Journal of Molecular Biology
Protein Elongation, Co-translational Folding and Targeting
Graphical abstract
Introduction
Translation elongation is the central phase of the protein synthesis which maintains protein production and affects protein folding, processing and—for some predestined proteins—selection for targeting to cellular compartments. Elongation entails three major steps: decoding, peptide bond formation and tRNA–mRNA translocation. Elongation proceeds rapidly, with an average of 10–25 aa incorporated into the nascent peptide per second in Escherichia coli [1]. Despite the high overall rate of protein production, elongation is not a uniform process, as periods of rapid synthesis are interrupted by pauses. For rapidly translated stretches, the overall rate is mostly limited by the codon-specific delivery of cognate aminoacyl-tRNA (aa-tRNA) into the A site of the ribosome. The abundance of the respective tRNAs and other factors, such as secondary structure elements in the mRNA, codon context, ribosome pausing and stalling, collisions between ribosomes in polysomes, or cooperation between translating ribosomes and the RNA polymerase machinery may contribute to local pauses and thus to the variation of translation rates.
The relation of speed and accuracy of translation and the mechanisms of peptide bond formation and translocation remain important issues in understanding the processivity of translation. Furthermore, the ribosome can alter the meaning of individual codons, alleviate the co-linearity of the sequences of the mRNA and the protein, or change the reading frame on particular mRNAs. These recording phenomena suggest how mRNA signals can redirect the ribosome to the synthesis of an alternative protein, thereby enriching the proteome.
Proteins may start to fold during translation elongation. Translational pauses were long suggested to affect folding. A peptide emerging from the exit tunnel encounters a number of proteins, such as protein biogenesis factors and chaperones. Interactions of the nascent protein with these factors ensure correct processing of the N terminus, help folding or keep unfolded and ensure that the proteins will find their destination in the cell, for example, are inserted into the plasma membrane. We present a view of translation elongation as a complex network of reactions that ensure the composition and quality of the cellular proteome.
Section snippets
Decoding
Speed and accuracy of protein synthesis are fundamental parameters that affect the fitness of the cell, the quality of the proteome and the evolution of ribosomes. At each round of elongation, the ribosome selects an aa-tRNA corresponding to the codon in the A site among other aa-tRNAs. Aa-tRNAs are delivered to the ribosome in a ternary complex with elongation factor (EF)-Tu and GTP. On the ribosome, the fidelity of translation is controlled at two basic selection stages (Fig. 1): (i) during
Recoding
While the fidelity of translation is generally high, some mRNAs contain signals which alter the rules for reading the information in the mRNA and lead to recoding. One example of recoding is provided by the selenocysteine (Sec) insertion system, which ensures the incorporation of Sec, the 21st natural proteinogenic amino acid, by reading a UAG stop codon with the help of a specialized tRNA, Sec-tRNASec, guided by a downstream stem/loop (SECIS, selenocysteine incorporation sequence) in the mRNA.
Co-translational Protein Folding
Folding of many proteins begins when the nascent peptide is still attached to the synthesizing ribosome (for recent reviews, see Refs. [121], [122], [123], [124], [125], [126], [127], [128], [129]). The nascent peptide travels through a polypeptide exit tunnel (Fig. 8). The tunnel covers about 30–40 aa of the nascent peptide, assuming an unfolded, fully stretched conformation. The width of the tunnel constrains the folding of the nascent peptide and does not permit formation of extended
Interactions of Nascent Peptides with Protein Biogenesis Factors on the Ribosome
Depending on sequence, folding properties and final destination of newly synthesized proteins in the cell, nascent peptides emerging from the ribosome interact with a number of ribosome-associated protein biogenesis factors (RPBs). In bacteria these include, among others, the chaperone trigger factor (TF), which prevents misfolding of the nascent peptide, the signal recognition particle (SRP), which promotes co-translational targeting of ribosome-nascent-chain complexes (RNCs) to the membrane,
Co-translational Membrane Targeting of Ribosomes Synthesizing Membrane Proteins
About one quarter of the bacterial proteome consists of proteins that are integrated into the plasma membrane. To avoid misfolding and aggregation due to exposed hydrophobic patches, membrane proteins are inserted into the membrane co-translationally by way of a protein conducting channel (translocon) located in the membrane. Ribosomes synthesizing membrane proteins are targeted to the translocon by the SRP pathway (for a recent review, see Ref. [172]). E. coli SRP consists of an RNA, 4.5S RNA,
Acknowledgments
We thank all present and former members of our labs for their contributions to the work reviewed here and Michael Pearson for preparing Fig. 3. Research in our laboratories is supported by the Max-Planck Society, grants of the Deutsche Forschungsgemeinschaft (SFB860, SFB1190 and FOR1805 to M.V.R.), and a grant of the Human Frontier Science Program (grant no. RGP0024-2010 to M.V.R.).
References (189)
- et al.
A primary role for release factor 3 in quality control during translation elongation in Escherichia coli
Cell
(2011) - et al.
A uniform response to mismatches in codon–anticodon complexes ensures ribosomal fidelity
Mol. Cell
(2006) - et al.
Kinetic determinants of high-fidelity tRNA discrimination on the ribosome
Mol. Cell
(2004) - et al.
Codon reading by tRNAAla with modified uridine in the wobble position
Mol. Cell
(2007) - et al.
Rates of aminoacyl-tRNA selection at 29 sense codons in vivo
J. Mol. Biol.
(1989) - et al.
Absolute in vivo translation rates of individual codons in Escherichia coli. The two glutamic acid codons GAA and GAG are translated with a threefold difference in rate
J. Mol. Biol.
(1991) - et al.
Different aa-tRNAs are selected uniformly on the ribosome
Mol. Cell
(2008) - et al.
Distortion of tRNA upon near-cognate codon recognition on the ribosome
J. Biol. Chem.
(2011) - et al.
Essential role of histidine 84 in elongation factor Tu for the chemical step of GTP hydrolysis on the ribosome
J. Mol. Biol.
(2003) The ribosome as a versatile catalyst: reactions at the peptidyl transferase center
Curr. Opin. Struct. Biol.
(2013)
Structural insights into the roles of water and the 2′ hydroxyl of the P site tRNA in the peptidyl transferase reaction
Mol. Cell
Modulation of the rate of peptidyl transfer on the ribosome by the nature of substrates
J. Biol. Chem.
An uncharged amine in the transition state of the ribosomal peptidyl transfer reaction
Chem. Biol.
Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome
Mol. Cell
Spontaneous intersubunit rotation in single ribosomes
Mol. Cell
Conformational changes of elongation factor G on the ribosome during tRNA translocation
Cell
Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation
Mol. Cell
Reverse translocation of tRNA in the ribosome
Mol. Cell
Movement of elongation factor G between compact and extended conformations
J. Mol. Biol.
Kinetically competent intermediates in the translocation step of protein synthesis
Mol. Cell
An elongation factor G-induced ribosome rearrangement precedes tRNA–mRNA translocation
Mol. Cell
Single-molecule fluorescence measurements of ribosomal translocation dynamics
Mol. Cell
Programmed − 1 frameshifting by kinetic partitioning during impeded translocation
Cell
Modulation of chemical composition and other parameters of the cell at different exponential growth rates
EcoSal Plus
A kinetic safety gate controlling the delivery of unnatural amino acids to the ribosome
J. Am. Chem. Soc.
Quality control by the ribosome following peptide bond formation
Nature
Optimization of speed and accuracy of decoding in translation
EMBO J.
Deducing the kinetics of protein synthesis in vivo from the transition rates measured in vitro
PLoS Comput. Biol.
Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection
Proc. Natl. Acad. Sci. U. S. A.
Accuracy of initial codon selection by aminoacyl-tRNAs on the mRNA-programmed bacterial ribosome
Proc. Natl. Acad. Sci. U. S. A.
Evolutionary optimization of speed and accuracy of decoding on the ribosome
Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci.
Exceptionally large entropy contributions enable the high rates of GTP hydrolysis on the ribosome
Sci. Rep.
Measurement of average decoding rates of the 61 sense codons in vivo
Elife
The mechanism for activation of GTP hydrolysis on the ribosome
Science
An active role for tRNA in decoding beyond codon:anticodon pairing
Science
The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA
Science
Intact aminoacyl-tRNA is required to trigger GTP hydrolysis by elongation factor Tu on the ribosome
Biochemistry
Structural insights into cognate versus near-cognate discrimination during decoding
EMBO J.
Missense suppressor mutations in 16S rRNA reveal the importance of helices h8 and h14 in aminoacyl-tRNA selection
RNA
Ribosome-induced tuning of GTP hydrolysis by a translational GTPase
Proc. Natl. Acad. Sci. U. S. A.
Role of a ribosomal RNA phosphate oxygen during the EF-G-triggered GTP hydrolysis
Proc. Natl. Acad. Sci. U. S. A.
Comment on “the mechanism for activation of GTP hydrolysis on the ribosome”
Science
Elongation factor G bound to the ribosome in an intermediate state of translocation
Science
Structure of EF-G-ribosome complex in a pretranslocation state
Nat. Struct. Mol. Biol.
The conformation of a catalytic loop is central to GTPase activity on the ribosome
Biochemistry
GTPase activation of elongation factors Tu and G on the ribosome
Biochemistry
Functional role of the C-terminal tail of the archaeal ribosomal stalk in recruitment of two elongation factors to the sarcin/ricin loop of 23S rRNA
Genes Cells
A tRNA body with high affinity for EF-Tu hastens ribosomal incorporation of unnatural amino acids
RNA
Inefficient delivery but fast peptide bond formation of unnatural l-aminoacyl-tRNAs in translation
J. Am. Chem. Soc.
Tuning the affinity of aminoacyl-tRNA to elongation factor Tu for optimal decoding
Proc. Natl. Acad. Sci. U. S. A.
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