Lysine Metabolism by Clostridia

Stadtman, Thressa C.

doi:10.1002/9780470122839.ch9

Cited by 21 publications

(21 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Isotope studies with clostridia have suggested the presence of at least two different lysine fermentation pathways, with catabolism of L-lysine proceeding via conversion to 3,5-diaminohexanoate and catabolism of D-lysine proceeding through 2,5-diaminohexanoate formation (Scheme 2 of Supporting Information) [50,60]. These pathways of lysine fermentation have been postulated for fusobacteria also; however, the results of the studies were not conclusive [51].…”

Section: Metabolism Of D-and L-lysinementioning

confidence: 99%

Proteomic investigation of amino acid catabolism in the indigenous gut anaerobe Fusobacterium varium

Potrykus¹,

White²,

Bearne³

2008

Proteomics

View full text Add to dashboard Cite

The butyrate-producing anaerobe Fusobacterium varium is an integral constituent of human gut microflora. Unlike many gut microorganisms, F. varium is capable of fermenting both amino acids and glucose. Although F. varium has been implicated in beneficial as well as pathological bacterium-host interactions, its genome has not been sequenced. To obtain a better understanding of the metabolic processes associated with amino acid fermentation by F. varium, we used a gel-based proteomic approach to examine the changes in the soluble proteome accompanying the utilization of eight different growth substrates: glucose, L-and D-glutamate, L-histidine, L-and D-lysine, and L-and D-serine. Using LC-MS/MS to analyze ,25% of the detected protein spots, we were able to identify 47 distinct proteins. While the intracellular concentrations of enzymes characteristic of a catabolic pathway for a specific amino acid were selectively increased in response to the presence of an excess of that amino acid in the growth medium, the concentrations of the core acetate-butyrate pathway enzymes remained relatively constant. Our analysis revealed (i) high intracellular concentrations of glutamate mutase and b-methylaspartate ammonia-lyase under all growth conditions, underscoring the importance of the methylaspartate pathway of glutamate catabolism in F. varium (ii) the presence of two enzymes of the hydroxyglutarate pathway of glutamate degradation in the proteome of F. varium ((R)-2-hydroxyglutaryl-CoA dehydratase and NAD-specific glutamate dehydrogenase) specifically when Lglutamate was the main energy source (iii) the presence of genes in the genome of F. varium encoding each of the enzymes of the hydroxyglutarate pathway (iv) the presence of both L-and Dserine ammonia-lyases (dehydratases) which permit F. varium to thrive on either L-or D-serine, respectively, and (v) the presence of aspartate-semialdehyde dehydrogenase and dihydrodipicolinate synthase, consistent with the ability of F. varium to synthesize meso-2,6-diaminopimelic acid as a component of its peptidoglycan. Proteins involved in other cellular processes, including oxidation-reduction reactions, protein synthesis and turnover, and transport were also identified.

show abstract

Section: Metabolism Of D-and L-lysinementioning

confidence: 99%

Proteomic investigation of amino acid catabolism in the indigenous gut anaerobe Fusobacterium varium

Potrykus¹,

White²,

Bearne³

2008

Proteomics

View full text Add to dashboard Cite

show abstract

“…5,6-LAM then converts l -β-lysine into l -3,5-DAH, a molecule poised for dehydrogenation and β-oxidation. Fermentation of d -lysine in Figure 1 begins with conversion to d -2,5-DAH by 5,6-LAM and proceeds to the formation of acetate and butyrate (1). …”

mentioning

confidence: 99%

Radical Triplets and Suicide Inhibition in Reactions of 4-Thia-d- and 4-Thia-l-lysine with Lysine 5,6-Aminomutase

et al. 2009

View full text Add to dashboard Cite

Lysine 5,6-aminomutase (5,6-LAM) catalyzes the interconversions of D-or L-lysine and the corresponding enantiomers of 2,5-diaminohexanoate, as well as the interconversion of L-β-lysine and L-3,5-diaminohexanoate. The reactions of 5,6-LAM are 5′-deoxyadenosylcobalamin-and pyridoxal-5′-phosphate (PLP)-dependent. Like other 5′-deoxyadenosylcobalamin-dependent enzymes, 5,6-LAM is thought to function by a radical mechanism. No free radicals can be detected by electron paramagnetic resonance (EPR) spectroscopy in reactions of 5,6-LAM with D-or L-lysine or with L-β-lysine. However, the substrate analogs 4-thia-L-lysine and 4-thia-D-lysine undergo early steps in the mechanism to form two radical species that are readily detected by EPR spectroscopy. Cob(II)alamin and 5′-deoxyadenosine derived from 5′-deoxyadenosylcobalamin are also detected. The radicals are proximal to and spin-coupled with low-spin Co 2+ in cob(II)alamin and appear as radical triplets. The radicals are reversibly formed but do not proceed to stable products, so that 4-thia-D-and L-lysine are suicide inhibitors. Inhibition attains equilibrium between the active Michaelis complex and the inhibited radical triplets. The structure of the transient 4-thia-L-lysine-radical is analogous to that of the first substrate-related radical in the putative isomerization mechanism. The second, persistent radical is more stable than the transient species and is assigned as a tautomer, in which a C6(H) of the transient radical is transferred to the carboxaldehyde carbon (C4′) of PLP. The persistent radical blocks the active site and inhibits the enzyme, but it decomposes very slowly at ≤ 1% of the rate of formation to regenerate the active enzyme. Fundamental differences between reversible suicide inactivation by 4-thia-D-or L-4-lysine and irreversible suicide inactivation by D- NIH Public Access Author ManuscriptBiochemistry. Author manuscript; available in PMC 2010 September 1. Figure 1 begins with conversion to D-2,5-DAH by 5,6-LAM and proceeds to the formation of acetate and butyrate (1).5,6-LAM is an adenosylcobalamin-and PLP-dependent enzyme that catalyzes the interconversion of D-or L-lysine with D-or L-2,5-DAH or of L-β-lysine with L-3,5-DAH (1-8).The mechanism of action of 2,3-LAM is well worked out, and the structure of the enzyme is fully compatible with the spectroscopic and chemical evidence supporting the mechanism (9, 10). The 2,3-LAM mechanism inspires the hypothetical chemical mechanism for 5,6-LAM shown in Scheme 1 (2,4,9), wherein the 5′-deoxyadenosyl radical from adenosylcobalamin initiates the chemistry by abstracting a C5(H) from lysine to generate the substrate-related radical 2, which is bound as the N ε -aldimine to PLP. Radical isomerization analogous to that in 2,3-LAM leads through the aziridincarbinyl intermediate 3 to the product-related radical 4, which is quenched by hydrogen transfer from 5′-deoxyadenosine. In contrast to 2,3-LAM, little experimental evidence bearing on the mechanism of action of 5,6-LAM is available, apart fr...

show abstract

“…The first two steps are catalyzed by lysine-2,3-aminomutase and ␤-lysine-5,6-aminomutase. Both enzymes have been biochemically characterized (3), and their corresponding genes have been identified (4,5).…”

mentioning

confidence: 99%

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

Kreimeyer¹,

Perret²,

Lechaplais

et al. 2007

Journal of Biological Chemistry

View full text Add to dashboard Cite

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.

show abstract

Lysine Metabolism by Clostridia

Cited by 21 publications

References 44 publications

Proteomic investigation of amino acid catabolism in the indigenous gut anaerobe Fusobacterium varium

Proteomic investigation of amino acid catabolism in the indigenous gut anaerobe Fusobacterium varium

Radical Triplets and Suicide Inhibition in Reactions of 4-Thia-d- and 4-Thia-l-lysine with Lysine 5,6-Aminomutase

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

Contact Info

Product

Resources

About