Protein Elongation, Co-translational Folding and Targeting

https://doi.org/10.1016/j.jmb.2016.03.022Get rights and content

Highlights

  • Ribosome dynamics control decoding and translocation.

  • A specialized translation factor is required for the synthesis of proline stretches.

  • Programmed ribosome frameshifting is due to impeded translocation.

  • The ribosomal peptide exit tunnel directs co-translational protein folding.

  • The translocon opens laterally on ribosome binding and signal peptide insertion.

Abstract

The elongation phase of protein synthesis defines the overall speed and fidelity of protein synthesis and affects protein folding and targeting. The mechanisms of reactions taking place during translation elongation remain important questions in understanding ribosome function. The ribosome—guided by signals in the mRNA—can recode the genetic information, resulting in alternative protein products. Co-translational protein folding and interaction of ribosomes and emerging polypeptides with associated protein biogenesis factors determine the quality and localization of proteins. In this review, we summarize recent findings on mechanisms of translation elongation in bacteria, including decoding and recoding, peptide bond formation, tRNA–mRNA translocation, co-translational protein folding, interaction with protein biogenesis factors and targeting of ribosomes synthesizing membrane proteins to the plasma membrane. The data provide insights into how the ribosome shapes composition and quality of the cellular proteome.

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.).

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