title: Functional proteomic view of metabolic regulation in "Aromatoleum aromaticum" strain EbN1.
abstract: The denitrifying "Aromatoleum aromaticum" strain EbN1 utilizes a wide range of aromatic and nonaromatic compounds under anoxic and oxic conditions. The recently determined genome revealed corresponding degradation pathways and predicted a fine-tuned regulatory network. In this study, differential proteomics (2-D DIGE and MS) was used to define degradation pathway-specific subproteomes and to determine their growth condition dependent regulation. Differential protein profiles were determined for cultures adapted to growth under 22 different substrate and redox conditions. In total, 354 different proteins were identified, 199 of which displayed significantly changed abundances. These regulated proteins mainly represented enzymes of the different degradation pathways, and revealed different degrees of growth condition specific regulation. In case of three substrate conditions (e.g. phenylalanine, anoxic), proteins previously predicted to be involved in their degradation were apparently not involved (e.g. Pdh, phenylacetaldehyde dehydrogenase). Instead, previously not considered proteins were specifically increased in abundance (e.g. EbA5005, predicted aldehyde:ferredoxin oxidoreductase), shedding new light on the respective pathways. Moreover, strong evidence was obtained for thus far unpredicted degradation pathways of three hitherto unknown substrates (e.g. o-aminobenzoate, anoxic). Comparing all identified regulated and nonregulated proteins provided first insights into regulatory hierarchies of special degradation pathways versus general metabolism in strain EbN1.
authors.affiliation: Max-Planck-Institute for Marine Microbiology, Bremen, Germany.
authors.forename: Lars
authors.initials: L
authors.lastname: Wöhlbrand
authors.forename: Birte
authors.initials: B
authors.lastname: Kallerhoff
authors.forename: Daniela
authors.initials: D
authors.lastname: Lange
authors.forename: Peter
authors.initials: P
authors.lastname: Hufnagel
authors.forename: Jürgen
authors.initials: J
authors.lastname: Thiermann
authors.forename: Richard
authors.initials: R
authors.lastname: Reinhardt
authors.forename: Ralf
authors.initials: R
authors.lastname: Rabus
mesh_terms: D000144:Acids, Acyclic / Q000378:metabolism; D000332:Aerobiosis; D000438:Alcohols / Q000378:metabolism; D000693:Anaerobiosis; D001426:Bacterial Proteins / Q000032:analysis / Q000378:metabolism*; D001555:Benzene Derivatives / Q000378:metabolism; D015180:Electrophoresis, Gel, Two-Dimensional; D004798:Enzymes / Q000032:analysis / Q000378:metabolism; D006841:Hydrocarbons, Aromatic / Q000378:metabolism; D007659:Ketones / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D020543:Proteome / Q000032:analysis / Q000378:metabolism*; D043362:Rhodocyclaceae / Q000378:metabolism*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D053719:Tandem Mass Spectrometry
chemical_list: D000144:Acids, Acyclic; D000438:Alcohols; D001426:Bacterial Proteins; D001555:Benzene Derivatives; D004798:Enzymes; D006841:Hydrocarbons, Aromatic; D007659:Ketones; D020543:Proteome