The DHTKD1 Pathogenic Mutation Encoding the G729R 2-oxoadipate dehydrogenase Affects Substrate Channeling in the 2-oxoadipate Dehydrogenase Complex in the L-lysine Degradation Pathway

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.

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Investigating the Molecular Determinants for Substrate Channeling in BphI–BphJ, an Aldolase–Dehydrogenase Complex from the Polychlorinated Biphenyls Degradation Pathway

Biochemistry ◽

10.1021/bi200960j ◽

2011 ◽

Vol 50 (39) ◽

pp. 8407-8416 ◽

Cited By ~ 19

Author(s):

Jason Carere ◽

Perrin Baker ◽

Stephen Y. K. Seah

Keyword(s):

Polychlorinated Biphenyls ◽

Degradation Pathway ◽

Substrate Channeling ◽

Molecular Determinants ◽

Dehydrogenase Complex

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

Life ◽

10.3390/life11050407 ◽

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.

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

Human Molecular Genetics ◽

10.1093/hmg/ddaa037 ◽

2020 ◽

Vol 29 (7) ◽

pp. 1168-1179 ◽

Cited By ~ 5

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.

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Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway

Nature Communications ◽

10.1038/s41467-019-11931-1 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 4

Author(s):

Nitish Sathyanarayanan ◽

Giuseppe Cannone ◽

Lokesh Gakhar ◽

Nainesh Katagihallimath ◽

Ramanathan Sowdhamini ◽

...

Keyword(s):

Conformational Changes ◽

Active Site ◽

Ring Opening ◽

Environmental Pollutants ◽

Degradation Pathway ◽

Substrate Channeling ◽

Enzyme Form ◽

X Ray Scattering ◽

Hydrophobic Tunnel ◽

Metabolite Channeling

Abstract Substrate channeling is a mechanism for the internal transfer of hydrophobic, unstable or toxic intermediates from the active site of one enzyme to another. Such transfer has previously been described to be mediated by a hydrophobic tunnel, the use of electrostatic highways or pivoting and by conformational changes. The enzyme PaaZ is used by many bacteria to degrade environmental pollutants. PaaZ is a bifunctional enzyme that catalyzes the ring opening of oxepin-CoA and converts it to 3-oxo-5,6-dehydrosuberyl-CoA. Here we report the structures of PaaZ determined by electron cryomicroscopy with and without bound ligands. The structures reveal that three domain-swapped dimers of the enzyme form a trilobed structure. A combination of small-angle X-ray scattering (SAXS), computational studies, mutagenesis and microbial growth experiments suggests that the key intermediate is transferred from one active site to the other by a mechanism of electrostatic pivoting of the CoA moiety, mediated by a set of conserved positively charged residues.

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The lysine degradation pathway: Subcellular compartmentalization and enzyme deficiencies

Molecular Genetics and Metabolism ◽

10.1016/j.ymgme.2020.07.010 ◽

2020 ◽

Vol 131 (1-2) ◽

pp. 14-22

Author(s):

João Leandro ◽

Sander M. Houten

Keyword(s):

Degradation Pathway ◽

Lysine Degradation ◽

Subcellular Compartmentalization

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Transcriptome Dynamics of Double Recessive Mutant, o2o2o16o16, Reveals the Transcriptional Mechanisms in the Increase of Its Lysine and Tryptophan Content in Maize

Genes ◽

10.3390/genes10040316 ◽

2019 ◽

Vol 10 (4) ◽

pp. 316 ◽

Cited By ~ 3

Author(s):

Wei Wang ◽

Yi Dai ◽

Mingchun Wang ◽

Wenpeng Yang ◽

Degang Zhao

Keyword(s):

Molecular Mechanisms ◽

Degradation Pathway ◽

Endosperm Development ◽

Rna Seq ◽

Wild Type ◽

Genes Encoding ◽

Recessive Mutant ◽

Lysine Degradation ◽

Tryptophan Content

In maize, pyramiding of o2 and o16 alleles can greatly improve the nutritional quality of grains. To dissect its molecular mechanism, we created a double recessive mutant line, o2o2o16o16, by introgression of the o2 and o16 alleles into the wild-type maize inbred line, by molecular marker-assisted backcross selection. The kernels (18 day after pollination (DAP), 28 DAP, and 38 DAP) of the o2o2o16o16 mutant and its parent lines were subject to RNA sequencing (RNA-Seq). The RNA-Seq analysis revealed that 59 differentially expressed genes (DEGs) were involved in lysine metabolism and 43 DEGs were involved in tryptophan metabolism. Among them, the genes encoding AK, ASADH, and Dap-F in the lysine synthesis pathway were upregulated at different stages of endosperm development, promoting the synthesis of lysine. Meanwhile, the genes encoding LKR/SDH and L-PO in the lysine degradation pathway were downregulated, inhibiting the degradation of lysine. Moreover, the genes encoding TAA and YUC in the tryptophan metabolic pathway were downregulated, restraining the degradation of tryptophan. Thus, pyramiding o2 and o16 alleles could increase the lysine and tryptophan content in maize. These above results would help to uncover the molecular mechanisms involved in the increase in lysine and the tryptophan content, through the introgression of o2 and o16 alleles into the wild-type maize.

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Anti-Microbiota Vaccines Modulate the Tick Microbiome in a Taxon-Specific Manner

Frontiers in Immunology ◽

10.3389/fimmu.2021.704621 ◽

2021 ◽

Vol 12 ◽

Author(s):

Lourdes Mateos-Hernández ◽

Dasiel Obregón ◽

Alejandra Wu-Chuang ◽

Jennifer Maye ◽

Jeremie Bornères ◽

...

Keyword(s):

Degradation Pathway ◽

Tick Feeding ◽

E Coli ◽

Live Bacteria ◽

Lysine Degradation ◽

And Function ◽

Functional Profiles ◽

The Impact ◽

Tick Microbiome ◽

Gut Microbiota Composition

The lack of tools for the precise manipulation of the tick microbiome is currently a major limitation to achieve mechanistic insights into the tick microbiome. Anti-tick microbiota vaccines targeting keystone bacteria of the tick microbiota alter tick feeding, but their impact on the taxonomic and functional profiles of the tick microbiome has not been tested. In this study, we immunized a vertebrate host model (Mus musculus) with live bacteria vaccines targeting keystone (i.e., Escherichia-Shigella) or non-keystone (i.e., Leuconostoc) taxa of tick microbiota and tested the impact of bacterial-specific antibodies (Abs) on the structure and function of tick microbiota. We also investigated the effect of these anti-microbiota vaccines on mice gut microbiota composition. Our results showed that the tick microbiota of ticks fed on Escherichia coli-immunized mice had reduced Escherichia-Shigella abundance and lower species diversity compared to ticks fed on control mice immunized with a mock vaccine. Immunization against keystone bacteria restructured the hierarchy of nodes in co-occurrence networks and reduced the resistance of the bacterial network to taxa removal. High levels of E. coli-specific IgM and IgG were negatively correlated with the abundance of Escherichia-Shigella in tick microbiota. These effects were not observed when Leuconostoc was targeted with vaccination against Leuconostoc mesenteroides. Prediction of functional pathways in the tick microbiome using PICRUSt2 revealed that E. coli vaccination reduced the abundance of lysine degradation pathway in tick microbiome, a result validated by qPCR. In contrast, the gut microbiome of immunized mice showed no significant alterations in the diversity, composition and abundance of bacterial taxa. Our results demonstrated that anti-tick microbiota vaccines are a safe, specific and an easy-to-use tool for manipulation of vector microbiome. These results guide interventions for the control of tick infestations and pathogen infection/transmission.

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First patient in Serbia with biochemically and genetically diagnosed pyridoxine-dependent epilepsy

Vojnosanitetski pregled ◽

10.2298/vsp150311244j ◽

2017 ◽

Vol 74 (6) ◽

pp. 594-597

Author(s):

Milos Jesic ◽

Maja Jesic ◽

Svetlana Buljugic ◽

Aleksandra Zivanovic

Keyword(s):

Cerebrospinal Fluid ◽

Inborn Error ◽

Autosomal Recessive ◽

Degradation Pathway ◽

Drug Resistant ◽

Gene Diagnosis ◽

Genetical Analysis ◽

Semialdehyde Dehydrogenase ◽

Lysine Degradation ◽

Reliable Marker

Introduction. Pyridoxine-dependent epilepsy (PDE) is a rare autosomal recessive inborn error of metabolism present with early-onset seizures resistant to common anticonvulsants. PDE has been shown to be caused by a defect of a ?-aminoadipic semialdehyde dehydrogenase (also known as ALDH7A1 or antiquitin) in the cerebral lysine degradation pathway. Its deficiency results in accumulation of ?-aminoadipic semialdehyde (?-AASA), piperideine -6-carboxylate and pipecolic acid, which serve as diagnostic markers in urine, plasma and cerebrospinal fluid of the disease. ?-Aminoadipic semialdehyde dehydrogenase is encoded by the ALDH7A1 or antiquitin gene and definite confirmation of diagnosis of PDE is made by genetic analysis. Case report. We present a first patient in Serbia who was diagnosed clinically, biochemically and genetically. We suspected PDE due to drug-resistant seizures in the seventh day of life when we attempted with pyridoxine. Since that time the patient has taken pyridoxine and the seizures have not recured. Our patient had markedly elevated ?- AASA in urine while on treatment with individual dosages of pyridoxine. Molecular-genetical analysis identified mutations of the ALDH7A1 (antiquitin) gene. Conclusion. ?-AASA is reliable marker to select PDF patient for molecular analysis of the ALDH7A1(antiquitin) gene. Diagnosis is confirmed by molecular- genetical analysis and pyridoxine withdrawal is no longer needed to establish the diagnosis of ?definite? PDE.

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