhance phenotypic variability of immunological repertoires, such as the T-cell receptor. A more conservative alternative is that the T-cell system may have evolved to balance the tradeoff between translation fidelity and speed, as has been discussed in other cellular contexts 34,35 . According to this possibility, reduction in modification allows cells to translate proteins more rapidly, i.e.…”

MMS2plot: an R package for visualizing multiple MS/MS spectra for groups of modified and non-modified peptides

“…This spectrum may also correspond to the substitution of F6 with Y6 [20]. Clearly, the aligned-spectra view shows more information than the single-spectrum view.…”