Pathways and substrate‐specific regulation of amino acid degradation in P haeobacter inhibens   DSM 17395 (archetype of the marine R oseobacter clade)

• Published in: Environmental microbiology Vol. 16; no. 1; pp. 218 - 238
• Main Authors: Drüppel, Katharina, Hensler, Michael, Trautwein, Kathleen, Koßmehl, Sebastian, Wöhlbrand, Lars, Schmidt‐Hohagen, Kerstin, Ulbrich, Marcus, Bergen, Nils, Meier‐Kolthoff, Jan P., Göker, Markus, Klenk, Hans‐Peter, Schomburg, Dietmar, Rabus, Ralf
• Format: Journal Article
• Language: English
• Published: 01.01.2014
• ISSN: 1462-2912; 1462-2920
• DOI: 10.1111/1462-2920.12276

Summary 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 P haeobacter 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, P h. 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 A zoarcus evansii . Histidine degradation is analogous to the P seudomonas ‐type H ut 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 P h. 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 P h. inhibens   DSM 17395 across 27 other complete genomes of R oseobacter clade members revealed most of them to be widespread among roseobacters.