title: Proteins in different Synechocystis compartments have distinguishing N-terminal features: a combined proteomics and multivariate sequence analysis.
abstract: 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.
authors.affiliation: Department of Chemistry, University of Bergen, Bergen, Norway.
authors.forename: Tarja
authors.initials: T
authors.lastname: Rajalahti
authors.forename: Fang
authors.initials: F
authors.lastname: Huang
authors.forename: Maria Rosén
authors.initials: MR
authors.lastname: Klement
authors.forename: Tatiana
authors.initials: T
authors.lastname: Pisareva
authors.forename: Maria
authors.initials: M
authors.lastname: Edman
authors.forename: Michael
authors.initials: M
authors.lastname: Sjöström
authors.forename: Ake
authors.initials: A
authors.lastname: Wieslander
authors.forename: Birgitta
authors.initials: B
authors.lastname: Norling
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000032:analysis / Q000737:chemistry*; D008565:Membrane Proteins / Q000032:analysis / Q000737:chemistry; D026901:Membrane Transport Proteins / Q000032:analysis / Q000737:chemistry; D008969:Molecular Sequence Data; D015999:Multivariate Analysis; D021381:Protein Transport; D020543:Proteome / Q000032:analysis*; D040901:Proteomics; D020539:Sequence Analysis, Protein; D012697:Serine Endopeptidases / Q000032:analysis / Q000737:chemistry; D046939:Synechocystis / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D008565:Membrane Proteins; D026901:Membrane Transport Proteins; D020543:Proteome; D012697:Serine Endopeptidases; C026515:type I signal peptidase