title: Pathways and substrate-specific regulation of amino acid degradation in Phaeobacter inhibens DSM 17395 (archetype of the marine Roseobacter clade).
abstract: Combining omics and enzymatic approaches, catabolic routes of nine selected amino acids (tryptophan, phenylalanine, methionine, leucine, isoleucine, valine, histidine, lysine and threonine) were elucidated in substrate-adapted cells of Phaeobacter inhibens DSM 17395 (displaying conspicuous morphotypes). The catabolic network [excluding tricarboxylic acid (TCA) cycle] was reconstructed from 71 genes (scattered across the chromosome; one-third newly assigned), with 69 encoded proteins and 20 specific metabolites identified, and activities of 10 different enzymes determined. For example, Ph. inhibens DSM 17395 does not degrade lysine via the widespread saccharopine pathway but might rather employ two parallel pathways via 5-aminopentanoate or 2-aminoadipate. Tryptophan degradation proceeds via kynurenine and 2-aminobenzoate; the latter is metabolized as known from Azoarcus evansii. Histidine degradation is analogous to the Pseudomonas-type Hut pathway via N-formyl-l-glutamate. For threonine, only one of the three genome-predicted degradation pathways (employing threonine 3-dehydrogenase) is used. Proteins of the individual peripheral degradation sequences in Ph. inhibens DSM 17395 were apparently substrate-specifically formed contrasting the non-modulated TCA cycle enzymes. Comparison of genes for the reconstructed amino acid degradation network in Ph. inhibens DSM 17395 across 27 other complete genomes of Roseobacter clade members revealed most of them to be widespread among roseobacters.
authors.affiliation: Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany.
authors.forename: Katharina
authors.initials: K
authors.lastname: Drüppel
authors.forename: Michael
authors.initials: M
authors.lastname: Hensler
authors.forename: Kathleen
authors.initials: K
authors.lastname: Trautwein
authors.forename: Sebastian
authors.initials: S
authors.lastname: Koßmehl
authors.forename: Lars
authors.initials: L
authors.lastname: Wöhlbrand
authors.forename: Kerstin
authors.initials: K
authors.lastname: Schmidt-Hohagen
authors.forename: Marcus
authors.initials: M
authors.lastname: Ulbrich
authors.forename: Nils
authors.initials: N
authors.lastname: Bergen
authors.forename: Jan P
authors.initials: JP
authors.lastname: Meier-Kolthoff
authors.forename: Markus
authors.initials: M
authors.lastname: Göker
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Klenk
authors.forename: Dietmar
authors.initials: D
authors.lastname: Schomburg
authors.forename: Ralf
authors.initials: R
authors.lastname: Rabus
mesh_terms: D000596:Amino Acids / Q000378:metabolism*; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D041904:Roseobacter / Q000235:genetics / Q000378:metabolism*; D013045:Species Specificity
chemical_list: D000596:Amino Acids; D001426:Bacterial Proteins