title: Probing the protein interaction network of Pseudomonas aeruginosa cells by chemical cross-linking mass spectrometry.
abstract: In pathogenic Gram-negative bacteria, interactions among membrane proteins are key mediators of host cell attachment, invasion, pathogenesis, and antibiotic resistance. Membrane protein interactions are highly dependent upon local properties and environment, warranting direct measurements on native protein complex structures as they exist in cells. Here we apply in vivo chemical cross-linking mass spectrometry, to reveal the first large-scale protein interaction network in Pseudomonas aeruginosa, an opportunistic human pathogen, by covalently linking interacting protein partners, thereby fixing protein complexes in vivo. A total of 626 cross-linked peptide pairs, including previously unknown interactions of many membrane proteins, are reported. These pairs not only define the existence of these interactions in cells but also provide linkage constraints for complex structure predictions. Structures of three membrane proteins, namely, SecD-SecF, OprF, and OprI are predicted using in vivo cross-linked sites. These findings improve understanding of membrane protein interactions and structures in cells.
authors: Department of Genome Sciences, University of Washington, 850 Republican Street, Seattle, WA 98109, USA.
authors: Arti T
authors: AT
authors: Navare
authors: Department of Genome Sciences, University of Washington, 850 Republican Street, Seattle, WA 98109, USA.
authors: Juan D
authors: JD
authors: Chavez
authors: Department of Genome Sciences, University of Washington, 850 Republican Street, Seattle, WA 98109, USA.
authors: Chunxiang
authors: C
authors: Zheng
authors: Department of Genome Sciences, University of Washington, 850 Republican Street, Seattle, WA 98109, USA.
authors: Chad R
authors: CR
authors: Weisbrod
authors: Department of Genome Sciences, University of Washington, 850 Republican Street, Seattle, WA 98109, USA.
authors: Jimmy K
authors: JK
authors: Eng
authors: Department of Microbiology, University of Washington Medical Center, 1959 N.E. Pacific Street, Seattle, WA 98195, USA.
authors: Richard
authors: R
authors: Siehnel
authors: Department of Microbiology, University of Washington Medical Center, 1959 N.E. Pacific Street, Seattle, WA 98195, USA.
authors: Pradeep K
authors: PK
authors: Singh
authors: Department of Genome Sciences, University of Washington, 850 Republican Street, Seattle, WA 98109, USA.
authors: Colin
authors: C
authors: Manoil
authors: Department of Genome Sciences, University of Washington, 850 Republican Street, Seattle, WA 98109, USA. Electronic address: jimbruce@uw.edu.
authors: James E
authors: JE
authors: Bruce
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D003432:Cross-Linking Reagents / Q000737:chemistry; D013058:Mass Spectrometry; D008565:Membrane Proteins / Q000737:chemistry / Q000378:metabolism; D026901:Membrane Transport Proteins / Q000737:chemistry / Q000378:metabolism; D008969:Molecular Sequence Data; D011485:Protein Binding; D020543:Proteome / Q000737:chemistry* / Q000378:metabolism; D011550:Pseudomonas aeruginosa / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D003432:Cross-Linking Reagents; D008565:Membrane Proteins; D026901:Membrane Transport Proteins; C547605:OprF protein, Pseudomonas aeruginosa; D020543:Proteome; C075767:secD protein, Bacteria; C075768:secF protein, Bacteria