title: Identification of the last unknown genes in the fermentation pathway of lysine.
abstract: Although the proteins of the lysine fermentation pathway were biochemically characterized more than thirty years ago, the genes encoding the proteins that catalyze three steps of this pathway are still unknown. We combined gene context, similarity of enzymatic mechanisms, and molecular weight comparisons with known proteins to select candidate genes for these three orphan proteins. We used a wastewater metagenomic collection of sequences to find and characterize the missing genes of the lysine fermentation pathway. After recombinant protein production and purification following cloning in Escherichia coli, we demonstrated that these genes (named kdd, kce, and kal) encode a l-erythro-3,5-diaminohexanoate dehydrogenase, a 3-keto-5-aminohexanoate cleavage enzyme, and a 3-aminobutyryl-CoA ammonia lyase, respectively. Because all of the genes of the pathway are now identified, we used this breakthrough to detect lysine-fermenting bacteria in sequenced genomes. We identified twelve bacteria that possess these genes and thus are expected to ferment lysine, and their gene organization is discussed.
authors.affiliation: CNRS-UMR 8030, Genoscope, 91057 Evry Cedex, France.
authors.forename: Annett
authors.initials: A
authors.lastname: Kreimeyer
authors.forename: Alain
authors.initials: A
authors.lastname: Perret
authors.forename: Christophe
authors.initials: C
authors.lastname: Lechaplais
authors.forename: David
authors.initials: D
authors.lastname: Vallenet
authors.forename: Claudine
authors.initials: C
authors.lastname: Médigue
authors.forename: Marcel
authors.initials: M
authors.lastname: Salanoubat
authors.forename: Jean
authors.initials: J
authors.lastname: Weissenbach
mesh_terms: D000594:Amino Acid Oxidoreductases / Q000235:genetics*; D000642:Ammonia-Lyases / Q000235:genetics*; D001419:Bacteria / Q000378:metabolism*; D001483:Base Sequence; D005285:Fermentation; D005798:Genes, Bacterial; D008239:Lysine / Q000378:metabolism*; D008969:Molecular Sequence Data; D005810:Multigene Family; D009249:NADP / Q000378:metabolism; D007652:Oxo-Acid-Lyases / Q000235:genetics*
chemical_list: D009249:NADP; D000594:Amino Acid Oxidoreductases; C020028:L-erythro-3,5-diaminohexanoate dehydrogenase; C021464:3-keto-5-aminohexanoate cleavage enzyme; D007652:Oxo-Acid-Lyases; C026842:3-aminobutyryl-CoA deaminase; D000642:Ammonia-Lyases; D008239:Lysine