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J. Biol. Chem., Vol. 282, Issue 11, 7809-7816, March 16, 2007

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Association of Protein Biogenesis Factors at the Yeast Ribosomal Tunnel Exit Is Affected by the Translational Status and Nascent Polypeptide Sequence^*

Uta Raue, Stefan Oellerer, and Sabine Rospert¹

From the Institute of Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Zellforschung and the Fakultät für Biologie, University of Freiburg, D-79104 Freiburg, Germany

Ribosome-associated protein biogenesis factors (RPBs) act during a short but critical period of protein biogenesis. The action of RPBs starts as soon as a nascent polypeptide becomes accessible from the outside of the ribosome and ends upon termination of translation. In yeast, RPBs include the chaperones Ssb1/2 and ribosome-associated complex, signal recognition particle, nascent polypeptide-associated complex (NAC), the aminopeptidases Map1 and Map2, and the N-terminal acetyltransferase NatA. Here, we provide the first comprehensive analysis of RPB binding at the yeast ribosomal tunnel exit as a function of translational status and polypeptide sequence. We measured the ratios of RPBs to ribosomes in yeast cells and determined RPB occupation of translating and non-translating ribosomes. The combined results imply a requirement for dynamic and coordinated interactions at the tunnel exit. Exclusively, NAC was associated with the majority of ribosomes regardless of their translational status. All other RPBs occupied only ribosomal subpopulations, binding with increased apparent affinity to randomly translating ribosomes as compared with non-translating ones. Analysis of RPB interaction with homogenous ribosome populations engaged in the translation of specific nascent polypeptides revealed that the affinities of Ssb1/2, NAC, and, as expected, signal recognition particle, were influenced by the amino acid sequence of the nascent polypeptide. Complementary cross-linking data suggest that not only affinity of RPBs to the ribosome but also positioning can be influenced in a nascent polypeptide-dependent manner.

Received for publication, December 13, 2006 , and in revised form, January 12, 2007.

^* This work was supported by the Fonds der Chemischen Industrie (to S. R.) and by Collaborative Research Center 388 (to S. R.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains supplemental Figs. S1 and S2 and supplemental Table S1.

¹ To whom correspondence should be addressed: Institute of Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Zellforschung, Herrmann-Herder-Str. 7, D-79104 Freiburg, Germany. Tel.: 49-761-2035259; Fax: 49-761-2035257; E-mail: sabine.rospert{at}biochemie.uni-freiburg.de.

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