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Protein targeting, translocation and insertion in Escherichia coli: Proteomic analysis of substrate-pathway relationships
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
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 [en]
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: urn:nbn:se:su:diva-6990ISBN: 978-91-7155-481-9 (print)OAI: oai:DiVA.org:su-6990DiVA: diva2:197421
Public defence
2007-09-07, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 12 A, Stockholm, 10:00 (English)
Opponent
Supervisors
Available from: 2007-08-13 Created: 2007-08-13 Last updated: 2009-05-12Bibliographically approved
List of papers
1. New Escherichia coli outer membrane proteins identified through prediction and experimental verification
Open this publication in new window or tab >>New Escherichia coli outer membrane proteins identified through prediction and experimental verification
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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.

Keyword
outer membrane protein, bioinformatics, SecB, autotransporter
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:su:diva-24380 (URN)10.1110/ps.051889506 (DOI)000236734200021 ()
Available from: 2007-08-13 Created: 2007-08-13 Last updated: 2017-12-13Bibliographically approved
2. Targeting and translocation of two lipoproteins in Escherichia coli via the SRP/Sec/YidC pathway
Open this publication in new window or tab >>Targeting and translocation of two lipoproteins in Escherichia coli via the SRP/Sec/YidC pathway
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2004 In: Journal of Biological Chemistry, ISSN 00219258, Vol. 279, no 30, 31026-32 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-24381 (URN)
Note
Part of urn:nbn:se:su:diva-6990Available from: 2007-08-13 Created: 2007-08-13Bibliographically approved
3. Defining the role of the Escherichia coli chaperone SecB using comparative proteomics
Open this publication in new window or tab >>Defining the role of the Escherichia coli chaperone SecB using comparative proteomics
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2006 In: Journal of Biological Chemistry, ISSN 00219258, no 281, 10024-34 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-24382 (URN)
Note
Part of urn:nbn:se:su:diva-6990Available from: 2007-08-13 Created: 2007-08-13Bibliographically approved
4. Effects of SecE depletion on the inner and outer membrane proteomes of Escherichia coli
Open this publication in new window or tab >>Effects of SecE depletion on the inner and outer membrane proteomes of Escherichia coli
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2008 (English)In: Journal of Bacteriology, ISSN 0021-9193, E-ISSN 1098-5530, Vol. 190, no 10, 3505-3525 p.Article in journal (Refereed) Published
Keyword
Bacterial Outer Membrane Proteins/metabolism, Cell Membrane/*metabolism, Escherichia coli/*genetics/metabolism, Escherichia coli Proteins/chemistry/*metabolism, Mass Spectrometry, Membrane Transport Proteins/chemistry/metabolism/*physiology, Proteome/*metabolism, Proteomics/*methods
Identifiers
urn:nbn:se:su:diva-16865 (URN)10.1128/JB.01631-07 (DOI)000255622500011 ()18296516 (PubMedID)
Available from: 2008-12-29 Created: 2008-12-29 Last updated: 2017-12-13Bibliographically approved

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