1
|
Houten SM, Dodatko T, Dwyer W, Violante S, Chen H, Stauffer B, DeVita RJ, Vaz FM, Cross JR, Yu C, Leandro J. Acyl-CoA dehydrogenase substrate promiscuity: Challenges and opportunities for development of substrate reduction therapy in disorders of valine and isoleucine metabolism. J Inherit Metab Dis 2023; 46:931-942. [PMID: 37309295 PMCID: PMC10526699 DOI: 10.1002/jimd.12642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/04/2023] [Accepted: 06/07/2023] [Indexed: 06/14/2023]
Abstract
Toxicity of accumulating substrates is a significant problem in several disorders of valine and isoleucine degradation notably short-chain enoyl-CoA hydratase (ECHS1 or crotonase) deficiency, 3-hydroxyisobutyryl-CoA hydrolase (HIBCH) deficiency, propionic acidemia (PA), and methylmalonic aciduria (MMA). Isobutyryl-CoA dehydrogenase (ACAD8) and short/branched-chain acyl-CoA dehydrogenase (SBCAD, ACADSB) function in the valine and isoleucine degradation pathways, respectively. Deficiencies of these acyl-CoA dehydrogenase (ACAD) enzymes are considered biochemical abnormalities with limited or no clinical consequences. We investigated whether substrate reduction therapy through inhibition of ACAD8 and SBCAD can limit the accumulation of toxic metabolic intermediates in disorders of valine and isoleucine metabolism. Using analysis of acylcarnitine isomers, we show that 2-methylenecyclopropaneacetic acid (MCPA) inhibited SBCAD, isovaleryl-CoA dehydrogenase, short-chain acyl-CoA dehydrogenase and medium-chain acyl-CoA dehydrogenase, but not ACAD8. MCPA treatment of wild-type and PA HEK-293 cells caused a pronounced decrease in C3-carnitine. Furthermore, deletion of ACADSB in HEK-293 cells led to an equally strong decrease in C3-carnitine when compared to wild-type cells. Deletion of ECHS1 in HEK-293 cells caused a defect in lipoylation of the E2 component of the pyruvate dehydrogenase complex, which was not rescued by ACAD8 deletion. MCPA was able to rescue lipoylation in ECHS1 KO cells, but only in cells with prior ACAD8 deletion. SBCAD was not the sole ACAD responsible for this compensation, which indicates substantial promiscuity of ACADs in HEK-293 cells for the isobutyryl-CoA substrate. Substrate promiscuity appeared less prominent for 2-methylbutyryl-CoA at least in HEK-293 cells. We suggest that pharmacological inhibition of SBCAD to treat PA should be investigated further.
Collapse
Affiliation(s)
- Sander M. Houten
- Department of Genetics and Genomic Sciences, 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
| | - William Dwyer
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sara Violante
- The Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Hongjie Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brandon Stauffer
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, 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
| | - Frédéric M. Vaz
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children’s Hospital, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Inborn errors of metabolism, Amsterdam, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Justin R. Cross
- The Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Chunli Yu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - João Leandro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| |
Collapse
|
2
|
Gong Y, Zhang Y, Li B, Xiao Y, Zeng Q, Xu K, Duan Y, He J, Ma H. Insight into Liver lncRNA and mRNA Profiling at Four Developmental Stages in Ningxiang Pig. BIOLOGY 2021; 10:310. [PMID: 33917834 PMCID: PMC8068270 DOI: 10.3390/biology10040310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/01/2021] [Accepted: 04/07/2021] [Indexed: 12/23/2022]
Abstract
Ningxiang pigs, a fat-type pig, are native to Ningxiang County in Hunan Province, with thousands of years of breeding history. This study aims to explore the expression profiles and functional networks on messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) in the liver. Liver tissue of Ningxiang piglets was collected at 30, 90, 150, and 210 days after birth (four development stages), and the mRNA and lncRNA expression was profiled. Compared to mRNA and lncRNA expression profiles, most differentially expressed mRNAs (DEmRNAs) were upregulated at 30 days; however, most DElncRNAs were downregulated at 210 days. Via Short Time-series Expression Miner (STEM) analysis and weighted gene co-expression network analysis (WGCNA), a complex interaction between mRNAs and lncRNAs was identified, indicating that lncRNAs may be a critical regulatory element for mRNAs. One module of genes in particular (module profile 4) was related to fibril organization, vasculogenesis, GTPase activator activity, and regulation of kinase activity. The mRNAs and lncRNAs in module profile 4 had a similar pattern of expression, indicating that they have functional and regulatory relationships. Only CAV1, PACSIN2, and CDC42 in the particular mRNA profile 4 were the target genes of lncRNAs in that profile, which shows the possible regulatory relationship between lncRNAs and mRNAs. The expression of these genes and lncRNAs in profile 4 was the highest at 30 days, and it is believed that these RNAs may play a critical role during the suckling period in order to meet the dietary requirements of piglets. In the lncRNA-mRNA co-expression network, the identified gene hubs and associated lncRNAs were shown to be involved in saccharide, lipid, and glucose metabolism, which may play an important role in the development and health of the liver. This result will lead to further investigation of liver lncRNA functions at various stages of development in Ningxiang pigs.
Collapse
Affiliation(s)
- Yan Gong
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Y.G.); (Y.Z.); (B.L.); (Y.X.); (Q.Z.); (J.H.)
| | - Yuebo Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Y.G.); (Y.Z.); (B.L.); (Y.X.); (Q.Z.); (J.H.)
| | - Biao Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Y.G.); (Y.Z.); (B.L.); (Y.X.); (Q.Z.); (J.H.)
| | - Yu Xiao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Y.G.); (Y.Z.); (B.L.); (Y.X.); (Q.Z.); (J.H.)
| | - Qinghua Zeng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Y.G.); (Y.Z.); (B.L.); (Y.X.); (Q.Z.); (J.H.)
- Ningxiang Pig Farm of Dalong Livestock Technology Co. Ltd., Ningxiang 410600, China
| | - Kang Xu
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agroecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Science, Changsha 410125, China; (K.X.); (Y.D.)
| | - Yehui Duan
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agroecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Science, Changsha 410125, China; (K.X.); (Y.D.)
| | - Jianhua He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Y.G.); (Y.Z.); (B.L.); (Y.X.); (Q.Z.); (J.H.)
| | - Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Y.G.); (Y.Z.); (B.L.); (Y.X.); (Q.Z.); (J.H.)
| |
Collapse
|
3
|
Site-directed mutation to improve the enzymatic activity of 5-carboxy-2-pentenoyl-CoA reductase for enhancing adipic acid biosynthesis. Enzyme Microb Technol 2019; 125:6-12. [DOI: 10.1016/j.enzmictec.2019.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 12/28/2018] [Accepted: 02/14/2019] [Indexed: 11/23/2022]
|
4
|
Rani N, Hazra S, Singh A, Surolia A. Functional annotation of putative fadE9 of Mycobacterium tuberculosis as isobutyryl-CoA dehydrogenase involved in valine catabolism. Int J Biol Macromol 2019; 122:45-57. [DOI: 10.1016/j.ijbiomac.2018.10.040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 10/10/2018] [Accepted: 10/10/2018] [Indexed: 12/21/2022]
|
5
|
Zhou J, Wang Y, Chen J, Xu M, Yang T, Zheng J, Zhang X, Rao Z. Rational Engineering of Bacillus cereus
Leucine Dehydrogenase Towards α-keto Acid Reduction for Improving Unnatural Amino Acid Production. Biotechnol J 2018; 14:e1800253. [DOI: 10.1002/biot.201800253] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/06/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Junping Zhou
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi Jiangsu Province 214122 China
| | - Yaling Wang
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi Jiangsu Province 214122 China
| | - Jiajie Chen
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi Jiangsu Province 214122 China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi Jiangsu Province 214122 China
| | - Taowei Yang
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi Jiangsu Province 214122 China
| | - Junxian Zheng
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi Jiangsu Province 214122 China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi Jiangsu Province 214122 China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi Jiangsu Province 214122 China
| |
Collapse
|
6
|
Jiang P, Fang X, Zhao Z, Yu X, Sun B, Yu H, Yang R. The effect of short/branched chain acyl-coenzyme A dehydrogenase gene on triglyceride synthesis of bovine mammary epithelial cells. Arch Anim Breed 2018. [DOI: 10.5194/aab-61-115-2018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. Short/branched chain acyl-CoA dehydrogenase (ACADSB) is a member of
the acyl-CoA dehydrogenase family of enzymes that catalyze the
dehydrogenation of acyl-CoA derivatives in the metabolism of fatty
acids. Our previous transcriptome analysis in dairy cattle showed
that ACADSB was differentially expressed and was associated with milk
fat metabolism. The aim of this study was to elucidate the
background of this differential expression and to evaluate the role
of ACADSB as a candidate for fat metabolism in dairy cattle. After
analysis of ACADSB mRNA abundance by qRT-PCR and Western blot,
overexpression and RNA interference (RNAi) vectors of ACADSB gene
were constructed and then transfected into bovine mammary
epithelial cells (bMECs) to examine the effects of ACADSB on
milk fat synthesis. The results showed that the ACADSB was
differentially expressed in mammary tissue of low and high milk fat
dairy cattle. Overexpression of ACADSB gene could significantly
increase the level of intracellular triglyceride (TG), while ACADSB
gene knockdown could significantly reduce the TG synthesis
in bMECs. This study suggested that the ACADSB was important in
TG synthesis in bMECs, and it could be a candidate gene
to regulate the metabolism of milk fat in dairy cattle.
Collapse
|
7
|
Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation. Sci Rep 2017; 7:40101. [PMID: 28067254 PMCID: PMC5220378 DOI: 10.1038/srep40101] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 11/30/2016] [Indexed: 01/15/2023] Open
Abstract
The Candidate Phyla Radiation (CPR) is a large group of bacteria, the scale of which approaches that of all other bacteria. CPR organisms are inferred to depend on other community members for many basic cellular building blocks and all appear to be obligate anaerobes. To date, there has been no evidence for any significant respiratory capacity in an organism from this radiation. Here we report a curated draft genome for 'Candidatus Parcunitrobacter nitroensis' a member of the Parcubacteria (OD1) superphylum of the CPR. The genome encodes versatile energy pathways, including fermentative and respiratory capacities, nitrogen and fatty acid metabolism, as well as the first complete electron transport chain described for a member of the CPR. The sequences of all of these enzymes are highly divergent from sequences found in other organisms, suggesting that these capacities were not recently acquired from non-CPR organisms. Although the wide respiration-based repertoire points to a different lifestyle compared to other CPR bacteria, we predict similar obligate dependence on other organisms or the microbial community. The results substantially expand the known metabolic potential of CPR bacteria, although sequence comparisons indicate that these capacities are very rare in members of this radiation.
Collapse
|
8
|
Bar-Even A, Milo R, Noor E, Tawfik DS. The Moderately Efficient Enzyme: Futile Encounters and Enzyme Floppiness. Biochemistry 2015. [DOI: 10.1021/acs.biochem.5b00621] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | | | - Elad Noor
- Institute
of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, CH-8093 Zurich, Switzerland
| | | |
Collapse
|
9
|
Kinetic and spectral properties of isovaleryl-CoA dehydrogenase and interaction with ligands. Biochimie 2014; 108:108-19. [PMID: 25450250 DOI: 10.1016/j.biochi.2014.11.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 11/10/2014] [Indexed: 11/21/2022]
Abstract
Isovaleryl-CoA dehydrogenase (IVD) catalyzes the conversion of isovaleryl-CoA to 3-methylcrotonyl-CoA and the transfer of electrons to the electron transfer flavoprotein (ETF). Recombinant human IVD purifies with bound CoA-persulfide. A modified purification protocol was developed to isolate IVD without bound CoA-persulfide and to protect the protein thiols from oxidation. The CoA-persulfide-free IVD specific activity was 112.5 μmol porcine ETF min(-)(1) mg(-)(1), which was ∼20-fold higher than that of its CoA-persulfide bound form. The Km and catalytic efficiency (kcat/Km) for isovaleryl-CoA were 1.0 μM and 4.3 × 10(6) M(-1) s(-1) per monomer, respectively, and its Km for ETF was 2.0 μM. Anaerobic titration of isovaleryl-CoA into an IVD solution resulted in a stable blue complex with increased absorbance at 310 nm, decreased absorbance at 373 and 447 nm, and the appearance of the charge transfer complex band at 584 nm. The apparent dissociation constant (KDapp) determined spectrally for isovaleryl-CoA was 0.54 μM. Isovaleryl-CoA, acetoacetyl-CoA, methylenecyclopropyl-acetyl-CoA, and ETF induced CD spectral changes at the 250-500 nm region while isobutyryl-CoA did not, suggesting conformational changes occur at the flavin ring that are ligand specific. Replacement of the IVD Trp166 with a Phe did not block IVD interaction with ETF, indicating that its indole ring is not essential for electron transfer to ETF. A twelve amino acid synthetic peptide that matches the sequence of the ETF docking peptide competitively inhibited the enzyme reaction when ETF was used as the electron acceptor with a Ki of 1.5 mM.
Collapse
|
10
|
Regulation of fatty acid oxidation in mouse cumulus-oocyte complexes during maturation and modulation by PPAR agonists. PLoS One 2014; 9:e87327. [PMID: 24505284 PMCID: PMC3914821 DOI: 10.1371/journal.pone.0087327] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 12/19/2013] [Indexed: 12/30/2022] Open
Abstract
Fatty acid oxidation is an important energy source for the oocyte; however, little is known about how this metabolic pathway is regulated in cumulus-oocyte complexes. Analysis of genes involved in fatty acid oxidation showed that many are regulated by the luteinizing hormone surge during in vivo maturation, including acyl-CoA synthetases, carnitine transporters, acyl-CoA dehydrogenases and acetyl-CoA transferase, but that many are dysregulated when cumulus-oocyte complexes are matured under in vitro maturation conditions using follicle stimulating hormone and epidermal growth factor. Fatty acid oxidation, measured as production of 3H2O from [3H]palmitic acid, occurs in mouse cumulus-oocyte complexes in response to the luteinizing hormone surge but is significantly reduced in cumulus-oocyte complexes matured in vitro. Thus we sought to determine whether fatty acid oxidation in cumulus-oocyte complexes could be modulated during in vitro maturation by lipid metabolism regulators, namely peroxisome proliferator activated receptor (PPAR) agonists bezafibrate and rosiglitazone. Bezafibrate showed no effect with increasing dose, while rosiglitazone dose dependently inhibited fatty acid oxidation in cumulus-oocyte complexes during in vitro maturation. To determine the impact of rosiglitazone on oocyte developmental competence, cumulus-oocyte complexes were treated with rosiglitazone during in vitro maturation and gene expression, oocyte mitochondrial activity and embryo development following in vitro fertilization were assessed. Rosiglitazone restored Acsl1, Cpt1b and Acaa2 levels in cumulus-oocyte complexes and increased oocyte mitochondrial membrane potential yet resulted in significantly fewer embryos reaching the morula and hatching blastocyst stages. Thus fatty acid oxidation is increased in cumulus-oocyte complexes matured in vivo and deficient during in vitro maturation, a known model of poor oocyte quality. That rosiglitazone further decreased fatty acid oxidation during in vitro maturation and resulted in poor embryo development points to the developmental importance of fatty acid oxidation and the need for it to be optimized during in vitro maturation to improve this reproductive technology.
Collapse
|
11
|
Liu X, Wu L, Deng G, Chen G, Li N, Chu X, Li D. Comparative studies of Acyl-CoA dehydrogenases for monomethyl branched chain substrates in amino acid metabolism. Bioorg Chem 2013; 47:1-8. [PMID: 23474214 DOI: 10.1016/j.bioorg.2012.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Revised: 12/05/2012] [Accepted: 12/07/2012] [Indexed: 12/21/2022]
Abstract
Short/branched chain acyl-CoA dehydrogenase (SBCAD), isovaleryl-CoA dehydrogenase (IVD), and isobutyryl-CoA dehydrogenase (IBD) are involved in metabolism of isoleucine, leucine, and valine, respectively. These three enzymes all belong to acyl-CoA dehydrogenase (ACD) family, and catalyze the dehydrogenation of monomethyl branched-chain fatty acid (mmBCFA) thioester derivatives. In the present work, the catalytic properties of rat SBCAD, IVD, and IBD, including their substrate specificity, isomerase activity, and enzyme inhibition, were comparatively studied. Our results indicated that SBCAD has its catalytic properties relatively similar to those of straight-chain acyl-CoA dehydrogenases in terms of their isomerase activity and enzyme inhibition, while IVD and IBD are different. IVD has relatively broader substrate specificity than those of the other two enzymes in accommodating various substrate analogs. The present study increased our understanding for the metabolism of monomethyl branched-chain fatty acids (mmBCFAs) and branched-chain amino acids (BCAAs), which should also be useful for selective control of a particular reaction through the design of specific inhibitors.
Collapse
Affiliation(s)
- Xiaojun Liu
- Department of Biology and Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, PR China
| | | | | | | | | | | | | |
Collapse
|
12
|
Hamill MJ, Jost M, Wong C, Bene NC, Drennan CL, Elliott SJ. Electrochemical characterization of Escherichia coli adaptive response protein AidB. Int J Mol Sci 2012; 13:16899-915. [PMID: 23443126 PMCID: PMC3546729 DOI: 10.3390/ijms131216899] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Revised: 11/26/2012] [Accepted: 12/03/2012] [Indexed: 11/16/2022] Open
Abstract
When exposed to known DNA-damaging alkylating agents, Escherichia coli cells increase production of four DNA repair enzymes: Ada, AlkA, AlkB, and AidB. The role of three enzymes (Ada, AlkA, and AlkB) in repairing DNA lesions has been well characterized, while the function of AidB is poorly understood. AidB has a distinct cofactor that is potentially related to the elusive role of AidB in adaptive response: a redox active flavin adenine dinucleotide (FAD). In this study, we report the thermodynamic redox properties of the AidB flavin for the first time, both for free protein and in the presence of potential substrates. We find that the midpoint reduction potential of the AidB flavin is within a biologically relevant window for redox chemistry at -181 mV, that AidB significantly stabilizes the flavin semiquinone, and that small molecule binding perturbs the observed reduction potential. Our electrochemical results combined with structural analysis allow for fresh comparisons between AidB and the homologous acyl-coenzyme A dehydrogenase (ACAD) family of enzymes. AidB exhibits several discrepancies from ACADs that suggest a novel catalytic mechanism distinct from that of the ACAD family enzymes.
Collapse
Affiliation(s)
- Michael J. Hamill
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA; E-Mails: (M.J.H.); (N.C.B.)
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA; E-Mails: (M.J.); (C.L.D.)
| | - Marco Jost
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA; E-Mails: (M.J.); (C.L.D.)
| | - Cintyu Wong
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA; E-Mails: (M.J.); (C.L.D.)
| | - Nicholas C. Bene
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA; E-Mails: (M.J.H.); (N.C.B.)
| | - Catherine L. Drennan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA; E-Mails: (M.J.); (C.L.D.)
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Environmental Health, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sean J. Elliott
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA; E-Mails: (M.J.H.); (N.C.B.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-617-358-2816; Fax: +1-617-353-6466
| |
Collapse
|
13
|
He M, Pei Z, Mohsen AW, Watkins P, Murdoch G, Van Veldhoven PP, Ensenauer R, Vockley J. Identification and characterization of new long chain acyl-CoA dehydrogenases. Mol Genet Metab 2011; 102:418-29. [PMID: 21237683 PMCID: PMC3073726 DOI: 10.1016/j.ymgme.2010.12.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 12/09/2010] [Indexed: 12/23/2022]
Abstract
Long-chain fatty acids are an important source of energy in muscle and heart where the acyl-CoA dehydrogenases (ACADs) participate in consecutive cycles of β-oxidation to generate acetyl-CoA and reducing equivalents for generating energy. However, the role of long-chain fatty acid oxidation in the brain and other tissues that do not rely on fat for energy is poorly understood. Here we characterize two new ACADs, ACAD10 and ACAD11, both with significant expression in human brain. ACAD11 utilizes substrates with primary carbon chain lengths between 20 and 26, with optimal activity towards C22CoA. The combination of ACAD11 with the newly characterized ACAD9 accommodates the full spectrum of long chain fatty acid substrates presented to mitochondrial β-oxidation in human cerebellum. ACAD10 has significant activity towards the branched-chain substrates R and S, 2 methyl-C15-CoA and is highly expressed in fetal but not adult brain. This pattern of expression is similar to that of LCAD, another ACAD previously shown to be involved in long branched chain fatty acid metabolism. Interestingly, the ACADs in human cerebellum were found to have restricted cellular distribution. ACAD9 was most highly expressed in the granular layer, ACAD11 in the white matter, and MCAD in the molecular layer and axons of specific neurons. This compartmentalization of ACADs in the human central nerve system suggests that β-oxidation in cerebellum participates in different functions other than generating energy, for example, the synthesis and/or degradation of unique cellular lipids and catabolism of aromatic amino acids, compounds that are vital to neuronal function.
Collapse
Affiliation(s)
- Miao He
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Zhengtong Pei
- Kennedy Krieger Institute and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Al-Walid Mohsen
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Paul Watkins
- Kennedy Krieger Institute and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Geoffrey Murdoch
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Paul P Van Veldhoven
- Laboratory of Lipid Biochemistry and Protein Interactions, Department of Molecular Cell Biology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Regina Ensenauer
- Ludwig-Maximilians University, Dr. von Hauner Children’s Hospital, Children’s Research Center, Munich, Germany
| | - Jerry Vockley
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Human Genetics, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA
| |
Collapse
|
14
|
Luís PBM, Ruiter JPN, Ijlst L, Tavares de Almeida I, Duran M, Mohsen AW, Vockley J, Wanders RJA, Silva MFB. Role of isovaleryl-CoA dehydrogenase and short branched-chain acyl-CoA dehydrogenase in the metabolism of valproic acid: implications for the branched-chain amino acid oxidation pathway. Drug Metab Dispos 2011; 39:1155-60. [PMID: 21430231 DOI: 10.1124/dmd.110.037606] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Many biological systems including the oxidative catabolic pathway for branched-chain amino acids (BCAAs) are affected in vivo by valproate therapy. In this study, we investigated the potential effect of valproic acid (VPA) and some of its metabolites on the metabolism of BCAAs. In vitro studies were performed using isovaleryl-CoA dehydrogenase (IVD), isobutyryl-CoA dehydrogenase (IBD), and short branched-chain acyl-CoA dehydrogenase (SBCAD), enzymes involved in the degradation pathway of leucine, valine, and isoleucine. The enzymatic activities of the three purified human enzymes were measured using optimized high-performance liquid chromatography procedures, and the respective kinetic parameters were determined in the absence and presence of VPA and the corresponding CoA and dephosphoCoA conjugates. Valproyl-CoA and valproyl-dephosphoCoA inhibited IVD activity significantly by a purely competitive mechanism with K(i) values of 74 ± 4 and 170 ± 12 μM, respectively. IBD activity was not affected by any of the tested VPA esters. However, valproyl-CoA did inhibit SBCAD activity by a purely competitive mechanism with a K(i) of 249 ± 29 μM. In addition, valproyl-dephosphoCoA inhibited SBCAD activity via a distinct mechanism (K(i) = 511 ± 96 μM) that appeared to be of the mixed type. Furthermore, we show that both SBCAD and IVD are active, using valproyl-CoA as a substrate. The catalytic efficiency of SBCAD turned out to be much higher than that of IVD, demonstrating that SBCAD is the most probable candidate for the first dehydrogenation step of VPA β-oxidation. Our data explain some of the effects of valproate on the branched-chain amino acid metabolism and shed new light on the biotransformation pathway of valproate.
Collapse
Affiliation(s)
- Paula B M Luís
- Research Institute for Medicines and Pharmaceutical Sciences-iMED.UL, Faculdade de Farmácia da Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Erb TJ, Fuchs G, Alber BE. (2S)-Methylsuccinyl-CoA dehydrogenase closes the ethylmalonyl-CoA pathway for acetyl-CoA assimilation. Mol Microbiol 2009; 73:992-1008. [PMID: 19703103 DOI: 10.1111/j.1365-2958.2009.06837.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Many organic substrates are metabolized via acetyl-coenzyme A (CoA) and enter central carbon metabolism at the level of this compound. We recently described the outlines of the ethylmalonyl-CoA pathway, a new acetyl-CoA assimilation strategy that operates in a number of bacteria such as Rhodobacter sphaeroides, Methylobacterium extorquens and streptomycetes and replaces the glyoxylate cycle. This new pathway involves a unique central reaction sequence catalysed by characteristic enzymes. Here, we identified and characterized (2S)-methylsuccinyl-CoA dehydrogenase from R. sphaeroides, a flavin adenine dinucleotide-containing enzyme that catalyses the last unknown step in the central part of the ethylmalonyl-CoA pathway, the oxidation of (2S)-methylsuccinyl-CoA to mesaconyl-(C1)-CoA. This enzyme is highly specific for its substrate and forms a distinct subgroup within the superfamily of flavin-dependent acyl-CoA dehydrogenases. Homology modelling and comparative sequence analyses with well-studied members of this superfamily identified amino acids that may contribute to the narrow substrate specificity of (2S)-methylsuccinyl-CoA dehydrogenase. The central part of the ethylmalonyl-CoA pathway was reconstituted in vitro using four recombinant enzymes. By this work, the ethylmalonyl-CoA pathway and its stereochemical course have been completely solved. This allowed defining the minimum set of enzymes necessary for its operation and to screen for further organisms following this acetyl-CoA assimilation strategy.
Collapse
Affiliation(s)
- Tobias J Erb
- Mikrobiologie, Institut für Biologie II, Schänzlestr 1, Albert-Ludwigs-Universität Freiburg, Freiburg i Br, Germany
| | | | | |
Collapse
|
16
|
Shen YQ, Lang BF, Burger G. Diversity and dispersal of a ubiquitous protein family: acyl-CoA dehydrogenases. Nucleic Acids Res 2009; 37:5619-31. [PMID: 19625492 PMCID: PMC2761260 DOI: 10.1093/nar/gkp566] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Acyl-CoA dehydrogenases (ACADs), which are key enzymes in fatty acid and amino acid catabolism, form a large, pan-taxonomic protein family with at least 13 distinct subfamilies. Yet most reported ACAD members have no subfamily assigned, and little is known about the taxonomic distribution and evolution of the subfamilies. In completely sequenced genomes from approximately 210 species (eukaryotes, bacteria and archaea), we detect ACAD subfamilies by rigorous ortholog identification combining sequence similarity search with phylogeny. We then construct taxonomic subfamily-distribution profiles and build phylogenetic trees with orthologous proteins. Subfamily profiles provide unparalleled insight into the organisms’ energy sources based on genome sequence alone and further predict enzyme substrate specificity, thus generating explicit working hypotheses for targeted biochemical experimentation. Eukaryotic ACAD subfamilies are traditionally considered as mitochondrial proteins, but we found evidence that in fungi one subfamily is located in peroxisomes and participates in a distinct β-oxidation pathway. Finally, we discern horizontal transfer, duplication, loss and secondary acquisition of ACAD genes during evolution of this family. Through these unorthodox expansion strategies, the ACAD family is proficient in utilizing a large range of fatty acids and amino acids—strategies that could have shaped the evolutionary history of many other ancient protein families.
Collapse
Affiliation(s)
- Yao-Qing Shen
- Robert Cedergren Center for Bioinformatics and Genomics, Biochemistry Department, Université de Montréal, 2900 Edouard-Montpetit, Montreal, QC, H3T 1J4, Canada.
| | | | | |
Collapse
|
17
|
Emerson JW, Dolled-Filhart M, Harris L, Rimm DL, Tuck DP. Quantitative assessment of tissue biomarkers and construction of a model to predict outcome in breast cancer using multiple imputation. Cancer Inform 2008; 7:29-40. [PMID: 19352457 PMCID: PMC2664700 DOI: 10.4137/cin.s911] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Missing data pose one of the greatest challenges in the rigorous evaluation of biomarkers. The limited availability of specimens with complete clinical annotation and quality biomaterial often leads to underpowered studies. Tissue microarray studies, for example, may be further handicapped by the loss of data points because of unevaluable staining, core loss, or the lack of tumor in the histospot. This paper presents a novel approach to these common problems in the context of a tissue protein biomarker analysis in a cohort of patients with breast cancer. Our analysis develops techniques based on multiple imputation to address the missing value problem. We first select markers using a training cohort, identifying a small subset of protein expression levels that are most useful in predicting patient survival. The best model is obtained by including both protein markers (including COX6C, GATA3, NAT1, and ESR1) and lymph node status. The use of either lymph node status or the four protein expression levels provides similar improvements in goodness-of-fit, with both significantly better than a baseline clinical model. Using the same multiple imputation strategy, we then validate the results out-of-sample on a larger independent cohort. Our approach of integrating multiple imputation with each stage of the analysis serves as an example that may be replicated or adapted in future studies with missing values.
Collapse
Affiliation(s)
- John W Emerson
- Department of Statistics, Yale University, New Haven, Connecticut 06520, USA
| | | | | | | | | |
Collapse
|
18
|
Maggio-Hall LA, Lyne P, Wolff JA, Keller NP. A single acyl-CoA dehydrogenase is required for catabolism of isoleucine, valine and short-chain fatty acids in Aspergillus nidulans. Fungal Genet Biol 2007; 45:180-9. [PMID: 17656140 PMCID: PMC2905684 DOI: 10.1016/j.fgb.2007.06.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2007] [Revised: 06/01/2007] [Accepted: 06/04/2007] [Indexed: 01/04/2023]
Abstract
An acyl-CoA dehydrogenase has been identified as part of the mitochondrial beta-oxidation pathway in the ascomycete fungus Aspergillus nidulans. Disruption of the scdA gene prevented use of butyric acid (C(4)) and hexanoic acid (C(6)) as carbon sources and reduced cellular butyryl-CoA dehydrogenase activity by 7.5-fold. While the mutant strain exhibited wild-type levels of growth on erucic acid (C(22:1)) and oleic acid (C(18:1)), some reduction in growth was observed with myristic acid (C(14)). The DeltascdA mutation was found to be epistatic to a mutation downstream in the beta-oxidation pathway (disruption of enoyl-CoA hydratase). The DeltascdA mutant was also unable to use isoleucine or valine as a carbon source. Transcription of scdA was observed in the presence of either fatty acids or amino acids. When the mutant was grown in medium containing either isoleucine or valine, organic acid analysis of culture supernatants showed accumulation of 2-oxo acid intermediates of branched chain amino acid catabolism, suggesting feedback inhibition of the upstream branched-chain alpha-keto acid dehydrogenase.
Collapse
Affiliation(s)
- Lori A. Maggio-Hall
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Paul Lyne
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Jon A. Wolff
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Nancy P. Keller
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Corresponding author: 882 Russell Labs, 1630 Linden Drive, Madison, Wisconsin 53706; Telephone: 608-262-9795; Fax: 608-263-2626;
| |
Collapse
|
19
|
Goetzman ES, Wang Y, He M, Mohsen AW, Ninness BK, Vockley J. Expression and characterization of mutations in human very long-chain acyl-CoA dehydrogenase using a prokaryotic system. Mol Genet Metab 2007; 91:138-47. [PMID: 17374501 PMCID: PMC2702680 DOI: 10.1016/j.ymgme.2007.01.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Accepted: 01/30/2007] [Indexed: 11/28/2022]
Abstract
Very long-chain acyl-CoA dehydrogenase (VLCAD) catalyzes the first enzymatic step in the mitochondrial beta-oxidation of fatty acids 14-20 carbons in length. More than 100 cases of VLCAD deficiency have been reported with the disease varying from a severe, often fatal neonatal form to a mild adult-onset form. VLCAD is distinguished from matrix-soluble acyl-CoA dehydrogenases by its unique C-terminal domain, homodimeric structure, and localization to the inner mitochondrial membrane. We have for the first time expressed and purified VLCAD using a bacterial system. Recombinant VLCAD had similar biochemical properties to those reported for native VLCAD and the bacterial system was used to study six previously described disease-causing missense mutations including the two most common mild mutations (T220M, V243A), a mutation leading to the severe disease phenotype (R429W), and three mutations in the C-terminal domain (A450P, L462P, and R573W). Of particular interest was the finding that the A450P and L462P bacterial extracts had normal or increased amounts of VLCAD antigen and activity. In the pure form L462P had roughly 30% of wild-type activity while A450P was normal. Using computer modeling both mutations were mapped to a predicted charged surface of VLCAD that we postulate interacts with the mitochondrial membrane. In a membrane pull down assay both mutants showed greatly reduced mitochondrial membrane association, suggesting a mechanism for the disease in these patients. In summary, the bacterial expression system developed here will significantly advance our understanding of both the clinical aspects of VLCAD deficiency and the basic biochemistry of the enzyme.
Collapse
Affiliation(s)
- Eric S Goetzman
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh, PA 15213, USA
| | | | | | | | | | | |
Collapse
|
20
|
Korman SH. Inborn errors of isoleucine degradation: a review. Mol Genet Metab 2006; 89:289-99. [PMID: 16950638 DOI: 10.1016/j.ymgme.2006.07.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Revised: 07/27/2006] [Accepted: 07/27/2006] [Indexed: 11/28/2022]
Abstract
Three inborn errors have been identified in the pathway of isoleucine degradation. Deficiency of beta-ketothiolase (beta-KT, also known as T2, mitochondrial acetoacetyl-CoA thiolase and acetyl-CoA acetyltransferase 1) is a well-described disorder which presents with acute episodic ketoacidosis. In contrast, short/branched-chain acyl-CoA dehydrogenase (SBCAD) and 2-methyl-3-hydroxybutyryl-CoA dehydrogenase (MHBD) deficiencies are recently described and relatively rare defects which present with predominantly neurological manifestations, although acute metabolic decompensation may occur in the early newborn period. Careful examination of urine organic acids is required for identification and differential diagnosis of these disorders, with awareness that the abnormalities may be subtle and variable. Tandem MS analysis of acylcarnitines may reveal elevated C5 (SBCAD) or C5:1 and/or OH-C5 species (MHBD and beta-KT deficiencies) but the abnormalities are non-diagnostic and may be intermittent or absent. Confirmation of diagnosis is therefore advisable by specific enzyme assay and/or mutation analysis of the ACAT1 (beta-KT), ACADSB (SBCAD) or HADH2 (MHBD) genes. The latter is located on the X chromosome, accounting for the milder clinical phenotype in females. If beta-KT deficiency is diagnosed early and treated by fasting avoidance and modest protein restriction, ketoacidosis episodes can be prevented and the prognosis is excellent. The role of treatment in SBCAD deficiency remains unclear pending further delineation of its clinical phenotype and pathogenicity, particularly regarding asymptomatic individuals detected by expanded newborn screening. The ineffectiveness of isoleucine restriction in MHBD deficiency is consistent with the additional roles of this multifunctional enzyme in sex steroid and neurosteroid metabolism and its interaction with amyloid-beta peptide.
Collapse
Affiliation(s)
- Stanley H Korman
- Metabolic Diseases Unit, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel.
| |
Collapse
|
21
|
Dolled-Filhart M, Rydén L, Cregger M, Jirström K, Harigopal M, Camp RL, Rimm DL. Classification of Breast Cancer Using Genetic Algorithms and Tissue Microarrays. Clin Cancer Res 2006; 12:6459-68. [PMID: 17085660 DOI: 10.1158/1078-0432.ccr-06-1383] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE A multitude of breast cancer mRNA profiling studies has stratified breast cancer and defined gene sets that correlate with outcome. However, the number of genes used to predict patient outcome or define tumor subtypes by RNA expression studies is variable, nonoverlapping, and generally requires specialized technologies that are beyond those used in the routine pathology laboratory. It would be ideal if the familiarity and streamlined nature of immunohistochemistry could be combined with the rigorously quantitative and highly specific properties of nucleic acid-based analysis to predict patient outcome. EXPERIMENTAL DESIGN We have used AQUA-based objective quantitative analysis of tissue microarrays toward the goal of discovery of a minimal number of markers with maximal prognostic or predictive value that can be applied to the conventional formalin-fixed, paraffin-embedded tissue section. RESULTS The minimal discovered multiplexed set of tissue biomarkers was GATA3, NAT1, and estrogen receptor. Genetic algorithms were then applied after division of our cohort into a training set of 223 breast cancer patients to discover a prospectively applicable solution that can define a subset of patients with 5-year survival of 96%. This algorithm was then validated on an internal validation set (n=223, 5-year survival=95.8%) and further validated on an independent cohort from Sweden, which showed 5-year survival of 92.7% (n=149). CONCLUSIONS With further validation, this test has both the familiarity and specificity for widespread use in management of breast cancer. More generally, this work illustrates the potential for multiplexed biomarker discovery on the tissue microarray platform.
Collapse
Affiliation(s)
- Marisa Dolled-Filhart
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520-8023, USA
| | | | | | | | | | | | | |
Collapse
|
22
|
Goetzman ES, He M, Nguyen TV, Vockley J. Functional analysis of acyl-CoA dehydrogenase catalytic residue mutants using surface plasmon resonance and circular dichroism. Mol Genet Metab 2006; 87:233-42. [PMID: 16376132 DOI: 10.1016/j.ymgme.2005.09.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2005] [Revised: 09/28/2005] [Accepted: 09/30/2005] [Indexed: 11/21/2022]
Abstract
The acyl-CoA dehydrogenases (ACDs) are a family of flavoenzymes involved in the metabolism of fatty acids and branched-chain amino acids. The ACDs share a similar structure and a common dehydrogenation mechanism in which a catalytic glutamate extracts a proton from an acyl-CoA substrate. The resulting charge-transfer complex subsequently passes electrons to electron-transferring flavoprotein (ETF). We previously generated catalytic residue mutants of human short-chain acyl-CoA dehydrogenase (SCAD) and isovaleryl-CoA dehydrogenase (IVD) that were difficult to characterize by traditional methods. In the present study, we developed a novel surface plasmon resonance-based assay to measure substrate binding to these mutants. Replacement of the catalytic glutamate in either SCAD or IVD with glycine resulted in a several-fold reduction in affinity for substrate. Circular dichroism studies substantiated our earlier findings that both SCAD E368G and IVD E254G are unable to form a charge-transfer complex with substrate/product. The CD spectra of IVD E254G also indicated a perturbation of the flavin environment, a finding supported by molecular modeling that predicted a shift in the conformation of a conserved tryptophan that lies in close proximity to the flavin. Lastly, competitive inhibition studies using the ETF fluorescence reduction assay suggested that SCAD E368G and IVD E254G do not effectively compete with the wild-type enzymes for the physiological electron acceptor ETF.
Collapse
Affiliation(s)
- Eric S Goetzman
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | | | | | | |
Collapse
|
23
|
Abstract
In the year 2003 there was a 17% increase in the number of publications citing work performed using optical biosensor technology compared with the previous year. We collated the 962 total papers for 2003, identified the geographical regions where the work was performed, highlighted the instrument types on which it was carried out, and segregated the papers by biological system. In this overview, we spotlight 13 papers that should be on everyone's 'must read' list for 2003 and provide examples of how to identify and interpret high-quality biosensor data. Although we still find that the literature is replete with poorly performed experiments, over-interpreted results and a general lack of understanding of data analysis, we are optimistic that these shortcomings will be addressed as biosensor technology continues to mature.
Collapse
Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
| | | |
Collapse
|
24
|
Goetzman ES, Mohsen AWA, Prasad K, Vockley J. Convergent evolution of a 2-methylbutyryl-CoA dehydrogenase from isovaleryl-CoA dehydrogenase in Solanum tuberosum. J Biol Chem 2004; 280:4873-9. [PMID: 15574432 DOI: 10.1074/jbc.m412640200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The potato cDNAs Solanum tuberosum isovaleryl-CoA dehydrogenases 1 and 2 (St-IVD1 and St-IVD2) encode proteins that are 84% identical to each other and 65 and 64% identical to human IVD, respectively. St-IVD2 protein was previously partially purified from potato tubers and confirmed to be an IVD. The function of St-IVD1 is unknown. In these experiments, both proteins were expressed in Escherichia coli and purified as intact homotetramers. The substrate preference profile of the St-IVD2 protein was similar to that of human IVD. However, recombinant St-IVD1 had maximal activity with 2-methylbutyryl-CoA, which in humans is dehydrogenated by short/branched-chain acyl-CoA dehydrogenase (SBCAD). Whereas molecular modeling predicts that the 2-methylbutyryl-CoA dehydrogenase (2MBCD) and IVD substrate binding pockets are nearly identical, 2MBCD has amino acid substitutions at five residues that are invariant among all of the known and putative IVDs. Site-directed mutagenesis was used to match the human IVD active site with that of potato 2MBCD. The resulting mutant IVD had detectable activity with 2-methylbutyryl-CoA and no activity with isovaleryl-CoA. The 2MBCD active site was compared with that of human SBCAD using molecular modeling. Residues Met-361 and Ala-365 of 2MBCD appear to partially substitute for the function of Tyr-380 in human SBCAD, binding the methyl branch linked to C2 of 2-methylbutyryl-CoA, whereas residues Val-88, Val-92, and Val-96 appear to bind the distal C4 methyl group. The presence of a 2MBCD in potato that is highly homologous to IVD is an example of convergent evolution within the acyl-CoA dehydrogenase family, leading to the independent occurrence of two enzymes (SBCAD and 2MBCD) specific for 2-methylbutyryl-CoA.
Collapse
Affiliation(s)
- Eric S Goetzman
- Department of Pediatrics, School of Medicine and Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | | | | | | |
Collapse
|
25
|
Nasser I, Mohsen AW, Jelesarov I, Vockley J, Macheroux P, Ghisla S. Thermal unfolding of medium-chain acyl-CoA dehydrogenase and iso(3)valeryl-CoA dehydrogenase: study of the effect of genetic defects on enzyme stability. Biochim Biophys Acta Mol Basis Dis 2004; 1690:22-32. [PMID: 15337167 DOI: 10.1016/j.bbadis.2004.04.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2003] [Revised: 04/20/2004] [Accepted: 04/21/2004] [Indexed: 10/26/2022]
Abstract
Genetic defects affecting acyl-CoA dehydrogenases (ACAD)-key enzymes in the degradation of fatty acids and branched chain amino acids-are increasingly recognized as being more widespread than originally thought. For the medium-chain acyl-CoA dehydrogenase (MCAD), the K304E mutation is the most common genetic defect among Caucasian populations. The effect of substrate or substrate analog binding on the stability of wild-type MCAD and isovaleryl-CoA dehydrogenase (i3VD) and their genetic mutants (K304E- and T168A-MCAD and A282V-i3VD) is examined. Binding to the mutant ACADs is generally approximately 10-fold weaker compared to wild-type proteins. Thermal stability of wt-MCAD (melting point approximately 53.6 degrees C) is significantly higher compared to wt-i3VD ( approximately 49.3 degrees C). With the exception of the A282V-i3VD mutant, a high degree of stabilization (5-11 degrees C) is induced by conversion into the reduced enzyme form complexed with product. The results are discussed based on the 3D-structures of the enzymes, and it is concluded that in the case of K304E-MCAD thermal stability as such is not a major contribution to the clinical phenotype. With the T168A-MCAD and A282V-i3VD mutants, however, the diminished thermal stability and minor stabilization by ligands must be regarded as an important factor contributing to the manifestation of the disease.
Collapse
Affiliation(s)
- Ibrahim Nasser
- Department of Biology, University of Konstanz, P.O. Box 5560-M644, D-78457 Konstanz, Germany
| | | | | | | | | | | |
Collapse
|
26
|
Cordente AG, López-Viñas E, Vázquez MI, Swiegers JH, Pretorius IS, Gómez-Puertas P, Hegardt FG, Asins G, Serra D. Redesign of carnitine acetyltransferase specificity by protein engineering. J Biol Chem 2004; 279:33899-908. [PMID: 15155769 DOI: 10.1074/jbc.m402685200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In eukaryotes, L-carnitine is involved in energy metabolism by facilitating beta-oxidation of fatty acids. Carnitine acetyltransferases (CrAT) catalyze the reversible conversion of acetyl-CoA and carnitine to acetylcarnitine and free CoA. To redesign the specificity of rat CrAT toward its substrates, we mutated Met564. The M564G mutated CrAT showed higher activity toward longer chain acyl-CoAs: activity toward myristoyl-CoA was 1250-fold higher than that of the wild-type CrAT, and lower activity toward its natural substrate, acetyl-CoA. Kinetic constants of the mutant CrAT showed modification in favor of longer acyl-CoAs as substrates. In the reverse case, mutation of the orthologous glycine (Gly553) to methionine in carnitine octanoyltransferase (COT) decreased activity toward its natural substrates, medium- and long-chain acyl-CoAs, and increased activity toward short-chain acyl-CoAs. Another CrAT mutant, M564A, was prepared and tested in the same way, with similar results. We conclude that Met564 blocks the entry of medium- and long-chain acyl-CoAs to the catalytic site of CrAT. Three-dimensional models of wild-type and mutated CrAT and COT support this hypothesis. We show for the first time that a single amino acid is able to determine the substrate specificity of CrAT and COT.
Collapse
Affiliation(s)
- Antonio G Cordente
- Department of Biochemistry and Molecular Biology, School of Pharmacy, University of Barcelona, Diagonal 643, E-08028 Barcelona, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Hoard-Fruchey HM, Goetzman E, Benson L, Naylor S, Vockley J. Mammalian Electron Transferring Flavoprotein·Flavoprotein Dehydrogenase Complexes Observed by Microelectrospray Ionization-Mass Spectrometry and Surface Plasmon Resonance. J Biol Chem 2004; 279:13786-91. [PMID: 14744856 DOI: 10.1074/jbc.m313914200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microelectrospray ionization-mass spectrometry was used to directly observe electron transferring flavoprotein.flavoprotein dehydrogenase interactions. When electron transferring flavoprotein and porcine dimethylglycine dehydrogenase or sarcosine dehydrogenase were incubated together in the absence of substrate, a relative molecular mass corresponding to the flavoprotein.electron transferring flavoprotein complex was observed, providing the first direct observation of these mammalian complexes. When an acyl-CoA dehydrogenase family member, human short chain acyl-CoA dehydrogenase, was incubated with dimethylglycine dehydrogenase and electron transferring flavoprotein, the microelectrospray ionization-mass spectrometry signal for the dimethylglycine dehydrogenase.electron transferring flavoprotein complex decreased, indicating that the acyl-CoA dehydrogenases have the ability to compete with the dimethylglycine dehydrogenase/sarcosine dehydrogenase family for access to electron transferring flavoprotein. Surface plasmon resonance solution competition experiments revealed affinity constants of 2.0 and 5.0 microm for the dimethylglycine dehydrogenase-electron transferring flavoprotein and short chain acyl-CoA dehydrogenase-electron transferring flavoprotein interactions, respectively, suggesting the same or closely overlapping binding motif(s) on electron transferring flavoprotein for dehydrogenase interaction.
Collapse
Affiliation(s)
- Heidi M Hoard-Fruchey
- Departments of Biochemistry and Molecular Biology and Medical Genetics, Mayo Clinic and Foundation, Rochester, Minnesota 55905, USA
| | | | | | | | | |
Collapse
|