scholarly journals Toward an Understanding Of the Structural and Mechanistic Aspects of Protein-Protein Interactions in 2-Oxo Acid Dehydrogenase Complexes

2021 ◽  
Author(s):  
Natalia S. Nemeria ◽  
Xu Zhang ◽  
Joao Leandro ◽  
Jieyu Zhou ◽  
Luying Yang ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Tca Cycle ◽  
Degradation Pathway ◽  
Protein Protein Interactions ◽  
Acid Dehydrogenase ◽  
The Tca Cycle ◽  
Hybrid Complex ◽  
Key Enzyme ◽  
Lysine Degradation ◽  
Dehydrogenase Complex

The 2-oxoglutarate dehydrogenase complex (OGDHc) is a key enzyme in the TCA cycle and represents one of the major regulators of mitochondrial metabolism through NADH and reactive oxygen species levels. The OGDHc impacts cell metabolic and cell signaling pathways through the coupling of 2-oxoglutarate metabolism to gene transcription related to tumor cell proliferation and aging. DHTKD1 is a gene encoding 2-oxoadipate dehydrogenase (E1a), which functions in the L-lysine degradation pathway. The potentially damaging variants in DHTKD1 have been associated to the (neuro) pathogenesis of several diseases. Evidence was obtained for the formation of a hybrid complex between the OGDHc and E1a, suggesting a potential cross talk between the two metabolic pathways and raising fundamental questions about their assembly. Here we reviewed the recent findings and advances in understanding of protein-protein interactions in OGDHc and 2-oxoadipate dehydrogenase complex (OADHc), an understanding that will create a scaffold to help design approaches to mitigate the effects of diseases associated with dysfunction of the TCA cycle or lysine degradation. A combination of biochemical, biophysical and structural approaches such as chemical cross-linking MS and cryo-EM appears particularly promising to provide vital information for the assembly of 2-oxo acid dehydrogenase complexes, their function and regulation.

scholarly journals Toward an Understanding of the Structural and Mechanistic Aspects of Protein-Protein Interactions in 2-Oxoacid Dehydrogenase Complexes

Life ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 407
Author(s):  
Natalia S. Nemeria ◽  
Xu Zhang ◽  
Joao Leandro ◽  
Jieyu Zhou ◽  
Luying Yang ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Tca Cycle ◽  
Degradation Pathway ◽  
Protein Protein Interactions ◽  
Gene Encoding ◽  
The Tca Cycle ◽  
Hybrid Complex ◽  
Key Enzyme ◽  
Lysine Degradation ◽  
Dehydrogenase Complex

The 2-oxoglutarate dehydrogenase complex (OGDHc) is a key enzyme in the tricarboxylic acid (TCA) cycle and represents one of the major regulators of mitochondrial metabolism through NADH and reactive oxygen species levels. The OGDHc impacts cell metabolic and cell signaling pathways through the coupling of 2-oxoglutarate metabolism to gene transcription related to tumor cell proliferation and aging. DHTKD1 is a gene encoding 2-oxoadipate dehydrogenase (E1a), which functions in the L-lysine degradation pathway. The potentially damaging variants in DHTKD1 have been associated to the (neuro) pathogenesis of several diseases. Evidence was obtained for the formation of a hybrid complex between the OGDHc and E1a, suggesting a potential cross talk between the two metabolic pathways and raising fundamental questions about their assembly. Here we reviewed the recent findings and advances in understanding of protein-protein interactions in OGDHc and 2-oxoadipate dehydrogenase complex (OADHc), an understanding that will create a scaffold to help design approaches to mitigate the effects of diseases associated with dysfunction of the TCA cycle or lysine degradation. A combination of biochemical, biophysical and structural approaches such as chemical cross-linking MS and cryo-EM appears particularly promising to provide vital information for the assembly of 2-oxoacid dehydrogenase complexes, their function and regulation.

scholarly journals DHTKD1 and OGDH display substrate overlap in cultured cells and form a hybrid 2-oxo acid dehydrogenase complex in vivo

2020 ◽  
Vol 29 (7) ◽  
pp. 1168-1179 ◽  
Author(s):  
João Leandro ◽  
Tetyana Dodatko ◽  
Jan Aten ◽  
Natalia S Nemeria ◽  
Xu Zhang ◽  
...  
Keyword(s):  
Cultured Cells ◽  
Cell Model ◽  
Glutaric Aciduria Type ◽  
Glutaric Aciduria Type 1 ◽  
Hek 293 ◽  
Acid Dehydrogenase ◽  
Lysine Degradation ◽  
Acid Dehydrogenase Complex ◽  
Dehydrogenase Complex

Abstract Glutaric aciduria type 1 (GA1) is an inborn error of lysine degradation characterized by a specific encephalopathy that is caused by toxic accumulation of lysine degradation intermediates. Substrate reduction through inhibition of DHTKD1, an enzyme upstream of the defective glutaryl-CoA dehydrogenase, has been investigated as a potential therapy, but revealed the existence of an alternative enzymatic source of glutaryl-CoA. Here, we show that loss of DHTKD1 in glutaryl-CoA dehydrogenase-deficient HEK-293 cells leads to a 2-fold decrease in the established GA1 clinical biomarker glutarylcarnitine and demonstrate that oxoglutarate dehydrogenase (OGDH) is responsible for this remaining glutarylcarnitine production. We furthermore show that DHTKD1 interacts with OGDH, dihydrolipoyl succinyltransferase and dihydrolipoamide dehydrogenase to form a hybrid 2-oxoglutaric and 2-oxoadipic acid dehydrogenase complex. In summary, 2-oxoadipic acid is a substrate for DHTKD1, but also for OGDH in a cell model system. The classical 2-oxoglutaric dehydrogenase complex can exist as a previously undiscovered hybrid containing DHTKD1 displaying improved kinetics towards 2-oxoadipic acid.

scholarly journals Protein/Protein Interactions in the Mammalian Heme Degradation Pathway

2014 ◽  
Vol 289 (43) ◽  
pp. 29836-29858 ◽  
Author(s):  
Andrea L. M. Spencer ◽  
Ireena Bagai ◽  
Donald F. Becker ◽  
Erik R. P. Zuiderweg ◽  
Stephen W. Ragsdale
Keyword(s):  
Protein Interactions ◽  
Degradation Pathway ◽  
Protein Protein Interactions ◽  
Heme Degradation

Alpha-ketoglutarate as an intermediate in glutamate metabolism by Peptococcus aerogenes

1972 ◽  
Vol 18 (6) ◽  
pp. 875-880 ◽  
Author(s):  
W. M. Johnson ◽  
D. W. S. Westlake
Keyword(s):  
Potential Energy ◽  
Glutamic Acid ◽  
Tca Cycle ◽  
The Other ◽  
Glutamate Metabolism ◽  
Fermentation Products ◽  
Acid Dehydrogenase ◽  
Specific Distribution ◽  
The Tca Cycle ◽  
Hydroxyglutaric Acid

The pathway from glutamic acid to α-hydroxyglutaric acid in Peptococcus aerogenes proceeds via α-ketoglutaric acid and is mediated by two NAD-dependent enzymes. One enzyme, an NAD-dependent glutamic acid dehydrogenase, oxidatively deaminates glutamic acid to α-ketoglutaric acid. The other enzyme, α-ketoglutaric acid reductase, reduces α-ketoglutaric acid to α-hydroxyglutaric acid in the presence of NADH. The demonstration of a very low level of α-ketoglutaric acid dehydrogenase activity in crude cell-free extracts indicates that the primary metabolic pathway for glutamic acid carbons proceeds via α-hydroxyglutaric acid and not via the TCA cycle. Potential energy-yielding mechanisms are discussed relative to the known specific distribution of glutamic acid carbon atoms in fermentation products.

scholarly journals Regulation of the acuF Gene, Encoding Phosphoenolpyruvate Carboxykinase in the Filamentous Fungus Aspergillus nidulans

2002 ◽  
Vol 184 (1) ◽  
pp. 183-190 ◽  
Author(s):  
Michael J. Hynes ◽  
Oliver W. Draht ◽  
Meryl A. Davis
Keyword(s):  
Carbon Source ◽  
Aspergillus Nidulans ◽  
Phosphoenolpyruvate Carboxykinase ◽  
Carbon Sources ◽  
Tca Cycle ◽  
Northern Blotting ◽  
Gene Encoding ◽  
The Tca Cycle ◽  
Key Enzyme ◽  
Acetate Utilization

ABSTRACT Phosphoenolpyruvate carboxykinase (PEPCK) is a key enzyme required for gluconeogenesis when microorganisms grow on carbon sources metabolized via the tricarboxylic acid (TCA) cycle. Aspergillus nidulans acuF mutants isolated by their inability to use acetate as a carbon source specifically lack PEPCK. The acuF gene has been cloned and shown to encode a protein with high similarity to PEPCK from bacteria, plants, and fungi. The regulation of acuF expression has been studied by Northern blotting and by the construction of lacZ fusion reporters. Induction by acetate is abolished in mutants unable to metabolize acetate via the TCA cycle, and induction by amino acids metabolized via 2-oxoglutarate is lost in mutants unable to form 2-oxoglutarate. Induction by acetate and proline is not additive, consistent with a single mechanism of induction. Malate and succinate result in induction, and it is proposed that PEPCK is controlled by a novel mechanism of induction by a TCA cycle intermediate or derivative, thereby allowing gluconeogenesis to occur during growth on any carbon source metabolized via the TCA cycle. It has been shown that the facB gene, which mediates acetate induction of enzymes specifically required for acetate utilization, is not directly involved in PEPCK induction. This is in contrast to Saccharomyces cerevisiae, where Cat8p and Sip4p, homologs of FacB, regulate PEPCK as well as the expression of other genes necessary for growth on nonfermentable carbon sources in response to the carbon source present. This difference in the control of gluconeogenesis reflects the ability of A. nidulans and other filamentous fungi to use a wide variety of carbon sources in comparison with S. cerevisiae. The acuF gene was also found to be subject to activation by the CCAAT binding protein AnCF, a protein homologous to the S. cerevisiae Hap complex and the mammalian NFY complex.

scholarly journals Massively parallel fitness profiling reveals multiple novel enzymes inPseudomonas putidalysine metabolism

2018 ◽  
Author(s):  
Mitchell G. Thompson ◽  
Jacquelyn M. Blake-Hedges ◽  
Pablo Cruz-Morales ◽  
Jesus F. Barajas ◽  
Samuel C. Curran ◽  
...  
Keyword(s):  
Tca Cycle ◽  
Central Metabolism ◽  
It Use ◽  
Catabolic Genes ◽  
Genome Wide ◽  
The Tca Cycle ◽  
A Genome ◽  
Domains Of Life ◽  
Lysine Degradation ◽  
Lysine Metabolism

AbstractDespite intensive study for 50 years, the biochemical and genetic links between lysine metabolism and central metabolism inPseudomonas putidaremain unresolved. To establish these biochemical links, we leveraged Random Barcode Transposon Sequencing (RB-TnSeq), a genome-wide assay measuring the fitness of thousands of genes in parallel, to identify multiple novel enzymes in both L- and D-lysine metabolism. We first describe three pathway enzymes that catabolize L-2-aminoadipate (L-2AA) to 2-ketoglutarate (2KG), connecting D-lysine to the TCA cycle. One of these enzymes, PP_5260, contains a DUF1338 domain, a family with no previously described biological function. Our work also identified the recently described CoA independent route of L-lysine degradation that metabolizes to succinate. We expanded on previous findings by demonstrating that glutarate hydroxylase CsiD is promiscuous in its 2-oxoacid selectivity. Proteomics of select pathway enzymes revealed that expression of catabolic genes is highly sensitive to particular pathway metabolites, implying intensive local and global regulation. This work demonstrates the utility of RB-TnSeq for discovering novel metabolic pathways in even well-studied bacteria, as well as a powerful tool for validating previous research.ImportanceP. putidalysine metabolism can produce multiple commodity chemicals, conferring great biotechnological value. Despite much research, connecting lysine catabolism to central metabolism inP. putidaremained undefined. Herein we use Random Barcode Transposon Sequencing to fill in the gaps of lysine metabolism inP. putida. We describe a route of 2-oxoadipate (2OA) catabolism in bacteria, which utilizes DUF1338 containing protein PP_5260. Despite its prevalence in many domains of life, DUF1338 containing proteins had no known biochemical function. We demonstrate PP_5260 is a metalloenzyme which catalyzes an unusual 2OA to D-2HG decarboxylation. Our screen also identified a recently described novel glutarate metabolic pathway. We validate previous results, and expand the understanding of glutarate hydroxylase CsiD by showing can it use either 2OA or 2KG as a cosubstrate. Our work demonstrates biological novelty can be rapidly identified using unbiased experimental genetics, and that RB-TnSeq can be used to rapidly validate previous results.

Compartmentalization and metabolic regulation of glycolysis

2021 ◽  
Vol 134 (20) ◽  
Author(s):  
Gregory G. Fuller ◽  
John K. Kim
Keyword(s):  
Protein Interactions ◽  
Mammalian Cells ◽  
Energy Production ◽  
Metabolic Regulation ◽  
Tca Cycle ◽  
Synaptic Function ◽  
Protein Protein Interactions ◽  
C Elegans ◽  
Physiological Importance ◽  
Condensate Formation

ABSTRACT Hypoxia inhibits the tricarboxylic acid (TCA) cycle and leaves glycolysis as the primary metabolic pathway responsible for converting glucose into usable energy. However, the mechanisms that compensate for this loss in energy production due to TCA cycle inactivation remain poorly understood. Glycolysis enzymes are typically diffuse and soluble in the cytoplasm under normoxic conditions. In contrast, recent studies have revealed dynamic compartmentalization of glycolysis enzymes in response to hypoxic stress in yeast, C. elegans and mammalian cells. These messenger ribonucleoprotein (mRNP) structures, termed glycolytic (G) bodies in yeast, lack membrane enclosure and display properties of phase-separated biomolecular condensates. Disruption of condensate formation correlates with defects such as impaired synaptic function in C. elegans neurons and decreased glucose flux in yeast. Concentrating glycolysis enzymes into condensates may lead to their functioning as ‘metabolons’ that enhance rates of glucose utilization for increased energy production. Besides condensates, glycolysis enzymes functionally associate in other organisms and specific tissues through protein–protein interactions and membrane association. However, as discussed in this Review, the functional consequences of coalescing glycolytic machinery are only just beginning to be revealed. Through ongoing studies, we anticipate the physiological importance of metabolic regulation mediated by the compartmentalization of glycolysis enzymes will continue to emerge.

scholarly journals Parasite-specific inserts in the bifunctional S-adenosylmethionine decarboxylase/ornithine decarboxylase of Plasmodium falciparum modulate catalytic activities and domain interactions

2004 ◽  
Vol 377 (2) ◽  
pp. 439-448 ◽  
Author(s):  
Lyn-Marie BIRKHOLTZ ◽  
Carsten WRENGER ◽  
Fourie JOUBERT ◽  
Gordon A. WELLS ◽  
Rolf D. WALTER ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Complex Formation ◽  
Ornithine Decarboxylase ◽  
Protein Interactions ◽  
Polyamine Metabolism ◽  
Protein Protein Interactions ◽  
Bifunctional Protein ◽  
Catalytic Activities ◽  
Adenosylmethionine Decarboxylase ◽  
Hybrid Complex

Polyamine biosynthesis of the malaria parasite, Plasmodium falciparum, is regulated by a single, hinge-linked bifunctional PfAdoMetDC/ODC [P. falciparum AdoMetDC (S-adenosylmethionine decarboxylase)/ODC (ornithine decarboxylase)] with a molecular mass of 330 kDa. The bifunctional nature of AdoMetDC/ODC is unique to Plasmodia and is shared by at least three species. The PfAdoMetDC/ODC contains four parasite-specific regions ranging in size from 39 to 274 residues. The significance of the parasite-specific inserts for activity and protein–protein interactions of the bifunctional protein was investigated by a single- and multiple-deletion strategy. Deletion of these inserts in the bifunctional protein diminished the corresponding enzyme activity and in some instances also decreased the activity of the neighbouring, non-mutated domain. Intermolecular interactions between AdoMetDC and ODC appear to be vital for optimal ODC activity. Similar results have been reported for the bifunctional P. falciparum dihydrofolate reductase-thymidylate synthase [Yuvaniyama, Chitnumsub, Kamchonwongpaisan, Vanichtanankul, Sirawaraporn, Taylor, Walkinshaw and Yuthavong (2003) Nat. Struct. Biol. 10, 357–365]. Co-incubation of the monofunctional, heterotetrameric ≈150 kDa AdoMetDC domain with the monofunctional, homodimeric ODC domain (≈180 kDa) produced an active hybrid complex of 330 kDa. The hinge region is required for bifunctional complex formation and only indirectly for enzyme activities. Deletion of the smallest, most structured and conserved insert in the ODC domain had the biggest impact on the activities of both decarboxylases, homodimeric ODC arrangement and hybrid complex formation. The remaining large inserts are predicted to be non-globular regions located on the surface of these proteins. The large insert in AdoMetDC in contrast is not implicated in hybrid complex formation even though distinct interactions between this insert and the two domains are inferred from the effect of its removal on both catalytic activities. Interference with essential protein–protein interactions mediated by parasite-specific regions therefore appears to be a viable strategy to aid the design of selective inhibitors of polyamine metabolism of P. falciparum.

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