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Published online before print March 7, 2006, 10.1110/ps.051889506
Protein Science (2006), 15:884-889. Published by Cold Spring Harbor Laboratory Press. Copyright © 2006 The Protein Society
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New Escherichia coli outer membrane proteins identified through prediction and experimental verification

Paola Marani1,2,4, Samuel Wagner1,4, Louise Baars1, Pierre Genevaux3, Jan-Willem De Gier1, Ingmarie Nilsson1, Rita Casadio2 and Gunnar Von Heijne1

1 Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
2 Laboratory of Biocomputing, CIRB/Department of Biology, University of Bologna, Bologna, Italy
3 Department of Microbiology and Molecular Medicine, Centre Meédical Universitaire, CH-1211 Geneva, Switzerland

(RECEIVED October 5, 2005; FINAL REVISION December 23, 2005; ACCEPTED December 23, 2005)

Many new Escherichia coli outer membrane proteins have recently been identified by proteomics techniques. However, poorly expressed proteins and proteins expressed only under certain conditions may escape detection when wild-type cells are grown under standard conditions. Here, we have taken a complementary approach where candidate outer membrane proteins have been identified by bioinformatics prediction, cloned and overexpressed, and finally localized by cell fractionation experiments. Out of eight predicted outer membrane proteins, we have confirmed the outer membrane localization for five—YftM, YaiO, YfaZ, CsgF, and YliI—and also provide preliminary data indicating that a sixth—YfaL—may be an outer membrane autotransporter.

Keywords: outer membrane protein; bioinformatics; SecB; autotransporter


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