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Transient ribosomal attenuation coordinates protein synthesis and co-translational folding

Nature Structural & Molecular Biology volume 16, pages 274–280 (2009)Cite this article

Abstract

Clustered codons that pair to low-abundance tRNA isoacceptors can form slow-translating regions in the mRNA and cause transient ribosomal arrest. We report that folding efficiency of the Escherichia coli multidomain protein SufI can be severely perturbed by alterations in ribosome-mediated translational attenuation. Such alterations were achieved by global acceleration of the translation rate with tRNA excess in vitro or by synonymous substitutions to codons with highly abundant tRNAs both in vitro and in vivo. Conversely, the global slow-down of the translation rate modulated by low temperature suppresses the deleterious effect of the altered translational attenuation pattern. We propose that local discontinuous translation temporally separates the translation of segments of the peptide chain and actively coordinates their co-translational folding.

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Figure 1: Prediction of the translation rate in the ORFs of the E. coli transcriptome.
Figure 2: SufI is translated via many transient intermediates, as predicted from the translation-rate profile (a) and experimentally detected in synchronized in vitro translation in an E. coli cell-free system (b).
Figure 3: Altering the pattern of the slow-translating patches perturbs the co-translational folding of SufI.
Figure 4: Decreased translation temperature counterbalances the altered pattern of intrinsic ribosomal attenuation.

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Acknowledgements

We thank M. Hayer-Hartl and U. Hartl and their groups (Max-Planck-Institute, Martinsried) for fruitful discussions, T. Palmer (University of Dundee) for providing SufI wild-type DNA and B. Berks (University of Oxford) for sharing unpublished data on the crystal structure of SufI, which was enormously helpful for our interpretations. We thank S. Arvidsson and B. Müller-Röber (University of Potsdam) for help with the RT-PCR. This work is supported by the Deutsche Forschungsgemeinschaft (Heisenberg award to Z.I. and IG73/4-1) and a Katholischer Akademischer Ausländer-Dienst fellowship to G.Z.

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  1. Department of Cellular Biochemistry, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany

    Gong Zhang, Magdalena Hubalewska & Zoya Ignatova

  2. Department of Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str 24-25, Potsdam-Golm, 14476, Germany

    Gong Zhang & Zoya Ignatova

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G.Z. and Z.I. designed the experiments and analyzed the results; G.Z. carried out the experiments, wrote the program for the genome-wide search and prepared manuscript figures; M.H. carried out the in vivo experiments; Z.I. wrote the manuscript and supervised the project; all authors read and made contributions to the final manuscript.

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Correspondence to Zoya Ignatova.

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Zhang, G., Hubalewska, M. & Ignatova, Z. Transient ribosomal attenuation coordinates protein synthesis and co-translational folding. Nat Struct Mol Biol 16, 274–280 (2009). https://doi.org/10.1038/nsmb.1554

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