1
|
Zdanowicz R, Afanasyev P, Pruška A, Harrison JA, Giese C, Boehringer D, Leitner A, Zenobi R, Glockshuber R. Stoichiometry and architecture of the human pyruvate dehydrogenase complex. SCIENCE ADVANCES 2024; 10:eadn4582. [PMID: 39018392 PMCID: PMC466950 DOI: 10.1126/sciadv.adn4582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 06/05/2024] [Indexed: 07/19/2024]
Abstract
The pyruvate dehydrogenase complex (PDHc) is a key megaenzyme linking glycolysis with the citric acid cycle. In mammalian PDHc, dihydrolipoamide acetyltransferase (E2) and the dihydrolipoamide dehydrogenase-binding protein (E3BP) form a 60-subunit core that associates with the peripheral subunits pyruvate dehydrogenase (E1) and dihydrolipoamide dehydrogenase (E3). The structure and stoichiometry of the fully assembled, mammalian PDHc or its core remained elusive. Here, we demonstrate that the human PDHc core is formed by 48 E2 copies that bind 48 E1 heterotetramers and 12 E3BP copies that bind 12 E3 homodimers. Cryo-electron microscopy, together with native and cross-linking mass spectrometry, confirmed a core model in which 8 E2 homotrimers and 12 E2-E2-E3BP heterotrimers assemble into a pseudoicosahedral particle such that the 12 E3BP molecules form six E3BP-E3BP intertrimer interfaces distributed tetrahedrally within the 60-subunit core. The even distribution of E3 subunits in the peripheral shell of PDHc guarantees maximum enzymatic activity of the megaenzyme.
Collapse
Affiliation(s)
- Rafal Zdanowicz
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Pavel Afanasyev
- Cryo-EM Knowledge Hub, ETH Zurich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Adam Pruška
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Julian A. Harrison
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Christoph Giese
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Daniel Boehringer
- Cryo-EM Knowledge Hub, ETH Zurich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Rudi Glockshuber
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| |
Collapse
|
2
|
Meinhold S, Zdanowicz R, Giese C, Glockshuber R. Dimerization of a 5-kDa domain defines the architecture of the 5-MDa gammaproteobacterial pyruvate dehydrogenase complex. SCIENCE ADVANCES 2024; 10:eadj6358. [PMID: 38324697 PMCID: PMC10849603 DOI: 10.1126/sciadv.adj6358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 01/11/2024] [Indexed: 02/09/2024]
Abstract
The Escherichia coli pyruvate dehydrogenase complex (PDHc) is a ~5 MDa assembly of the catalytic subunits pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). The PDHc core is a cubic complex of eight E2 homotrimers. Homodimers of the peripheral subunits E1 and E3 associate with the core by binding to the peripheral subunit binding domain (PSBD) of E2. Previous reports indicated that 12 E1 dimers and 6 E3 dimers bind to the 24-meric E2 core. Using an assembly arrested E2 homotrimer (E23), we show that two of the three PSBDs in the E23 dimerize, that each PSBD dimer cooperatively binds two E1 dimers, and that E3 dimers only bind to the unpaired PSBD in E23. This mechanism is preserved in wild-type PDHc, with an E1 dimer:E2 monomer:E3 dimer stoichiometry of 16:24:8. The conserved PSBD dimer interface indicates that PSBD dimerization is the previously unrecognized architectural determinant of gammaproteobacterial PDHc megacomplexes.
Collapse
Affiliation(s)
| | | | - Christoph Giese
- ETH Zürich, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | | |
Collapse
|
3
|
Wang MM, Huang YY, Liu WB, Xiao K, Wang X, Guo HX, Zhang YL, Fan JW, Li XF, Jiang GZ. Interactive effects of dietary leucine and isoleucine affect amino acid profile and metabolism through AKT/TOR signaling pathways in blunt snout bream (Megalobrama amblycephala). FISH PHYSIOLOGY AND BIOCHEMISTRY 2024; 50:385-401. [PMID: 36525145 DOI: 10.1007/s10695-022-01161-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
The purpose of this research is to explore the interaction between dietary leucine and isoleucine levels on whole-body composition, plasma and liver biochemical indexes, amino acids deposition in the liver, and amino acid metabolism of blunt snout bream (Megalobrama amblycephala). The test fish (average weight: 56.00 ± 0.55 g) were fed one of six diets at random containing two leucine levels (1.70% and 2.50%) and three isoleucine levels (1.00%, 1.20%, and 1.40%) for 8 weeks. The results showed that the final weight and weight gain rate were the highest in the fish fed low-level leucine and high-level isoleucine diets (P > 0.05). Furthermore, the crude lipid content was significantly adjusted by diets with diverse levels of leucine and isoleucine (P < 0.05). In addition, interactive effects of these two branched-chain amino acids (BCAAs) were found on plasma total protein, blood ammonia, and blood urea nitrogen of test fish (P < 0.05). Additionally, the liver amino acid profiles were significantly influenced by the interactive effects of the two BCAAs (P < 0.05). Moreover, interactive effects of dietary leucine and isoleucine were significantly observed in the expressions of amino acid metabolism-related genes (P < 0.05). These findings suggested that dietary leucine and isoleucine had interaction. Meanwhile, the interaction between them was more conducive to the growth and quality improvement of blunt snout bream when the dietary leucine level was 1.70% and isoleucine level was 1.40%.
Collapse
Affiliation(s)
- Mang-Mang Wang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Yang-Yang Huang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Wen-Bin Liu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Kang Xiao
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Xi Wang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Hui-Xing Guo
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Yi-Lin Zhang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Jing-Wei Fan
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Xiang-Fei Li
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Guang-Zhen Jiang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China.
| |
Collapse
|
4
|
Szabo E, Nagy B, Czajlik A, Komlodi T, Ozohanics O, Tretter L, Ambrus A. Mitochondrial Alpha-Keto Acid Dehydrogenase Complexes: Recent Developments on Structure and Function in Health and Disease. Subcell Biochem 2024; 104:295-381. [PMID: 38963492 DOI: 10.1007/978-3-031-58843-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The present work delves into the enigmatic world of mitochondrial alpha-keto acid dehydrogenase complexes discussing their metabolic significance, enzymatic operation, moonlighting activities, and pathological relevance with links to underlying structural features. This ubiquitous family of related but diverse multienzyme complexes is involved in carbohydrate metabolism (pyruvate dehydrogenase complex), the citric acid cycle (α-ketoglutarate dehydrogenase complex), and amino acid catabolism (branched-chain α-keto acid dehydrogenase complex, α-ketoadipate dehydrogenase complex); the complexes all function at strategic points and also participate in regulation in these metabolic pathways. These systems are among the largest multienzyme complexes with at times more than 100 protein chains and weights ranging up to ~10 million Daltons. Our chapter offers a wealth of up-to-date information on these multienzyme complexes for a comprehensive understanding of their significance in health and disease.
Collapse
Affiliation(s)
- Eszter Szabo
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Balint Nagy
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Andras Czajlik
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Timea Komlodi
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Oliver Ozohanics
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Laszlo Tretter
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Attila Ambrus
- Department of Biochemistry, Semmelweis University, Budapest, Hungary.
| |
Collapse
|
5
|
Palmieri EM, Holewinski R, McGinity CL, Pierri CL, Maio N, Weiss JM, Tragni V, Miranda KM, Rouault TA, Andresson T, Wink DA, McVicar DW. Pyruvate dehydrogenase operates as an intramolecular nitroxyl generator during macrophage metabolic reprogramming. Nat Commun 2023; 14:5114. [PMID: 37607904 PMCID: PMC10444860 DOI: 10.1038/s41467-023-40738-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 08/04/2023] [Indexed: 08/24/2023] Open
Abstract
M1 macrophages enter a glycolytic state when endogenous nitric oxide (NO) reprograms mitochondrial metabolism by limiting aconitase 2 and pyruvate dehydrogenase (PDH) activity. Here, we provide evidence that NO targets the PDH complex by using lipoate to generate nitroxyl (HNO). PDH E2-associated lipoate is modified in NO-rich macrophages while the PDH E3 enzyme, also known as dihydrolipoamide dehydrogenase (DLD), is irreversibly inhibited. Mechanistically, we show that lipoate facilitates NO-mediated production of HNO, which interacts with thiols forming irreversible modifications including sulfinamide. In addition, we reveal a macrophage signature of proteins with reduction-resistant modifications, including in DLD, and identify potential HNO targets. Consistently, DLD enzyme is modified in an HNO-dependent manner at Cys477 and Cys484, and molecular modeling and mutagenesis show these modifications impair the formation of DLD homodimers. In conclusion, our work demonstrates that HNO is produced physiologically. Moreover, the production of HNO is dependent on the lipoate-rich PDH complex facilitating irreversible modifications that are critical to NO-dependent metabolic rewiring.
Collapse
Affiliation(s)
- Erika M Palmieri
- Cancer Innovation Laboratory, NCI-Frederick, Frederick, MD, 21702, USA
| | - Ronald Holewinski
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | | | - Ciro L Pierri
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Pharmacy-Pharmaceutical Sciences, University of Bari, Via E. Orabona, 4, Bari, 70125, Italy
| | - Nunziata Maio
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Jonathan M Weiss
- Cancer Innovation Laboratory, NCI-Frederick, Frederick, MD, 21702, USA
| | - Vincenzo Tragni
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Pharmacy-Pharmaceutical Sciences, University of Bari, Via E. Orabona, 4, Bari, 70125, Italy
| | - Katrina M Miranda
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Tracey A Rouault
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - David A Wink
- Cancer Innovation Laboratory, NCI-Frederick, Frederick, MD, 21702, USA
| | - Daniel W McVicar
- Cancer Innovation Laboratory, NCI-Frederick, Frederick, MD, 21702, USA.
| |
Collapse
|
6
|
Salinas ND, Ma R, Dickey TH, McAleese H, Ouahes T, Long CA, Miura K, Lambert LE, Tolia NH. A potent and durable malaria transmission-blocking vaccine designed from a single-component 60-copy Pfs230D1 nanoparticle. NPJ Vaccines 2023; 8:124. [PMID: 37596283 PMCID: PMC10439124 DOI: 10.1038/s41541-023-00709-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/12/2023] [Indexed: 08/20/2023] Open
Abstract
Malaria transmission-blocking vaccines (TBVs) reduce disease transmission by breaking the continuous cycle of infection between the human host and the mosquito vector. Domain 1 (D1) of Pfs230 is a leading TBV candidate and comprises the majority of transmission-reducing activity (TRA) elicited by Pfs230. Here we show that the fusion of Pfs230D1 to a 60-copy multimer of the catalytic domain of dihydrolipoyl acetyltransferase protein (E2p) results in a single-component nanoparticle composed of 60 copies of the fusion protein with high stability, homogeneity, and production yields. The nanoparticle presents a potent human transmission-blocking epitope within Pfs230D1, indicating the antigen is correctly oriented on the surface of the nanoparticle. Two vaccinations of New Zealand White rabbits with the Pfs230D1 nanoparticle elicited a potent and durable antibody response with high TRA when formulated in two distinct adjuvants suitable for translation to human use. This single-component nanoparticle vaccine may play a key role in malaria control and has the potential to improve production pipelines and the cost of manufacturing of a potent and durable TBV.
Collapse
Affiliation(s)
- Nichole D Salinas
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rui Ma
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Thayne H Dickey
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Holly McAleese
- Vaccine Development Unit, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tarik Ouahes
- Vaccine Development Unit, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Carole A Long
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Kazutoyo Miura
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Lynn E Lambert
- Vaccine Development Unit, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Niraj H Tolia
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
7
|
Roosterman D, Cottrell GS. Discovery of a second citric acid cycle complex. Heliyon 2023; 9:e15968. [PMID: 37251852 PMCID: PMC10209337 DOI: 10.1016/j.heliyon.2023.e15968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/31/2023] Open
Abstract
Together, Nobel Prize honoured work, mathematics, physics and the laws of nature have drawn a concept of clockwise cycling carboxylic acids in Krebs' Citric Acid Cycle. A Citric Acid Cycle complex is defined by specific substrate, product and regulation. Recently, the Citric Acid Cycle 1.1 complex was introduced as an NAD+-regulated cycle with the substrate, lactic acid and the product, malic acid. Here, we introduce the concept of the Citric Acid Cycle 2.1 complex as an FAD-regulated cycle with the substrate, malic acid and the products, succinic acid or citric acid. The function of the Citric Acid Cycle 2.1 complex is to balance stress situations within the cell. We propose that the biological function of Citric Acid Cycle 2.1 in muscles is to accelerate recovery of ATP; whereas in white tissue adipocytes our testing of the theoretical concept led to the storage of energy as lipids.
Collapse
|
8
|
A Missense Variant in PDK1 Associated with Severe Neurodevelopmental Delay and Epilepsy. Biomedicines 2022; 10:biomedicines10123171. [PMID: 36551928 PMCID: PMC9775741 DOI: 10.3390/biomedicines10123171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 12/13/2022] Open
Abstract
The pyruvate dehydrogenase complex (PDC) is responsible for the conversion of pyruvate into acetyl-CoA, which is used for energy conversion in cells. PDC activity is regulated by phosphorylation via kinases and phosphatases (PDK/PDP). Variants in all subunits of the PDC and in PDK3 have been reported, with varying phenotypes including lactic acidosis, neurodevelopmental delay, peripheral neuropathy, or seizures. Here, we report a de novo heterozygous missense variant in PDK1 (c.1139G > A; p.G380D) in a girl with developmental delay and early onset severe epilepsy. To investigate the role of PDK1G380D in energy metabolism and neuronal development, we used a zebrafish model. In zebrafish embryos we show a reduced number of cells with mitochondria with membrane potential, reduced movements, and a delay in neuronal development. Furthermore, we observe a reduction in the phosphorylation of PDH-E1α by PDKG380D, which suggests a disruption in the regulation of PDC activity. Finally, in patient fibroblasts, a mild reduction in the ratio of phosphorylated PDH over total PDH-E1α was detected. In summary, our findings support the notion that this aberrant PDK1 activity is the cause of clinical symptoms in the patient.
Collapse
|
9
|
How evolution dismantles and reassembles multienzyme complexes. Proc Natl Acad Sci U S A 2022; 119:2120286118. [PMID: 34996854 PMCID: PMC8740704 DOI: 10.1073/pnas.2120286118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
10
|
Škerlová J, Berndtsson J, Nolte H, Ott M, Stenmark P. Structure of the native pyruvate dehydrogenase complex reveals the mechanism of substrate insertion. Nat Commun 2021; 12:5277. [PMID: 34489474 PMCID: PMC8421416 DOI: 10.1038/s41467-021-25570-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/13/2021] [Indexed: 02/07/2023] Open
Abstract
The pyruvate dehydrogenase complex (PDHc) links glycolysis to the citric acid cycle by converting pyruvate into acetyl-coenzyme A. PDHc encompasses three enzymatically active subunits, namely pyruvate dehydrogenase, dihydrolipoyl transacetylase, and dihydrolipoyl dehydrogenase. Dihydrolipoyl transacetylase is a multidomain protein comprising a varying number of lipoyl domains, a peripheral subunit-binding domain, and a catalytic domain. It forms the structural core of the complex, provides binding sites for the other enzymes, and shuffles reaction intermediates between the active sites through covalently bound lipoyl domains. The molecular mechanism by which this shuttling occurs has remained elusive. Here, we report a cryo-EM reconstruction of the native E. coli dihydrolipoyl transacetylase core in a resting state. This structure provides molecular details of the assembly of the core and reveals how the lipoyl domains interact with the core at the active site.
Collapse
Affiliation(s)
- Jana Škerlová
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jens Berndtsson
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Hendrik Nolte
- grid.419502.b0000 0004 0373 6590Max-Planck-Institute for Biology of Ageing, Cologne, Germany
| | - Martin Ott
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden ,grid.8761.80000 0000 9919 9582Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Pål Stenmark
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden ,grid.4514.40000 0001 0930 2361Department of Experimental Medical Science, Lund University, Lund, Sweden
| |
Collapse
|
11
|
Xiong L, Pei J, Wu X, Kalwar Q, Yan P, Guo X. Effect of Gender to Fat Deposition in Yaks Based on Transcriptomic and Metabolomics Analysis. Front Cell Dev Biol 2021; 9:653188. [PMID: 34504837 PMCID: PMC8421605 DOI: 10.3389/fcell.2021.653188] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 07/22/2021] [Indexed: 12/14/2022] Open
Abstract
Fat deposition in yaks plays an important part in survival, multiplication, and meat quality. In this work, the characteristic of fat deposition in male yaks (MYs) and female yaks (FYs) and the regulations of gender to yak fat deposition were explored by mRNA-Seq and non-targeted metabolomics analyses. FYs possessed a higher body fat rate (BFR) of visceral fat, fat content in longissimus dorsi (LD) and liver, and subcutaneous fat thickness (p < 0.05). The fat and cholesterol synthesis in liver and the fat transport in FY blood increased. The fat metabolism in yaks is the combined effect of carbohydrate, fatty acid, and amino acid metabolism by tricarboxylic acid (TCA) cycle, and an increase of triglyceride (TG) synthesis was accompanied by an increase of steroid synthesis. The high levels of myo-inositol and cortisol (COR) (p < 0.01) activated the calcium signaling in FY subcutaneous fat, followed by the increase of adipocyte secretion, and resulted in more leptin (LEP) secretion (p < 0.01). Then peroxisome proliferator-activated receptor (PPAR) signaling was activated by the focal adhesions and ECM-receptor interaction. Finally, the TG and steroid synthesis increased by the expression regulation of ME1, SCD, ELOVL6, DGAT2, DBI, LPL, CPT1, PLIN1, LIPA, DHCR24, and SQLE gene. The above genes can be considered as the candidate genes for yak with higher fat amount in molecular breeding in the future. This study can provide a theoretical basis for improving the meat quality and breeding of yaks.
Collapse
Affiliation(s)
- Lin Xiong
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Jie Pei
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Xiaoyun Wu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Qudratullah Kalwar
- Department of Animal Reproduction, Shaheed Benazir Bhutto University of Veterinary and Animal Sciences, Sakrand, Pakistan
| | - Ping Yan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Xian Guo
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| |
Collapse
|
12
|
Leandro J, Dodatko T, Aten J, Nemeria NS, Zhang X, Jordan F, Hendrickson RC, Sanchez R, Yu C, DeVita RJ, Houten SM. DHTKD1 and OGDH display substrate overlap in cultured cells and form a hybrid 2-oxo acid dehydrogenase complex in vivo. Hum Mol Genet 2021; 29:1168-1179. [PMID: 32160276 DOI: 10.1093/hmg/ddaa037] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/27/2020] [Accepted: 03/04/2020] [Indexed: 11/14/2022] Open
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.
Collapse
Affiliation(s)
- João Leandro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tetyana Dodatko
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jan Aten
- Department of Pathology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, 1105 AZ The Netherlands
| | - Natalia S Nemeria
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA
| | - Xu Zhang
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA
| | - Frank Jordan
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA
| | - Ronald C Hendrickson
- Microchemistry and Proteomics Core, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Roberto Sanchez
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chunli Yu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Mount Sinai Genomics, Inc., Stamford, CT 06902, USA
| | - Robert J DeVita
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sander M Houten
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| |
Collapse
|
13
|
Nemeria NS, Zhang X, Leandro J, Zhou J, Yang L, Houten SM, Jordan F. Toward an Understanding of the Structural and Mechanistic Aspects of Protein-Protein Interactions in 2-Oxoacid Dehydrogenase Complexes. Life (Basel) 2021; 11:407. [PMID: 33946784 PMCID: PMC8146983 DOI: 10.3390/life11050407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/24/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Natalia S. Nemeria
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA; (J.Z.); (L.Y.)
| | - Xu Zhang
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA; (J.Z.); (L.Y.)
| | - Joao Leandro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (J.L.); (S.M.H.)
| | - Jieyu Zhou
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA; (J.Z.); (L.Y.)
| | - Luying Yang
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA; (J.Z.); (L.Y.)
| | - Sander M. Houten
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (J.L.); (S.M.H.)
| | - Frank Jordan
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ 07102, USA; (J.Z.); (L.Y.)
| |
Collapse
|
14
|
Nagy B, Polak M, Ozohanics O, Zambo Z, Szabo E, Hubert A, Jordan F, Novaček J, Adam-Vizi V, Ambrus A. Structure of the dihydrolipoamide succinyltransferase (E2) component of the human alpha-ketoglutarate dehydrogenase complex (hKGDHc) revealed by cryo-EM and cross-linking mass spectrometry: Implications for the overall hKGDHc structure. Biochim Biophys Acta Gen Subj 2021; 1865:129889. [PMID: 33684457 DOI: 10.1016/j.bbagen.2021.129889] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/05/2021] [Accepted: 03/02/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND The human mitochondrial alpha-ketoglutarate dehydrogenase complex (hKGDHc) converts KG to succinyl-CoA and NADH. Malfunction of and reactive oxygen species generation by the hKGDHc as well as its E1-E2 subcomplex are implicated in neurodegenerative disorders, ischemia-reperfusion injury, E3-deficiency and cancers. METHODS We performed cryo-EM, cross-linking mass spectrometry (CL-MS) and molecular modeling analyses to determine the structure of the E2 component of the hKGDHc (hE2k); hE2k transfers a succinyl group to CoA and forms the structural core of hKGDHc. We also assessed the overall structure of the hKGDHc by negative-stain EM and modeling. RESULTS We report the 2.9 Å resolution cryo-EM structure of the hE2k component. The cryo-EM map comprises density for hE2k residues 151-386 - the entire (inner) core catalytic domain plus a few additional residues -, while residues 1-150 are not observed due to the inherent flexibility of the N-terminal region. The structure of the latter segment was also determined by CL-MS and homology modeling. Negative-stain EM on in vitro assembled hKGDHc and previous data were used to build a putative overall structural model of the hKGDHc. CONCLUSIONS The E2 core of the hKGDHc is composed of 24 hE2k chains organized in octahedral (8 × 3 type) assembly. Each lipoyl domain is oriented towards the core domain of an adjacent chain in the hE2k homotrimer. hE1k and hE3 are most likely tethered at the edges and faces, respectively, of the cubic hE2k assembly. GENERAL SIGNIFICANCE The revealed structural information will support the future pharmacologically targeting of the hKGDHc.
Collapse
Affiliation(s)
- Balint Nagy
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Martin Polak
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Oliver Ozohanics
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Zsofia Zambo
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Eszter Szabo
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Agnes Hubert
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Frank Jordan
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Jiří Novaček
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Vera Adam-Vizi
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Attila Ambrus
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary.
| |
Collapse
|
15
|
Jin J, Chen H, Wang N, Zhu K, Liu H, Shi D, Xin J, Liu H. A Novel Lipoate-Protein Ligase, Mhp-LplJ, Is Required for Lipoic Acid Metabolism in Mycoplasma hyopneumoniae. Front Microbiol 2021; 11:631433. [PMID: 33584596 PMCID: PMC7873978 DOI: 10.3389/fmicb.2020.631433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 12/30/2020] [Indexed: 11/21/2022] Open
Abstract
Lipoic acid is a conserved cofactor necessary for the activation of several critical enzyme complexes in the aerobic metabolism of 2-oxoacids and one-carbon metabolism. Lipoate metabolism enzymes are key for lipoic acid biosynthesis and salvage. In this study, we found that Mycoplasma hyopneumoniae (M. hyopneumoniae) Mhp-Lpl, which had been previously shown to have lipoate-protein ligase activity against glycine cleavage system H protein (GcvH) in vitro, did not lipoylate the lipoate-dependent subunit of dihydrolipoamide dehydrogenase (PdhD). Further studies indicated that a new putative lipoate-protein ligase in M. hyopneumoniae, MHP_RS00640 (Mhp-LplJ), catalyzes free lipoic acid attachment to PdhD in vitro. In a model organism, Mhp-LplJ exhibited lipoate and octanoate ligase activities against PdhD. When the enzyme activity of Mhp-LplJ was disrupted by lipoic acid analogs, 8-bromooctanoic acid (8-BrO) and 6,8-dichlorooctanoate (6,8-diClO), M. hyopneumoniae growth was arrested in vitro. Taken together, these results indicate that Mhp-LplJ plays a vital role in lipoic acid metabolism of M. hyopneumoniae, which is of great significance to further understand the metabolism of M. hyopneumoniae and develop new antimicrobials against it.
Collapse
Affiliation(s)
- Jin Jin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.,Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Huan Chen
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment and SUSTech-HKU Joint Laboratories for Matrix Biology and Diseases, Southern University of Science and Technology, Shenzhen, China
| | - Ning Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Kemeng Zhu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Huanhuan Liu
- College of Life Science, Yangtze University, Kingchow, China
| | - Dongfang Shi
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Jiuqing Xin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Henggui Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| |
Collapse
|
16
|
Roosterman D, Cottrell GS. Rethinking the Citric Acid Cycle: Connecting Pyruvate Carboxylase and Citrate Synthase to the Flow of Energy and Material. Int J Mol Sci 2021; 22:ijms22020604. [PMID: 33435350 PMCID: PMC7827294 DOI: 10.3390/ijms22020604] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 12/22/2022] Open
Abstract
In 1937, Sir H. A Krebs first published the Citric Acid Cycle, a unidirectional cycle with carboxylic acids. The original concept of the Citric Acid Cycle from Krebs’ 1953 Nobel Prize lecture illustrates the unidirectional degradation of lactic acid to water, carbon dioxide and hydrogen. Here, we add the heart lactate dehydrogenase•proton-linked monocarboxylate transporter 1 complex, connecting the original Citric Acid Cycle to the flow of energy and material. The heart lactate dehydrogenase•proton-linked monocarboxylate transporter 1 complex catalyses the first reaction of the Citric Acid Cycle, the oxidation of lactate to pyruvate, and thus secures the provision of pyruvic acid. In addition, we modify Krebs’ original concept by feeding the cycle with oxaloacetic acid. Our concept enables the integration of anabolic processes and allows adaption of the organism to recover ATP faster.
Collapse
|
17
|
Roosterman D, Cottrell GS. The two-cell model of glucose metabolism: a hypothesis of schizophrenia. Mol Psychiatry 2021; 26:1738-1747. [PMID: 33402704 PMCID: PMC8440173 DOI: 10.1038/s41380-020-00980-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 11/16/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023]
Abstract
Schizophrenia is a chronic and severe mental disorder that affects over 20 million people worldwide. Common symptoms include distortions in thinking, perception, emotions, language, and self awareness. Different hypotheses have been proposed to explain the development of schizophrenia, however, there are no unifying features between the proposed hypotheses. Schizophrenic patients have perturbed levels of glucose in their cerebrospinal fluid, indicating a disturbance in glucose metabolism. We have explored the possibility that disturbances in glucose metabolism can be a general mechanism for predisposition and manifestation of the disease. We discuss glucose metabolism as a network of signaling pathways. Glucose and glucose metabolites can have diverse actions as signaling molecules, such as regulation of transcription factors, hormone and cytokine secretion and activation of neuronal cells, such as microglia. The presented model challenges well-established concepts in enzyme kinetics and glucose metabolism. We have developed a 'two-cell' model of glucose metabolism, which can explain the effects of electroconvulsive therapy and the beneficial and side effects of olanzapine treatment. Arrangement of glycolytic enzymes into metabolic signaling complexes within the 'two hit' hypothesis, allows schizophrenia to be formulated in two steps. The 'first hit' is the dysregulation of the glucose signaling pathway. This dysregulation of glucose metabolism primes the central nervous system for a pathological response to a 'second hit' via the astrocytic glycogenolysis signaling pathway.
Collapse
Affiliation(s)
- Dirk Roosterman
- Ruhr Universität Bochum, LWL-Hospital of Psychiatry, Bochum, Germany.
| | - Graeme Stuart Cottrell
- grid.9435.b0000 0004 0457 9566School of Pharmacy, University of Reading, Reading, RG6 6AP UK
| |
Collapse
|
18
|
Bezerra GA, Foster WR, Bailey HJ, Hicks KG, Sauer SW, Dimitrov B, McCorvie TJ, Okun JG, Rutter J, Kölker S, Yue WW. Crystal structure and interaction studies of human DHTKD1 provide insight into a mitochondrial megacomplex in lysine catabolism. IUCRJ 2020; 7:693-706. [PMID: 32695416 PMCID: PMC7340257 DOI: 10.1107/s205225252000696x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/22/2020] [Indexed: 05/05/2023]
Abstract
DHTKD1 is a lesser-studied E1 enzyme among the family of 2-oxoacid de-hydrogenases. In complex with E2 (di-hydro-lipo-amide succinyltransferase, DLST) and E3 (dihydrolipo-amide de-hydrogenase, DLD) components, DHTKD1 is involved in lysine and tryptophan catabolism by catalysing the oxidative de-carboxyl-ation of 2-oxoadipate (2OA) in mitochondria. Here, the 1.9 Å resolution crystal structure of human DHTKD1 is solved in complex with the thi-amine diphosphate co-factor. The structure reveals how the DHTKD1 active site is modelled upon the well characterized homologue 2-oxoglutarate (2OG) de-hydrogenase but engineered specifically to accommodate its preference for the longer substrate of 2OA over 2OG. A 4.7 Å resolution reconstruction of the human DLST catalytic core is also generated by single-particle electron microscopy, revealing a 24-mer cubic scaffold for assembling DHTKD1 and DLD protomers into a megacomplex. It is further demonstrated that missense DHTKD1 variants causing the inborn error of 2-amino-adipic and 2-oxoadipic aciduria impact on the complex formation, either directly by disrupting the interaction with DLST, or indirectly through destabilizing the DHTKD1 protein. This study provides the starting framework for developing DHTKD1 modulators to probe the intricate mitochondrial energy metabolism.
Collapse
Affiliation(s)
- Gustavo A. Bezerra
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - William R. Foster
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Henry J. Bailey
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Kevin G. Hicks
- Department of Biochemistry, University of Utah School of Medicine, USA
| | - Sven W. Sauer
- Division of Child Neurology and Metabolic Medicine, Centre for Pediatrics and Adolescent Medicine, Clinic I, University Hospital Heidelberg, Germany
| | - Bianca Dimitrov
- Division of Child Neurology and Metabolic Medicine, Centre for Pediatrics and Adolescent Medicine, Clinic I, University Hospital Heidelberg, Germany
| | - Thomas J. McCorvie
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Jürgen G. Okun
- Division of Child Neurology and Metabolic Medicine, Centre for Pediatrics and Adolescent Medicine, Clinic I, University Hospital Heidelberg, Germany
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, USA
| | - Stefan Kölker
- Division of Child Neurology and Metabolic Medicine, Centre for Pediatrics and Adolescent Medicine, Clinic I, University Hospital Heidelberg, Germany
| | - Wyatt W. Yue
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| |
Collapse
|
19
|
Zhu K, Chen H, Jin J, Wang N, Ma G, Huang J, Feng Y, Xin J, Zhang H, Liu H. Functional Identification and Structural Analysis of a New Lipoate Protein Ligase in Mycoplasma hyopneumoniae. Front Cell Infect Microbiol 2020; 10:156. [PMID: 32373550 PMCID: PMC7186572 DOI: 10.3389/fcimb.2020.00156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/24/2020] [Indexed: 11/13/2022] Open
Abstract
Mycoplasma hyopneumoniae (M. hyopneumoniae) is the causative agent of pandemic pneumonia among pigs, namely, swine enzootic pneumonia. Although M. hyopneumoniae was first identified in 1965, little is known regarding its metabolic pathways, which might play a pivotal role during disease pathogenesis. Lipoate is an essential cofactor for enzymes important for central metabolism. However, the lipoate metabolism pathway in M. hyopneumoniae is definitely unclear. Here, we identified a novel gene, lpl, encoding a lipoate protein ligase in the genome of M. hyopneumoniae (Mhp-Lpl). This gene contains 1,032 base pairs and encodes a protein of 343 amino acids, which is between 7.5 and 36.09% identical to lipoate protein ligases (Lpls) of other species. Similar to its homologs in other species, Mhp-Lpl catalyzes the ATP-dependent activation of lipoate to lipoyl-AMP and the transfer of the activated lipoyl onto the lipoyl domains of M. hyopneumoniae GcvH (Mhp H) in vitro. Enzymatic and mutagenesis analysis indicate that residue K56 within the SKT sequence of Mhp H protein is the lipoyl moiety acceptor site. The three-dimensional structure showed typical lipoate protein ligase folding, with a large N-terminal domain and a small C-terminal domain. The large N-terminal domain is responsible for the full enzymatic activity of Mhp-Lpl. The identification and characterization of Mhp-Lpl will be beneficial to our understanding of M. hyopneumoniae metabolism. Summary Lipoic acid is an essential cofactor for the activation of some enzyme complexes involved in key metabolic processes. Lipoate protein ligases (Lpls) are responsible for the metabolism of lipoic acid. To date, little is known regarding the Lpls in M. hyopneumoniae. In this study, we identified a lipoate protein ligase of M. hyopneumoniae. We further analyzed the function, overall structure and ligand-binding site of this protein. The lipoate acceptor site on M. hyopneumoniae GcvH was also identified. Together, these findings reveal that Lpl exists in M. hyopneumoniae and will provide a basis for further exploration of the pathway of lipoic acid metabolism in M. hyopneumoniae.
Collapse
Affiliation(s)
- Kemeng Zhu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
| | - Huan Chen
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment and SUSTech-HKU Joint Laboratories for Matrix Biology and Diseases, Southern University of Science and Technology, Shenzhen, China.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jin Jin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ning Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
| | - Guixing Ma
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment and SUSTech-HKU Joint Laboratories for Matrix Biology and Diseases, Southern University of Science and Technology, Shenzhen, China
| | - Jiandong Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Youjun Feng
- Department of Pathogen Biology and Microbiology, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiuqing Xin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hongmin Zhang
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment and SUSTech-HKU Joint Laboratories for Matrix Biology and Diseases, Southern University of Science and Technology, Shenzhen, China
| | - Henggui Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
| |
Collapse
|
20
|
Dynamic Relay of Protein-Bound Lipoic Acid in Staphylococcus aureus. J Bacteriol 2019; 201:JB.00446-19. [PMID: 31451544 DOI: 10.1128/jb.00446-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/21/2019] [Indexed: 12/19/2022] Open
Abstract
Staphylococcus aureus competes for myriad essential nutrients during host infection. One of these nutrients is the organosulfur compound lipoic acid, a cofactor required for the activity of several metabolic enzyme complexes. In S. aureus, these include the E2 subunits of three α-ketoacid dehydrogenases and two H proteins, GcvH of the glycine cleavage system and its paralog, GcvH-L. We previously determined that the S. aureus amidotransferase LipL is required for lipoylation of the E2 subunits of pyruvate dehydrogenase (PDH) and branched-chain 2-oxoacid dehydrogenase (BCODH) complexes. The results from this study, coupled with those from Bacillus subtilis, suggested that LipL catalyzes lipoyl transfer from H proteins to E2 subunits. However, to date, the range of LipL targets, the extent of LipL-dependent lipoic acid shuttling between lipoyl domain-containing proteins, and the importance of lipoyl relay in pathogenesis remain unknown. Here, we demonstrate that LipL uses both lipoyl-H proteins as the substrates for lipoyl transfer to all E2 subunits. Moreover, LipL facilitates lipoyl relay between E2 subunits and between H proteins, a property that potentially constitutes an adaptive response to nutrient scarcity in the host, as LipL is required for virulence during infection. Together, these observations support a role for LipL in facilitating flexible lipoyl relay between proteins and highlight the complexity of protein lipoylation in S. aureus IMPORTANCE Protein lipoylation is a posttranslational modification that is evolutionarily conserved from bacteria to humans. Lipoic acid modifications are found on five proteins in S. aureus, four of which are components of major metabolic enzymes. In some bacteria, the amidotransferase LipL is critical for the attachment of lipoic acid to these proteins, and yet it is unclear to what extent LipL facilitates the transfer of this cofactor. We find that S. aureus LipL flexibly shuttles lipoic acid among metabolic enzyme subunits, alluding to a dynamic redistribution mechanism within the bacterial cell. This discovery exemplifies a potential means by which bacteria optimize the use of scarce nutrients when resources are limited.
Collapse
|
21
|
Andi B, Soares AS, Shi W, Fuchs MR, McSweeney S, Liu Q. Structure of the dihydrolipoamide succinyltransferase catalytic domain from Escherichia coli in a novel crystal form: a tale of a common protein crystallization contaminant. Acta Crystallogr F Struct Biol Commun 2019; 75:616-624. [PMID: 31475929 PMCID: PMC6718150 DOI: 10.1107/s2053230x19011488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/15/2019] [Indexed: 12/12/2022] Open
Abstract
The crystallization of amidase, the ultimate enzyme in the Trp-dependent auxin-biosynthesis pathway, from Arabidopsis thaliana was attempted using protein samples with at least 95% purity. Cube-shaped crystals that were assumed to be amidase crystals that belonged to space group I4 (unit-cell parameters a = b = 128.6, c = 249.7 Å) were obtained and diffracted to 3.0 Å resolution. Molecular replacement using structures from the PDB containing the amidase signature fold as search models was unsuccessful in yielding a convincing solution. Using the Sequence-Independent Molecular replacement Based on Available Databases (SIMBAD) program, it was discovered that the structure corresponded to dihydrolipoamide succinyltransferase from Escherichia coli (PDB entry 1c4t), which is considered to be a common crystallization contaminant protein. The structure was refined to an Rwork of 23.0% and an Rfree of 27.2% at 3.0 Å resolution. The structure was compared with others of the same protein deposited in the PDB. This is the first report of the structure of dihydrolipoamide succinyltransferase isolated without an expression tag and in this novel crystal form.
Collapse
Affiliation(s)
- Babak Andi
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Alexei S. Soares
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Wuxian Shi
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Martin R. Fuchs
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Sean McSweeney
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Qun Liu
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| |
Collapse
|
22
|
Prajapati S, Haselbach D, Wittig S, Patel MS, Chari A, Schmidt C, Stark H, Tittmann K. Structural and Functional Analyses of the Human PDH Complex Suggest a "Division-of-Labor" Mechanism by Local E1 and E3 Clusters. Structure 2019; 27:1124-1136.e4. [PMID: 31130485 DOI: 10.1016/j.str.2019.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 01/17/2019] [Accepted: 04/11/2019] [Indexed: 11/27/2022]
Abstract
The pseudo-atomic structural model of human pyruvate dehydrogenase complex (PDHc) core composed of full-length E2 and E3BP components, calculated from our cryoelectron microscopy-derived density maps at 6-Å resolution, is similar to those of prokaryotic E2 structures. The spatial organization of human PDHc components as evidenced by negative-staining electron microscopy and native mass spectrometry is not homogeneous, and entails the unanticipated formation of local clusters of E1:E2 and E3BP:E3 complexes. Such uneven, clustered organization translates into specific duties for E1-E2 clusters (oxidative decarboxylation and acetyl transfer) and E3BP-E3 clusters (regeneration of reduced lipoamide) corresponding to half-reactions of the PDHc catalytic cycle. The addition of substrate coenzyme A modulates the conformational landscape of PDHc, in particular of the lipoyl domains, extending the postulated multiple random coupling mechanism. The conformational and associated chemical landscapes of PDHc are thus not determined entirely stochastically, but are restrained and channeled through an asymmetric architecture and further modulated by substrate binding.
Collapse
Affiliation(s)
- Sabin Prajapati
- Department of Molecular Enzymology, Göttingen Centre for Molecular Biosciences and Albrecht-von-Haller Institute, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany; Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Am Fassberg 11, 37077 Göttingen, Germany
| | - David Haselbach
- Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Am Fassberg 11, 37077 Göttingen, Germany
| | - Sabine Wittig
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, 06120 Halle/Saale, Germany
| | - Mulchand S Patel
- Jacobs School of Medicine and Biomedical Sciences, Department of Biochemistry, University at Buffalo, 955 Main Street, Buffalo, NY 14203, USA
| | - Ashwin Chari
- Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Am Fassberg 11, 37077 Göttingen, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, 06120 Halle/Saale, Germany.
| | - Holger Stark
- Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Kai Tittmann
- Department of Molecular Enzymology, Göttingen Centre for Molecular Biosciences and Albrecht-von-Haller Institute, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany; Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Am Fassberg 11, 37077 Göttingen, Germany.
| |
Collapse
|
23
|
Zdraljevic S, Fox BW, Strand C, Panda O, Tenjo FJ, Brady SC, Crombie TA, Doench JG, Schroeder FC, Andersen EC. Natural variation in C. elegans arsenic toxicity is explained by differences in branched chain amino acid metabolism. eLife 2019; 8:40260. [PMID: 30958264 PMCID: PMC6453569 DOI: 10.7554/elife.40260] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 03/26/2019] [Indexed: 12/29/2022] Open
Abstract
We find that variation in the dbt-1 gene underlies natural differences in Caenorhabditis elegans responses to the toxin arsenic. This gene encodes the E2 subunit of the branched-chain α-keto acid dehydrogenase (BCKDH) complex, a core component of branched-chain amino acid (BCAA) metabolism. We causally linked a non-synonymous variant in the conserved lipoyl domain of DBT-1 to differential arsenic responses. Using targeted metabolomics and chemical supplementation, we demonstrate that differences in responses to arsenic are caused by variation in iso-branched chain fatty acids. Additionally, we show that levels of branched chain fatty acids in human cells are perturbed by arsenic treatment. This finding has broad implications for arsenic toxicity and for arsenic-focused chemotherapeutics across human populations. Our study implicates the BCKDH complex and BCAA metabolism in arsenic responses, demonstrating the power of C. elegans natural genetic diversity to identify novel mechanisms by which environmental toxins affect organismal physiology. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
Collapse
Affiliation(s)
- Stefan Zdraljevic
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, United States.,Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Bennett William Fox
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | | | - Oishika Panda
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States.,The Buck Institute for Research on Aging, Novato, United States
| | - Francisco J Tenjo
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Shannon C Brady
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, United States.,Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Tim A Crombie
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, United States
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Erik C Andersen
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, United States.,Department of Molecular Biosciences, Northwestern University, Evanston, United States.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, United States
| |
Collapse
|
24
|
Ambrus A. An Updated View on the Molecular Pathomechanisms of Human Dihydrolipoamide Dehydrogenase Deficiency in Light of Novel Crystallographic Evidence. Neurochem Res 2019; 44:2307-2313. [PMID: 30847858 PMCID: PMC6776566 DOI: 10.1007/s11064-019-02766-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 12/22/2022]
Abstract
Dihydrolipoamide dehydrogenase (LADH, E3) deficiency is a rare (autosomal, recessive) genetic disorder generally presenting with an onset in the neonatal age and early death; the highest carrier rate has been found among Ashkenazi Jews. Acute clinical episodes usually involve severe metabolic decompensation and lactate acidosis that result in neurological, cardiological, and/or hepatological manifestations. Clinical severity is due to the fact that LADH is a common E3 subunit to the alpha-ketoglutarate, pyruvate, alpha-ketoadipate, and branched-chain alpha-keto acid dehydrogenase complexes, and is also a constituent in the glycine cleavage system, thus a loss in LADH function adversely affects multiple key metabolic routes. However, the severe clinical pictures frequently still do not parallel the LADH activity loss, which implies the involvement of auxiliary biochemical mechanisms; enhanced reactive oxygen species generation as well as affinity loss for multienzyme complexes proved to be key auxiliary exacerbating pathomechanisms. This review provides an overview and an up-to-date molecular insight into the pathomechanisms of this disease in light of the structural conclusions drawn from the first crystal structure of a disease-causing hE3 variant determined recently in our laboratory.
Collapse
Affiliation(s)
- Attila Ambrus
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, 37-47 Tuzolto Street, Budapest, 1094, Hungary.
| |
Collapse
|
25
|
Cao X, Koch T, Steffens L, Finkensieper J, Zigann R, Cronan JE, Dahl C. Lipoate-binding proteins and specific lipoate-protein ligases in microbial sulfur oxidation reveal an atpyical role for an old cofactor. eLife 2018; 7:e37439. [PMID: 30004385 PMCID: PMC6067878 DOI: 10.7554/elife.37439] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/12/2018] [Indexed: 01/02/2023] Open
Abstract
Many Bacteria and Archaea employ the heterodisulfide reductase (Hdr)-like sulfur oxidation pathway. The relevant genes are inevitably associated with genes encoding lipoate-binding proteins (LbpA). Here, deletion of the gene identified LbpA as an essential component of the Hdr-like sulfur-oxidizing system in the Alphaproteobacterium Hyphomicrobium denitrificans. Thus, a biological function was established for the universally conserved cofactor lipoate that is markedly different from its canonical roles in central metabolism. LbpAs likely function as sulfur-binding entities presenting substrate to different catalytic sites of the Hdr-like complex, similar to the substrate-channeling function of lipoate in carbon-metabolizing multienzyme complexes, for example pyruvate dehydrogenase. LbpAs serve a specific function in sulfur oxidation, cannot functionally replace the related GcvH protein in Bacillus subtilis and are not modified by the canonical E. coli and B. subtilis lipoyl attachment machineries. Instead, LplA-like lipoate-protein ligases encoded in or in immediate vicinity of hdr-lpbA gene clusters act specifically on these proteins.
Collapse
Affiliation(s)
- Xinyun Cao
- Department of BiochemistryUniversity of IllinoisUrbanaUnited States
| | - Tobias Koch
- Institut für Mikrobiologie and BiotechnologieRheinische Friedrich-Wilhelms-Universität BonnBonnGermany
| | - Lydia Steffens
- Institut für Mikrobiologie and BiotechnologieRheinische Friedrich-Wilhelms-Universität BonnBonnGermany
| | - Julia Finkensieper
- Institut für Mikrobiologie and BiotechnologieRheinische Friedrich-Wilhelms-Universität BonnBonnGermany
| | - Renate Zigann
- Institut für Mikrobiologie and BiotechnologieRheinische Friedrich-Wilhelms-Universität BonnBonnGermany
| | - John E Cronan
- Department of BiochemistryUniversity of IllinoisUrbanaUnited States
- Department of MicrobiologyUniversity of IllinoisUrbanaUnited States
| | - Christiane Dahl
- Institut für Mikrobiologie and BiotechnologieRheinische Friedrich-Wilhelms-Universität BonnBonnGermany
| |
Collapse
|
26
|
Roosterman D, Meyerhof W, Cottrell GS. Proton Transport Chains in Glucose Metabolism: Mind the Proton. Front Neurosci 2018; 12:404. [PMID: 29962930 PMCID: PMC6014028 DOI: 10.3389/fnins.2018.00404] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 05/25/2018] [Indexed: 01/11/2023] Open
Abstract
The Embden-Meyerhof-Parnas (EMP) pathway comprises eleven cytosolic enzymes interacting to metabolize glucose to lactic acid [CH3CH(OH)COOH]. Glycolysis is largely considered as the conversion of glucose to pyruvate (CH3COCOO-). We consider glycolysis to be a cellular process and as such, transporters mediating glucose uptake and lactic acid release and enable the flow of metabolites through the cell, must be considered as part of the EMP pathway. In this review, we consider the flow of metabolites to be coupled to a flow of energy that is irreversible and sufficient to form ordered structures. This latter principle is highlighted by discussing that lactate dehydrogenase (LDH) complexes irreversibly reduce pyruvate/H+ to lactate [CH3CH(OH)COO-], or irreversibly catalyze the opposite reaction, oxidation of lactate to pyruvate/H+. However, both LDH complexes are considered to be driven by postulated proton transport chains. Metabolism of glucose to two lactic acids is introduced as a unidirectional, continuously flowing pathway. In an organism, cell membrane-located proton-linked monocarboxylate transporters catalyze the final step of glycolysis, the release of lactic acid. Consequently, both pyruvate and lactate are discussed as intermediate products of glycolysis and substrates of regulated crosscuts of the glycolytic flow.
Collapse
Affiliation(s)
| | - Wolfgang Meyerhof
- Center for Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
| | | |
Collapse
|
27
|
Guo C, Li D, Liu C, Guo Z, Chen Y. Facile derivatization of ultratrace carboxylic acids in saliva for quantification by HPLC-MS/MS. Anal Bioanal Chem 2018; 410:4293-4300. [PMID: 29748756 DOI: 10.1007/s00216-018-1078-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/03/2018] [Accepted: 04/11/2018] [Indexed: 11/29/2022]
Abstract
It remains an issue to directly quantify trace biologically important carboxyl compounds in body fluids. Herein we propose an innovative method to determine α-lipoic acid, 2-(β-carboxyethyl)-6-hydroxy-2,7,8-trimethylchroman, prostaglandin E2, cholic acid, and chenodeoxycholic acid in saliva. The method consists of two successive steps: fast and direct labeling of the target analytes with N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide followed by ultrahigh-performance liquid chromatography-tandem mass spectrometry analysis. The method exhibited a wide linear range from 2.5 to 2500 pg/mL, with linear coefficients greater than 0.9963 and limits of detection and quantification as low as 0.10 and 0.33 pg/mL, respectively. The method precision was evaluated, with relative standard deviations ranging from 2.12% to 10.63% for intraday assays and from 2.98% to 12.88% for interday assays. The recoveries were measured by our spiking saliva samples with standards at three different levels, and ranged from 72.5% to 98.0%. Real applicability was validated by direct quantification of trace target analytes in human saliva, with simple pretreatment, use of a small sample volume, and a short analysis time. Graphical abstract Sequential steps to extract, label, and determine the ultratrace carboxylic acids in saliva. CDCA chenodeoxycholic acid, γ-CEHC 2-(β-carboxyethyl)-6-hydroxy-2,7,8-trimethylchroman, α-LA α-lipoic acid, PGE2 prostaglandin E2, UHPLC-MS/MS ultrahigh-performance liquid chromatography-tandem mass spectrometry.
Collapse
Affiliation(s)
- Chao Guo
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dongmei Li
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,School of Pharmacy, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Cuimei Liu
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenpeng Guo
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yi Chen
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Beijing National Laboratory for Molecular Sciences, Beijing, 100190, China.
| |
Collapse
|
28
|
Jiang J, Baiesc FL, Hiromasa Y, Yu X, Hui WH, Dai X, Roche TE, Zhou ZH. Atomic Structure of the E2 Inner Core of Human Pyruvate Dehydrogenase Complex. Biochemistry 2018; 57:2325-2334. [PMID: 29608861 DOI: 10.1021/acs.biochem.8b00357] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pyruvate dehydrogenase complex (PDC) is a large multienzyme complex that catalyzes the irreversible conversion of pyruvate to acetyl-coenzyme A with reduction of NAD+. Distinctive from PDCs in lower forms of life, in mammalian PDC, dihydrolipoyl acetyltransferase (E2; E2p in PDC) and dihydrolipoamide dehydrogenase binding protein (E3BP) combine to form a complex that plays a central role in the organization, regulation, and integration of catalytic reactions of PDC. However, the atomic structure and organization of the mammalian E2p/E3BP heterocomplex are unknown. Here, we report the structure of the recombinant dodecahedral core formed by the C-terminal inner-core/catalytic (IC) domain of human E2p determined at 3.1 Å resolution by cryo electron microscopy (cryoEM). The structure of the N-terminal fragment and four other surface areas of the human E2p IC domain exhibit significant differences from those of the other E2 crystal structures, which may have implications for the integration of E3BP in mammals. This structure also allowed us to obtain a homology model for the highly homologous IC domain of E3BP. Analysis of the interactions of human E2p or E3BP with their adjacent IC domains in the dodecahedron provides new insights into the organization of the E2p/E3BP heterocomplex and suggests a potential contribution by E3BP to catalysis in mammalian PDC.
Collapse
Affiliation(s)
- Jiansen Jiang
- Department of Microbiology, Immunology and Molecular Genetics , University of California, Los Angeles , Los Angeles , California 90095 , United States.,California Nanosystems Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Flavius L Baiesc
- Department of Microbiology, Immunology and Molecular Genetics , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Yasuaki Hiromasa
- Faculty of Agriculture, Attached Promotive Center for International Education and Research of Agriculture , Kyushu University , Fukuoka 812-8581 , Japan.,Department of Biochemistry and Molecular Biophysics , Kansas State University , Manhattan , Kansas 66506 , United States
| | - Xuekui Yu
- Department of Microbiology, Immunology and Molecular Genetics , University of California, Los Angeles , Los Angeles , California 90095 , United States.,California Nanosystems Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Wong Hoi Hui
- California Nanosystems Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Xinghong Dai
- Department of Microbiology, Immunology and Molecular Genetics , University of California, Los Angeles , Los Angeles , California 90095 , United States.,California Nanosystems Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Thomas E Roche
- Department of Biochemistry and Molecular Biophysics , Kansas State University , Manhattan , Kansas 66506 , United States
| | - Z Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics , University of California, Los Angeles , Los Angeles , California 90095 , United States.,California Nanosystems Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| |
Collapse
|
29
|
Dong G, Cao L, Ryde U. Insight into the reaction mechanism of lipoyl synthase: a QM/MM study. J Biol Inorg Chem 2018; 23:221-229. [PMID: 29204715 PMCID: PMC5816104 DOI: 10.1007/s00775-017-1522-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 11/28/2017] [Indexed: 11/26/2022]
Abstract
Lipoyl synthase (LipA) catalyses the final step of the biosynthesis of the lipoyl cofactor by insertion of two sulfur atoms at the C6 and C8 atoms of the protein-bound octanoyl substrate. In this reaction, two [4Fe4S] clusters and two molecules of S-adenosyl-L-methionine are used. One of the two FeS clusters is responsible for the generation of a powerful oxidant, the 5'-deoxyadenosyl radical (5'-dA•). The other (the auxiliary cluster) is the source of both sulfur atoms that are inserted into the substrate. In this paper, the spin state of the FeS clusters and the reaction mechanism is investigated by the combined quantum mechanical and molecular mechanics approach. The calculations show that the ground state of the two FeS clusters, both in the [4Fe4S]2+ oxidation state, is a singlet state with antiferromagnetically coupled high-spin Fe ions and that there is quite a large variation of the energies of the various broken-symmetry states, up to 40 kJ/mol. For the two S-insertion reactions, the highest energy barrier is found for the hydrogen-atom abstraction from the octanoyl substrate by 5'-dA•. The formation of 5'-dA• is very facile for LipA, with an energy barrier of 6 kJ/mol for the first S-insertion reaction and without any barrier for the second S-insertion reaction. In addition, the first S ion attack on the C6 radical of octanoyl was found to take place directly by the transfer of the H6 from the substrate to 5'-dA•, whereas for the second S-insertion reaction, a C8 radical intermediate was formed with a rate-limiting barrier of 71 kJ/mol.
Collapse
Affiliation(s)
- Geng Dong
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, 221 00, Lund, Sweden.
| | - Lili Cao
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| |
Collapse
|
30
|
Rowland EA, Snowden CK, Cristea IM. Protein lipoylation: an evolutionarily conserved metabolic regulator of health and disease. Curr Opin Chem Biol 2017; 42:76-85. [PMID: 29169048 DOI: 10.1016/j.cbpa.2017.11.003] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/01/2017] [Accepted: 11/03/2017] [Indexed: 02/07/2023]
Abstract
Lipoylation is a rare, but highly conserved lysine posttranslational modification. To date, it is known to occur on only four multimeric metabolic enzymes in mammals, yet these proteins are staples in the core metabolic landscape. The dysregulation of these mitochondrial proteins is linked to a range of human metabolic disorders. Perhaps most striking is that lipoylation itself, the proteins that add or remove the modification, as well as the proteins it decorates are all evolutionarily conserved from bacteria to humans, highlighting the importance of this essential cofactor. Here, we discuss the biological significance of protein lipoylation, the importance of understanding its regulation in health and disease states, and the advances in mass spectrometry-based proteomic technologies that can aid these studies.
Collapse
Affiliation(s)
- Elizabeth A Rowland
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, United States
| | - Caroline K Snowden
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, United States
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, United States.
| |
Collapse
|
31
|
Schmiesing J, Lohmöller B, Schweizer M, Tidow H, Gersting SW, Muntau AC, Braulke T, Mühlhausen C. Disease-causing mutations affecting surface residues of mitochondrial glutaryl-CoA dehydrogenase impair stability, heteromeric complex formation and mitochondria architecture. Hum Mol Genet 2017; 26:538-551. [PMID: 28062662 DOI: 10.1093/hmg/ddw411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 11/28/2016] [Indexed: 01/22/2023] Open
Abstract
The neurometabolic disorder glutaric aciduria type 1 (GA1) is caused by mutations in the GCDH gene encoding the mitochondrial matrix protein glutaryl-CoA dehydrogenase (GCDH), which forms homo- and heteromeric complexes. Twenty percent of all pathogenic mutations affect single amino acid residues on the surface of GCDH resulting in a severe clinical phenotype. We report here on heterologous expression studies of 18 missense mutations identified in GA1 patients affecting surface amino acids. Western blot and pulse chase experiments revealed that the stability of half of the GCDH mutants was significantly reduced. In silico analyses showed that none of the mutations impaired the 3D structure of GCDH. Immunofluorescence co-localisation studies in HeLa cells demonstrated that all GCDH mutants were correctly translocated into mitochondria. Surprisingly, the expression of p.Arg88Cys GCDH as well as further substitutions by alanine, lysine, or methionine but not histidine or leucine resulted in the disruption of mitochondrial architecture forming longitudinal structures composed of stacks of cristae and partial loss of the outer mitochondrial membrane. The expression of mitochondrial fusion or fission proteins was not affected in these cells. Bioluminescence resonance energy transfer analyses revealed that all GCDH mutants exhibit an increased binding affinity to electron transfer flavoprotein beta, whereas only p.Tyr155His GCDH showed a reduced interaction with dihydrolipoamide succinyl transferase. Our data underscore the impact of GCDH protein interactions mediated by amino acid residues on the surface of GCDH required for proper enzymatic activity.
Collapse
Affiliation(s)
- Jessica Schmiesing
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Benjamin Lohmöller
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michaela Schweizer
- Center of Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Henning Tidow
- The Hamburg Centre for Ultrafast Imaging & Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Søren W Gersting
- Department of Molecular Pediatrics, Dr. von Hauner Childrens Hospital, Ludwig-Maximilians-University, Munich, Germany and
| | - Ania C Muntau
- University Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Braulke
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Chris Mühlhausen
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,University Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| |
Collapse
|
32
|
Conditional knock-out of lipoic acid protein ligase 1 reveals redundancy pathway for lipoic acid metabolism in Plasmodium berghei malaria parasite. Parasit Vectors 2017; 10:315. [PMID: 28655332 PMCID: PMC5488443 DOI: 10.1186/s13071-017-2253-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/19/2017] [Indexed: 11/04/2022] Open
Abstract
Background Lipoic acid is a cofactor for α-keto acid dehydrogenase system that is involved in the central energy metabolism. In the apicomplexan parasite, Plasmodium, lipoic acid protein ligase 1 (LplA1) and LplA2 catalyse the ligation of acquired lipoic acid to the dehydrogenase complexes in the mitochondrion. The enzymes LipB and LipA mediate lipoic acid synthesis and ligation to the enzymes in the apicoplast. These enzymes in the lipoic acid metabolism machinery have been shown to play important roles in the biology of Plasmodium parasites, but the relationship between the enzymes is not fully elucidated. Methods We used an anhydrotetracycline (ATc)-inducible transcription system to generate transgenic P. berghei parasites in which the lplA1 gene was conditionally knocked out (LplA1-cKO). Phenotypic changes and the lplA1 and lplA2 gene expression profiles of cloned LplA1-cKO parasites were analysed. Results LplA1-cKO parasites showed severely impaired growth in vivo in the first 8 days of infection, and retarded blood-stage development in vitro, in the absence of ATc. However, these parasites resumed viability in the late stage of infection and mounted high levels of parasitemia leading to the death of the hosts. Although lplA1 mRNA expression was regulated tightly by ATc during the whole course of infection, lplA2 mRNA expression was significantly increased in the late stage of infection only in the LplA1-cKO parasites that were not exposed to ATc. Conclusions The lplA2 gene can be activated as an alternative pathway to compensate for the loss of LplA1 activity and to maintain lipoic acid metabolism. Electronic supplementary material The online version of this article (doi:10.1186/s13071-017-2253-y) contains supplementary material, which is available to authorized users.
Collapse
|
33
|
Ambrus A, Adam-Vizi V. Human dihydrolipoamide dehydrogenase (E3) deficiency: Novel insights into the structural basis and molecular pathomechanism. Neurochem Int 2017; 117:5-14. [PMID: 28579060 DOI: 10.1016/j.neuint.2017.05.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 05/22/2017] [Accepted: 05/30/2017] [Indexed: 11/18/2022]
Abstract
This review summarizes our present view on the molecular pathogenesis of human (h) E3-deficiency caused by a variety of genetic alterations with a special emphasis on the moonlighting biochemical phenomena related to the affected (dihydro)lipoamide dehydrogenase (LADH, E3, gene: dld), in particular the generation of reactive oxygen species (ROS). E3-deficiency is a rare autosomal recessive genetic disorder frequently presenting with a neonatal onset and premature death; the highest carrier rate of a single pathogenic dld mutation (1:94-1:110) was found among Ashkenazi Jews. Patients usually die during acute episodes that generally involve severe metabolic decompensation and lactic acidosis leading to neurological, cardiological, and/or hepatological manifestations. The disease owes its severity to the fact that LADH is the common E3 subunit of the alpha-ketoglutarate (KGDHc), pyruvate (PDHc), and branched-chain α-keto acid dehydrogenase complexes and is also part of the glycine cleavage system, hence the malfunctioning of LADH simultaneously incapacitates several central metabolic pathways. Nevertheless, the clinical pictures are usually not unequivocally portrayed through the loss of LADH activities and imply auxiliary mechanisms that exacerbate the symptoms and outcomes of this disorder. Enhanced ROS generation by disease-causing hE3 variants as well as by the E1-E2 subcomplex of the hKGDHc likely contributes to selected pathogeneses of E3-deficiency, which could be targeted by specific drugs or antioxidants; lipoic acid was demonstrated to be a potent inhibitor of ROS generation by hE3 in vitro. Flavin supplementation might prove to be beneficial for those mutations triggering FAD loss in the hE3 component. Selected pathogenic hE3 variants lose their affinity for the E2 component of the hPDHc, a mechanism which warrants scrutiny also for other E3-haboring complexes.
Collapse
Affiliation(s)
- Attila Ambrus
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, Hungary.
| | - Vera Adam-Vizi
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, Hungary.
| |
Collapse
|
34
|
Takeda T, Matsuo Y, Nishida K, Fujiki A, Hattori Y, Koga T, Ishii Y, Yamada H. α-Lipoic acid potentially targets AMP-activated protein kinase and energy production in the fetal brain to ameliorate dioxin-produced attenuation in fetal steroidogenesis. J Toxicol Sci 2017; 42:13-23. [PMID: 28070105 DOI: 10.2131/jts.42.13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Our previous studies demonstrated that treating pregnant rats with dioxins, including 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), targets the pituitary expression of luteinizing hormone (LH) to attenuate testicular steroidogenesis in fetuses, resulting in the imprinting of sexual immaturity of the offspring after reaching maturity. Furthermore, we found that although TCDD disturbs the tricarboxylic acid (TCA) cycle in the fetal hypothalamus, maternal co-treatment with α-lipoic acid (α-LA), a cofactor of the TCA cycle, restores a TCDD-produced reduction in the LH-evoked steroidogenesis as well as the TCA cycle activity in fetuses. However, the mechanism underlying the beneficial effect of α-LA remains to be fully elucidated. To address this issue, we compared the effect of α-LA with that of thiamine, another cofactor of the TCA cycle. As with α-LA, supplying thiamine to dams exposed to TCDD alleviates the reduced level of not only hypothalamic ATP but also pituitary LH and testicular steroidogenic protein in fetuses. However, thiamine had a much weaker effect than α-LA. In agreement with ATP attenuation, TCDD activated AMP-activated protein kinase (AMPK), a negative regulator of LH production, whereas the supplementation of α-LA allowed recovery from this defect. Furthermore, α-LA restored the TCDD-produced reduction in the pituitary expression of the receptor for gonadotropin-releasing hormone (GnRH), an upstream regulator of LH synthesis. These results suggest that α-LA rescues TCDD-produced attenuation during fetal steroidogenesis due not only to facilitation of energy production through the TCA cycle but also through suppression of AMPK activation, and the pituitary GnRH receptor may serve as a mediator of these effects.
Collapse
Affiliation(s)
- Tomoki Takeda
- Graduate School of Pharmaceutical Sciences, Kyushu University
| | | | | | | | | | | | | | | |
Collapse
|
35
|
Vatrinet R, Leone G, De Luise M, Girolimetti G, Vidone M, Gasparre G, Porcelli AM. The α-ketoglutarate dehydrogenase complex in cancer metabolic plasticity. Cancer Metab 2017; 5:3. [PMID: 28184304 PMCID: PMC5289018 DOI: 10.1186/s40170-017-0165-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 01/18/2017] [Indexed: 02/07/2023] Open
Abstract
Deregulated metabolism is a well-established hallmark of cancer. At the hub of various metabolic pathways deeply integrated within mitochondrial functions, the α-ketoglutarate dehydrogenase complex represents a major modulator of electron transport chain activity and tricarboxylic acid cycle (TCA) flux, and is a pivotal enzyme in the metabolic reprogramming following a cancer cell’s change in bioenergetic requirements. By contributing to the control of α-ketoglutarate levels, dynamics, and oxidation state, the α-ketoglutarate dehydrogenase is also essential in modulating the epigenetic landscape of cancer cells. In this review, we will discuss the manifold roles that this TCA enzyme and its substrate play in cancer.
Collapse
Affiliation(s)
- Renaud Vatrinet
- Dipartimento Farmacia e Biotecnologie (FABIT), Università di Bologna, Via Selmi 3, 40126 Bologna, Italy.,Dipartimento Scienze Mediche e Chirurgiche (DIMEC), U.O. Genetica Medica, Pol. Universitario S. Orsola-Malpighi, Università di Bologna, Via Massarenti 9, 40138 Bologna, Italy
| | - Giulia Leone
- Dipartimento Farmacia e Biotecnologie (FABIT), Università di Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Monica De Luise
- Dipartimento Scienze Mediche e Chirurgiche (DIMEC), U.O. Genetica Medica, Pol. Universitario S. Orsola-Malpighi, Università di Bologna, Via Massarenti 9, 40138 Bologna, Italy
| | - Giulia Girolimetti
- Dipartimento Scienze Mediche e Chirurgiche (DIMEC), U.O. Genetica Medica, Pol. Universitario S. Orsola-Malpighi, Università di Bologna, Via Massarenti 9, 40138 Bologna, Italy
| | - Michele Vidone
- Dipartimento Scienze Mediche e Chirurgiche (DIMEC), U.O. Genetica Medica, Pol. Universitario S. Orsola-Malpighi, Università di Bologna, Via Massarenti 9, 40138 Bologna, Italy
| | - Giuseppe Gasparre
- Dipartimento Scienze Mediche e Chirurgiche (DIMEC), U.O. Genetica Medica, Pol. Universitario S. Orsola-Malpighi, Università di Bologna, Via Massarenti 9, 40138 Bologna, Italy
| | - Anna Maria Porcelli
- Dipartimento Farmacia e Biotecnologie (FABIT), Università di Bologna, Via Selmi 3, 40126 Bologna, Italy
| |
Collapse
|
36
|
Wu N, Yu Y, Li T, Ji X, Jiang L, Zong J, Huang H. Investigating the Influence of MoS2 Nanosheets on E. coli from Metabolomics Level. PLoS One 2016; 11:e0167245. [PMID: 27907068 PMCID: PMC5132170 DOI: 10.1371/journal.pone.0167245] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/10/2016] [Indexed: 12/13/2022] Open
Abstract
Molybdenum disulfide, a type of two-dimensional layered material with unique properties, has been widely used in many fields. However, an exact understanding of its toxicity remains elusive, let alone its effects on the environmental microbial community. In this study, we utilized metabolomics technology to explore the effects of different concentrations of molybdenum disulfide nanosheets on Escherichia coli for the first time. The results showed that with increasing concentration of molybdenum disulfide nanosheets, the survival rate of Escherichia coli was decreased and the release of lactic dehydrogenase was increased. At the same time, intracellular concentrations of reactive oxygen species were dramatically increased. In addition, metabolomics analysis showed that high concentrations of molybdenum disulfide nanosheets (100, 1000 μg/mL) could significantly affect the metabolic profile of Escherichia coli, including glycine, serine and threonine metabolism, protein biosynthesis, urea cycle and pyruvate metabolism. These results will be beneficial for molybdenum disulfide toxicity assessment and further applications.
Collapse
Affiliation(s)
- Na Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Yadong Yu
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing, China
- * E-mail: (YY); (HH)
| | - Tao Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Xiaojun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Ling Jiang
- College of food science and light industry, Nanjing Tech University, Nanjing, China
| | - Jiajun Zong
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - He Huang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
- * E-mail: (YY); (HH)
| |
Collapse
|
37
|
Han C, Yang L, Choi HH, Baddour J, Achreja A, Liu Y, Li Y, Li J, Wan G, Huang C, Ji G, Zhang X, Nagrath D, Lu X. Amplification of USP13 drives ovarian cancer metabolism. Nat Commun 2016; 7:13525. [PMID: 27892457 PMCID: PMC5133706 DOI: 10.1038/ncomms13525] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 10/12/2016] [Indexed: 12/25/2022] Open
Abstract
Dysregulated energetic metabolism has been recently identified as a hallmark of cancer. Although mutations in metabolic enzymes hardwire metabolism to tumourigenesis, they are relatively infrequent in ovarian cancer. More often, cancer metabolism is re-engineered by altered abundance and activity of the metabolic enzymes. Here we identify ubiquitin-specific peptidase 13 (USP13) as a master regulator that drives ovarian cancer metabolism. USP13 specifically deubiquitinates and thus upregulates ATP citrate lyase and oxoglutarate dehydrogenase, two key enzymes that determine mitochondrial respiration, glutaminolysis and fatty acid synthesis. The USP13 gene is co-amplified with PIK3CA in 29.3% of high-grade serous ovarian cancers and its overexpression is significantly associated with poor clinical outcome. Inhibiting USP13 remarkably suppresses ovarian tumour progression and sensitizes tumour cells to the treatment of PI3K/AKT inhibitor. Our results reveal an important metabolism-centric role of USP13, which may lead to potential therapeutics targeting USP13 in ovarian cancers. Cancer cells need to reprogramme their metabolism to allow rapid cell proliferation. Here, the authors show that USP13 is amplified in ovarian cancer and its protein product, a deubiquitinase, drives tumour progression by rewiring the metabolism of cancer cells by stabilising two critical metabolic enzymes.
Collapse
Affiliation(s)
- Cecil Han
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Lifeng Yang
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| | - Hyun Ho Choi
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Joelle Baddour
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| | - Abhinav Achreja
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| | - Yunhua Liu
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Yujing Li
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jiada Li
- The State Key Laboratory of Medical Genetics and School of Life Sciences, Central South University, Changsha 410008, China
| | - Guohui Wan
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Cheng Huang
- Drug Discovery Laboratory, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Guang Ji
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Xinna Zhang
- Department of Gynaecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Deepak Nagrath
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA.,Department of Bioengineering, Rice University, Houston, Texas 77005, USA
| | - Xiongbin Lu
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| |
Collapse
|
38
|
Transport of pyruvate into mitochondria is involved in methylmercury toxicity. Sci Rep 2016; 6:21528. [PMID: 26899208 PMCID: PMC4761912 DOI: 10.1038/srep21528] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 01/26/2016] [Indexed: 01/24/2023] Open
Abstract
We have previously demonstrated that the overexpression of enzymes involved in the production of pyruvate, enolase 2 (Eno2) and D-lactate dehydrogenase (Dld3) renders yeast highly sensitive to methylmercury and that the promotion of intracellular pyruvate synthesis may be involved in intensifying the toxicity of methylmercury. In the present study, we showed that the addition of pyruvate to culture media in non-toxic concentrations significantly enhanced the sensitivity of yeast and human neuroblastoma cells to methylmercury. The results also suggested that methylmercury promoted the transport of pyruvate into mitochondria and that the increased pyruvate concentrations in mitochondria were involved in intensifying the toxicity of methylmercury without pyruvate being converted to acetyl-CoA. Furthermore, in human neuroblastoma cells, methylmercury treatment alone decreased the mitochondrial membrane potential, and the addition of pyruvate led to a further significant decrease. In addition, treatment with N-acetylcysteine (an antioxidant) significantly alleviated the toxicity of methylmercury and significantly inhibited the intensification of methylmercury toxicity by pyruvate. Based on these data, we hypothesize that methylmercury exerts its toxicity by raising the level of pyruvate in mitochondria and that mitochondrial dysfunction and increased levels of reactive oxygen species are involved in the action of pyruvate.
Collapse
|
39
|
Abstract
Two vitamins, biotin and lipoic acid, are essential in all three domains of life. Both coenzymes function only when covalently attached to key metabolic enzymes. There they act as "swinging arms" that shuttle intermediates between two active sites (= covalent substrate channeling) of key metabolic enzymes. Although biotin was discovered over 100 years ago and lipoic acid 60 years ago, it was not known how either coenzyme is made until recently. In Escherichia coli the synthetic pathways for both coenzymes have now been worked out for the first time. The late steps of biotin synthesis, those involved in assembling the fused rings, were well described biochemically years ago, although recent progress has been made on the BioB reaction, the last step of the pathway in which the biotin sulfur moiety is inserted. In contrast, the early steps of biotin synthesis, assembly of the fatty acid-like "arm" of biotin were unknown. It has now been demonstrated that the arm is made by using disguised substrates to gain entry into the fatty acid synthesis pathway followed by removal of the disguise when the proper chain length is attained. The BioC methyltransferase is responsible for introducing the disguise, and the BioH esterase is responsible for its removal. In contrast to biotin, which is attached to its cognate proteins as a finished molecule, lipoic acid is assembled on its cognate proteins. An octanoyl moiety is transferred from the octanoyl acyl carrier protein of fatty acid synthesis to a specific lysine residue of a cognate protein by the LipB octanoyltransferase followed by sulfur insertion at carbons C-6 and C-8 by the LipA lipoyl synthetase. Assembly on the cognate proteins regulates the amount of lipoic acid synthesized, and, thus, there is no transcriptional control of the synthetic genes. In contrast, transcriptional control of the biotin synthetic genes is wielded by a remarkably sophisticated, yet simple, system, exerted through BirA, a dual-function protein that both represses biotin operon transcription and ligates biotin to its cognate proteins.
Collapse
|
40
|
Ambrus A, Nemeria NS, Torocsik B, Tretter L, Nilsson M, Jordan F, Adam-Vizi V. Formation of reactive oxygen species by human and bacterial pyruvate and 2-oxoglutarate dehydrogenase multienzyme complexes reconstituted from recombinant components. Free Radic Biol Med 2015; 89:642-50. [PMID: 26456061 PMCID: PMC4684775 DOI: 10.1016/j.freeradbiomed.2015.10.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 09/18/2015] [Accepted: 10/03/2015] [Indexed: 01/25/2023]
Abstract
Individual recombinant components of pyruvate and 2-oxoglutarate dehydrogenase multienzyme complexes (PDHc, OGDHc) of human and Escherichia coli (E. coli) origin were expressed and purified from E. coli with optimized protocols. The four multienzyme complexes were each reconstituted under optimal conditions at different stoichiometric ratios. Binding stoichiometries for the highest catalytic efficiency were determined from the rate of NADH generation by the complexes at physiological pH. Since some of these complexes were shown to possess 'moonlighting' activities under pathological conditions often accompanied by acidosis, activities were also determined at pH 6.3. As reactive oxygen species (ROS) generation by the E3 component of hOGDHc is a pathologically relevant feature, superoxide generation by the complexes with optimal stoichiometry was measured by the acetylated cytochrome c reduction method in both the forward and the reverse catalytic directions. Various known affectors of physiological activity and ROS production, including Ca(2+), ADP, lipoylation status or pH, were investigated. The human complexes were also reconstituted with the most prevalent human pathological mutant of the E3 component, G194C and characterized; isolated human E3 with the G194C substitution was previously reported to have an enhanced ROS generating capacity. It is demonstrated that: i. PDHc, similarly to OGDHc, is able to generate ROS and this feature is displayed by both the E. coli and human complexes, ii. Reconstituted hPDHc generates ROS at a significantly higher rate as compared to hOGDHc in both the forward and the reverse reactions when ROS generation is calculated for unit mass of their common E3 component, iii. The E1 component or E1-E2 subcomplex generates significant amount of ROS only in hOGDHc; iv. Incorporation of the G194C variant of hE3, the result of a disease-causing mutation, into reconstituted hOGDHc and hPDHc indeed leads to a decreased activity of both complexes and higher ROS generation by only hOGDHc and only in its reverse reaction.
Collapse
Affiliation(s)
- Attila Ambrus
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, 1094, Hungary
| | - Natalia S Nemeria
- Department of Chemistry, Rutgers, the State University, Newark, NJ 07102, USA
| | - Beata Torocsik
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, 1094, Hungary
| | - Laszlo Tretter
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, 1094, Hungary
| | - Mattias Nilsson
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, 1094, Hungary
| | - Frank Jordan
- Department of Chemistry, Rutgers, the State University, Newark, NJ 07102, USA
| | - Vera Adam-Vizi
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, 1094, Hungary.
| |
Collapse
|
41
|
Trujillo M, Alvarez B, Radi R. One- and two-electron oxidation of thiols: mechanisms, kinetics and biological fates. Free Radic Res 2015; 50:150-71. [PMID: 26329537 DOI: 10.3109/10715762.2015.1089988] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The oxidation of biothiols participates not only in the defense against oxidative damage but also in enzymatic catalytic mechanisms and signal transduction processes. Thiols are versatile reductants that react with oxidizing species by one- and two-electron mechanisms, leading to thiyl radicals and sulfenic acids, respectively. These intermediates, depending on the conditions, participate in further reactions that converge on different stable products. Through this review, we will describe the biologically relevant species that are able to perform these oxidations and we will analyze the mechanisms and kinetics of the one- and two-electron reactions. The processes undergone by typical low-molecular-weight thiols as well as the particularities of specific thiol proteins will be described, including the molecular determinants proposed to account for the extraordinary reactivities of peroxidatic thiols. Finally, the main fates of the thiyl radical and sulfenic acid intermediates will be summarized.
Collapse
Affiliation(s)
- Madia Trujillo
- a Departamento de Bioquímica , Facultad de Medicina, Universidad de la República , Montevideo , Uruguay .,b Center for Free Radical and Biomedical Research , Universidad de la República , Montevideo , Uruguay , and
| | - Beatriz Alvarez
- b Center for Free Radical and Biomedical Research , Universidad de la República , Montevideo , Uruguay , and.,c Laboratorio de Enzimología, Facultad de Ciencias , Universidad de la República , Montevideo , Uruguay
| | - Rafael Radi
- a Departamento de Bioquímica , Facultad de Medicina, Universidad de la República , Montevideo , Uruguay .,b Center for Free Radical and Biomedical Research , Universidad de la República , Montevideo , Uruguay , and
| |
Collapse
|
42
|
Song L, Liu D. Mutations in the three Arabidopsis genes that encode the E2 subunit of the mitochondrial pyruvate dehydrogenase complex differentially affect enzymatic activity and plant growth. PLANT CELL REPORTS 2015; 34:1919-26. [PMID: 26194327 DOI: 10.1007/s00299-015-1838-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/23/2015] [Accepted: 07/01/2015] [Indexed: 05/24/2023]
Abstract
Three members of the E2 subunit of the Arabidopsis mitochondrial pyruvate dehydrogenase (mtPDC) complex differentially affect mtPDC activity and plant growth. In all organisms, the mitochondrial pyruvate dehydrogenase complex (mtPDC) consists of three components: E1, E2, and E3. In this multi-enzyme complex, the E2 subunits form the core structure. In Arabidopsis, the E2 subunits are encoded by three genes: mtE2-1, mtE2-2, and mtE2-3. The contribution of each mtE2 gene to total mtPDC activity, however, is unknown. In this study, we show that knockdown of the expression of the mtE2-1 gene to 17% of that in the wild type has only a slight effect on plant growth whereas knockout of mtE2-2 leads to an embryo-lethal phenotype. The nearly null mutation of mtE2-3 does not cause any developmental abnormality. Based on these results, we conclude that mtE2-2 plays a major role in determining the total activity of the mtPDC in Arabidopsis while mtE2-1 and mtE2-3 are more or less functionally redundant with mtE2-2 under normal growth condition. Our results provide genetic evidence for a recently proposed novel mechanism that regulates plant mtPDC activity.
Collapse
Affiliation(s)
- Li Song
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Dong Liu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, People's Republic of China.
| |
Collapse
|
43
|
Abstract
The tricarboxylic acid (TCA) cycle plays two essential roles in metabolism. First, under aerobic conditions the cycle is responsible for the total oxidation of acetyl-CoA that is derived mainly from the pyruvate produced by glycolysis. Second, TCA cycle intermediates are required in the biosynthesis of several amino acids. Although the TCA cycle has long been considered a "housekeeping" pathway in Escherichia coli and Salmonella enterica, the pathway is highly regulated at the transcriptional level. Much of this control is exerted in response to respiratory conditions. The TCA cycle gene-protein relationship and mutant phenotypes have been well studied, although a few loose ends remain. The realization that a "shadow" TCA cycle exists that proceeds through methylcitrate has cleared up prior ambiguities. The glyoxylate bypass has long been known to be essential for growth on carbon sources such as acetate or fatty acids because this pathway allowsnet conversion of acetyl-CoA to metabolic intermediates. Strains lacking this pathway fail to grow on these carbon sources, since acetate carbon entering the TCA cycle is quantitatively lost as CO2 resulting in the lack of a means to replenish the dicarboxylic acids consumed in amino acid biosynthesis. The TCA cycle gene-protein relationship and mutant phenotypes have been well studied, although the identity of the small molecule ligand that modulates transcriptional control of the glyoxylate cycle genes by binding to the IclR repressor remains unknown. The activity of the cycle is also exerted at the enzyme level by the reversible phosphorylation of the TCA cycle enzyme isocitrate dehydrogenase catalyzed by a specific kinase/phosphatase to allow isocitratelyase to compete for isocitrate and cleave this intermediate to glyoxylate and succinate.
Collapse
|
44
|
Abstract
Two vitamins, biotin and lipoic acid, are essential in all three domains of life. Both coenzymes function only when covalently attached to key metabolic enzymes. There they act as "swinging arms" that shuttle intermediates between two active sites (= covalent substrate channeling) of key metabolic enzymes. Although biotin was discovered over 100 years ago and lipoic acid was discovered 60 years ago, it was not known how either coenzyme is made until recently. In Escherichia coli the synthetic pathways for both coenzymes have now been worked out for the first time. The late steps of biotin synthesis, those involved in assembling the fused rings, were well described biochemically years ago, although recent progress has been made on the BioB reaction, the last step of the pathway, in which the biotin sulfur moiety is inserted. In contrast, the early steps of biotin synthesis, assembly of the fatty acid-like "arm" of biotin, were unknown. It has now been demonstrated that the arm is made by using disguised substrates to gain entry into the fatty acid synthesis pathway followed by removal of the disguise when the proper chain length is attained. The BioC methyltransferase is responsible for introducing the disguise and the BioH esterase for its removal. In contrast to biotin, which is attached to its cognate proteins as a finished molecule, lipoic acid is assembled on its cognate proteins. An octanoyl moiety is transferred from the octanoyl-ACP of fatty acid synthesis to a specific lysine residue of a cognate protein by the LipB octanoyl transferase, followed by sulfur insertion at carbons C6 and C8 by the LipA lipoyl synthetase. Assembly on the cognate proteins regulates the amount of lipoic acid synthesized, and thus there is no transcriptional control of the synthetic genes. In contrast, transcriptional control of the biotin synthetic genes is wielded by a remarkably sophisticated, yet simple, system exerted through BirA, a dual-function protein that both represses biotin operon transcription and ligates biotin to its cognate protein.
Collapse
|
45
|
Cheon W, Lim K. Change of gene expression on protein uptake composition and hindlimb-suspension in rat skeletal muscle. J Exerc Nutrition Biochem 2015; 19:107-13. [PMID: 26244129 PMCID: PMC4523800 DOI: 10.5717/jenb.2015.15052508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 05/20/2015] [Accepted: 05/25/2015] [Indexed: 11/13/2022] Open
Abstract
[Purpose] This study was to investigate changes in BCAT and BCKDH genes by Hindlimb-Suspension (HS) and protein intake composition (casein, Whey protein) in rats. [Methods] Following 5-day preliminary feeding, forty-eight male 5 weeks old Sprague Dawley albino rats (110g) divided into 17% protein intake group (24 rats) and 30% protein intake group (24 rats), and each group divided further into Hindlimb-Suspension group (HS; 12 rats) and control group(CON; 12 rats). Eventually, this study was performed with Whey protein intake group (HS; 6 rats, CON; 6 rats) and casein intake group (HS; 6 rats, CON; 6 rats). For analysis purposes, total RNA was extracted from isolated skeletal muscles, and mRNA expression was analyzed using Real Time PCR. Two-way ANOVA was performed to examine the difference in BCATm and BCKDH mRNA expression on protein uptake and myoatrophy. post-hoc test was perform on interaction if any, and significance level was set at p<0.05. [Results] In this study, BCATm and BCKDH gene analysis in rat skeletal muscles by hindlimb-suspension and protein intake composition resulted in significant higher BCATm expression in 30% dietary protein group and hindlimb-suspension group that control group. In addition, regarding BCKDH, BCKDH was significantly higher in hindlimb-suspended 30% protein intake group than control group. [Conclusion] Overall, protein intake and myoatrophy demonstrated close relationship in skeletal muscles. Therefore, it is likely to affect effectively in prevention or recovery of exercise induced muscle disorder. This effect is considered to be applied to maintain and improve health of not only athletes but also the general public. Additionally it would be applied in convalescent rehabilitation due to skeletal muscle atrophy.
Collapse
Affiliation(s)
- Wookwang Cheon
- Department of Physical Education, Keimyung University, Daegu, Republic of Korea
| | - Kiwon Lim
- Department of Physical Education, Konkuk University, Seoul, Republic of Korea
| |
Collapse
|
46
|
Pashaj A, Xia M, Moreau R. α-Lipoic acid as a triglyceride-lowering nutraceutical. Can J Physiol Pharmacol 2015; 93:1029-41. [PMID: 26235242 DOI: 10.1139/cjpp-2014-0480] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Considering the current obesity epidemic in the United States (>100 million adults are overweight or obese), the prevalence of hypertriglyceridemia is likely to grow beyond present statistics of ∼30% of the population. Conventional therapies for managing hypertriglyceridemia include lifestyle modifications such as diet and exercise, pharmacological approaches, and nutritional supplements. It is critically important to identify new strategies that would be safe and effective in lowering hypertriglyceridemia. α-Lipoic acid (LA) is a naturally occurring enzyme cofactor found in the human body in small quantities. A growing body of evidence indicates a role of LA in ameliorating metabolic dysfunction and lipid anomalies primarily in animals. Limited human studies suggest LA is most efficacious in situations where blood triglycerides are markedly elevated. LA is commercially available as dietary supplements and is clinically shown to be safe and effective against diabetic polyneuropathies. LA is described as a potent biological antioxidant, a detoxification agent, and a diabetes medicine. Given its strong safety record, LA may be a useful nutraceutical, either alone or in combination with other lipid-lowering strategies, when treating severe hypertriglyceridemia and diabetic dyslipidemia. This review examines the current evidence regarding the use of LA as a means of normalizing blood triglycerides. Also presented are the leading mechanisms of action of LA on triglyceride metabolism.
Collapse
Affiliation(s)
- Anjeza Pashaj
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.,Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Mengna Xia
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.,Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Régis Moreau
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.,Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| |
Collapse
|
47
|
McLaughlin M, Lanz N, Goldman P, Lee KH, Booker S, Drennan C. Caught in the Act: Snapshots of Sulfur Insertion by Lipoyl Synthase. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.895.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Martin McLaughlin
- Dept. of Chemistry MITCambridgeMAUnited States
- Dept. of Chemistry Penn State UniversityState CollegePAUnited States
| | - Nicholas Lanz
- Dept. of Biochemistry & Molecular Biology Penn State University State CollegePAUnited States
| | | | - Kyung Hoon Lee
- Dept. of Chemistry Penn State UniversityState CollegePAUnited States
| | - Squire Booker
- Dept. of Chemistry Penn State UniversityState CollegePAUnited States
- Dept. of Biochemistry & Molecular Biology Penn State University State CollegePAUnited States
| | - Catherine Drennan
- Dept. of Chemistry MITCambridgeMAUnited States
- Dept. of BiologyMITCambridgeMAUnited States
- Howard Hughes Medical Institute MITCambridgeMAUnited States
| |
Collapse
|
48
|
Ortegon P, Poot-Hernández AC, Perez-Rueda E, Rodriguez-Vazquez K. Comparison of Metabolic Pathways in Escherichia coli by Using Genetic Algorithms. Comput Struct Biotechnol J 2015; 13:277-85. [PMID: 25973143 PMCID: PMC4423528 DOI: 10.1016/j.csbj.2015.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 11/21/2022] Open
Abstract
In order to understand how cellular metabolism has taken its modern form, the conservation and variations between metabolic pathways were evaluated by using a genetic algorithm (GA). The GA approach considered information on the complete metabolism of the bacterium Escherichia coli K-12, as deposited in the KEGG database, and the enzymes belonging to a particular pathway were transformed into enzymatic step sequences by using the breadth-first search algorithm. These sequences represent contiguous enzymes linked to each other, based on their catalytic activities as they are encoded in the Enzyme Commission numbers. In a posterior step, these sequences were compared using a GA in an all-against-all (pairwise comparisons) approach. Individual reactions were chosen based on their measure of fitness to act as parents of offspring, which constitute the new generation. The sequences compared were used to construct a similarity matrix (of fitness values) that was then considered to be clustered by using a k-medoids algorithm. A total of 34 clusters of conserved reactions were obtained, and their sequences were finally aligned with a multiple-sequence alignment GA optimized to align all the reaction sequences included in each group or cluster. From these comparisons, maps associated with the metabolism of similar compounds also contained similar enzymatic step sequences, reinforcing the Patchwork Model for the evolution of metabolism in E. coli K-12, an observation that can be expanded to other organisms, for which there is metabolism information. Finally, our mapping of these reactions is discussed, with illustrations from a particular case.
Collapse
Affiliation(s)
- Patricia Ortegon
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, IIMAS, Universidad Nacional Autónoma de México, Mexico
| | - Augusto C. Poot-Hernández
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, IIMAS, Universidad Nacional Autónoma de México, Mexico
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Ernesto Perez-Rueda
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
- Unidad Multidisciplinaria de Docencia e Investigación, Sisal Facultad de Ciencias, Sisal, Yucatán, UNAM, Mexico
- Correspondence to: E. Perez-Rueda, Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
| | - Katya Rodriguez-Vazquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, IIMAS, Universidad Nacional Autónoma de México, Mexico
- Correspondence to: K. Rodriguez-Vazquez, Departamento de Ingeniería de Sistemas Computacionales y Automatización, IIMAS, Universidad Nacional Autónoma de México, Mexico.
| |
Collapse
|
49
|
Neels JG, Grimaldi PA. Physiological functions of peroxisome proliferator-activated receptor β. Physiol Rev 2014; 94:795-858. [PMID: 24987006 DOI: 10.1152/physrev.00027.2013] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The peroxisome proliferator-activated receptors, PPARα, PPARβ, and PPARγ, are a family of transcription factors activated by a diversity of molecules including fatty acids and fatty acid metabolites. PPARs regulate the transcription of a large variety of genes implicated in metabolism, inflammation, proliferation, and differentiation in different cell types. These transcriptional regulations involve both direct transactivation and interaction with other transcriptional regulatory pathways. The functions of PPARα and PPARγ have been extensively documented mainly because these isoforms are activated by molecules clinically used as hypolipidemic and antidiabetic compounds. The physiological functions of PPARβ remained for a while less investigated, but the finding that specific synthetic agonists exert beneficial actions in obese subjects uplifted the studies aimed to elucidate the roles of this PPAR isoform. Intensive work based on pharmacological and genetic approaches and on the use of both in vitro and in vivo models has considerably improved our knowledge on the physiological roles of PPARβ in various cell types. This review will summarize the accumulated evidence for the implication of PPARβ in the regulation of development, metabolism, and inflammation in several tissues, including skeletal muscle, heart, skin, and intestine. Some of these findings indicate that pharmacological activation of PPARβ could be envisioned as a therapeutic option for the correction of metabolic disorders and a variety of inflammatory conditions. However, other experimental data suggesting that activation of PPARβ could result in serious adverse effects, such as carcinogenesis and psoriasis, raise concerns about the clinical use of potent PPARβ agonists.
Collapse
Affiliation(s)
- Jaap G Neels
- Institut National de la Santé et de la Recherche Médicale U 1065, Mediterranean Center of Molecular Medicine (C3M), Team "Adaptive Responses to Immuno-metabolic Dysregulations," Nice, France; and Faculty of Medicine, University of Nice Sophia-Antipolis, Nice, France
| | - Paul A Grimaldi
- Institut National de la Santé et de la Recherche Médicale U 1065, Mediterranean Center of Molecular Medicine (C3M), Team "Adaptive Responses to Immuno-metabolic Dysregulations," Nice, France; and Faculty of Medicine, University of Nice Sophia-Antipolis, Nice, France
| |
Collapse
|
50
|
Heublein M, Burguillos MA, Vögtle FN, Teixeira PF, Imhof A, Meisinger C, Ott M. The novel component Kgd4 recruits the E3 subunit to the mitochondrial α-ketoglutarate dehydrogenase. Mol Biol Cell 2014; 25:3342-9. [PMID: 25165143 PMCID: PMC4214781 DOI: 10.1091/mbc.e14-07-1178] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
By binding to both the E1-E2 core and the E3 subunit, Kgd4 acts as a molecular adaptor that is necessary to form a stable α-ketoglutarate dehydrogenase enzyme complex. The mitochondrial citric acid cycle is a central hub of cellular metabolism, providing intermediates for biosynthetic pathways and channeling electrons to the respiratory chain complexes. In this study, we elucidated the composition and organization of the multienzyme complex α-ketoglutarate dehydrogenase (α-KGDH). In addition to the three classical E1-E3 subunits, we identified a novel component, Kgd4 (Ymr31/MRPS36), which was previously assigned to be a subunit of the mitochondrial ribosome. Biochemical analyses demonstrate that this protein plays an evolutionarily conserved role in the organization of mitochondrial α-KGDH complexes of fungi and animals. By binding to both the E1-E2 core and the E3 subunit, Kgd4 acts as a molecular adaptor that is necessary to a form a stable α-KGDH enzyme complex. Our work thus reveals a novel subunit of a key citric acid–cycle enzyme and shows how this large complex is organized.
Collapse
Affiliation(s)
- Manfred Heublein
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Miguel A Burguillos
- Cancer Centrum Karolinska, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - F Nora Vögtle
- Institute for Biochemistry and Molecular Biology and BIOSS (Centre for Biological Signaling Studies), University of Freiburg, D-79104 Freiburg, Germany
| | - Pedro F Teixeira
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Axel Imhof
- Zentrallabor für Proteinanalytik, Adolf-Butenandt Institut, LMU München, D-80336 München, Germany
| | - Chris Meisinger
- Institute for Biochemistry and Molecular Biology and BIOSS (Centre for Biological Signaling Studies), University of Freiburg, D-79104 Freiburg, Germany
| | - Martin Ott
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| |
Collapse
|