title: High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris.
abstract: Cell membranes represent the "front line" of cellular defense and the interface between a cell and its environment. To determine the range of proteins and protein complexes that are present in the cell membranes of a target organism, we have utilized a "tagless" process for the system-wide isolation and identification of native membrane protein complexes. As an initial subject for study, we have chosen the Gram-negative sulfate-reducing bacterium Desulfovibrio vulgaris. With this tagless methodology, we have identified about two-thirds of the outer membrane- associated proteins anticipated. Approximately three-fourths of these appear to form homomeric complexes. Statistical and machine-learning methods used to analyze data compiled over multiple experiments revealed networks of additional protein-protein interactions providing insight into heteromeric contacts made between proteins across this region of the cell. Taken together, these results establish a D. vulgaris outer membrane protein data set that will be essential for the detection and characterization of environment-driven changes in the outer membrane proteome and in the modeling of stress response pathways. The workflow utilized here should be effective for the global characterization of membrane protein complexes in a wide range of organisms.
authors.affiliation: Lawrence Berkeley National Laboratory, Berkeley, California, United States. pjwalian@lbl.gov
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Walian
authors.forename: Simon
authors.initials: S
authors.lastname: Allen
authors.forename: Maxim
authors.initials: M
authors.lastname: Shatsky
authors.forename: Lucy
authors.initials: L
authors.lastname: Zeng
authors.forename: Evelin D
authors.initials: ED
authors.lastname: Szakal
authors.forename: Haichuan
authors.initials: H
authors.lastname: Liu
authors.forename: Steven C
authors.initials: SC
authors.lastname: Hall
authors.forename: Susan J
authors.initials: SJ
authors.lastname: Fisher
authors.forename: Bonita R
authors.initials: BR
authors.lastname: Lam
authors.forename: Mary E
authors.initials: ME
authors.lastname: Singer
authors.forename: Jil T
authors.initials: JT
authors.lastname: Geller
authors.forename: Steven E
authors.initials: SE
authors.lastname: Brenner
authors.forename: John-Marc
authors.initials: JM
authors.lastname: Chandonia
authors.forename: Terry C
authors.initials: TC
authors.lastname: Hazen
authors.forename: H Ewa
authors.initials: HE
authors.lastname: Witkowska
authors.forename: Mark D
authors.initials: MD
authors.lastname: Biggin
authors.forename: Bing K
authors.initials: BK
authors.lastname: Jap
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry / Q000302:isolation & purification*; D002462:Cell Membrane / Q000737:chemistry; D002852:Chromatography, Ion Exchange; D016969:Desulfovibrio vulgaris / Q000737:chemistry* / Q000201:enzymology; D003902:Detergents / Q000737:chemistry; D004591:Electrophoresis, Polyacrylamide Gel; D004926:Escherichia coli / Q000737:chemistry; D057166:High-Throughput Screening Assays / Q000379:methods*; D013058:Mass Spectrometry; D008565:Membrane Proteins / Q000737:chemistry / Q000302:isolation & purification*; D008970:Molecular Weight; D046912:Multiprotein Complexes / Q000737:chemistry / Q000302:isolation & purification*; D019897:Periplasm / Q000737:chemistry / Q000201:enzymology; D025941:Protein Interaction Mapping / Q000379:methods; D060066:Protein Interaction Maps; D020543:Proteome / Q000737:chemistry; D040901:Proteomics / Q000379:methods; D017386:Sequence Homology, Amino Acid; D012995:Solubility
chemical_list: D001425:Bacterial Outer Membrane Proteins; D003902:Detergents; D008565:Membrane Proteins; D046912:Multiprotein Complexes; D020543:Proteome