scholarly journals The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation

2016 ◽  
Author(s):  
Khanh Dao Duc ◽  
Yun S. Song
Keyword(s):  
Electrostatic Interactions ◽  
Elongation Rate ◽  
Ribosome Profiling ◽  
Rate Variation ◽  
Biophysical Properties ◽  
Translation Elongation ◽  
Nascent Polypeptide ◽  
Exit Tunnel ◽  
Pass Through ◽  
The Impact

ABSTRACTPrevious studies have shown that translation elongation is regulated by multiple factors, but the observed heterogeneity remains only partially explained. To dissect quantitatively the different determinants of elongation speed, we use probabilistic modeling to estimate initiation and local elongation rates from ribosome profiling data. This model-based approach allows us to quantify the extent of interference between ribosomes on the same transcript. We show that neither interference nor the distribution of slow codons is sufficient to explain the observed heterogeneity. Instead, we find that electrostatic interactions between the ribosomal exit tunnel and specific parts of the nascent polypeptide govern the elongation rate variation as the polypeptide makes its initial pass through the tunnel. Once the N-terminus has escaped the tunnel, the hydropathy of the nascent polypeptide within the ribosome plays a major role in modulating the speed. We show that our results are consistent with the biophysical properties of the tunnel.

scholarly journals Inferring efficiency of translation initiation and elongation from ribosome profiling

2020 ◽  
Vol 48 (17) ◽  
pp. 9478-9490
Author(s):  
Juraj Szavits-Nossan ◽  
Luca Ciandrini
Keyword(s):  
Protein Synthesis ◽  
Mathematical Modelling ◽  
Translation Initiation ◽  
Mrna Translation ◽  
Elongation Rate ◽  
Ribosome Profiling ◽  
Translation Elongation ◽  
Recent Advances ◽  
Two Stages

Abstract One of the main goals of ribosome profiling is to quantify the rate of protein synthesis at the level of translation. Here, we develop a method for inferring translation elongation kinetics from ribosome profiling data using recent advances in mathematical modelling of mRNA translation. Our method distinguishes between the elongation rate intrinsic to the ribosome’s stepping cycle and the actual elongation rate that takes into account ribosome interference. This distinction allows us to quantify the extent of ribosomal collisions along the transcript and identify individual codons where ribosomal collisions are likely. When examining ribosome profiling in yeast, we observe that translation initiation and elongation are close to their optima and traffic is minimized at the beginning of the transcript to favour ribosome recruitment. However, we find many individual sites of congestion along the mRNAs where the probability of ribosome interference can reach $50\%$. Our work provides new measures of translation initiation and elongation efficiencies, emphasizing the importance of rating these two stages of translation separately.

scholarly journals Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing

2019 ◽  
Author(s):  
Alaaddin Bulak Arpat ◽  
Angélica Liechti ◽  
Mara De Matos ◽  
René Dreos ◽  
Peggy Janich ◽  
...  
Keyword(s):  
Protein Production ◽  
Evolutionary Conservation ◽  
Ribosome Profiling ◽  
Translation Rate ◽  
Translation Elongation ◽  
Peptide Motifs ◽  
Functional Relevance ◽  
Polypeptide Structure ◽  
The Impact ◽  
Pause Site

AbstractTranslation initiation is the major regulatory step defining the rate of protein production from an mRNA. Meanwhile, the impact of non-uniform ribosomal elongation rates is largely unknown. Using a modified ribosome profiling protocol based on footprints from two closely packed ribosomes (disomes), we have mapped ribosomal collisions transcriptome-wide in mouse liver. We uncover that the stacking of an elongating onto a paused ribosome occurs frequently and scales with translation rate, trapping ∼10% of translating ribosomes in the disome state. A distinct class of pause sites, independent of translation rate, is indicative of deterministic pausing signals. Pause site association with specific amino acids, peptide motifs and nascent polypeptide structure, is suggestive of programmed pausing as a widespread mechanism associated with protein folding. Evolutionary conservation at disome sites indicates functional relevance of translational pausing. Collectively, our disome profiling approach allows unique insights into gene regulation occurring at the step of translation elongation.

scholarly journals Widespread Alterations in Translation Elongation in the Brain of Juvenile Fmr1 Knock-Out Mice

2018 ◽  
Author(s):  
Sohani Das Sharma ◽  
Jordan B. Metz ◽  
Hongyu Li ◽  
Benjamin D. Hobson ◽  
Nicholas Hornstein ◽  
...  
Keyword(s):  
Fragile X Syndrome ◽  
Translation Initiation ◽  
Rna Binding ◽  
Fragile X ◽  
Ribosome Profiling ◽  
Translation Elongation ◽  
Knock Out ◽  
Knock Out Mice ◽  
Mrna Binding ◽  
The Impact

SummaryFMRP is a polysome-associated RNA-binding protein encoded by Fmr1 that is lost in Fragile X syndrome. Increasing evidence suggests that FMRP regulates both translation initiation and elongation, but the gene-specificity of these effects is unclear. To elucidate the impact of Fmr1 loss on translation, we used ribosome profiling for genome-wide measurements of ribosomal occupancy and positioning in the cortex of 24 day-old Fmr1 knock-out mice. We found a remarkably coherent reduction in ribosome footprint abundance per mRNA for previously identified, high-affinity mRNA binding partners of FMRP, and an increase for terminal oligo-pyrimidine (TOP) motif-containing genes canonically controlled by mTOR-4EBP-eIF4E signaling. Amino acid motif- and gene-level analyses both showed a widespread reduction of translational pausing in Fmr1 knock-out mice. Our findings are consistent with a model of FMRP-mediated regulation of both translation initiation through eIF4E and elongation that is disrupted in Fragile X syndrome.

scholarly journals Inferring efficiency of translation initiation and elongation from ribosome profiling

2019 ◽  
Author(s):  
Juraj Szavits-Nossan ◽  
Luca Ciandrini
Keyword(s):  
Protein Synthesis ◽  
Mathematical Modelling ◽  
Translation Initiation ◽  
Mrna Translation ◽  
Elongation Rate ◽  
Ribosome Profiling ◽  
Translation Elongation ◽  
Recent Advances ◽  
Two Stages

ABSTRACTOne of the main goals of ribosome profiling is to quantify the rate of protein synthesis at the level of translation. Here, we develop a method for inferring translation elongation kinetics from ribosome profiling data using recent advances in the mathematical modelling of mRNA translation. Our method distinguishes between the elongation rate intrinsic to the ribosome’s stepping cycle and the actual elongation rate that takes into account ribosome interference. This distinction allows us to quantify the extent of ribosomal collisions along the transcript and identify individual codons where ribosomal collisions are likely. When examining ribosome profiling in yeast, we observe that translation initiation and elongation are close to their optima, and traffic is minimised at the beginning of the transcript to favour ribosome recruitment. However, we find many individual sites of congestion along the mRNAs where the probability of ribosome interference can reach 50%. Our work provides new measures of translation initiation and elongation efficiencies, emphasising the importance of rating these two stages of translation separately.

scholarly journals Rqc1 and other yeast proteins containing highly positively charged sequences are not targets of the RQC complex

2019 ◽  
Author(s):  
Géssica C. Barros ◽  
Rodrigo D. Requião ◽  
Rodolfo L. Carneiro ◽  
Claudio A. Masuda ◽  
Mariana H. Moreira ◽  
...  
Keyword(s):  
Electrostatic Interactions ◽  
Translation Termination ◽  
Ribosome Profiling ◽  
Translation Efficiency ◽  
Ribosome Stalling ◽  
Reporter Systems ◽  
Exit Tunnel ◽  
Endogenous Proteins ◽  
Ribosome Exit Tunnel ◽  
Positively Charged

ABSTRACTHighly positively charged protein segments are known to result in poor translation efficiency. This effect is explained by ribosome stalling caused by electrostatic interactions between the nascent peptide and the negatively charged ribosome exit tunnel, leading to translation termination followed by protein degradation mediated by the RQC complex. These polybasic sequences are mainly studied in the context of artificial reporter systems. Examples of endogenous yeast proteins targeted by the RQC complex are Rqc1, a protein essential for RQC function, and Sdd1. Both contain polybasic sequences that are thought to activate the RQC, leading to protein down-regulation. Here, we investigated whether the RQC complex regulates other endogenous proteins with polybasic sequences. We show by bioinformatics, ribosome profiling data analysis, and western blot that endogenous proteins containing polybasic sequences similar to, or even more positively charged than those of Rqc1 and Sdd1, are not targeted by the RQC complex suggesting that endogenous polybasic sequences are not sufficient to induce this type of regulation. Finally, our results also suggest that Rqc1 is regulated post-translationally by the E3 component of the RQC complex Ltn1, in a manner independent of the RQC complex.

scholarly journals Accurate design of translational output by a neural network model of ribosome distribution

2017 ◽  
Author(s):  
Robert J Tunney ◽  
Nicholas J McGlincy ◽  
Monica E Graham ◽  
Nicki Naddaf ◽  
Lior Pachter ◽  
...  
Keyword(s):  
Neural Network ◽  
Fluorescent Protein ◽  
Synonymous Codon ◽  
Full Range ◽  
Rna Stability ◽  
Ribosome Profiling ◽  
Translation Elongation ◽  
Accurate Design ◽  
The Impact

Synonymous codon choice can have dramatic effects on ribosome speed, RNA stability, and protein expression. Ribosome profiling experiments have underscored that ribosomes do not move uniformly along mRNAs, exposing a need for models of coding sequences that capture the full range of empirically observed variation. We present a method, Ixnos, that models this variation in translation elongation using a feedforward neural network to predict the translation elongation rate at each codon as a function of its sequence neighborhood. Our approach revealed sequence features affecting translation elongation and quantified the impact of large technical biases in ribosome profiling. We applied our model to design synonymous variants of a fluorescent protein spanning the range of possible translation speeds predicted with our model. We found that levels of the fluorescent protein in yeast closely tracked the predicted translation speeds across their full range. We therefore demonstrate that our model captures information determining translation dynamics in vivo, and that control of translation elongation alone is sufficient to produce large, quantitative differences in protein output.

scholarly journals Nascent polypeptide within the exit tunnel ensures continuous translation elongation by stabilizing the translating ribosome

2021 ◽  
Author(s):  
Yuhei Chadani ◽  
Nobuyuki Sugata ◽  
Tatsuya Niwa ◽  
Yosuke Ito ◽  
Shintaro Iwasaki ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Amino Acid Residues ◽  
Translation Elongation ◽  
Ribosomal Subunits ◽  
Nascent Polypeptide ◽  
Nascent Chain ◽  
Exit Tunnel ◽  
Living Organisms

SummaryContinuous translation elongation, irrespective of amino acid sequences, is a prerequisite for living organisms to produce their proteomes. However, the risk of elongation abortion is concealed within nascent polypeptide products. Negatively charged sequences with occasional intermittent prolines, termed intrinsic ribosome destabilization (IRD) sequences, destabilizes the translating ribosomal complex. Thus, some nascent chain sequences lead to premature translation cessation. Here, we show that the risk of IRD is maximal at the N-terminal regions of proteins encoded by dozens of Escherichia coli genes. In contrast, most potential IRD sequences in the middle of open reading frames remain cryptic. We found two elements in nascent chains that counteract IRD: the nascent polypeptide itself that spans the exit tunnel and its bulky amino acid residues that occupy the tunnel entrance region. Thus, nascent polypeptide products have a built-in ability to ensure elongation continuity by serving as a bridge and thus by protecting the large and small ribosomal subunits from dissociation.

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