Optimization of speed and accuracy of decoding in translation

Wohlgemuth, Ingo; Pohl, Corinna; Rodnina, Marina V.

doi:10.1038/emboj.2010.229

Cited by 106 publications

(145 citation statements)

References 42 publications

(128 reference statements)

Supporting

Mentioning

132

Contrasting

Unclassified

Order By: Relevance

“…The Mg 2 þ concentration is crucial for speed and fidelity of decoding 16 ; however, its effect on recoding events, such as bypassing, is not known. At low Mg 2 þ concentration, the gene 60 mRNA was translated up to the stop codon at the beginning of the gap, but the full-length byp was not formed (we have added 3.5-4.0 mM Mg 2 þ , corresponding to about 1.0-1.5 mM of free Mg 2 þ , taking into account the Mg 2 þ bound to GTP and phosphoenol pyruvate present in the reaction mixture 16 ; see Methods). At higher concentrations of Mg 2 þ (5-7 mM added), the byp was formed (23%).…”

Section: Resultsmentioning

confidence: 99%

High-efficiency translational bypassing of non-coding nucleotides specified by mRNA structure and nascent peptide

et al. 2014

View full text Add to dashboard Cite

The gene product 60 (gp60) of bacteriophage T4 is synthesized as a single polypeptide chain from a discontinuous reading frame as a result of bypassing of a non-coding mRNA region of 50 nucleotides by the ribosome. To identify the minimum set of signals required for bypassing, we recapitulated efficient translational bypassing in an in vitro reconstituted translation system from Escherichia coli. We find that the signals, which promote efficient and accurate bypassing, are specified by the gene 60 mRNA sequence. Systematic analysis of the mRNA suggests unexpected contributions of sequences upstream and downstream of the non-coding gap region as well as of the nascent peptide. During bypassing, ribosomes glide forward on the mRNA track in a processive way. Gliding may have a role not only for gp60 synthesis, but also during regular mRNA translation for reading frame selection during initiation or tRNA translocation during elongation.

show abstract

Section: Resultsmentioning

confidence: 99%

High-efficiency translational bypassing of non-coding nucleotides specified by mRNA structure and nascent peptide

et al. 2014

View full text Add to dashboard Cite

show abstract

“…On the other hand, it has been argued that similar K M values for the cognate and non-cognate complexes would lead to slow cognate amino acid incorporation owing to competition by the large excess of incorrect ternary complexes over correct ones [65,66]. However, competition experiments showed that, although the presence of excess bulk ternary complexes reduced the rate of GTP hydrolysis for the cognate ternary complex about 10-fold, this is not reflected in a decrease of the rate of cognate peptide bond formation, because the rate of GTP hydrolysis even at high concentrations of inhibitory ternary complexes is higher than the rate of peptide bond formation, buffering the inhibition by competition (figure 3b) [37]. Thus, the high speed of GTP hydrolysis on cognate codons in fact causes a loss of intrinsically available selectivity, but at the same time precludes that the rate of amino acid incorporation is decreased by competition with bulk ternary complexes.…”

Section: Trade-off Between Speed and Accuracymentioning

confidence: 99%

“…Based on the available data, the reaction rate is limited by the accommodation of the aa-tRNA in the peptidyl transferase centre on the 50S subunit [37,57]. Computer simulations of accommodation suggested a stepwise movement of the tRNA through a corridor of conserved rRNA bases, which engage in various interactions with the tRNA during this movement [58].…”

Section: The Crucial Forward Steps Of Decodingmentioning

confidence: 99%

“…Measurements in vitro using reconstituted translation systems working at conditions optimized for speed and fidelity account for an error frequency of about 10 24 -10 23 (figure 3a) [24,30,31,37]. The much lower in vitro error frequency of 10 27 reported recently [63] can now be attributed to the use of extremely low concentrations of free Mg 2þ that destabilized near-cognate codon recognition complexes much more than cognate ones, leading to an artificially high incorporation of cognate relative to near-cognate amino acids [37]. The about 1000-fold difference between the k 22 values imply a large difference in the thermodynamic stability, DDG8, between cognate and near-cognate codonrecognition complexes [29,31,43,64].…”

Section: Trade-off Between Speed and Accuracymentioning

confidence: 99%

“…For the GTPase reaction on the ribosome, one possible reason for this difference to the enzyme-catalysed reactions is the necessity to optimize speed and fidelity at the same time; the optimization of subsequent peptide bond formation beyond the efficiency of the GTPase would be unnecessary. In fact, the ribosome accelerates the peptidyl transfer reaction by a factor of about 10 7 -10 8 [37,42,68], i.e. it is much less efficient than many protein enzymes that accelerate reactions by up to 10 23 -fold [69].…”

Section: Trade-off Between Speed and Accuracymentioning

confidence: 99%

See 2 more Smart Citations

Evolutionary optimization of speed and accuracy of decoding on the ribosome

Wohlgemuth

Pohl

Mittelstaet

et al. 2011

Phil. Trans. R. Soc. B

Self Cite

132

159

View full text Add to dashboard Cite

Speed and accuracy of protein synthesis are fundamental parameters for the fitness of living cells, the quality control of translation, and the evolution of ribosomes. The ribosome developed complex mechanisms that allow for a uniform recognition and selection of any cognate aminoacyl-tRNA (aa-tRNA) and discrimination against any near-cognate aa-tRNA, regardless of the nature or position of the mismatch. This review describes the principles of the selection-kinetic partitioning and induced fit-and discusses the relationship between speed and accuracy of decoding, with a focus on bacterial translation. The translational machinery apparently has evolved towards high speed of translation at the cost of fidelity.Keywords: ribosome; protein synthesis; translation fidelity; tRNA; error frequency; mRNA decoding SPEED AND ACCURACY OF TRANSLATIONProtein synthesis on the ribosome is a fundamentally important process that consumes a large part of the energy resources of the cell. Ribosomes are universal macromolecular machines built of two subunits, the small subunit (30S subunit in bacteria), where mRNA decoding takes place, and the large subunit (50S subunit in bacteria), which harbours the catalytic site for peptide bond formation. The decoding and peptidyl transferase centres consist of RNA, suggesting that the ribosome originates from the RNA world. Intuitively, one would expect that the ribosome has evolved to produce proteins with maximum speed and accuracy at minimum metabolic cost. The aim of this review is to discuss the mechanisms by which this is achieved and potential limits to the optimization of the ribosome performance. Protein synthesis entails four major phases: initiation, elongation, termination and recycling. During initiation, the ribosome selects an mRNA and, assisted by initiation factors, places the initiator tRNA on the appropriate start codon in the P site. In the subsequent elongation phase, amino acids are added to the growing peptide in a cyclic process. Aminoacyl-tRNAs (aa-tRNAs) enter the ribosome in a tight complex with elongation factor Tu (EF-Tu) and guanosine-5 0 -triphosphate (GTP). Following the recognition of the codon by the anticodon of aa-tRNA and GTP hydrolysis by EF-Tu, aa-tRNA is accommodated in the A site of the 50S subunit and takes part in peptide bond formation. The rate of protein elongation in bacteria is between 4 and 22 amino acids per second at 378C [1-5]; thus, a protein of an average length of 330 amino acids [6] is completed in about 10-80 s. The times required for initiation, termination and ribosome recycling (around 1 s each [3]) are short enough to make elongation rate-limiting for protein synthesis [7]. Translation of a particular codon depends on both the nature and abundance of the respective tRNAs, particularly on the non-random use of synonymous codons and the availability of the respective isoacceptor tRNAs [8]. The overall rate of translation is limited by the codon-specific rates of cognate ternary complex delivery to the A site and is further attenuated ...

show abstract

Translational Control under Stress: Reshaping the Translatome

2019

View full text Add to dashboard Cite

Adequate reprogramming of cellular metabolism in response to stresses or suboptimal growth conditions involves a myriad of coordinated changes that serve to promote cell survival. As protein synthesis is an energetically expensive process, its regulation under stress is of critical importance. Reprogramming of messenger RNA (mRNA) translation involves well‐understood stress‐activated kinases that target components of translation initiation machinery, resulting in the robust inhibition of general translation and promotion of the translation of stress‐responsive proteins. Translational arrest of mRNAs also results in the accumulation of transcripts in cytoplasmic foci called stress granules. Recent studies focus on the key roles of transfer RNA (tRNA) in stress‐induced translational reprogramming. These include stress‐specific regulation of tRNA pools, codon‐biased translation influenced by tRNA modifications, tRNA miscoding, and tRNA cleavage. In combination, signal transduction pathways and tRNA metabolism changes regulate translation during stress, resulting in adaptation and cell survival. This review examines molecular mechanisms that regulate protein synthesis in response to stress.

show abstract

Optimization of speed and accuracy of decoding in translation

Cited by 106 publications

References 42 publications

High-efficiency translational bypassing of non-coding nucleotides specified by mRNA structure and nascent peptide

High-efficiency translational bypassing of non-coding nucleotides specified by mRNA structure and nascent peptide

Evolutionary optimization of speed and accuracy of decoding on the ribosome

Translational Control under Stress: Reshaping the Translatome

Contact Info

Product

Resources

About