title: Proteome and carbon flux analysis of Pseudomonas aeruginosa clinical isolates from different infection sites.
abstract: Pseudomonas aeruginosa is known as opportunistic pathogen frequently isolated from different infection sites. To investigate the expression rates of P. aeruginosa proteins commonly expressed by different clinical isolates, absolute protein quantities were determined employing a gel-free and data-independent LC-IMS(E) approach. Moreover, the metabolic diversity of these isolates was investigated by (13) C-metabolic flux analyses. 812 proteins were reproducibly identified and absolutely quantified for the reference strain P. aeruginosa PAO1, 363 of which were also identified and relatively quantified in all isolates. Whilst the majority of these proteins were expressed in constant amounts, expression rates of 42 proteins were highly variable between the isolates. Notably, the outer membrane protein OprH and the response regulator PhoP were strongly expressed in burned wounds isolates compared to lung/urinary tract isolates. Moreover, proteins involved in iron/amino acids uptake were found to be highly abundant in urinary tract isolates. The fluxome data revealed a conserved glycolysis, and a niche-specific divergence in fluxes through the glyoxylate shunt and the TCA cycle among the isolates. The integrated proteome/fluxome analysis did not indicate straightforward correlation between the protein amount and flux, but rather points to additional layers of regulation that mediate metabolic adaption of P. aeruginosa to different host environments. All MS data have been deposited in the ProteomeXchange with identifier PXD002373 (http://proteomecentral.proteomexchange.org/dataset/PXD002373).
authors.affiliation: Institute of Microbiology, University of Greifswald, Greifswald, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Lassek
authors.affiliation: Institute of Biochemical Engineering, TU Braunschweig, Braunschweig, Germany.
authors.forename: Antje
authors.initials: A
authors.lastname: Berger
authors.affiliation: Institute of Microbiology, University of Greifswald, Greifswald, Germany.
authors.forename: Daniela
authors.initials: D
authors.lastname: Zühlke
authors.affiliation: Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
authors.forename: Christoph
authors.initials: C
authors.lastname: Wittmann
authors.affiliation: Institute of Microbiology, University of Greifswald, Greifswald, Germany.|Helmholtz Centre for Infection Research, Braunschweig, Germany.
authors.forename: Katharina
authors.initials: K
authors.lastname: Riedel
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D002056:Burns / Q000382:microbiology; D057486:Carbon Cycle / Q000235:genetics; D002952:Citric Acid Cycle / Q000235:genetics*; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D063990:Gene Ontology; D014644:Genetic Variation; D006038:Glyoxylates / Q000378:metabolism; D006801:Humans; D058977:Molecular Sequence Annotation; D018410:Pneumonia, Bacterial / Q000382:microbiology; D020543:Proteome / Q000235:genetics* / Q000378:metabolism; D011552:Pseudomonas Infections / Q000382:microbiology*; D011550:Pseudomonas aeruginosa / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D014552:Urinary Tract Infections / Q000382:microbiology
chemical_list: D001425:Bacterial Outer Membrane Proteins; D001426:Bacterial Proteins; D006038:Glyoxylates; C402926:OprH protein, Pseudomonas aeruginosa; D020543:Proteome; C061064:PhoP protein, Bacteria; C031150:glyoxylic acid
keywords: Core proteome; Fluxome; LC-IMSE; Microbiology