The Metabolism of Hydroxypyruvate

Discovery of a New, Recurrent Enzyme in Bacterial Phosphonate Degradation: (R)-1-Hydroxy-2-aminoethylphosphonate Ammonia-lyase

Phosphonates represent an important source of bioavailable phosphorus in certain environments. Accordingly, many microorganisms (particularly marine bacteria) possess catabolic pathways to degrade these molecules. One example is the widespread hydrolytic route for the breakdown of 2-aminoethylphosphonate (AEP, the most common biogenic phosphonate). In this pathway, the aminotransferase PhnW initially converts AEP into phosphonoacetaldehyde (PAA), which is then cleaved by the hydrolase PhnX to yield acetaldehyde and phosphate. This work focuses on a pyridoxal 5'-phosphate-dependent enzyme that is encoded in >13% of the bacterial gene clusters containing the phnW-phnX combination. This enzyme (which we termed PbfA) is annotated as a transaminase, but there is no obvious need for an additional transamination reaction in the established AEP degradation pathway. We report here that PbfA from the marine bacterium Vibrio splendidus catalyzes an elimination reaction on the naturally occurring compound (R)-1-hydroxy-2-aminoethylphosphonate (R-HAEP). The reaction releases ammonia and generates PAA, which can be then hydrolyzed by PhnX. In contrast, PbfA is not active toward the S enantiomer of HAEP or other HAEP-related compounds such as ethanolamine and d,l-isoserine, indicating a very high substrate specificity. We also show that R-HAEP (despite being structurally similar to AEP) is not processed efficiently by the PhnW-PhnX couple in the absence of PbfA. In summary, the reaction catalyzed by PbfA serves to funnel R-HAEP into the hydrolytic pathway for AEP degradation, expanding the scope and the usefulness of the pathway itself.

Revealing Donor Substrate-Dependent Mechanistic Control on DXPS, an Enzyme in Bacterial Central Metabolism

The thiamin diphosphate-dependent enzyme 1-deoxy-d-xylulose 5-phosphate synthase (DXPS) catalyzes the formation of DXP from pyruvate (donor) and d-glyceraldehyde 3-phosphate (d-GAP, acceptor). DXPS is essential in bacteria but absent in human metabolism, highlighting it as a potential antibacterial drug target. The enzyme possesses unique structural and mechanistic features that enable development of selective inhibition strategies and raise interesting questions about DXPS function in bacterial pathogens. DXPS distinguishes itself within the ThDP enzyme class by its exceptionally large active site and random sequential mechanism in DXP formation. In addition, DXPS displays catalytic promiscuity and relaxed acceptor substrate specificity, yet previous studies have suggested a preference for pyruvate as the donor substrate when d-GAP is the acceptor substrate. However, such donor specificity studies are potentially hindered by a lack of knowledge about specific, alternative donor-acceptor pairs. In this study, we exploited the promiscuous oxygenase activity of DXPS to uncover alternative donor substrates for DXPS. Characterization of glycolaldehyde, hydroxypyruvate, and ketobutyrate as donor substrates revealed differences in stabilization of enzyme-bound intermediates and acceptor substrate usage, illustrating the influence of the donor substrate on reaction mechanism and acceptor specificity. In addition, we found that DXPS prevents abortive acetyl-ThDP formation from a DHEThDP carbanion/enamine intermediate, similar to transketolase, supporting the potential physiological relevance of this intermediate on DXPS. Taken together, these results offer clues toward alternative roles for DXPS in bacterial pathogen metabolism.

Chemical reactivity drives spatiotemporal organisation of bacterial metabolism

In this review, we examine how bacterial metabolism is shaped by chemical constraints acting on the material and dynamic layout of enzymatic networks and beyond. These are moulded not only for optimisation of given metabolic objectives (e.g. synthesis of a particular amino acid or nucleotide) but also for curbing the detrimental reactivity of chemical intermediates. Besides substrate channelling, toxicity is avoided by barriers to free diffusion (i.e. compartments) that separate otherwise incompatible reactions, along with ways for distinguishing damaging vs. harmless molecules. On the other hand, enzymes age and their operating lifetime must be tuned to upstream and downstream reactions. This time dependence of metabolic pathways creates time-linked information, learning and memory. These features suggest that the physical structure of existing biosystems, from operon assemblies to multicellular development may ultimately stem from the need to restrain chemical damage and limit the waste inherent to basic metabolic functions. This provides a new twist of our comprehension of fundamental biological processes in live systems as well as practical take-home lessons for the forward DNA-based engineering of novel biological objects.

The decarbonylation of ionized β-hydroxypyruvic acid: the hydrogen-bridged radical cation [CH2=O...H...==C-OH].+studied by experiment and theory

The intriguing gas-phase ion chemistry of β-hydroxypyruvic acid (HPA), HOCH2C(==O)COOH, has been investigated using tandem mass spectrometry (metastable ion (MI) and (multiple) collision-induced dissociation (CID) experiments, neutralization-reionization mass spectrometry (NRMS),18O and D isotopic labelling on both the acid and its methyl ester) in conjunction with computational chemistry (ab initio MO and density functional theories). HPA does not enolize upon evaporation, but it retains its keto structure. When ionized, decarbonylation occurs and, depending on the internal-energy content, this dissociation reaction proceeds via two distinct routes. The source-generated, high-energy ions lose the keto C==O, not via a least-motion extrusion into ionized glycolic acid, HOCH2COOH.+, but via a rearrangement that yields the title H-bridged radical cation CH2==O...H...O==C-OH.+for which Δ Hf0= 99 ± 3 kcal/mol. The long-lived low-energy ions enolize prior to decarbonylation and lose the carboxyl C==O. Again, this is not a least-motion extrusion (which would produce the most stable isomer, HOC(H)==C(OH)2.+Δ Hf0= 73 kcal/mol) but a rearrangement yielding the ion-dipole complex HOC(H)C==C==O.+/H2O. The methyl ester of HPA behaves analogously, yielding CH2==O...H...O==C-OCH3.+and HOC(H)C==C==O.+/ CH3OH upon decarbonylation of the high- and low-energy ions, respectively. Decarboxylation into the ylidion CH2OH2.+characterizes the dissociation chemistry of both the title H-bridged ion and its glycolic acid isomer HOCH2COOH.+. A computational analysis of this reaction (which satisfies the experimental observations) leads to the proposal that the decarboxylation of the acid occurs via CH2-O(H)...H...==C==O.+as the key intermediate, whereas the title H-bridged ion follows a higher energy route that involves ion-dipole rotations leading to the ionized carbene HO(H2)CO-C-OH.+and the distonic ion H2O-C(H2)-O-C==O.+as key intermediates.Key words: tandem mass spectrometry, hydrogen-bridged radical cation, hydroxypyruvic acid, ab initio calculations, keto-enol tautomerization,18O labelling.

Hepatic oxalate production: the role of hydroxypyruvate

The metabolism of hydroxypyruvate to oxalate was studied in isolated rat hepatocytes. [14C]Oxalate was produced from [2-14C]- and [3-14C]- but not [1-14C]hydroxypyruvate. No oxalate was produced from similarly labeled pyruvate. The mechanism by which hydroxypyruvate is metabolized to oxalate involves decarboxylation at the carbon 1 position as the initial step. This activity was distinct from that which produced CO2 from the carbon 1 position of pyruvate. Hydroxypyruvate decarboxylase activity was found mainly in the mitochondria, with the remainder (25%) in the cytosol. No activity was present in the peroxisomes, the probable site of oxalate production from glycolate and glyoxylate. Hydroxypyruvate, but not pyruvate stimulated [14C]oxalate production from [U-14C]fructose, suggesting that hydroxypyruvate is either an intermediate in the fructose-oxalate pathway, or that it prevents carbon from leaving that pathway. The lack of effect of pyruvate in this regard is evidence against redox being the primary effect of hydroxypyruvate and focuses attention on hydroxypyruvate and its precursors as important sources of carbon for oxalate synthesis from both carbohydrate and protein.

Hyperoxaluria in L-glyceric aciduria: possible nonenzymic mechanism

Hydroxypyruvate inhibited the oxidation of [1-14C]glyoxylate to [14C] oxalate whether catalyzed by a purified preparation of glycolic acid oxidase from human liver, lactate dehydrogenase, a human liver extract, or a lobe of rat liver. It also brought about the nonenzymic decarboxylation of [1-14C]glyoxylate when it was present in the above assay systems. Radioactive isotope dilution and high-performance liquid chromatography analysis revealed the autooxidation of hydroxypyruvate to oxalate on standing in buffered solution at pH 7.4. In view of these observations, the current hypothesis of the role of lactate dehydrogenase in inducing hyperoxaluria in L-glyceric aciduria has been reexamined, and a possible nonenzymic mechanism by which oxalate may originate from hydroxypyruvate under such conditions has been proposed.