Inferring translational heterogeneity from Saccharomyces cerevisiae ribosome profiling

Abstract

Translation of mRNAs into proteins by the ribosome is the most important step of protein biosynthesis. Accordingly, translation is tightly controlled and heavily regulated to maintain cellular homeostasis. Ribosome profiling (Ribo‐seq) has revolutionized the study of translation by revealing many of its underlying mechanisms. However, equally many aspects of translation remain mysterious, in part also due to persisting challenges in the interpretation of data obtained from Ribo‐seq experiments. Here, we show that some of the variability observed in Ribo‐seq data has biological origins and reflects programmed heterogeneity of translation. Through a comparative analysis of Ribo‐seq data from Saccharomyces cerevisiae, we systematically identify short 3‐codon sequences that are differentially translated (DT) across mRNAs, that is, identical sequences that are translated sometimes fast and sometimes slowly beyond what can be attributed to variability between experiments. Remarkably, the thus identified DT sequences link to mechanisms known to regulate translation elongation and are enriched in genes important for protein and organelle biosynthesis. Our results thus highlight examples of translational heterogeneity that are encoded in the genomic sequences and tuned to optimizing cellular homeostasis. More generally, our work highlights the power of Ribo‐seq to understand the complexities of translation regulation.

Single-cell expression predicts neuron-specific protein homeostasis networks

“…Gene expression in general is inherently stochastic [ 59 ], as now quantifiable by single-cell genomics [ 60 ]. Moreover, some of that variability may be further amplified through translational heterogeneity [ 61 ]. The suppression of expression noise is costly [ 62 ], and some fluctuations are even functional, for instance in cell-fate decisions [ 63 ] or during differentiation [ 64 ].…”

Heterogeneous folding landscapes and predetermined breaking points within a protein family

“…However, any comparative analyses depends on a level of resolution that serves as a common denominator. The hope is that the presented results will motivate future studies to characterize in vivo protein folding landscapes include the role of the protein termini [53], and the interplay between translation, folding, and protein export pathways [54].…”

Single-cell expression predicts neuron specific protein homeostasis networks

“…Gene expression in general is inherently stochastic (Raj and van Oudenaarden, 2008), as now quantifiable by single-cell genomics (Jariani et al, 2020). Moreover, some of that variability may be further amplified through translational heterogeneity (do Couto Bordignon and Pechmann, 2021). The suppression of expression noise is costly (Lestas et al, 2010), and some fluctuations are even functional, for instance in cell-fate decisions (Coomer et al, 2022) or during differentiation (Wada et al, 2018).…”