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J. Biol. Chem., Vol. 282, Issue 10, 7191-7197, March 9, 2007

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Identification of the Last Unknown Genes in the Fermentation Pathway of Lysine^*

From the CNRS-UMR 8030, Genoscope, 91057 Evry Cedex, France

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.

Received for publication, October 18, 2006 , and in revised form, December 12, 2006.

^* This work was supported by the Consortium National de la Recherche Genomique. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The nucleotide sequence(s) reported in this paper has been submitted to the GenBank^TM/EBI Data Bank with accession number(s) CU151840, CU151841, and CU151896.

The on-line version of this article (available at http://www.jbc.org) contains supplemental data.

¹ These authors contributed equally to this work.

² To whom correspondence may be addressed: CNRS-UMR 8030, Genoscope, 2 Rue Gaston Crémieux, 91057 Evry Cedex, France. Tel.: 33-1-60-87-45-90; Fax: 33-1-60-87-25-14; E-mail: akreimey{at}genoscope.cns.fr. ³ To whom correspondence may be addressed: CNRS-UMR 8030, Genoscope, 2 Rue Gaston Crémieux, 91057 Evry Cedex, France. Tel.: 33-1-60-87-45-90; Fax: 33-1-60-87-25-14; E-mail: aperret{at}genoscope.cns.fr.

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