Figure 1.
The lysine fermentation pathway.
Lysine is converted to β-lysine by lysine-2,3 aminomutase (1) and then to L-erythro-3,5-diaminohexanoate by β-lysine-5,6-aminomutase (2). This compound is deaminated and oxidized by a NAD(P)-dependent L-erythro-3,5-diaminohexanoate dehydrogenase (3) to yield 3-keto-5-aminohexanoate. It is further converted into 3-aminobutyryl-CoA and acetoacetate in the presence of acetyl-CoA by 3-keto-5-aminohexanoate cleavage enzyme (4). 3-aminobutyryl-CoA is deaminated to crotonyl-CoA by an ammonia lyase (5). Crotonyl-CoA is reduced to butyryl-CoA by butyryl-CoA dehydrogenase (6), which reacts with acetoacetate to form butyrate and acetoacetyl-CoA through the action of acetoacetate:butyrate CoA transferase (7). The latter compound is converted to acetate via acetyl-CoA and acetyl phosphate by acetoacetyl-CoA thiolase (8), phosphate acetyltransferase (9), and acetate kinase (10), respectively.
Figure 2.
Models of the gene cluster organization for lysine fermentation.
(A): Fusobacterium nucleatum ATCC 25586; (B): a contig sequence affiliated with the Bacteroidetes phylum originating from the metagenome of the anaerobic digester of a wastewater treatment plant; (C): the reconstructed genome of “Candidatus Cloacamonas acidaminovorans”, an uncultivated bacterium found in this digester (only the ID number of the CLOAM genes are reported). The symbol “//” means an interruption of >5.5 kb in the cluster. HP indicates a gene encoding a Hypothetical Protein; mutS a gene encoding a MutS family protein.
Figure 3.
The hypothetical alternative metabolism of 3-aminobutyryl-CoA.
Table 1.
Kinetic parameters of 3-aminobutyryl-CoA transamination.
Figure 4.
Structure of the different NAC-thioesters and their corresponding products after β-transamination catalyzed by Kat in the presence of α-ketoglutarate.
Table 2.
Identification of NAC-thioesters formed by Kat.
Figure 5.
The alternative lysine fermentation pathway.
Enzymes involved are L-lysine-2,3-aminomutase (1); β-L-lysine-5,6-aminomutase (2); 3,5-diaminohexanoate dehydrogenase (3); 3-keto-5-aminohexanoate cleavage enzyme (4); 3-aminobutyryl-CoA aminotransferase (Kat; 5); butyrate-acetoacetate CoA transferase (6); glutamate dehydrogenase (7); acetoacetyl-CoA thiolase (8); phosphate acetyltransferase (9); acetate kinase (10); butyryl-CoA dehydrogenase (11); butyrate-acetoacetate CoA transferase (12).
Table 3.
Occurrences in the metagenome from the anaerobic digester of a wastewater treatment plant of the genes known to be involved in lysine fermentation.
Figure 6.
ASMC tree based on sequence and structural similarities of modelled active sites for 1343 enzymes belonging to the aminotransferases class III family (see Material and Methods).
Known enzymatic activities are reported. Green: Adenosylmethionine-8-amino-7-oxononanoate transaminase. Red: 3-aminobutyryl-CoA transaminase. Orange: glutamate-1-semialdehyde-2, 1-aminomutase. Yellow: diaminobutyrate-2-oxoglutarate transaminase. Pink: taurine-pyruvate aminotransferase. Blue: ornithine, acetylornithine, pyruvate, 4-aminobutyrate, and diaminobutyrate-2-oxoglutarate transaminases.