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  • 1. Kwon, Joseph
    et al.
    Oh, Jeehyun
    Park, Chiyoul
    Cho, Kun
    Kim, Seung Il
    Kim, Soohyun
    Lee, Sunghoon
    Bhak, Jong
    Norling, Birgitta
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Choi, Jejong-Soon
    Systematic cyanobacterial membrane proteome analysis by combining acid hydrolysis and digestive enzymes with nano-liquid chromatography-Fourier transform mass spectrometry2010Ingår i: Journal of Chromatography A, ISSN 0021-9673, E-ISSN 1873-3778, Vol. 1217, nr 3, s. 285-293Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The identification of membrane proteins is currently under-represented since the trans-membrane domains of membrane proteins have a hydrophobic property. Membrane proteins have mainly been analyzed by cleaving and identifying exposed hydrophilic domains. We developed the membrane proteomics method for targeting integral membrane proteins by the following sequential process: in-solution acid hydrolysis, reverse phase chromatographic separation, trypsin or chymotrypsin digestion and nano-liquid chromatography-Fourier transform mass spectrometry. When we employed total membrane proteins of Synechocystis sp. PCC 6803, 155 integral membrane proteins out of a predictable 706 were identified in a single application, corresponding to 22% of a genome. The combined methods of acid hydrolysis-trypsin (AT) and acid hydrolysis-chymotrypsin (AC) identified both hydrophilic and hydrophobic domains of integral membrane proteins, respectively. The systematic approach revealed a more concrete data in mapping the repertoire of cyanobacterial membrane and membrane-linked proteome.

  • 2.
    Pisareva, Tatiana
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Kwon, Joseph
    Oh, Jihyun
    Kim, Young H.
    Ge, Changrong
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Wieslander, Åke
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Choi, Jong-Soon
    Norling, Birgitta
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Model for Membrane Organization and Protein Sorting in the Cyanobacterium Synechocystis sp. PCC 6803 Inferred from Proteomics and Multivariate Sequence Analyses2011Ingår i: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 10, nr 8, s. 3617-3631Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Cyanobacteria are unique eubacteria with an organized subcellular compartmentalization of highly differentiated internal thylakoid membranes (TM), in addition to the outer and plasma membranes (PM). This leads to a complicated system for transport and sorting of proteins into the different membranes and compartments. By shotgun and gel-based proteomics of plasma and thylakoid membranes from the cyanobacterium Synechocystis sp. PCC 6803, a large number of membrane proteins were identified. Proteins localized uniquely in each membrane were used as a platform describing a model for cellular membrane organization and protein intermembrane sorting and were analyzed by multivariate sequence analyses to trace potential differences in sequence properties important for insertion and sorting to the correct membrane. Sequence traits in the C-terminal region, but not in the N-terminal nor in any individual transmembrane segments, were discriminatory between the TM and PM classes. The results are consistent with a contact zone between plasma and thylakoid membranes, which may contain short-lived "hemifusion" protein traffic connection assemblies. Insertion of both integral and peripheral membrane proteins is suggested to occur through common translocons in these subdomains, followed by a potential translation arrest and structure-based sorting into the correct membrane compartment.

  • 3.
    Pisareva, Tatiana
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Shumskaya, Maria
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Carlberg, Inger
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Norling, Birgitta
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Inactivation of Leader Peptidase T strongly influences the thylakoid membrane organization in the cyanobacterium Synechocystis sp. PCC 6803Manuskript (preprint) (Övrigt vetenskapligt)
  • 4.
    Pisareva, Tatiana
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Shumskaya, Maria
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Maddalo, Gianluca
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    Ilag, Leopold
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    Norling, Birgitta
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Proteomics of Synechocystis sp. PCC 6803 Identification of novel integral plasma membrane proteins: Identification of novel integral plasma membrane proteins2007Ingår i: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 274, nr 3, s. 791-804Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The cyanobacterial plasma membrane is an essential cell barrier with functions such as the control of taxis, nutrient uptake and secretion. These functions are carried out by integral membrane proteins, which are difficult to identify using standard proteomic methods. In this study, integral proteins were enriched from purified plasma membranes of Synechocystis sp. PCC 6803 using urea wash followed by protein resolution in 1D SDS/PAGE. In total, 51 proteins were identified by peptide mass fingerprinting using MALDI-TOF MS. More than half of the proteins were predicted to be integral with 1–12 transmembrane helices. The majority of the proteins had not been identified previously, and include members of metalloproteases, chemotaxis proteins, secretion proteins, as well as type 2 NAD(P)H dehydrogenase and glycosyltransferase. The obtained results serve as a useful reference for further investigations of the address codes for targeting of integral membrane proteins in cyanobacteria.

  • 5. Rajalahti, Tarja
    et al.
    Huang, Fang
    Klement, Maria Rosén
    Pisareva, Tatiana
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Edman, Maria
    Sjöström, Michael
    Wieslander, Åke
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Norling, Birgitta
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Proteins in different Synechocystis compartments have distinguishing N-terminal features: a combined proteomics and multivariate sequence analysis2007Ingår i: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 6, nr 7, s. 2420-2434Artikel i tidskrift (Refereegranskat)
    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.

  • 6.
    Srivastava, Renu
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Pisareva, Tatiana
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Norling, Birgitta
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Proteomic studies of the thylakoid membrane of Synechocystis sp. PCC 68032005Ingår i: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 5, nr 18, s. 4905-4916Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Purified thylakoid membranes from the cyanobacterium Synechocystis sp. PCC 6803 were used for the first time in proteomic studies. The membranes were prepared by a combination of sucrose density centrifugation and aqueous polymer two-phase partitioning. In total, 76 different proteins were identified from 2- and 1-D gels by MALDI-TOF MS analysis. Twelve of the identified proteins have a predicted Sec/Tat signal peptide. Fourteen of the proteins were known, or predicted to be, integral membrane proteins. Among the proteins identified were subunits of the well-characterized thylakoid membrane constituents Photosystem I and II, ATP synthase, cytochrome b6f-complex, NADH dehydrogenase, and phycobilisome complex. In addition, novel thylakoid membrane proteins, both integral and peripheral were found, including enzymes involved in protein folding and pigment biosynthesis. The latter were the chlorophyll biosynthesis enzymes, light-dependent protochlorophyllide reductase and geranylgeranyl reductase as well as phytoene desaturase involved in carotenoid biosynthesis and a water-soluble carotenoid-binding protein. Interestingly, in view of the protein sorting mechanism in cyanobacteria, one of the two signal peptidases type I of Synechocystis was found in the thylakoid membrane, whereas the second one has been identified previously in the plasma membrane. Sixteen proteins are hypothetical proteins with unknown function.

  • 7. Zhang, Li-Fang
    et al.
    Yang, Hao-Meng
    Cui, Su-Xia
    Hu, Jia
    Wang, Jie
    Kuang, Ting-Yun
    Norling, Birgitta
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Huang, Fang
    Proteomic analysis of plasma membranes of cyanobacterium Synechocystis sp. Strain PCC 6803 in response to high pH stress.2009Ingår i: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 8, nr 6, s. 2892-902Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Cyanobacteria are unique prokaryotes possessing plasma-, outer- and thylakoid membranes. The plasma membrane of a cyanobacterial cell serves as a crucial barrier against its environment and is essential for biogenesis of cyanobacterial photosystems. Previously, we have identified 79 different proteins in the plasma membrane of Synechocystis sp. Strain PCC 6803 based on 2D- and 1D- gels and MALDI-TOF MS. In this work, we have performed a proteomic study screening for high-pH-stress proteins in Synechocystis. 2-D gel profiles of plasma membranes isolated from both control and high pH-treated cells were constructed and compared quantitatively based on different protein staining methods including DIGE analysis. A total of 55 differentially expressed protein spots were identified using MALDI-TOF MS and MALDI-TOF/TOF MS, corresponding to 39 gene products. Twenty-five proteins were enhanced/induced and 14 reduced by high pH. One-third of the enhanced/induced proteins were transport and binding proteins of ABC transporters including 3 phosphate transport proteins. Other proteins include MinD involved in cell division, Cya2 in signaling and proteins involved in photosynthesis and respiration. Furthermore, among these proteins regulated by high pH, eight were found to be hypothetical proteins. Functional significance of the high-pH-stress proteins is discussed integrating current knowledge on cyanobacterial cell physiology.

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