David T. Chuang

Simultaneous steady-state and dynamic 13C NMR can differentiate alternative routes of pyruvate metabolism in living cancer cells

Background: 13C hyperpolarization sensitively and non-destructively detects pyruvate-lactate exchanges in cancer cells. Results: Combining 13C hyperpolarization with isotopomer analysis allowed many pyruvate-dependent pathways to be quantified simultaneously. Conclusion: Monitoring H[13C]O3− production from hyperpolarized [1-13C]pyruvate yielded a quantitative readout of oncogene-regulated pyruvate dehydrogenase activity. Significance: This approach might enable a broader quantitative assessment of metabolic activity in tumors. Metabolic reprogramming facilitates cancer cell growth, so quantitative metabolic flux measurements could produce useful biomarkers. However, current methods to analyze flux in vivo provide either a steady-state overview of relative activities (infusion of 13C and analysis of extracted metabolites) or a dynamic view of a few reactions (hyperpolarized 13C spectroscopy). Moreover, although hyperpolarization has successfully quantified pyruvate-lactate exchanges, its ability to assess mitochondrial pyruvate metabolism is unproven in cancer. Here, we combined 13C hyperpolarization and isotopomer analysis to quantify multiple fates of pyruvate simultaneously. Two cancer cell lines with divergent pyruvate metabolism were incubated with thermally polarized [3-13C]pyruvate for several hours, then briefly exposed to hyperpolarized [1-13C]pyruvate during acquisition of NMR spectra using selective excitation to maximize detection of H[13C]O3− and [1-13C]lactate. Metabolites were then extracted and subjected to isotopomer analysis to determine relative rates of pathways involving [3-13C]pyruvate. Quantitation of hyperpolarized H[13C]O3− provided a single definitive metabolic rate, which was then used to convert relative rates derived from isotopomer analysis into quantitative fluxes. This revealed that H[13C]O3− appearance reflects activity of pyruvate dehydrogenase rather than pyruvate carboxylation followed by subsequent decarboxylation reactions. Glucose substantially altered [1-13C]pyruvate metabolism, enhancing exchanges with [1-13C]lactate and suppressing H[13C]O3− formation. Furthermore, inhibiting Akt, an oncogenic kinase that stimulates glycolysis, reversed these effects, indicating that metabolism of pyruvate by both LDH and pyruvate dehydrogenase is subject to the acute effects of oncogenic signaling on glycolysis. The data suggest that combining 13C isotopomer analyses and dynamic hyperpolarized 13C spectroscopy may enable quantitative flux measurements in living tumors.

Molecular and biochemical basis of intermediate maple syrup urine disease. Occurrence of homozygous G245R and F364C mutations at the E1 alpha locus of Hispanic-Mexican patients.

Maple syrup urine disease (MSUD) is caused by a deficiency of the mitochondrial branched-chain alpha-keta acid dehydrogenase (BCKAD) complex. The multienzyme complex comprises five enzyme components, including the E1 decarboxylase with a heterotetrameric (alpha 2 beta 2) structure. Four unrelated Hispanic-Mexican MSUD patients with the intermediate clinical phenotype were diagnosed 7 to 22 mo after birth during evaluation for developmental delay. Three of the four patients were found homozygous for G to A transition at base 895 (exon 7) of the E1 alpha locus, which changes Gly-245 to Arg (G245R) in that subunit. The remaining patient was homozygous for T to G transversion at base 1,253 in the E1 alpha gene, which converts Phe-364 to Cys (F364C) in the gene product. Transfection studies in E1 alpha-deficient lymphoblasts indicate that both G245R and F364C mutant E1 alpha subunits were unable to significantly reconstitute BCKAD activity. Western blotting showed that both mutant E1 alpha subunits in transfected cells failed to efficiently rescue the normal E1 beta through assembly. The putative assembly defect was confirmed by pulse-chase labeling of E1 subunits in a chaperone-augmented bacterial overexpression system. The kinetics of initial assembly of the G245R E1 alpha subunit with the normal E1 beta was shown to be slower than the normal E1 alpha. No detectable assembly of the F364C E1 alpha with normal E1 beta was observed during the 2 h chase. Small amounts of recombinant mutant E1 proteins were produced after 15 h induction with isopropyl thiogalactoside and exhibited very low or no E1 activity. Our study establishes that G245R and F364C mutations in the E1 alpha subunit disrupt both the E1 heterotetrameric assembly and function of the BCKAD complex. Moreover, the results suggest that the G245R mutant E1 alpha allele may be important in the Hispanic-Mexican population.

Maple syrup urine disease in Mennonites. Evidence that the Y393N mutation in E1 alpha impedes assembly of the E1 component of branched-chain alpha-keto acid dehydrogenase complex.

Maple Syrup Urine Disease (MSUD) in Mennonites is associated with homozygosity for a T to A transversion in the E1 alpha gene of the branched-chain alpha-keto acid dehydrogenase complex. This causes a tyrosine to asparagine substitution at position 393 (Y393N). To assess the functional significance of this missense mutation, we have carried out transfection studies using E1 alpha-deficient MSUD lymphoblasts (Lo) as a host. The level of E1 beta subunit is also greatly reduced in Lo cells. Efficient episomal expression in lymphoblasts was achieved using the EBO vector. The inserts employed were chimeric bovine-human cDNAs which encode mitochondrial import competent E1 alpha subunit precursors. Transfection with normal E1 alpha cDNA into Lo cells restored decarboxylation activity of intact cells. Western blotting showed that both E1 alpha and E1 beta subunits were markedly increased. Introduction of Y393N mutant E1 alpha cDNA failed to produce any measurable decarboxylation activity. Mutant E1 alpha subunit was expressed at a normal level, however, the E1 beta subunit was undetectable. These results provide the first evidence that Y393N mutation is the cause of MSUD. Moreover, this mutation impedes the assembly of E1 alpha with E1 beta into a stable alpha 2 beta 2 structure, resulting in the degradation of the free E1 beta subunit.

GroEL/GroES-dependent Reconstitution of α2β2 Tetramers of Human Mitochondrial Branched Chain α-Ketoacid Decarboxylase OBLIGATORY INTERACTION OF CHAPERONINS WITH AN αβ DIMERIC INTERMEDIATE

The decarboxylase component (E1) of the human mitochondrial branched chain α-ketoacid dehydrogenase multienzyme complex (∼4–5 × 103 kDa) is a thiamine pyrophosphate-dependent enzyme, comprising two 45.5-kDa α subunits and two 37.8-kDa β subunits. In the present study, His6-tagged E1 α2β2 tetramers (171 kDa) denatured in 8 m urea were competently reconstituted in vitro at 23 °C with an absolute requirement for chaperonins GroEL/GroES and Mg-ATP. Unexpectedly, the kinetics for the recovery of E1 activity was very slow with a rate constant of 290 m −1 s−1. Renaturation of E1 with a similarly slow kinetics was also achieved using individual GroEL-α and GroEL-β complexes as combined substrates. However, the β subunit was markedly more prone to misfolding than the α in the absence of GroEL. The α subunit was released as soluble monomers from the GroEL-α complex alone in the presence of GroES and Mg-ATP. In contrast, the β subunit discharged from the GroEL-β complex readily rebound to GroEL when the α subunit was absent. Analysis of the assembly state showed that the His6-α and β subunits released from corresponding GroEL-polypeptide complexes assembled into a highly structured but inactive 85.5-kDa αβ dimeric intermediate, which subsequently dimerized to produce the active α2β2tetrameter. The purified αβ dimer isolated from Escherichia coli lysates was capable of binding to GroEL to produce a stable GroEL-αβ ternary complex. Incubation of this novel ternary complex with GroES and Mg-ATP resulted in recovery of E1 activity, which also followed slow kinetics with a rate constant of 138m −1 s−1. Dimers were regenerated from the GroEL-αβ complex, but they needed to interact with GroEL/GroES again, thereby perpetuating the cycle until the conversion from dimers to tetramers was complete. Our study describes an obligatory role of chaperonins in priming the dimeric intermediate for subsequent tetrameric assembly, which is a slow step in the reconstitution of E1 α2β2 tetramers.

GroEL/GroES Promote Dissociation/Reassociation Cycles of a Heterodimeric Intermediate during α2β2Protein Assembly ITERATIVE ANNEALING AT THE QUATERNARY STRUCTURE LEVEL

Whereas the mechanism of GroEL/GroES-mediated protein folding has been extensively studied, the role of these chaperonins in oligomeric protein assembly remains poorly understood. In the present study, we investigated the interaction of the chaperonins with an αβ heterodimeric intermediate during the α2β2 assembly of human mitochondrial branched-chain α-ketoacid dehydrogenase/decarboxylase (BCKD). Incubation of the recombinant His6-tagged BCKD in 400 mm KSCN for 45 min at 23 °C caused a complete dissociation of the α2β2 heterotetramers into inactive αβ heterodimers. Dilution of the denaturant resulted in a rapid recovery of BCKD independent of the chaperonins GroEL/GroES. Prolonged incubation of BCKD in 400 mm KSCN resulted in the generation of nonproductive or “bad” heterodimers, which were unable to undergo spontaneous reactivation but capable of binding to GroEL to form a stable GroEL-αβ complex. Incubation of this complex with GroES and Mg-ATP led to the slow reactivation of BCKD with a second-order rate constant k = 480m −1 s−1. Mixing experiments with radiolabeled and unlabeled protein substrates provided direct evidence that GroEL/GroES promote dissociation and subunit exchange between bad heterodimers. This was accompanied by the transformation of bad heterodimers to their “good” or productive counterparts. The good heterodimers were capable of spontaneous dimerization to initially form an inactive heterotetrameric species, followed by conversion to active heterotetramers. However, a large fraction of bad heterodimers were regenerated and rebound to GroEL. The cycle was perpetuated until the reconstitution of active BCKD was complete. Our data support the thesis that chaperonins GroEL/GroES mediate iterative annealing of nonproductive assembly intermediates at the quaternary structure level. This step is essential for an efficient subsequent higher order oligomerization.

Molecular Phenotypes in Cultured Maple Syrup Urine Disease Cells

The activity of the branched-chain alpha-keto acid dehydrogenase complex is deficient in patients with the inherited maple syrup urine disease (MSUD). To elucidate the molecular basis of this metabolic disorder, we have isolated three overlapping cDNA clones encoding the E1 alpha subunit of the human enzyme complex. The composite human E1 alpha cDNA consists of 1783 base pairs encoding the entire human E1 alpha subunit of 400 amino acids with calculated Mr = 45,552. The human E1 alpha and the previously isolated human E2 cDNAs were used as probes in Northern blot analysis with cultured fibroblasts and lymphoblasts from seven unrelated MSUD patients. The results along with those of Western blotting have revealed five distinct molecular phenotypes according to mRNA and protein-subunit contents. These consist of type I, where the levels of E1 alpha mRNA and E1 alpha and E1 beta subunits are normal in cells, but E1 activity is deficient; Type II, where the E1 alpha mRNA is present in normal quantity, whereas the contents of E1 alpha and E1 beta subunits are reduced; Type III, where the level of E1 alpha mRNA is markedly reduced with a concomitant loss of E1 alpha and E1 beta subunits; Type IV, where the contents of both E2 mRNA and E2 subunits are markedly reduced; and Type V, where the E2 mRNA is normally expressed, but the E2 subunit is markedly reduced or completely absent. Type V includes thiamin-responsive (WG-34) and certain classical MSUD cells. These molecular phenotypes have demonstrated the complexity of MSUD and identified the affected gene in different patients for further characterization.

Molecular cloning of the mature E1b-β subunit of human branched-chain α-keto acid dehydrogenase complex

We have isolated a cDNA encoding the E1b‐β subunit of the human branched‐chain α‐keto acid dehydrogenase complex. The human E1b‐β cDNA is 1401 base pairs in length. It encodes the entire mature E1b‐β subunit consisting of 342 amino acid residues, and a mitochondrial targeting presequence of 31 residues. The calculated molecular mass of the mature human E1b‐β subunit is 37 851 Da, and the calculated isoelectric point is pH 5.18. A hydropathy plot shows that the human E1b‐β subunit is highly hydrophobic. Northern blot analysis shows that the human E1b‐β mRNA is approximately 1.4 kb in size. It is present at the normal level in fibroblasts from two unrelated maple syrup urine disease patients.

A distinct variant of intermediate maple syrup urine disease

Branched chain α‐ketoacid dehydrogenase (BCKAD) deficiency, or maple syrup urine disease (MSUD), can be categorized as classical, intermediate, intermittent or thiamine responsive, based on generally concordant in vitro BCKAD activity and severity of phenotype. We present clinical and enzymatic data on a boy with intermediate maple syrup urine disease, and suggest that he represents a novel category of mutation. He presented at age 10 months in ketoacidotic coma, with a history of irritability, poor feeding and growth and developmental delay. Branched chain amino acid restriction effected normal growth and developmental parameters by age 42 months. In contrast to previous patients with intermediate MSUD, his fibroblasts and fibroblast extracts failed to decarboxylate [1‐14C]‐α‐ketoisovalerate (KIV). The defect is not in mitochondrial transport of substrate, but rather in the catalytic activity of the E1 component of the BCKAD. Disrupted cells of the proband exhibited negligible BCKAD activity over a wide range of keto acid substrate concentrations, irrespective of the presence of added thiamine pyrophosphate (TPP). These results differ from the sigmoidal kinetics observed using classical MSUD extracts, and the hyperbolic kinetics with control preparations under the same assay conditions. We propose that the structurally altered enzyme possesses reduced but not negligible activity in vivo, and exists as an unstable complex in vitro under assay conditions used, even in the presence of added TPP.

Interactions of GroEL/GroES with a Heterodimeric Intermediate during α2β2 Assembly of Mitochondrial Branched-chain α-Ketoacid Dehydrogenase cis CAPPING OF THE NATIVE-LIKE 86-kDa INTERMEDIATE BY GroES

We showed previously that the interaction of an αβ heterodimeric intermediate with GroEL/GroES is essential for efficient α2β2 assembly of human mitochondrial branched-chain α-ketoacid dehydrogenase. In the present study, we further characterized the mode of interaction between the chaperonins and the native-like αβ heterodimer. The αβ heterodimer, as an intact entity, was found to bind to GroEL at a 1:1 stoichiometry with a K D of 1.1 × 10− 7 m. The 1:1 molar ratio of the GroEL-αβ complex was confirmed by the ability of the complex to bind a stoichiometric amount of denatured lysozyme in thetrans cavity. Surprisingly, in the presence of Mg-ADP, GroES was able to cap the GroEL-αβ complex in cis, despite the size of 86 kDa of the heterodimer (with a His6tag and a linker). Incubation of the GroEL-αβ complex with Mg-ATP, but not AMP-PNP, resulted in the release of α monomers. In the presence of Mg-ATP, the β subunit was also released but was unable to assemble with the α subunit, and rebound to GroEL. The apparent differential subunit release from GroEL is explained, in part, by the significantly higher binding affinity of the β subunit (K D < 4.15 × 10− 9 m) than the α (K D = 1.6 × 10− 8 m) for GroEL. Incubation of the GroEL-αβ complex with Mg-ATP and GroES resulted in dissociation and discharge of both the α and β subunits from GroEL. The β subunit upon binding to GroEL underwent further folding in thecis cavity sequestered by GroES. This step rendered the β subunit competent for reassociation with the soluble α subunit to produce a new heterodimer. We propose that this mechanism is responsible for the iterative annealing of the kinetically trapped heterodimeric intermediate, leading to an efficient α2β2 assembly of human branched-chain α-ketoacid dehydrogenase.

Inhibition of the bovine branched-chain 2-oxo acid dehydrogenase complex and its kinase by arylidenepyruvates

A novel class of inhibitors for the branched-chain 2-oxo acid dehydrogenase (BCOAD) complex has been synthesized and studied. The sodium salts of arylidenepyruvates: e.g., furfurylidenepyruvate (compound I), 4-(3-thienyl)-2-oxo-3-butenoate (compound II), cinnamalpyruvate (compound III) and 4-(2-thienyl)-2-oxo-3-butenoate (compound IV) inhibit the overall and kinase reactions of the BCOAD complex from bovine liver. Inhibitions of the overall reaction occur at the decarboxylase (E1) step as determined by a spectrophotometric assay with 2,6-dichlorophenolindophenol as an electron acceptor. Inhibition of the E1 reaction by compound I (Ki = 0.5 microM) is competitive, whereas inhibitions by compounds II (Ki = 150 microM) and III (Ki = 500 microM) are non-competitive with respect to the substrate 2-oxoisovalerate. The Km value for 2-oxoisovalerate is 6.7 microM as measured by the E1 assay. Inhibition of the E1 step by compounds I, II and III are reversible at low inhibitor concentrations based on the Michaelis-Menten kinetics observed. By comparison, compound I does not significantly inhibit pyruvate and 2-oxoglutarate dehydrogenase complexes. The arylidenepyruvates (compounds I, II and IV) inhibit the BCOAD kinase reaction in a manner similar to the substrate 2-oxo acids. The inhibition of the kinase reaction by compound I is non-competitive with respect to ATP, with an apparent Ki value of 4.5 mM. The results suggest that arylidenepyruvates may be useful probes for elucidating the reaction mechanisms of the BCOAD complex and its kinase.