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New Escherichia coli outer membrane proteins identified through prediction and experimental verification
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. University of Bologna, Italy.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
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2006 (English)In: Protein Science, ISSN 0961-8368, E-ISSN 1469-896X, Vol. 15, no 4, 884-889 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2006. Vol. 15, no 4, 884-889 p.
Keyword [en]
outer membrane protein, bioinformatics, SecB, autotransporter
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:su:diva-24380DOI: 10.1110/ps.051889506ISI: 000236734200021OAI: oai:DiVA.org:su-24380DiVA: diva2:197417
Available from: 2007-08-13 Created: 2007-08-13 Last updated: 2017-12-13Bibliographically approved
In thesis
1. Protein targeting, translocation and insertion in Escherichia coli: Proteomic analysis of substrate-pathway relationships
Open this publication in new window or tab >>Protein targeting, translocation and insertion in Escherichia coli: Proteomic analysis of substrate-pathway relationships
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Approximately 10% of the open reading frames in the genome of the Gram-negative bacterium E. coli encodes secretory proteins, and 20% encodes integral inner membrane proteins (IMPs). These proteins are sorted to their correct cellular compartments (the periplasm and the outer and inner membranes) by specialized targeting and translocation/insertion systems. So far, a very limited set of model proteins have been used to study proteins sorting requirements in E. coli. The main objective of all the papers presented in this thesis was to determine the targeting and translocation/insertion requirements of more E. coli proteins. In papers I and II, this was done using focused approaches. Selected model proteins (lipoproteins and putative outer membrane proteins) were expressed from plasmids and their targeting and translocation were analysed in vitro by crosslinking experiments and/or in vivo by pulse-chase analysis in different E. coli mutant strains. In papers III a comparative sub-proteome analysis was carried out to define the role of the cytoplasmic chaperone SecB in protein targeting. In paper IV, a similar approach was used to study how protein translocation and insertion is affected upon depletion of the essential Sec-translocon component SecE. The ‘global’ approach used in paper III and IV allowed us to study protein targeting and translocation/insertion requirements on a proteome level. This led to the identification of several novel SecB substrates and a large number of potential Sec-translocon independent IMPs.

Place, publisher, year, edition, pages
Stockholm: Institutionen för biokemi och biofysik, 2007. 132 p.
Keyword
protein biogenesis, targeting, translocation, insertion, SecB, SecE, E. coli
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
Biochemistry
Identifiers
urn:nbn:se:su:diva-6990 (URN)978-91-7155-481-9 (ISBN)
Public defence
2007-09-07, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 12 A, Stockholm, 10:00 (English)
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Available from: 2007-08-13 Created: 2007-08-13 Last updated: 2009-05-12Bibliographically approved

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