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Penicillin-binding protein 5 can form a homo-oligomeric complex in the inner membrane of Escherichia coli
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
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2011 (English)In: Protein Science, ISSN 0961-8368, E-ISSN 1469-896X, Vol. 20, no 9, 1520-1529 p.Article in journal (Refereed) Published
Abstract [en]

Penicillin-binding protein 5 (PBP5) is a DD-carboxypeptidase, which cleaves the terminal D-alanine from the muramyl pentapeptide in the peptidoglycan layer of Escherichia coli and other bacteria. In doing so, it varies the substrates for transpeptidation and plays a key role in maintaining cell shape. In this study, we have analyzed the oligomeric state of PBP5 in detergent and in its native environment, the inner membrane. Both approaches indicate that PBP5 exists as a homo-oligomeric complex, most likely as a homo-dimer. As the crystal structure of the soluble domain of PBP5 (i.e., lacking the membrane anchor) shows a monomer, we used our experimental data to generate a model of the homo-dimer. This model extends our understanding of PBP5 function as it suggests how PBP5 can interact with the peptidoglycan layer. It suggests that the stem domains interact and the catalytic domains have freedom to move from the position observed in the crystal structure. This would allow the catalytic domain to have access to pentapeptides at different distances from the membrane.

Place, publisher, year, edition, pages
2011. Vol. 20, no 9, 1520-1529 p.
Keyword [en]
membrane protein, homo-oligomer, penicillin-binding protein, peptidoglycan biogenesis
National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
URN: urn:nbn:se:su:diva-62902DOI: 10.1002/pro.677ISI: 000294383900006OAI: oai:DiVA.org:su-62902DiVA: diva2:445465
Available from: 2011-10-04 Created: 2011-10-04 Last updated: 2017-12-08Bibliographically approved
In thesis
1. Cell division in Escherichia coli
Open this publication in new window or tab >>Cell division in Escherichia coli
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The Gram-negative bacterium Escherichia coli is a model system to describe the biochemistry and cell biology of cell division in bacteria. This process can be divided into three major steps. The first step involves the replication of the DNA, followed by an elongation step in which the cells become twice as long. In the last step the elongated cell constricts in the middle and the two daughter cells are separated. The cell division process in E. coli has been extensively studied for at least 50 years and a lot is known, however many details are still vague. New proteins involved in the process continue to be identified and the number of these proteins as well as the interactions among them are not yet fully known. It is therefore not completely understood how the contraction proceeds to form two daughter cells. In this thesis, I have carried out experiments that contribute to our understanding of cell division in E. coli. Using fluorescence microscopy I show that the contraction of the inner membrane in dividing E. coli proceeds in a linear fashion and that the periplasm closes after the cytoplasm. I have also analyzed the oligomeric state of two proteins involved in the cell division and I show that the early cell division protein ZipA can dimerize. This could explain how this protein can bundle FtsZ protofilaments, as it could bridge two protofilaments. Penicillin-binding protein 5 (PBP5) has been found to localize to the septum and it has been suggested to be connected to cell division. I have found that PBP5 forms a homo-oligomeric complex, most likely a dimer. The dimer can be modeled in a back-to-back conformation with the catalytic domains being flexible. This allows PBP5 to reach for pentapeptides of the peptidoglycan at different distances from the membrane. An understanding of the mechanisms used by the cell division proteins and their protein: protein interactions can be a first step towards determining new antibiotic targets.

Place, publisher, year, edition, pages
Stockholm: Department of Biochemistry and Biophysics, Stockholm University, 2011. 61 p.
National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
urn:nbn:se:su:diva-62908 (URN)978-91-7447-339-1 (ISBN)
Public defence
2011-11-18, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 14:00 (English)
Opponent
Supervisors
Note
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Submitted. Paper 4: Manuscript. Available from: 2011-10-27 Created: 2011-10-04 Last updated: 2011-10-18Bibliographically approved
2. Protein complexes of the Escherichia coli cell envelope
Open this publication in new window or tab >>Protein complexes of the Escherichia coli cell envelope
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The cell envelope of Escherichia coli, as for all living cells, is a magnificent semi-permeable membrane barrier that facilitates protection as well as enables fundamental contact with the exterior world. The envelope comprises a mixture of phospholipids, organized in two bilayers, which are stabilized by a rigid peptidoglycan layer. There are also a large number of proteins, which can be lipid-integrated or attached. Infact, it is anticipated that approximately 30-40% of the cellular proteome of E. coli could be associated with the envelope. These proteins are involved in the transport of small molecules and nutrients, the biogenesis of the envelope, metabolism, signaling, channeling and cellular movement and attachment.

The focus of this thesis is to understand the cell envelope of E. coli by understanding the proteins it holds. Three main questions have been addressed: 1) Which proteins are present? 2) How do these proteins interact? 3) How are the interactions brought about? To answer these questions we have designed and optimized methods suitable for proteome-wide separation, visualization and characterization of membrane proteins and protein complexes. We present reference proteome and interactome maps of the envelope, which further our understanding of the assembly and composition of the cell envelope. In many instances our studies have provided a first step towards understanding protein function(s) and for carrying out meaningful biochemical and structural analysis. We have also developed parallel approaches, which have enabled us to dissect the assembly process for two specific membrane protein complexes, a homo-dimer of penicillin binding protein 5 and the respiratory oxidase cytochrome bo3. These studies have extended our understanding of the relationship between structure and function of protein complexes.

Place, publisher, year, edition, pages
Stockholm: Department of Biochemistry and Biophysics, Stockholm University, 2010. 82 p.
National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
urn:nbn:se:su:diva-42248 (URN)978-91-7447-118-2 (ISBN)
Public defence
2010-10-11, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 14:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Submitted. Paper 4: Manuscript. Paper 5: Manuscript.

Available from: 2010-09-20 Created: 2010-08-19 Last updated: 2014-08-01Bibliographically approved

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