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Proteins in different Synechocystis compartments have distinguishing N-terminal features: a combined proteomics and multivariate sequence analysis
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
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2007 (English)In: Journal of Proteome Research, ISSN 1535-3893, Vol. 6, no 7, 2420-2434 p.Article in journal (Refereed) Published
Abstract [en]

Cyanobacteria have a cell envelope consisting of a plasma membrane, a periplasmic space with a peptidoglycan layer, and an outer membrane. A third, separate membrane system, the intracellular thylakoid membranes, is the site for both photosynthesis and respiration. All membranes and luminal spaces have unique protein compositions, which impose an intriguing mechanism for protein sorting of extracytoplasmic proteins due to single sets of translocation protein genes. It is shown here by multivariate sequence analyses of many experimentally identified proteins in Synechocystis, that proteins routed for the different extracytosolic compartments have correspondingly different physicochemical properties in their signal peptide and mature N-terminal segments. The full-length mature sequences contain less significant information. From these multivariate, N-terminal property-profile models for proteins with single experimental localization, proteins with ambiguous localization could, to a large extent, be predicted to a defined compartment. The sequence properties involve amino acids varying especially in volume and polarizability and at certain positions in the sequence segments, in a manner typical for the various compartment classes. Potential means of the cell to recognize the property features are discussed, involving the translocation channels and two Type I signal peptidases with different cellular localization, and charge features at their membrane interfaces.

Place, publisher, year, edition, pages
2007. Vol. 6, no 7, 2420-2434 p.
Keyword [en]
Amino Acid Sequence, Bacterial Proteins/analysis/*chemistry, Membrane Proteins/analysis/chemistry, Membrane Transport Proteins/analysis/chemistry, Molecular Sequence Data, Multivariate Analysis, Protein Transport, Proteome/*analysis, Proteomics, Sequence Analysis; Protein, Serine Endopeptidases/analysis/chemistry, Synechocystis/*chemistry
URN: urn:nbn:se:su:diva-12056DOI: 10.1021/pr0605973ISI: 000247792300002PubMedID: 17508731OAI: diva2:178576
Available from: 2008-01-15 Created: 2008-01-15 Last updated: 2009-09-04Bibliographically approved
In thesis
1. A model for membrane organization and protein sorting in the cyanobacterium Synechocystis sp. PCC 6803
Open this publication in new window or tab >>A model for membrane organization and protein sorting in the cyanobacterium Synechocystis sp. PCC 6803
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Cyanobacteria constitute a unique group of eubacteria, possessing outer and plasma membranes as well as internal thylakoid membranes, the site for both photosynthesis and respiration. The combination of sucrose density centrifugation and two-phase partitioning methods leads to purification of different membranes from the cyanobacterium Synechocystis sp. PCC 6803 (referred to as Synechocystis). The standard proteomics methods, based on 1D- and 2D-gel electrophoresis, followed by protein digestion and MALDI-TOF MS, led to identification of 76 thylakoid and 51 plasma membrane proteins. In order to increase the number of identified proteins a shotgun proteomics approach was employed. Proteins were digested in complex mixtures, followed by LC separation of obtained peptides coupled to MS/MS. This approach led to identification of 379 different thylakoid and plasma membrane proteins, of which 124 were integral membrane proteins. 

The complex membrane organization of Synechocystis requires a unique system for transport and sorting of proteins into extracytosolic cell compartments. Obtained gel-based and shotgun proteomics data as well as results of the multivariate sequence analysis of both soluble and integral membrane proteins allowed to suggest a new mechanism for membrane organization and protein sorting in Synechocystis. The plasma and thylakoid membranes are proposed to be dynamically connected and both soluble and integral membrane proteins are inserted into connection points.

The Synechocystis genome possesses two genes encoding leader peptidases. Proteomic studies revealed that Sll0716 is localized in the thylakoid membrane (LepT), whereas Slr1377 in the plasma membrane (LepP). The BN/SDS-PAGE of the total membranes from mutant LepT revealed that LepT is directly involved in the processing of several photosynthetic and lumenal subunits, required for the assembly and function of PSI and maintaining of the thylakoid membrane organization in Synechocystis.



Place, publisher, year, edition, pages
Stockholm: Department of Biochemistry and Biophysics, Stockholm University, 2009. 63 p.
National Category
Biochemistry and Molecular Biology
Research subject
urn:nbn:se:su:diva-29043 (URN)978-91-7155-917-3 (ISBN)
Public defence
2009-09-30, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 12 A, Stockholm, 10:00 (English)
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: In progress. Paper 5: In progress. Available from: 2009-09-08 Created: 2009-08-07 Last updated: 2011-05-03Bibliographically approved

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