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J. Biol. Chem., Vol. 280, Issue 41, 34409-34419, October 14, 2005

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Protein Complexes of the Escherichia coli Cell Envelope^*

Filippa Stenberg, Peter Chovanec1, Sarah L. Maslen, Carol V. Robinson, Leopold L. Ilag¶, Gunnar von Heijne, and Daniel O. Daley2

From the Department of Biochemistry and Biophysics and ^¶Stockholm University Proteomics Facility, Department of Analytical Chemistry, Stockholm University, Stockholm SE-106 91, Sweden and the Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom

Protein complexes are an intrinsic aspect of life in the membrane. Knowing which proteins are assembled in these complexes is therefore essential to understanding protein function(s). Unfortunately, recent high throughput protein interaction studies have failed to deliver any significant information on proteins embedded in the membrane, and many membrane protein complexes remain ill defined. In this study, we have optimized the blue native-PAGE technique for the study of membrane protein complexes in the inner and outer membranes of Escherichia coli. In combination with second dimension SDS-PAGE and mass spectrometry, we have been able to identify 43 distinct protein complexes. In addition to a number of well characterized complexes, we have identified known and orphan proteins in novel oligomeric states. For two orphan proteins, YhcB and YjdB, our findings enable a tentative functional assignment. We propose that YhcB is a hitherto unidentified additional subunit of the cytochrome bd oxidase and that YjdB, which co-localizes with the ZipA protein, is involved in cell division. Our reference two-dimensional blue native-SDS-polyacrylamide gels will facilitate future studies of the assembly and composition of E. coli membrane protein complexes during different growth conditions and in different mutant backgrounds.

Received for publication, June 14, 2005 , and in revised form, July 14, 2005.

^* This work was supported by grants from the Swedish Foundation for Strategic Research, the Swedish Research Council, the Swedish Cancer Foundation, and the Marianne and Marcus Wallenberg Foundation (to G. v. H.) and by an EMBO Long Term Fellowship (to D. O. D.). 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. 1 and 2.

¹ Present address: Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, United Kingdom.

² To whom correspondence should be addressed: Dept. of Biochemistry and Biophysics Stockholm University, SE-106 91 Stockholm, Sweden. Tel.: 46-8-16-24-21; Fax: 46-8-15-36-79; E-mail: ddaley{at}dbb.su.se.

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