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J. Biol. Chem., Vol. 281, Issue 15, 10024-10034, April 14, 2006

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Defining the Role of the Escherichia coli Chaperone SecB Using Comparative Proteomics^*

Louise Baars, A. Jimmy Ytterberg, David Drew, Samuel Wagner, Claudia Thilo^¶, Klaas Jan van Wijk, and Jan-Willem de Gier¹

From the Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University SE-106 91 Stockholm, Sweden, the Department of Plant Biology, Cornell University, Ithaca, New York 14853, and the ^¶Center for Infectious Medicine, Karolinska Institute, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden

To improve understanding and identify novel substrates of the cytoplasmic chaperone SecB in Escherichia coli, we analyzed a secB null mutant using comparative proteomics. The secB null mutation did not affect cell growth but caused significant differences at the proteome level. In the absence of SecB, dynamic protein aggregates containing predominantly secretory proteins accumulated in the cytoplasm. Unprocessed secretory proteins were detected in radiolabeled whole cell lysates. Furthermore, the assembly of a large fraction of the outer membrane proteome was slowed down, whereas its steady state composition was hardly affected. In response to aggregation and delayed sorting of secretory proteins, cytoplasmic chaperones DnaK, GroEL/ES, ClpB, IbpA/B, and HslU were up-regulated severalfold, most likely to stabilize secretory proteins during their delayed translocation and/or rescue aggregated secretory proteins. The SecB/A dependence of 12 secretory proteins affected by the secB null mutation (DegP, FhuA, FkpA, OmpT, OmpX, OppA, TolB, TolC, YbgF, YcgK, YgiW, and YncE) was confirmed by "classical" pulse-labeling experiments. Our study more than triples the number of known SecB-dependent secretory proteins and shows that the primary role of SecB is to facilitate the targeting of secretory proteins to the Sec-translocase.

Received for publication, September 8, 2005 , and in revised form, December 9, 2005.

^* This work was supported by grants from the Swedish Research Council, Carl Tryggers Stiftelse, Marianne and Marcus Wallenberg Foundation, and the EMBO Young Investigator Programme (to J.-W. d. G.), a grant from The Swedish Foundation for International Cooperation in Research and Higher Education (STINT) (to J.-W. d. G. and K. J. v. W.), and proteomics infrastructure was supported by a grant from New York State Office of Science, Technology and Academic Research (to K. J. v. W.). 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 Tables S1–S4.

¹ To whom correspondence should be addressed. Tel.: 46-8-162420; Fax: 46-8-153679; E-mail: degier{at}dbb.su.se.

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