title: Proteomic characterization of the Pseudomonas putida KT2440 global response to a monocyclic aromatic compound by iTRAQ analysis and 1DE-MudPIT.
abstract: Pseudomonas putida KT2440 is a metabolically versatile soil bacterium. To examine the effects of an aromatic compound on the proteome of this bacterium, cytosolic proteins induced by the presence of benzoate and succinate were analyzed using two liquid chromatography (LC)-based proteomic approaches: an isobaric tag for relative and absolute quantitation (iTRAQ) for quantitative analysis and one-dimensional gel electrophoresis/multidimensional protein identification technology (1-DE MudPIT) for protein identification. In total, 1286 proteins were identified by 1-DE MudPIT; this represents around 23.3% of the total proteome. In contrast, 570 proteins were identified and quantified by iTRAQ analysis. Of these, 55 and 52 proteins were up- and down-regulated, respectively, in the presence of benzoate. The proteins up-regulated included benzoate degradation enzymes, chemotaxis-related proteins, and ABC transporters. Enzymes related to nitrogen metabolism and pyruvate metabolism were down-regulated. These data suggest that a combination of 1-DE MudPIT and iTRAQ is an appropriate method for comprehensive proteomic analysis of biodegradative bacteria.
authors.affiliation: Division of Life Science, Korea Basic Science Institute, Daejeon, Republic of Korea.
authors.forename: Sung-Ho
authors.initials: SH
authors.lastname: Yun
authors.forename: Gun Wook
authors.initials: GW
authors.lastname: Park
authors.forename: Jin Young
authors.initials: JY
authors.lastname: Kim
authors.forename: Sang Oh
authors.initials: SO
authors.lastname: Kwon
authors.forename: Chi-Won
authors.initials: CW
authors.lastname: Choi
authors.forename: Sun-Hee
authors.initials: SH
authors.lastname: Leem
authors.forename: Kyung-Hoon
authors.initials: KH
authors.lastname: Kwon
authors.forename: Jong Shin
authors.initials: JS
authors.lastname: Yoo
authors.forename: Chulhyun
authors.initials: C
authors.lastname: Lee
authors.forename: Soohyun
authors.initials: S
authors.lastname: Kim
authors.forename: Seung Il
authors.initials: SI
authors.lastname: Kim
mesh_terms: D000890:Anti-Infective Agents / Q000494:pharmacology*; D001426:Bacterial Proteins / Q000096:biosynthesis*; D001565:Benzoates / Q000494:pharmacology*; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects*; D020543:Proteome / Q000096:biosynthesis*; D040901:Proteomics / Q000379:methods*; D016958:Pseudomonas putida / Q000378:metabolism*
chemical_list: D000890:Anti-Infective Agents; D001426:Bacterial Proteins; D001565:Benzoates; D020543:Proteome