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Rutherford C, Speirs C, Williams JJL, Ewart MA, Mancini SJ, Hawley SA, Delles C, Viollet B, Costa-Pereira AP, Baillie GS, Salt IP, Palmer TM. Phosphorylation of Janus kinase 1 (JAK1) by AMP-activated protein kinase (AMPK) links energy sensing to anti-inflammatory signaling. Sci Signal 2016; 9:ra109. [DOI: 10.1126/scisignal.aaf8566] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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202
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Parker N, Wang Y, Meinke D. Analysis of Arabidopsis Accessions Hypersensitive to a Loss of Chloroplast Translation. PLANT PHYSIOLOGY 2016; 172:1862-1875. [PMID: 27707889 PMCID: PMC5100756 DOI: 10.1104/pp.16.01291] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/03/2016] [Indexed: 05/04/2023]
Abstract
Natural accessions of Arabidopsis (Arabidopsis thaliana) differ in their ability to tolerate a loss of chloroplast translation. These differences can be attributed in part to variation in a duplicated nuclear gene (ACC2) that targets homomeric acetyl-coenzyme A carboxylase (ACCase) to plastids. This functional redundancy allows limited fatty acid biosynthesis to occur in the absence of heteromeric ACCase, which is encoded in part by the plastid genome. In the presence of functional ACC2, tolerant alleles of several nuclear genes, not yet identified, enhance the growth of seedlings and embryos disrupted in chloroplast translation. ACC2 knockout mutants, by contrast, are hypersensitive. Here we describe an expanded search for hypersensitive accessions of Arabidopsis, evaluate whether all of these accessions are defective in ACC2, and characterize genotype-to-phenotype relationships for homomeric ACCase variants identified among 855 accessions with sequenced genomes. Null alleles with ACC2 nonsense mutations, frameshift mutations, small deletions, genomic rearrangements, and defects in RNA splicing are included among the most sensitive accessions examined. By contrast, most missense mutations affecting highly conserved residues failed to eliminate ACC2 function. Several accessions were identified where sensitivity could not be attributed to a defect in either ACC2 or Tic20-IV, the chloroplast membrane channel required for ACC2 uptake. Overall, these results underscore the central role of ACC2 in mediating Arabidopsis response to a loss of chloroplast translation, highlight future applications of this system to analyzing chloroplast protein import, and provide valuable insights into the mutational landscape of an important metabolic enzyme that is highly conserved throughout eukaryotes.
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Affiliation(s)
- Nicole Parker
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, Oklahoma 74078
| | - Yixing Wang
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, Oklahoma 74078
| | - David Meinke
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, Oklahoma 74078
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203
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Gómez E, Muñoz M, Simó C, Ibáñez C, Carrocera S, Martín-González D, Cifuentes A. Non-invasive metabolomics for improved determination of embryonic sex markers in chemically defined culture medium. J Chromatogr A 2016; 1474:138-144. [PMID: 27823786 DOI: 10.1016/j.chroma.2016.10.080] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/26/2016] [Accepted: 10/31/2016] [Indexed: 11/25/2022]
Abstract
Metabolic differences between early male and female embryos can be reflected in culture medium (CM). We used a single bovine embryo culture step (24h) supporting improved birth rates under chemically defined conditions (CDC) to investigate biomarker detection of embryonic sex in contrast to classical BSA-containing medium. In vitro matured slaughterhouse oocytes were fertilized in vitro with a single bull. Embryos were initially cultured in synthetic oviduct fluid with BSA. On day-6, morulae were cultured individually in droplets with (BSA) or without protein (CDC). On day-7, expanded blastocysts were sexed (amelogenin gene amplification) and CM was stored at -145°C until metabolomic analysis by UHPLC-TOF MS. N=10 embryos per group (i.e. male-protein; female-protein; male-non-protein; female-non-protein) were produced. Statistical analysis revealed N=6 metabolites with different concentrations in CM, N=5 in male embryos (methionine, tryptophan, N-stearoyl-valine, biotin and pipecolic acid), N=1 in female embryos (threonine) (P<0.05 in BSA; P<10-7 in CDC). Only the clear threshold between males and females in CDC allowed correct classification of 100% males and 91% females within 5 out of 6 biomarkers (one female outlier showing the male biomarker profile). The use of CDC represents a critical aspect in the efficient detection of embryonic sex biomarkers by metabolomics.
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Affiliation(s)
- E Gómez
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Centro de Biotecnología Animal, Área de Genética y Reproducción Animal, Camino de Rioseco 1225, 33394 Gijón, Spain, Spain
| | - M Muñoz
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Centro de Biotecnología Animal, Área de Genética y Reproducción Animal, Camino de Rioseco 1225, 33394 Gijón, Spain, Spain.
| | - C Simó
- Foodomics Lab & Metabolomics Platform, CIAL, CSIC, Nicolas Cabrera 9, 28049 Madrid, Spain
| | - C Ibáñez
- Foodomics Lab & Metabolomics Platform, CIAL, CSIC, Nicolas Cabrera 9, 28049 Madrid, Spain
| | - S Carrocera
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Centro de Biotecnología Animal, Área de Genética y Reproducción Animal, Camino de Rioseco 1225, 33394 Gijón, Spain, Spain
| | - D Martín-González
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Centro de Biotecnología Animal, Área de Genética y Reproducción Animal, Camino de Rioseco 1225, 33394 Gijón, Spain, Spain
| | - A Cifuentes
- Foodomics Lab & Metabolomics Platform, CIAL, CSIC, Nicolas Cabrera 9, 28049 Madrid, Spain
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204
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Choi PH, Jo J, Lin YC, Lin MH, Chou CY, Dietrich LEP, Tong L. A distinct holoenzyme organization for two-subunit pyruvate carboxylase. Nat Commun 2016; 7:12713. [PMID: 27708276 PMCID: PMC5059739 DOI: 10.1038/ncomms12713] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 07/26/2016] [Indexed: 01/15/2023] Open
Abstract
Pyruvate carboxylase (PC) has important roles in metabolism and is crucial for virulence for some pathogenic bacteria. PC contains biotin carboxylase (BC), carboxyltransferase (CT) and biotin carboxyl carrier protein (BCCP) components. It is a single-chain enzyme in eukaryotes and most bacteria, and functions as a 500 kD homo-tetramer. In contrast, PC is a two-subunit enzyme in a collection of Gram-negative bacteria, with the α subunit containing the BC and the β subunit the CT and BCCP domains, and it is believed that the holoenzyme has α4β4 stoichiometry. We report here the crystal structures of a two-subunit PC from Methylobacillus flagellatus. Surprisingly, our structures reveal an α2β4 stoichiometry, and the overall architecture of the holoenzyme is strikingly different from that of the homo-tetrameric PCs. Biochemical and mutagenesis studies confirm the stoichiometry and other structural observations. Our functional studies in Pseudomonas aeruginosa show that its two-subunit PC is important for colony morphogenesis. Pyruvate carboxylases are homotetrameric enzymes in eukaryotes and most bacteria. Here, the authors report the structure of an unusual two-subunit form of the enzyme from the Gram-negative bacterium Methylobacillus flagellates, revealing an unexpected α2β4 stoichiometry.
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Affiliation(s)
- Philip H Choi
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Jeanyoung Jo
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Yu-Cheng Lin
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Min-Han Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Chi-Yuan Chou
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Lars E P Dietrich
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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205
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Cao Z, Xia Z, Zhou Y, Yang X, Hao H, Peng N, Liu S, Zhu Y. Methylcrotonoyl-CoA carboxylase 1 potentiates RLR-induced NF-κB signaling by targeting MAVS complex. Sci Rep 2016; 6:33557. [PMID: 27629939 PMCID: PMC5024325 DOI: 10.1038/srep33557] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/30/2016] [Indexed: 02/07/2023] Open
Abstract
RNA virus infections are detected by the RIG-I family of receptors, which signal through the adaptor molecule mitochondrial antiviral signaling (MAVS). MAVS then recruits the adaptor’s tumor necrosis factor receptor-associated factor (TRAF) 3 and TRAF6, which in turn activate IRF3 and NF-κB, respectively, to induce interferons (IFNs) and inflammatory responses. Here we show that the biotin-containing enzyme methylcrotonoyl-CoA carboxylase 1 (MCCC1) enhances virus-induced, MAVS-mediated IFN and inflammatory cytokine expression through the NF-κB signaling pathway. MCCC1 knockdown strongly inhibits induction of IFNs and inflammatory cytokines. Furthermore, MCCC1 shows extensive antiviral activity toward RNA viruses, including influenza A virus, human enterovirus 71, and vesicular stomatitis virus. Here, we have elucidated the mechanism underlying MCCC1-mediated inhibition of viral replication. MCCC1 interacts with MAVS and components of the MAVS signalosome and contributes to enhanced production of type I IFNs and pro-inflammatory cytokines by promoting phosphorylation of the IκB kinase (IKK) complex and NF-κB inhibitor-α (IκBα), as well as NF-κB nuclear translocation. This process leads to activation of IFNs and cytokine expression and subsequent activation of IFN-stimulated genes, including double-stranded RNA-dependent protein kinase PKR and myxovirus resistance protein 1. These findings demonstrate that MCCC1 plays an essential role in virus-triggered, MAVS-mediated activation of NF-κB signaling.
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Affiliation(s)
- Zhongying Cao
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhangchuan Xia
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yaqin Zhou
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaodan Yang
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hua Hao
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Nanfang Peng
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Shi Liu
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ying Zhu
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan 430072, China
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206
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Hagmann A, Hunkeler M, Stuttfeld E, Maier T. Hybrid Structure of a Dynamic Single-Chain Carboxylase from Deinococcus radiodurans. Structure 2016; 24:1227-1236. [DOI: 10.1016/j.str.2016.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 05/04/2016] [Accepted: 06/02/2016] [Indexed: 11/28/2022]
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207
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Chang CY, Chang CP, Chakraborty S, Wang SW, Tseng YK, Wang CC. Modulating the Structure and Function of an Aminoacyl-tRNA Synthetase Cofactor by Biotinylation. J Biol Chem 2016; 291:17102-11. [PMID: 27330079 DOI: 10.1074/jbc.m116.734343] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Indexed: 12/20/2022] Open
Abstract
Arc1p is a yeast-specific tRNA-binding protein that forms a ternary complex with glutamyl-tRNA synthetase (GluRSc) and methionyl-tRNA synthetase (MetRS) in the cytoplasm to regulate their catalytic activities and subcellular distributions. Despite Arc1p not being involved in any known biotin-dependent reaction, it is a natural target of biotin modification. Results presented herein show that biotin modification had no obvious effect on the growth-supporting activity, subcellular distribution, tRNA binding, or interactions of Arc1p with GluRSc and MetRS. Nevertheless, biotinylation of Arc1p was temperature dependent; raising the growth temperature from 30 to 37 °C drastically reduced its biotinylation level. As a result, Arc1p purified from a yeast culture that had been grown overnight at 37 °C was essentially biotin free. Non-biotinylated Arc1p was more heat stable, more flexible in structure, and more effective than its biotinylated counterpart in promoting glutamylation activity of the otherwise inactive GluRSc at 37 °C in vitro Our study suggests that the structure and function of Arc1p can be modulated via biotinylation in response to temperature changes.
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Affiliation(s)
| | | | - Shruti Chakraborty
- the Department of Biotechnology, University of Calcutta, Kolkata 700019, India, and
| | - Shao-Win Wang
- the Division of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan Town, Miaoli 35053, Taiwan
| | - Yi-Kuan Tseng
- the Graduate Institute of Statistics, National Central University, Jungli District, Taoyuan 32001, Taiwan
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208
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Skagia A, Zografou C, Vezyri E, Venieraki A, Katinakis P, Dimou M. Cyclophilin PpiB is involved in motility and biofilm formation via its functional association with certain proteins. Genes Cells 2016; 21:833-51. [PMID: 27306110 DOI: 10.1111/gtc.12383] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/09/2016] [Indexed: 12/24/2022]
Abstract
PpiB belongs to the superfamily of peptidyl-prolyl cis/trans isomerases (PPIases, EC: 5.2.1.8), which catalyze the rate-limiting protein folding step at peptidyl-prolyl bonds and control several biological processes. In this study, we show that PpiB acts as a negative effector of motility and biofilm formation ability of Escherichia coli. We identify multicopy suppressors of each ΔppiB phenotype among putative PpiB prey proteins which upon deletion are often characterized by analogous phenotypes. Many putative preys show similar gene expression in wild-type and ΔppiB genetic backgrounds implying possible post-translational modifications by PpiB. We further conducted in vivo and in vitro interaction screens to determine which of them represent true preys. For DnaK, acetyl-CoA carboxylase, biotin carboxylase subunit (AccC) and phosphate acetyltransferase (Pta) we also showed a direct role of PpiB in the functional control of these proteins because it increased the measured enzyme activity of each protein and further interfered with DnaK localization and the correct folding of AccC. Taken together, these results indicate that PpiB is involved in diverse regulatory mechanisms to negatively modulate motility and biofilm formation via its functional association with certain protein substrates.
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Affiliation(s)
- Aggeliki Skagia
- Laboratory of General and Agricultural Microbiology, Faculty of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
| | - Chrysoula Zografou
- Laboratory of General and Agricultural Microbiology, Faculty of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
| | - Eleni Vezyri
- Laboratory of General and Agricultural Microbiology, Faculty of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
| | - Anastasia Venieraki
- Laboratory of General and Agricultural Microbiology, Faculty of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
| | - Panagiotis Katinakis
- Laboratory of General and Agricultural Microbiology, Faculty of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
| | - Maria Dimou
- Laboratory of General and Agricultural Microbiology, Faculty of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
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209
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TASK-1 Regulates Apoptosis and Proliferation in a Subset of Non-Small Cell Lung Cancers. PLoS One 2016; 11:e0157453. [PMID: 27294516 PMCID: PMC4905626 DOI: 10.1371/journal.pone.0157453] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 05/31/2016] [Indexed: 12/29/2022] Open
Abstract
Lung cancer is the leading cause of cancer deaths worldwide; survival times are poor despite therapy. The role of the two-pore domain K+ (K2P) channel TASK-1 (KCNK3) in lung cancer is at present unknown. We found that TASK-1 is expressed in non-small cell lung cancer (NSCLC) cell lines at variable levels. In a highly TASK-1 expressing NSCLC cell line, A549, a characteristic pH- and hypoxia-sensitive non-inactivating K+ current was measured, indicating the presence of functional TASK-1 channels. Inhibition of TASK-1 led to significant depolarization in these cells. Knockdown of TASK-1 by siRNA significantly enhanced apoptosis and reduced proliferation in A549 cells, but not in weakly TASK-1 expressing NCI-H358 cells. Na+-coupled nutrient transport across the cell membrane is functionally coupled to the efflux of K+ via K+ channels, thus TASK-1 may potentially influence Na+-coupled nutrient transport. In contrast to TASK-1, which was not differentially expressed in lung cancer vs. normal lung tissue, we found the Na+-coupled nutrient transporters, SLC5A3, SLC5A6, and SLC38A1, transporters for myo-inositol, biotin and glutamine, respectively, to be significantly overexpressed in lung adenocarcinomas. In summary, we show for the first time that the TASK-1 channel regulates apoptosis and proliferation in a subset of NSCLC.
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210
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Proximity-dependent biotin labelling in yeast using the engineered ascorbate peroxidase APEX2. Biochem J 2016; 473:2463-9. [PMID: 27274088 DOI: 10.1042/bcj20160106] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/07/2016] [Indexed: 11/17/2022]
Abstract
The engineered ascorbate peroxidase (APEX2) has been effectively employed in mammalian cells to identify protein-protein interactions. APEX2 fused to a protein of interest covalently tags nearby proteins with biotin-phenol (BP) when H2O2 is added to the cell culture medium. Subsequent affinity purification of biotinylated proteins allows for identification by MS. BP labelling occurs in 1 min, providing temporal control of labelling. The APEX2 tool enables proteomic mapping of subcellular compartments as well as identification of dynamic protein complexes, and has emerged as a new methodology for proteomic analysis. Despite these advantages, a related APEX2 approach has not been developed for yeast. Here we report methods to enable APEX2-mediated biotin labelling in yeast. Our work demonstrated that high osmolarity and disruption of cell wall integrity permits live-cell biotin labelling in Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively. Under these conditions, APEX2 permitted targeted and proximity-dependent labelling of proteins. The methods described herein set the stage for large-scale proteomic studies in yeast. With modifications, the method is also expected to be effective in other organisms with cell walls, such as bacteria and plants.
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211
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He L, Hamm JA, Reddy A, Sams D, Peliciari-Garcia RA, McGinnis GR, Bailey SM, Chow CW, Rowe GC, Chatham JC, Young ME. Biotinylation: a novel posttranslational modification linking cell autonomous circadian clocks with metabolism. Am J Physiol Heart Circ Physiol 2016; 310:H1520-32. [PMID: 27084392 PMCID: PMC4935513 DOI: 10.1152/ajpheart.00959.2015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 04/08/2016] [Indexed: 01/07/2023]
Abstract
Circadian clocks are critical modulators of metabolism. However, mechanistic links between cell autonomous clocks and metabolic processes remain largely unknown. Here, we report that expression of the biotin transporter slc5a6 gene is decreased in hearts of two distinct genetic mouse models of cardiomyocyte-specific circadian clock disruption [i.e., cardiomyocyte-specific CLOCK mutant (CCM) and cardiomyocyte-specific BMAL1 knockout (CBK) mice]. Biotinylation is an obligate posttranslational modification for five mammalian carboxylases: acetyl-CoA carboxylase α (ACCα), ACCβ, pyruvate carboxylase (PC), methylcrotonyl-CoA carboxylase (MCC), and propionyl-CoA carboxylase (PCC). We therefore hypothesized that the cardiomyocyte circadian clock impacts metabolism through biotinylation. Consistent with decreased slc5a6 expression, biotinylation of all carboxylases is significantly decreased (10-46%) in CCM and CBK hearts. In association with decreased biotinylated ACC, oleate oxidation rates are increased in both CCM and CBK hearts. Consistent with decreased biotinylated MCC, leucine oxidation rates are significantly decreased in both CCM and CBK hearts, whereas rates of protein synthesis are increased. Importantly, feeding CBK mice with a biotin-enriched diet for 6 wk normalized myocardial 1) ACC biotinylation and oleate oxidation rates; 2) PCC/MCC biotinylation (and partially restored leucine oxidation rates); and 3) net protein synthesis rates. Furthermore, data suggest that the RRAGD/mTOR/4E-BP1 signaling axis is chronically activated in CBK and CCM hearts. Finally we report that the hepatocyte circadian clock also regulates both slc5a6 expression and protein biotinylation in the liver. Collectively, these findings suggest that biotinylation is a novel mechanism by which cell autonomous circadian clocks influence metabolic pathways.
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Affiliation(s)
- Lan He
- Division of Cardiovascular Disease, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - J Austin Hamm
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Alex Reddy
- Division of Cardiovascular Disease, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - David Sams
- Division of Cardiovascular Disease, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Graham R McGinnis
- Division of Cardiovascular Disease, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Shannon M Bailey
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama; and
| | - Chi-Wing Chow
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York
| | - Glenn C Rowe
- Division of Cardiovascular Disease, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - John C Chatham
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama; and
| | - Martin E Young
- Division of Cardiovascular Disease, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama;
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212
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The dynamic organization of fungal acetyl-CoA carboxylase. Nat Commun 2016; 7:11196. [PMID: 27073141 PMCID: PMC4833862 DOI: 10.1038/ncomms11196] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 03/01/2016] [Indexed: 12/12/2022] Open
Abstract
Acetyl-CoA carboxylases (ACCs) catalyse the committed step in fatty-acid biosynthesis: the ATP-dependent carboxylation of acetyl-CoA to malonyl-CoA. They are important regulatory hubs for metabolic control and relevant drug targets for the treatment of the metabolic syndrome and cancer. Eukaryotic ACCs are single-chain multienzymes characterized by a large, non-catalytic central domain (CD), whose role in ACC regulation remains poorly characterized. Here we report the crystal structure of the yeast ACC CD, revealing a unique four-domain organization. A regulatory loop, which is phosphorylated at the key functional phosphorylation site of fungal ACC, wedges into a crevice between two domains of CD. Combining the yeast CD structure with intermediate and low-resolution data of larger fragments up to intact ACCs provides a comprehensive characterization of the dynamic fungal ACC architecture. In contrast to related carboxylases, large-scale conformational changes are required for substrate turnover, and are mediated by the CD under phosphorylation control. Acetyl-CoA carboxylases are central regulatory hubs of fatty acid metabolism and are important targets for drug development in obesity and cancer. Here, the authors demonstrate that the regulation of these highly dynamic enzymes in fungi is governed by a mechanism based on phosphorylation-dependent conformational variability.
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213
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Abstract
The metabolite 2-oxoglutarate (also known as α-ketoglutarate, 2-ketoglutaric acid, or oxoglutaric acid) lies at the intersection between the carbon and nitrogen metabolic pathways. This compound is a key intermediate of one of the most fundamental biochemical pathways in carbon metabolism, the tricarboxylic acid (TCA) cycle. In addition, 2-oxoglutarate also acts as the major carbon skeleton for nitrogen-assimilatory reactions. Experimental data support the conclusion that intracellular levels of 2-oxoglutarate fluctuate according to nitrogen and carbon availability. This review summarizes how nature has capitalized on the ability of 2-oxoglutarate to reflect cellular nutritional status through evolution of a variety of 2-oxoglutarate-sensing regulatory proteins. The number of metabolic pathways known to be regulated by 2-oxoglutarate levels has increased significantly in recent years. The signaling properties of 2-oxoglutarate are highlighted by the fact that this metabolite regulates the synthesis of the well-established master signaling molecule, cyclic AMP (cAMP), in Escherichia coli.
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214
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The Role of Biotin in Bacterial Physiology and Virulence: a Novel Antibiotic Target for
Mycobacterium tuberculosis. Microbiol Spectr 2016; 4. [DOI: 10.1128/microbiolspec.vmbf-0008-2015] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ABSTRACT
Biotin is an essential cofactor for enzymes present in key metabolic pathways such as fatty acid biosynthesis, replenishment of the tricarboxylic acid cycle, and amino acid metabolism. Biotin is synthesized
de novo
in microorganisms, plants, and fungi, but this metabolic activity is absent in mammals, making biotin biosynthesis an attractive target for antibiotic discovery. In particular, biotin biosynthesis plays important metabolic roles as the sole source of biotin in all stages of the
Mycobacterium tuberculosis
life cycle due to the lack of a transporter for scavenging exogenous biotin. Biotin is intimately associated with lipid synthesis where the products form key components of the mycobacterial cell membrane that are critical for bacterial survival and pathogenesis. In this review we discuss the central role of biotin in bacterial physiology and highlight studies that demonstrate the importance of its biosynthesis for virulence. The structural biology of the known biotin synthetic enzymes is described alongside studies using structure-guided design, phenotypic screening, and fragment-based approaches to drug discovery as routes to new antituberculosis agents.
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215
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Acetyl-CoA carboxylase inhibition by ND-630 reduces hepatic steatosis, improves insulin sensitivity, and modulates dyslipidemia in rats. Proc Natl Acad Sci U S A 2016; 113:E1796-805. [PMID: 26976583 DOI: 10.1073/pnas.1520686113] [Citation(s) in RCA: 203] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Simultaneous inhibition of the acetyl-CoA carboxylase (ACC) isozymes ACC1 and ACC2 results in concomitant inhibition of fatty acid synthesis and stimulation of fatty acid oxidation and may favorably affect the morbidity and mortality associated with obesity, diabetes, and fatty liver disease. Using structure-based drug design, we have identified a series of potent allosteric protein-protein interaction inhibitors, exemplified by ND-630, that interact within the ACC phosphopeptide acceptor and dimerization site to prevent dimerization and inhibit the enzymatic activity of both ACC isozymes, reduce fatty acid synthesis and stimulate fatty acid oxidation in cultured cells and in animals, and exhibit favorable drug-like properties. When administered chronically to rats with diet-induced obesity, ND-630 reduces hepatic steatosis, improves insulin sensitivity, reduces weight gain without affecting food intake, and favorably affects dyslipidemia. When administered chronically to Zucker diabetic fatty rats, ND-630 reduces hepatic steatosis, improves glucose-stimulated insulin secretion, and reduces hemoglobin A1c (0.9% reduction). Together, these data suggest that ACC inhibition by representatives of this series may be useful in treating a variety of metabolic disorders, including metabolic syndrome, type 2 diabetes mellitus, and fatty liver disease.
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216
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Lipids and bariatric procedures Part 2 of 2: scientific statement from the American Society for Metabolic and Bariatric Surgery (ASMBS), the National Lipid Association (NLA), and Obesity Medicine Association (OMA) 1. Surg Obes Relat Dis 2016; 12:468-495. [DOI: 10.1016/j.soard.2016.01.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 01/08/2016] [Indexed: 12/17/2022]
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217
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Phillips BE, Geletzke AK, Smith PB, Podany AB, Chacon A, Kelleher SL, Patterson AD, Soybel DI. Impaired recovery from peritoneal inflammation in a mouse model of mild dietary zinc restriction. Mol Nutr Food Res 2016; 60:672-81. [DOI: 10.1002/mnfr.201500688] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/30/2015] [Accepted: 10/31/2015] [Indexed: 12/31/2022]
Affiliation(s)
| | | | - Philip B. Smith
- Departments of Veterinary and Biomedical Sciences; University Park PA USA
- The Huck Institutes of the Life Sciences; University Park PA USA
| | | | | | - Shannon L. Kelleher
- Departments of Surgery; Hershey PA USA
- Cellular and Molecular Physiology; Hershey PA USA
| | - Andrew D. Patterson
- Departments of Veterinary and Biomedical Sciences; University Park PA USA
- Molecular Toxicology; University Park PA USA
| | - David I. Soybel
- Departments of Surgery; Hershey PA USA
- Cellular and Molecular Physiology; Hershey PA USA
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218
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Structural basis for specificity and promiscuity in a carrier protein/enzyme system from the sulfur cycle. Proc Natl Acad Sci U S A 2015; 112:E7166-75. [PMID: 26655737 DOI: 10.1073/pnas.1506386112] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The bacterial Sox (sulfur oxidation) pathway is an important route for the oxidation of inorganic sulfur compounds. Intermediates in the Sox pathway are covalently attached to the heterodimeric carrier protein SoxYZ through conjugation to a cysteine on a protein swinging arm. We have investigated how the carrier protein shuttles intermediates between the enzymes of the Sox pathway using the interaction between SoxYZ and the enzyme SoxB as our model. The carrier protein and enzyme interact only weakly, but we have trapped their complex by using a "suicide enzyme" strategy in which an engineered cysteine in the SoxB active site forms a disulfide bond with the incoming carrier arm cysteine. The structure of this trapped complex, together with calorimetric data, identifies sites of protein-protein interaction both at the entrance to the enzyme active site tunnel and at a second, distal, site. We find that the enzyme distinguishes between the substrate and product forms of the carrier protein through differences in their interaction kinetics and deduce that this behavior arises from substrate-specific stabilization of a conformational change in the enzyme active site. Our analysis also suggests how the carrier arm-bound substrate group is able to outcompete the adjacent C-terminal carboxylate of the carrier arm for binding to the active site metal ions. We infer that similar principles underlie carrier protein interactions with other enzymes of the Sox pathway.
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219
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Alissandratos A, Easton CJ. Biocatalysis for the application of CO2 as a chemical feedstock. Beilstein J Org Chem 2015; 11:2370-87. [PMID: 26734087 PMCID: PMC4685893 DOI: 10.3762/bjoc.11.259] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 11/20/2015] [Indexed: 11/23/2022] Open
Abstract
Biocatalysts, capable of efficiently transforming CO2 into other more reduced forms of carbon, offer sustainable alternatives to current oxidative technologies that rely on diminishing natural fossil-fuel deposits. Enzymes that catalyse CO2 fixation steps in carbon assimilation pathways are promising catalysts for the sustainable transformation of this safe and renewable feedstock into central metabolites. These may be further converted into a wide range of fuels and commodity chemicals, through the multitude of known enzymatic reactions. The required reducing equivalents for the net carbon reductions may be drawn from solar energy, electricity or chemical oxidation, and delivered in vitro or through cellular mechanisms, while enzyme catalysis lowers the activation barriers of the CO2 transformations to make them more energy efficient. The development of technologies that treat CO2-transforming enzymes and other cellular components as modules that may be assembled into synthetic reaction circuits will facilitate the use of CO2 as a renewable chemical feedstock, greatly enabling a sustainable carbon bio-economy.
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Affiliation(s)
| | - Christopher J Easton
- Research School of Chemistry, Australian National University, Canberra ACT 2601, Australia
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220
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Biotin-dependent functions in adiposity: a study of monozygotic twin pairs. Int J Obes (Lond) 2015; 40:788-95. [PMID: 26601567 DOI: 10.1038/ijo.2015.237] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 10/16/2015] [Accepted: 11/06/2015] [Indexed: 12/28/2022]
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221
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Jurado AR, Huang CS, Zhang X, Zhou ZH, Tong L. Structure and substrate selectivity of the 750-kDa α6β6 holoenzyme of geranyl-CoA carboxylase. Nat Commun 2015; 6:8986. [PMID: 26593090 PMCID: PMC4673880 DOI: 10.1038/ncomms9986] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 10/22/2015] [Indexed: 01/15/2023] Open
Abstract
Geranyl-CoA carboxylase (GCC) is essential for the growth of Pseudomonas organisms with geranic acid as the sole carbon source. GCC has the same domain organization and shares strong sequence conservation with the related biotin-dependent carboxylases 3-methylcrotonyl-CoA carboxylase (MCC) and propionyl-CoA carboxylase (PCC). Here we report the crystal structure of the 750-kDa α6β6 holoenzyme of GCC, which is similar to MCC but strikingly different from PCC. The structures provide evidence in support of two distinct lineages of biotin-dependent acyl-CoA carboxylases, one carboxylating the α carbon of a saturated organic acid and the other carboxylating the γ carbon of an α-β unsaturated acid. Structural differences in the active site region of GCC and MCC explain their distinct substrate preferences. Especially, a glycine residue in GCC is replaced by phenylalanine in MCC, which blocks access by the larger geranyl-CoA substrate. Mutation of this residue in the two enzymes can change their substrate preferences. The structures of the biotin-dependent carboxylases have revealed details of their function. Here, the authors describe the first structure of Pseudomonas geranyl-CoA carboxylase, and compare it with the previously characterised homologous 3-methylcrotonyl-CoA carboxylase.
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Affiliation(s)
- Ashley R Jurado
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Christine S Huang
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Xing Zhang
- California NanoSystems Institute, University of California, Los Angeles, California 90095, USA
| | - Z Hong Zhou
- California NanoSystems Institute, University of California, Los Angeles, California 90095, USA.,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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222
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Wei J, Tong L. Crystal structure of the 500-kDa yeast acetyl-CoA carboxylase holoenzyme dimer. Nature 2015; 526:723-7. [PMID: 26458104 PMCID: PMC4838907 DOI: 10.1038/nature15375] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Accepted: 08/04/2015] [Indexed: 12/13/2022]
Abstract
Acetyl-CoA carboxylase (ACC) has crucial roles in fatty acid metabolism and is an attractive target for drug discovery against diabetes, cancer and other diseases. Saccharomyces cerevisiae ACC (ScACC) is crucial for the production of very-long-chain fatty acids and the maintenance of the nuclear envelope. ACC contains biotin carboxylase (BC) and carboxyltransferase (CT) activities, and its biotin is linked covalently to the biotin carboxyl carrier protein (BCCP). Most eukaryotic ACCs are 250-kilodalton (kDa), multi-domain enzymes and function as homodimers and higher oligomers. They contain a unique, 80-kDa central region that shares no homology with other proteins. Although the structures of the BC, CT and BCCP domains and other biotin-dependent carboxylase holoenzymes are known, there is currently no structural information on the ACC holoenzyme. Here we report the crystal structure of the full-length, 500-kDa holoenzyme dimer of ScACC. The structure is remarkably different from that of the other biotin-dependent carboxylases. The central region contains five domains and is important for positioning the BC and CT domains for catalysis. The structure unexpectedly reveals a dimer of the BC domain and extensive conformational differences compared to the structure of the BC domain alone, which is a monomer. These structural changes reveal why the BC domain alone is catalytically inactive and define the molecular mechanism for the inhibition of eukaryotic ACC by the natural product soraphen A and by phosphorylation of a Ser residue just before the BC domain core in mammalian ACC. The BC and CT active sites are separated by 80 Å, and the entire BCCP domain must translocate during catalysis.
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Affiliation(s)
- Jia Wei
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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223
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Sedel F, Bernard D, Mock DM, Tourbah A. Targeting demyelination and virtual hypoxia with high-dose biotin as a treatment for progressive multiple sclerosis. Neuropharmacology 2015; 110:644-653. [PMID: 26327679 DOI: 10.1016/j.neuropharm.2015.08.028] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/24/2015] [Accepted: 08/18/2015] [Indexed: 12/30/2022]
Abstract
Progressive multiple sclerosis (MS) is a severely disabling neurological condition, and an effective treatment is urgently needed. Recently, high-dose biotin has emerged as a promising therapy for affected individuals. Initial clinical data have shown that daily doses of biotin of up to 300 mg can improve objective measures of MS-related disability. In this article, we review the biology of biotin and explore the properties of this ubiquitous coenzyme that may explain the encouraging responses seen in patients with progressive MS. The gradual worsening of neurological disability in patients with progressive MS is caused by progressive axonal loss or damage. The triggers for axonal loss in MS likely include both inflammatory demyelination of the myelin sheath and primary neurodegeneration caused by a state of virtual hypoxia within the neuron. Accordingly, targeting both these pathological processes could be effective in the treatment of progressive MS. Biotin is an essential co-factor for five carboxylases involved in fatty acid synthesis and energy production. We hypothesize that high-dose biotin is exerting a therapeutic effect in patients with progressive MS through two different and complementary mechanisms: by promoting axonal remyelination by enhancing myelin production and by reducing axonal hypoxia through enhanced energy production. This article is part of the Special Issue entitled 'Oligodendrocytes in Health and Disease'.
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Affiliation(s)
- Frédéric Sedel
- MedDay Pharmaceuticals, ICM-Brain and Spine Institute-IPEPs, Groupe Hospitalier Pitié Salpêtrière, 47 Boulevard de l'Hopital, 75013 Paris, France.
| | - Delphine Bernard
- MedDay Pharmaceuticals, ICM-Brain and Spine Institute-IPEPs, Groupe Hospitalier Pitié Salpêtrière, 47 Boulevard de l'Hopital, 75013 Paris, France.
| | - Donald M Mock
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, 4301 W Markham Street, Little Rock, AR 72205, USA; Department of Pediatrics, University of Arkansas for Medical Sciences, 4301 W Markham Street, Little Rock, AR 72205, USA.
| | - Ayman Tourbah
- Department of Neurology and Faculté de Médecine de Reims, CHU de Reims, URCA, 45 Rue Cognacq Jay, 51092 Reims Cedex, France.
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224
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Obesity and cancer progression: is there a role of fatty acid metabolism? BIOMED RESEARCH INTERNATIONAL 2015; 2015:274585. [PMID: 25866768 PMCID: PMC4383231 DOI: 10.1155/2015/274585] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 11/24/2014] [Indexed: 12/30/2022]
Abstract
Currently, there is renewed interest in elucidating the metabolic characteristics of cancer and how these characteristics may be exploited as therapeutic targets. Much attention has centered on glucose, glutamine and de novo lipogenesis, yet the metabolism of fatty acids that arise from extracellular, as well as intracellular, stores as triacylglycerol has received much less attention. This review focuses on the key pathways of fatty acid metabolism, including uptake, esterification, lipolysis, and mitochondrial oxidation, and how the regulators of these pathways are altered in cancer. Additionally, we discuss the potential link that fatty acid metabolism may serve between obesity and changes in cancer progression.
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225
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Bogdanova VS, Zaytseva OO, Mglinets AV, Shatskaya NV, Kosterin OE, Vasiliev GV. Nuclear-cytoplasmic conflict in pea (Pisum sativum L.) is associated with nuclear and plastidic candidate genes encoding acetyl-CoA carboxylase subunits. PLoS One 2015; 10:e0119835. [PMID: 25789472 PMCID: PMC4366379 DOI: 10.1371/journal.pone.0119835] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/16/2015] [Indexed: 11/18/2022] Open
Abstract
In crosses of wild and cultivated peas (Pisum sativum L.), nuclear-cytoplasmic incompatibility frequently occurs manifested as decreased pollen fertility, male gametophyte lethality, sporophyte lethality. High-throughput sequencing of plastid genomes of one cultivated and four wild pea accessions differing in cross-compatibility was performed. Candidate genes for involvement in the nuclear-plastid conflict were searched in the reconstructed plastid genomes. In the annotated Medicago truncatula genome, nuclear candidate genes were searched in the portion syntenic to the pea chromosome region known to harbor a locus involved in the conflict. In the plastid genomes, a substantial variability of the accD locus represented by nucleotide substitutions and indels was found to correspond to the pattern of cross-compatibility among the accessions analyzed. Amino acid substitutions in the polypeptides encoded by the alleles of a nuclear locus, designated as Bccp3, with a complementary function to accD, fitted the compatibility pattern. The accD locus in the plastid genome encoding beta subunit of the carboxyltransferase of acetyl-coA carboxylase and the nuclear locus Bccp3 encoding biotin carboxyl carrier protein of the same multi-subunit enzyme were nominated as candidate genes for main contribution to nuclear-cytoplasmic incompatibility in peas. Existence of another nuclear locus involved in the accD-mediated conflict is hypothesized.
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Affiliation(s)
- Vera S. Bogdanova
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
| | - Olga O. Zaytseva
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Anatoliy V. Mglinets
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalia V. Shatskaya
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
| | - Oleg E. Kosterin
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Gennadiy V. Vasiliev
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
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226
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Ehebauer MT, Zimmermann M, Jakobi AJ, Noens EE, Laubitz D, Cichocki B, Marrakchi H, Lanéelle MA, Daffé M, Sachse C, Dziembowski A, Sauer U, Wilmanns M. Characterization of the mycobacterial acyl-CoA carboxylase holo complexes reveals their functional expansion into amino acid catabolism. PLoS Pathog 2015; 11:e1004623. [PMID: 25695631 PMCID: PMC4347857 DOI: 10.1371/journal.ppat.1004623] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 12/11/2014] [Indexed: 01/22/2023] Open
Abstract
Biotin-mediated carboxylation of short-chain fatty acid coenzyme A esters is a key
step in lipid biosynthesis that is carried out by multienzyme complexes to extend
fatty acids by one methylene group. Pathogenic mycobacteria have an unusually high
redundancy of carboxyltransferase genes and biotin carboxylase genes, creating
multiple combinations of protein/protein complexes of unknown overall composition and
functional readout. By combining pull-down assays with mass spectrometry, we
identified nine binary protein/protein interactions and four validated holo
acyl-coenzyme A carboxylase complexes. We investigated one of these - the AccD1-AccA1
complex from Mycobacterium tuberculosis with hitherto unknown
physiological function. Using genetics, metabolomics and biochemistry we found that
this complex is involved in branched amino-acid catabolism with methylcrotonyl
coenzyme A as the substrate. We then determined its overall architecture by electron
microscopy and found it to be a four-layered dodecameric arrangement that matches the
overall dimensions of a distantly related methylcrotonyl coenzyme A holo complex. Our
data argue in favor of distinct structural requirements for biotin-mediated
γ-carboxylation of α−β unsaturated acid esters and will
advance the categorization of acyl-coenzyme A carboxylase complexes. Knowledge about
the underlying structural/functional relationships will be crucial to make the target
category amenable for future biomedical applications. Tuberculosis is deadly human disease caused by infection with the bacterium
Mycobacterium tuberculosis. This pathogen has a complex
metabolism with many genes required for the synthesis of components of its unique
cell envelope. We have investigated a family of closely related genes coding for
different acyl CoA carboxylase enzyme complexes with previously unexplained genetic
redundancy that have been thought to have an involvement in the synthesis of these
cell envelope components. We identified five functional multienzyme complexes. Of the
two complexes with hitherto unknown function we chose to investigate, one
specifically and to our surprise it is required for the degradation of the amino acid
leucine. To our knowledge this is the first demonstration that mycobacteria have a
specific pathway for leucine degradation and thus broaden the functional diversity
associated with acyl CoA carboxylase coding genes.
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Affiliation(s)
| | | | - Arjen J. Jakobi
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg,
Germany
- European Molecular Biology Laboratory, Structural Biology and Computational
Biology Programme, Heidelberg, Germany
| | - Elke E. Noens
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg,
Germany
| | - Daniel Laubitz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw,
Poland
- Department of Genetics & Biotechnology, Warsaw University, Warsaw,
Poland
| | - Bogdan Cichocki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw,
Poland
- Department of Genetics & Biotechnology, Warsaw University, Warsaw,
Poland
| | - Hedia Marrakchi
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de
Biologie Structurale, Tuberculosis & Infection Biology Department, Toulouse,
France; Université Paul Sabatier, Toulouse, France
| | - Marie-Antoinette Lanéelle
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de
Biologie Structurale, Tuberculosis & Infection Biology Department, Toulouse,
France; Université Paul Sabatier, Toulouse, France
| | - Mamadou Daffé
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de
Biologie Structurale, Tuberculosis & Infection Biology Department, Toulouse,
France; Université Paul Sabatier, Toulouse, France
| | - Carsten Sachse
- European Molecular Biology Laboratory, Structural Biology and Computational
Biology Programme, Heidelberg, Germany
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw,
Poland
- Department of Genetics & Biotechnology, Warsaw University, Warsaw,
Poland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich,
Switzerland
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg,
Germany
- Center for Structural Systems Biology, Hamburg, Germany
- * E-mail:
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227
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Tsuji A, Nakamura T, Shibata K. Biotin-deficient diet induces chromosome misalignment and spindle defects in mouse oocytes. Biosci Biotechnol Biochem 2015; 79:292-9. [DOI: 10.1080/09168451.2014.968090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Abstract
Increased abnormal oocytes due to meiotic chromosome misalignment and spindle defects lead to elevated rates of infertility, miscarriage, and trisomic conceptions. Here, we investigated the effect of biotin deficiency on oocyte quality. Three-week-old female ICR mice were fed a biotin-deficient or control diet (0, 0.004 g biotin/kg diet) for 21 days. On day 22, these mouse oocytes were analyzed by immunofluorescence. Due to biotin, undernutrition increased the frequency of abnormal oocytes (the biotin deficient vs. control: 40 vs. 16%). Next, the remaining mice in the biotin-deficient group were fed a control or biotin-deficient diet from day 22 to 42. Although biotin nutritional status in the recovery group was restored, the frequency of abnormal oocytes in the recovery group was still higher than that in the control group (48 vs. 18%). Our results indicate that steady, sufficient biotin intake is required for the production of high-quality oocytes in mice.
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Affiliation(s)
- Ai Tsuji
- Department of Nutrition, School of Human Cultures, The University of Shiga Prefecture, Hikone, Japan
| | - Toshinobu Nakamura
- Department of Animal Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Katsumi Shibata
- Department of Nutrition, School of Human Cultures, The University of Shiga Prefecture, Hikone, Japan
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228
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Gerhardt EC, Rodrigues TE, Müller-Santos M, Pedrosa FO, Souza EM, Forchhammer K, Huergo LF. The Bacterial signal transduction protein GlnB regulates the committed step in fatty acid biosynthesis by acting as a dissociable regulatory subunit of acetyl-CoA carboxylase. Mol Microbiol 2015; 95:1025-35. [DOI: 10.1111/mmi.12912] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Edileusa C.M. Gerhardt
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular; Universidade Federal do Paraná; CEP 81531-990 CP 19046 Curitiba PR Brazil
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin der Eberhard-Karls Universität Tübingen; Auf der Morgenstelle 28 Tübingen 72076 Germany
| | - Thiago E. Rodrigues
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular; Universidade Federal do Paraná; CEP 81531-990 CP 19046 Curitiba PR Brazil
| | - Marcelo Müller-Santos
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular; Universidade Federal do Paraná; CEP 81531-990 CP 19046 Curitiba PR Brazil
| | - Fabio O. Pedrosa
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular; Universidade Federal do Paraná; CEP 81531-990 CP 19046 Curitiba PR Brazil
| | - Emanuel M. Souza
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular; Universidade Federal do Paraná; CEP 81531-990 CP 19046 Curitiba PR Brazil
| | - Karl Forchhammer
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin der Eberhard-Karls Universität Tübingen; Auf der Morgenstelle 28 Tübingen 72076 Germany
| | - Luciano F. Huergo
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular; Universidade Federal do Paraná; CEP 81531-990 CP 19046 Curitiba PR Brazil
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229
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Sedel F, Papeix C, Bellanger A, Touitou V, Lebrun-Frenay C, Galanaud D, Gout O, Lyon-Caen O, Tourbah A. High doses of biotin in chronic progressive multiple sclerosis: a pilot study. Mult Scler Relat Disord 2015; 4:159-69. [PMID: 25787192 DOI: 10.1016/j.msard.2015.01.005] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 12/26/2014] [Accepted: 01/12/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND No drug has been found to have any impact on progressive multiple sclerosis (MS). Biotin is a vitamin acting as a coenzyme for carboxylases involved in key steps of energy metabolism and fatty acids synthesis. Among others, biotin activates acetylCoA carboxylase, a potentially rate-limiting enzyme in myelin synthesis. OBJECTIVES The aim of this pilot study is to assess the clinical efficacy and safety of high doses of biotin in patients suffering from progressive MS. STUDY DESIGN Uncontrolled, non-blinded proof of concept study METHODS 23 consecutive patients with primary and secondary progressive MS originated from three different French MS reference centers were treated with high doses of biotin (100-300mg/day) from 2 to 36 months (mean=9.2 months). Judgement criteria varied according to clinical presentations and included quantitative and qualitative measures. RESULTS In four patients with prominent visual impairment related to optic nerve injury, visual acuity improved significantly. Visual evoked potentials in two patients exhibited progressive reappearance of P100 waves, with normalization of latencies in one case. Proton magnetic resonance spectroscopy (H-MRS) in one case showed a progressive normalization of the Choline/Creatine ratio. One patient with left homonymous hemianopia kept on improving from 2 to 16 months following treatment׳s onset. Sixteen patients out of 18 (89%) with prominent spinal cord involvement were considered as improved as confirmed by blinded review of videotaped clinical examination in 9 cases. In all cases improvement was delayed from 2 to 8 months following treatment׳s onset. CONCLUSIONS These preliminary data suggest that high doses of biotin might have an impact on disability and progression in progressive MS. Two double-blind placebo-controlled trials are on going.
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Affiliation(s)
- Frédéric Sedel
- Neurology Department, AP-HP, Salpêtrière Hospital, Paris, France; Neuro-Metabolic Unit and Reference Center for Lysosomal Diseases, GRC13UPMC, Pierre & Marie Curie University-Paris 6, AP-HP, Salpêtrière Hospital, Paris, France
| | - Caroline Papeix
- Neurology Department, AP-HP, Salpêtrière Hospital, Paris, France
| | | | - Valérie Touitou
- Department of Ophthalmology, AP-HP, Salpêtrière Hospital, Paris, France
| | | | - Damien Galanaud
- Department of Neuroradiology, Pierre & Marie Curie University-Paris 6, Paris, France
| | - Olivier Gout
- Department of Neurology, Fondation Ophtalmologique Adolphe de Rothschild, Paris, France
| | | | - Ayman Tourbah
- Neurology Department, CHU de Reims & Faculté de Médecine de Reims, Champagne-Ardennes University, France; Laboratoire de Psychopathologie et de Neuropsychologie, EA 2027 Paris VIII University, Saint Denis, France.
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230
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Valdés-Ramos R, Guadarrama-López AL, Martínez-Carrillo BE, Benítez-Arciniega AD. Vitamins and type 2 diabetes mellitus. Endocr Metab Immune Disord Drug Targets 2015; 15:54-63. [PMID: 25388747 PMCID: PMC4435229 DOI: 10.2174/1871530314666141111103217] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 10/30/2014] [Accepted: 10/31/2014] [Indexed: 12/14/2022]
Abstract
The present review evaluates the relationship between type 2 diabetes mellitus and individual or combined vitamins. Antioxidant vitamins A, C and E are found decreased in diabetic subjects, possibly due to an increased need to control the excessive oxidative stress produced by abnormalities in glucose metabolism. On the other hand, retinol binding protein exerts a modulating effect, as it has adipokine functions. With respect to the B group vitamins, thiamin, pyridoxine and biotin have been found decreased but the mechanisms are not clear, however supplementation has shown some improvement of the metabolic control in diabetic patients. The absorption of folic acid and vitamin B12 is importantly decreased by the prolongued use of metformin, which is the first choice drug in uncomplicated diabetes, thus these two nutrients have been found deficient in the disease and most probably need to be supplemented regularly. On the other hand, vitamin D is considered a risk factor for the development of diabetes as well as its complications, particularly cardiovascular ones. Although some studies have found an association of vitamin K intake with glucose metabolism further research is needed. Studies on the use of multivitamin supplements have shown unconclusive results. After reviewing the evidence, no real recommendation on the use of vitamin supplements in type 2 diabetes mellitus can be issued, however patients using metformin during prolongued periods may need folic acid and vitamin B12.
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231
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Lümmen P, Khajehali J, Luther K, Van Leeuwen T. The cyclic keto-enol insecticide spirotetramat inhibits insect and spider mite acetyl-CoA carboxylases by interfering with the carboxyltransferase partial reaction. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2014; 55:1-8. [PMID: 25281882 DOI: 10.1016/j.ibmb.2014.09.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 09/19/2014] [Accepted: 09/20/2014] [Indexed: 06/03/2023]
Abstract
Acetyl-CoA carboxylase (ACC) catalyzes the committed and rate-limiting step in fatty acid biosynthesis. The two partial reactions, carboxylation of biotin followed by carboxyl transfer to the acceptor acetyl-CoA, are performed by two separate domains in animal ACCs. The cyclic keto-enol insecticides and acaricides have been proposed to inhibit insect ACCs. In this communication, we show that the enol derivative of the cylic keto-enol insecticide spirotetramat inhibited ACCs partially purified from the insect species Myzus persicae and Spodoptera frugiperda, as well as the spider mite (Tetranychus urticae) ACC which was expressed in insect cells using a recombinant baculovirus. Steady-state kinetic analysis revealed competitive inhibition with respect to the carboxyl acceptor, acetyl-CoA, indicating that spirotetramat-enol bound to the carboxyltransferase domain of ACC. Interestingly, inhibition with respect to the biotin carboxylase substrate ATP was uncompetitive. Amino acid residues in the carboxyltransferase domains of plant ACCs are important for binding of established herbicidal inhibitors. Mutating the spider mite ACC at the homologous positions, for example L1736 to either isoleucine or alanine, and A1739 to either valine or serine, did not affect the inhibition of the spider mite ACC by spirotetramat-enol. These results indicated different binding modes of the keto-enols and the herbicidal chemical families.
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Affiliation(s)
| | - Jahangir Khajehali
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Kai Luther
- BayerCropScience AG, 40789 Monheim, Germany
| | - Thomas Van Leeuwen
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium; Institute for Biodiversity and Ecosystems Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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232
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Propionyl coenzyme A (propionyl-CoA) carboxylase in Haloferax mediterranei: Indispensability for propionyl-CoA assimilation and impacts on global metabolism. Appl Environ Microbiol 2014; 81:794-804. [PMID: 25398867 DOI: 10.1128/aem.03167-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Propionyl coenzyme A (propionyl-CoA) is an important intermediate during the biosynthesis and catabolism of intracellular carbon storage of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) in haloarchaea. However, the haloarchaeal propionyl-CoA carboxylase (PCC) and its physiological significance remain unclear. In this study, we identified a PCC that catalyzed propionyl-CoA carboxylation with an acetyl-CoA carboxylation side activity in Haloferax mediterranei. Gene knockout/complementation demonstrated that the PCC enzyme consisted of a fusion protein of a biotin carboxylase and a biotin-carboxyl carrier protein (PccA [HFX_2490]), a carboxyltransferase component (PccB [HFX_2478]), and an essential small subunit (PccX [HFX_2479]). Knockout of pccBX led to an inability to utilize propionate and a higher intracellular propionyl-CoA level, indicating that the PCC enzyme is indispensable for propionyl-CoA utilization. Interestingly, H. mediterranei DBX (pccBX-deleted strain) displayed multiple phenotypic changes, including retarded cell growth, decreased glucose consumption, impaired PHBV biosynthesis, and wrinkled cells. A propionyl-CoA concentration equivalent to the concentration that accumulated in DBX cells was demonstrated to inhibit succinyl-CoA synthetase of the tricarboxylic acid cycle in vitro. Genome-wide microarray analysis showed that many genes for glycolysis, pyruvate oxidation, PHBV accumulation, electron transport, and stress responses were affected in DBX. This study not only identified the haloarchaeal PCC for the metabolism of propionyl-CoA, an important intermediate in haloarchaea, but also demonstrated that impaired propionyl-CoA metabolism affected global metabolism in H. mediterranei.
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233
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Tran TH, Hsiao YS, Jo J, Chou CY, Dietrich LEP, Walz T, Tong L. Structure and function of a single-chain, multi-domain long-chain acyl-CoA carboxylase. Nature 2014; 518:120-4. [PMID: 25383525 PMCID: PMC4319993 DOI: 10.1038/nature13912] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 10/02/2014] [Indexed: 01/15/2023]
Abstract
Biotin-dependent carboxylases are widely distributed in nature and have important functions in the metabolism of fatty acids, amino acids, carbohydrates, cholesterol and other compounds 1–6. Defective mutations in several of these enzymes have been linked to serious metabolic diseases in humans, and acetyl-CoA carboxylase (ACC) is a target for drug discovery against diabetes, cancer and other diseases 7–9. We report here the identification and biochemical, structural and functional characterizations of a novel single-chain (120 kD), multi-domain biotin-dependent carboxylase in bacteria. It has preference for long-chain acyl-CoA substrates, although it is also active toward short- and medium-chain acyl-CoAs, and we have named it long-chain acyl-CoA carboxylase (LCC). The holoenzyme is a homo-hexamer with molecular weight of 720 kD. The 3.0 Å crystal structure of Mycobacterium avium subspecies paratuberculosis LCC (MapLCC) holoenzyme revealed an architecture that is strikingly different compared to those of related biotin-dependent carboxylases 10,11. In addition, the domains of each monomer have no direct contacts with each other. They are instead extensively swapped in the holoenzyme, such that one cycle of catalysis involves the participation of four monomers. Functional studies in Pseudomonas aeruginosa suggest that the enzyme is involved in the utilization of selected carbon and nitrogen sources.
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Affiliation(s)
- Timothy H Tran
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Yu-Shan Hsiao
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jeanyoung Jo
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Chi-Yuan Chou
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Lars E P Dietrich
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Thomas Walz
- 1] Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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234
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Tytgat HLP, Schoofs G, Driesen M, Proost P, Van Damme EJM, Vanderleyden J, Lebeer S. Endogenous biotin-binding proteins: an overlooked factor causing false positives in streptavidin-based protein detection. Microb Biotechnol 2014; 8:164-8. [PMID: 25211245 PMCID: PMC4321382 DOI: 10.1111/1751-7915.12150] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/16/2014] [Accepted: 07/16/2014] [Indexed: 11/29/2022] Open
Abstract
Biotinylation is widely used in DNA, RNA and protein probing assays as this molecule has generally no impact on the biological activity of its substrate. During the streptavidin-based detection of glycoproteins in Lactobacillus rhamnosus GG with biotinylated lectin probes, a strong positive band of approximately 125 kDa was observed, present in different cellular fractions. This potential glycoprotein reacted heavily with concanavalin A (ConA), a lectin that specifically binds glucose and mannose residues. Surprisingly, this protein of 125 kDa could not be purified using a ConA affinity column. Edman degradation of the protein, isolated via cation and anion exchange chromatography, lead to the identification of the band as pyruvate carboxylase, an enzyme of 125 kDa that binds biotin as a cofactor. Detection using only the streptavidin conjugate resulted in more false positive signals of proteins, also in extracellular fractions, indicating biotin-associated proteins. Indeed, biotin is a known cofactor of numerous carboxylases. The potential occurence of false positive bands with biotinylated protein probes should thus be considered when using streptavidin-based detection, e.g. by developing a blot using only the streptavidin conjugate. To circumvent these false positives, alternative approaches like detection based on digoxigenin labelling can also be used.
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Affiliation(s)
- Hanne L P Tytgat
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium; Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, Leuven, Belgium
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235
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Kaundun SS. Resistance to acetyl-CoA carboxylase-inhibiting herbicides. PEST MANAGEMENT SCIENCE 2014; 70:1405-17. [PMID: 24700409 DOI: 10.1002/ps.3790] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 03/21/2014] [Accepted: 04/03/2014] [Indexed: 05/12/2023]
Abstract
Resistance to acetyl-CoA carboxylase herbicides is documented in at least 43 grass weeds and is particularly problematic in Lolium, Alopecurus and Avena species. Genetic studies have shown that resistance generally evolves independently and can be conferred by target-site mutations at ACCase codon positions 1781, 1999, 2027, 2041, 2078, 2088 and 2096. The level of resistance depends on the herbicides, recommended field rates, weed species, plant growth stages, specific amino acid changes and the number of gene copies and mutant ACCase alleles. Non-target-site resistance, or in essence metabolic resistance, is prevalent, multigenic and favoured under low-dose selection. Metabolic resistance can be specific but also broad, affecting other modes of action. Some target-site and metabolic-resistant biotypes are characterised by a fitness penalty. However, the significance for resistance regression in the absence of ACCase herbicides is yet to be determined over a practical timeframe. More recently, a fitness benefit has been reported in some populations containing the I1781L mutation in terms of vegetative and reproductive outputs and delayed germination. Several DNA-based methods have been developed to detect known ACCase resistance mutations, unlike metabolic resistance, as the genes remain elusive to date. Therefore, confirmation of resistance is still carried out via whole-plant herbicide bioassays. A growing number of monocotyledonous crops have been engineered to resist ACCase herbicides, thus increasing the options for grass weed control. While the science of ACCase herbicide resistance has progressed significantly over the past 10 years, several avenues provided in the present review remain to be explored for a better understanding of resistance to this important mode of action.
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Affiliation(s)
- Shiv S Kaundun
- Syngenta, Jealott's Hill International Research Centre, Biological Sciences, Bracknell, Berkshire, UK
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236
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Comparative proteomic analysis of ovary for Chinese rare minnow (Gobiocypris rarus) exposed to chlorophenol chemicals. J Proteomics 2014; 110:172-82. [PMID: 25106787 DOI: 10.1016/j.jprot.2014.07.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/09/2014] [Accepted: 07/23/2014] [Indexed: 11/21/2022]
Abstract
UNLABELLED Pentachlorophenol (PCP) and 2,4,6-trichlorophenol (TCP) are suspected of disrupting the endocrine system and thus affecting human and wildlife reproduction, but the potential common mechanisms and biomarkers of chlorophenols (CPs) in the ovary are not fully elucidated. In the present study, the female rare minnow (Gobiocypris rarus) was exposed to PCP (0.5, 5.0, and 50 μg/L), TCP (1.0, 10, and 100 μg/L) and 17β-estradiol (as a positive control) for 28 days, and the matrix-assisted laser desorption/ionization (MALDI) tandem time-of-flight (TOF/TOF) mass spectrometry analysis was employed to investigate the alteration of protein expression in the ovary. After comparison of the protein profiles from treated and control groups, 22 protein spots were observed to be altered in abundance (>2-fold) from female treated groups, and 14 protein spots were identified successfully. These proteins were related to molecular response patterns, endocrine effects, metabolic pathways, and even the possible carcinogens in response to CP exposure. The seven differentially expressed mRNA encoding proteins were measured by quantitative real-time PCR (QRT-PCR) and histopathology was also measured. Our data demonstrate that alterations of multiple pathways may be associated with the toxic effects of CPs on ovaries. BIOLOGICAL SIGNIFICANCE Although numerous studies have shown the affection of the endocrine system with exposure to chlorophenols (CPs), there is little report on the alterations of protein expression in the ovaries from rare minnows following exposure to PCP or TCP. In the present study, a comparative proteomic approach using two dimensional gel electrophoresis and mass spectrometry (MALDI-TOF/TOF MS) has been developed to identify certain proteins in the ovaries of Chinese rare minnow, whose abundance changes during exposure to CPs. After comparison of the protein profiles from treated and control groups, 22 protein spots were observed to be altered in abundance (>2-fold) from female treated groups, and 14 protein spots were identified successfully. These proteins were related to molecular response patterns, endocrine effects, metabolic pathways, and even the possible carcinogens in response to CP exposure. Because the mechanism often involves changes in the expression of multiple proteins rather than a single protein, a global analysis of the protein alterations can result in valuable information to understand the CP action mechanism. All the above results demonstrate that the Vtg, SUMO, Lec-3 and PIMT protein are potential biomarkers and involved in the toxicity pathway of CP exposure in aquatic animals, which should be the primary focus of studies on the CP ovary toxicity mechanism in the future.
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237
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Park S, Hwang IW, Makishima Y, Perales-Clemente E, Kato T, Niederländer NJ, Park EY, Terzic A. Spot14/Mig12 heterocomplex sequesters polymerization and restrains catalytic function of human acetyl-CoA carboxylase 2. J Mol Recognit 2014; 26:679-88. [PMID: 24277613 PMCID: PMC4283044 DOI: 10.1002/jmr.2313] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 08/20/2013] [Accepted: 08/21/2013] [Indexed: 01/17/2023]
Abstract
Acetyl-CoA carboxylase 2 (ACC2) is an isoform of ACC functioning as a negative regulator of fatty acid β-oxidation. Spot14, a thyroid hormone responsive protein, and Mig12, a Spot14 paralog, have recently been identified as regulators of fatty acid synthesis targeting ACC1, a distinctive subtype of ACC. Here, we examined whether Spot14/Mig12 modulates ACC2. Nanoscale protein topography mapped putative protein-protein interactions between purified human Spot14/Mig12 and ACC2, validated by functional assays. Human ACC2 displayed consistent enzymatic activity, and homogeneous particle distribution was probed by atomic force microscopy. Citrate-induced polymerization and enzymatic activity of ACC2 were restrained by the addition of the recombinant Spot14/Mig12 heterocomplex but only partially by the oligo-heterocomplex, demonstrating that the heterocomplex is a designated metabolic inhibitor of human ACC2. Moreover, Spot14/Mig12 demonstrated a sequestering role preventing an initial ACC2 nucleation step during filamentous polymer formation. Thus, the Spot14/Mig12 heterocomplex controls human ACC2 polymerization and catalytic function, emerging as a previously unrecognized molecular regulator in catalytic lipid metabolism.
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Affiliation(s)
- Sungjo Park
- Center for Regenerative Medicine, Mayo Clinic, Rochester, MN, USA; Marriott Heart Disease Research Program, Division of Cardiovascular Diseases, Departments of Medicine, Molecular Pharmacology and Experimental Therapeutics, and Medical Genetics, Mayo Clinic, Rochester, MN, USA
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238
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Sheng X, Liu Y. QM/MM Study of the Reaction Mechanism of the Carboxyl Transferase Domain of Pyruvate Carboxylase from Staphylococcus aureus. Biochemistry 2014; 53:4455-66. [DOI: 10.1021/bi500020r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiang Sheng
- School
of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- School
of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
- Northwest
Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810001, China
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239
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Lasso G, Yu LPC, Gil D, Lázaro M, Tong L, Valle M. Functional conformations for pyruvate carboxylase during catalysis explored by cryoelectron microscopy. Structure 2014; 22:911-22. [PMID: 24882745 DOI: 10.1016/j.str.2014.04.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 04/20/2014] [Accepted: 04/24/2014] [Indexed: 01/15/2023]
Abstract
The tetrameric enzyme pyruvate carboxylase (PC), a biotin-dependent carboxylase, produces oxaloacetate by two consecutive reactions that take place in distant active sites. Previous crystal structures revealed two different configurations for PC tetramers, the so-called symmetric and asymmetric, which were understood as characteristic molecular architectures for PC from different organisms. We have analyzed PC samples from Staphylococcus aureus while the enzyme generates oxaloacetate, expecting PC tetramers to display the conformational landscape relevant for its functioning. Using cryoelectron microscopy (cryo-EM) and sorting techniques, we detect previously defined symmetric and asymmetric architectures, demonstrating that PC maps both arrangements by large conformational changes. Furthermore, we observe that each configuration is coupled to one of the two consecutive enzymatic reactions. The findings describe the structural transitions relevant for the allosteric control of the multifunctional PC and demonstrate that by cryo-EM and classification, we can characterize freely working macromolecules.
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Affiliation(s)
- Gorka Lasso
- Structural Biology Unit, Center for Cooperative Research in Biosciences, CIC bioGUNE, 48160 Derio, Spain
| | - Linda P C Yu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - David Gil
- Structural Biology Unit, Center for Cooperative Research in Biosciences, CIC bioGUNE, 48160 Derio, Spain
| | - Melisa Lázaro
- Structural Biology Unit, Center for Cooperative Research in Biosciences, CIC bioGUNE, 48160 Derio, Spain
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Mikel Valle
- Structural Biology Unit, Center for Cooperative Research in Biosciences, CIC bioGUNE, 48160 Derio, Spain; Department of Biochemistry and Molecular Biology, University of the Basque Country, P.O. Box 644, 48080 Bilbao, Spain.
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240
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Lamaziere A, Wolf C, Quinn PJ. How lipidomics provides new insight into drug discovery. Expert Opin Drug Discov 2014; 9:819-36. [DOI: 10.1517/17460441.2014.914026] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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241
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Su B, Ryan RO. Metabolic biology of 3-methylglutaconic acid-uria: a new perspective. J Inherit Metab Dis 2014; 37:359-68. [PMID: 24407466 PMCID: PMC4016128 DOI: 10.1007/s10545-013-9669-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 11/20/2013] [Accepted: 11/26/2013] [Indexed: 10/25/2022]
Abstract
Over the past 25 years a growing number of distinct syndromes/mutations associated with compromised mitochondrial function have been identified that share a common feature: urinary excretion of 3-methylglutaconic acid (3MGA). In the leucine degradation pathway, carboxylation of 3-methylcrotonyl CoA leads to formation of 3-methylglutaconyl CoA while 3-methylglutaconyl CoA hydratase converts this metabolite to 3-hydroxy-3-methylglutaryl CoA (HMG CoA). In "primary" 3MGA-uria, mutations in the hydratase are directly responsible for the accumulation of 3MGA. On the other hand, in all "secondary" 3MGA-urias, no defect in leucine catabolism exists and the metabolic origin of 3MGA is unknown. Herein, a path to 3MGA from mitochondrial acetyl CoA is proposed. The pathway is initiated when syndrome-associated mutations/DNA deletions result in decreased Krebs cycle flux. When this occurs, acetoacetyl CoA thiolase condenses two acetyl CoA into acetoacetyl CoA plus CoASH. Subsequently, HMG CoA synthase 2 converts acetoacetyl CoA and acetyl CoA to HMG CoA. Under syndrome-specific metabolic conditions, 3-methylglutaconyl CoA hydratase converts HMG CoA into 3-methylglutaconyl CoA in a reverse reaction of the leucine degradation pathway. This metabolite fails to proceed further up the leucine degradation pathway owing to the kinetic properties of 3-methylcrotonyl CoA carboxylase. Instead, hydrolysis of the CoA moiety of 3-methylglutaconyl CoA generates 3MGA, which appears in urine. If experimentally confirmed, this pathway provides an explanation for the occurrence of 3MGA in multiple disorders associated with compromised mitochondrial function.
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Affiliation(s)
- Betty Su
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA, 94609, USA
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242
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Ma Q, Akhter Y, Wilmanns M, Ehebauer MT. Active site conformational changes upon reaction intermediate biotinyl-5'-AMP binding in biotin protein ligase from Mycobacterium tuberculosis. Protein Sci 2014; 23:932-9. [PMID: 24723382 DOI: 10.1002/pro.2475] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 03/25/2014] [Accepted: 03/28/2014] [Indexed: 11/07/2022]
Abstract
Protein biotinylation, a rare form of post-translational modification, is found in enzymes required for lipid biosynthesis. In mycobacteria, this process is essential for the formation of their complex and distinct cell wall and has become a focal point of drug discovery approaches. The enzyme responsible for this process, biotin protein ligase, substantially varies in different species in terms of overall structural organization, regulation of function and substrate specificity. To advance the understanding of the molecular mechanism of biotinylation in Mycobacterium tuberculosis we have biochemically and structurally characterized the corresponding enzyme. We report the high-resolution crystal structures of the apo-form and reaction intermediate biotinyl-5'-AMP-bound form of M. tuberculosis biotin protein ligase. Binding of the reaction intermediate leads to clear disorder-to-order transitions. We show that a conserved lysine, Lys138, in the active site is essential for biotinylation.
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Affiliation(s)
- Qingjun Ma
- European Molecular Biology Laboratory, EMBL-Hamburg, c/o DESY, Building 25A, Notkestrasse 85, 22603, Hamburg, Germany
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243
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Human acetyl-CoA carboxylase 2 expressed in silkworm Bombyx mori exhibits posttranslational biotinylation and phosphorylation. Appl Microbiol Biotechnol 2014; 98:8201-9. [PMID: 24740690 PMCID: PMC4163189 DOI: 10.1007/s00253-014-5715-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 03/23/2014] [Indexed: 12/26/2022]
Abstract
Biotin-dependent human acetyl-CoA carboxylases (ACCs) are integral in homeostatic lipid metabolism. By securing posttranslational biotinylation, ACCs perform coordinated catalytic functions allosterically regulated by phosphorylation/dephosphorylation and citrate. The production of authentic recombinant ACCs is heeded to provide a reliable tool for molecular studies and drug discovery. Here, we examined whether the human ACC2 (hACC2), an isoform of ACC produced using the silkworm BmNPV bacmid system, is equipped with proper posttranslational modifications to carry out catalytic functions as the silkworm harbors an inherent posttranslational modification machinery. Purified hACC2 possessed genuine biotinylation capacity probed by biotin-specific streptavidin and biotin antibodies. In addition, phosphorylated hACC2 displayed limited catalytic activity whereas dephosphorylated hACC2 revealed an enhanced enzymatic activity. Moreover, hACC2 polymerization, analyzed by native page gel analysis and atomic force microscopy imaging, was allosterically regulated by citrate and the phosphorylation/dephosphorylation modulated citrate-induced hACC2 polymerization process. Thus, the silkworm BmNPV bacmid system provides a reliable eukaryotic protein production platform for structural and functional analysis and therapeutic drug discovery applications implementing suitable posttranslational biotinylation and phosphorylation.
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244
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van Karnebeek CD, Sly WS, Ross CJ, Salvarinova R, Yaplito-Lee J, Santra S, Shyr C, Horvath GA, Eydoux P, Lehman AM, Bernard V, Newlove T, Ukpeh H, Chakrapani A, Preece MA, Ball S, Pitt J, Vallance HD, Coulter-Mackie M, Nguyen H, Zhang LH, Bhavsar AP, Sinclair G, Waheed A, Wasserman WW, Stockler-Ipsiroglu S. Mitochondrial carbonic anhydrase VA deficiency resulting from CA5A alterations presents with hyperammonemia in early childhood. Am J Hum Genet 2014; 94:453-61. [PMID: 24530203 DOI: 10.1016/j.ajhg.2014.01.006] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 01/14/2014] [Indexed: 12/26/2022] Open
Abstract
Four children in three unrelated families (one consanguineous) presented with lethargy, hyperlactatemia, and hyperammonemia of unexplained origin during the neonatal period and early childhood. We identified and validated three different CA5A alterations, including a homozygous missense mutation (c.697T>C) in two siblings, a homozygous splice site mutation (c.555G>A) leading to skipping of exon 4, and a homozygous 4 kb deletion of exon 6. The deleterious nature of the homozygous mutation c.697T>C (p.Ser233Pro) was demonstrated by reduced enzymatic activity and increased temperature sensitivity. Carbonic anhydrase VA (CA-VA) was absent in liver in the child with the homozygous exon 6 deletion. The metabolite profiles in the affected individuals fit CA-VA deficiency, showing evidence of impaired provision of bicarbonate to the four enzymes that participate in key pathways in intermediary metabolism: carbamoylphosphate synthetase 1 (urea cycle), pyruvate carboxylase (anaplerosis, gluconeogenesis), propionyl-CoA carboxylase, and 3-methylcrotonyl-CoA carboxylase (branched chain amino acids catabolism). In the three children who were administered carglumic acid, hyperammonemia resolved. CA-VA deficiency should therefore be added to urea cycle defects, organic acidurias, and pyruvate carboxylase deficiency as a treatable condition in the differential diagnosis of hyperammonemia in the neonate and young child.
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Affiliation(s)
- Clara D van Karnebeek
- Division of Biochemical Diseases, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3V4, Canada; Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3V4, Canada; Treatable Intellectual Disability Endeavour in British Columbia, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada; Center for Molecular Medicine and Therapeutics, Child and Family Research Institute, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada.
| | - William S Sly
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Colin J Ross
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3V4, Canada; Treatable Intellectual Disability Endeavour in British Columbia, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada; Center for Molecular Medicine and Therapeutics, Child and Family Research Institute, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Ramona Salvarinova
- Division of Biochemical Diseases, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3V4, Canada; Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3V4, Canada; Treatable Intellectual Disability Endeavour in British Columbia, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Joy Yaplito-Lee
- Metabolic Genetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Saikat Santra
- Department of Clinical Inherited Metabolic Disorders, Birmingham Children's Hospital, Birmingham B4 6NH, UK
| | - Casper Shyr
- Treatable Intellectual Disability Endeavour in British Columbia, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada; Center for Molecular Medicine and Therapeutics, Child and Family Research Institute, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada; Department of Medical Genetics, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Gabriella A Horvath
- Division of Biochemical Diseases, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3V4, Canada; Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3V4, Canada; Treatable Intellectual Disability Endeavour in British Columbia, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Patrice Eydoux
- Treatable Intellectual Disability Endeavour in British Columbia, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada; Department of Medical Genetics, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3N1, Canada; Department of Pathology & Laboratory Medicine, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Anna M Lehman
- Treatable Intellectual Disability Endeavour in British Columbia, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada; Department of Medical Genetics, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Virginie Bernard
- Treatable Intellectual Disability Endeavour in British Columbia, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada; Center for Molecular Medicine and Therapeutics, Child and Family Research Institute, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada; Department of Medical Genetics, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Theresa Newlove
- Treatable Intellectual Disability Endeavour in British Columbia, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada; Department of Psychology, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Henry Ukpeh
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3V4, Canada
| | - Anupam Chakrapani
- Department of Clinical Inherited Metabolic Disorders, Birmingham Children's Hospital, Birmingham B4 6NH, UK
| | - Mary Anne Preece
- Department of Newborn Screening and Biochemical Genetics, Birmingham Children's Hospital, Birmingham B4 6NH, UK
| | - Sarah Ball
- Department of Newborn Screening and Biochemical Genetics, Birmingham Children's Hospital, Birmingham B4 6NH, UK
| | - James Pitt
- Metabolic Genetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Hilary D Vallance
- Treatable Intellectual Disability Endeavour in British Columbia, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada; Biochemical Genetics Laboratory, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3N1, Canada; Department of Pathology & Laboratory Medicine, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Marion Coulter-Mackie
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3V4, Canada; Treatable Intellectual Disability Endeavour in British Columbia, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Hien Nguyen
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Lin-Hua Zhang
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3V4, Canada; Treatable Intellectual Disability Endeavour in British Columbia, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada; Center for Molecular Medicine and Therapeutics, Child and Family Research Institute, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Amit P Bhavsar
- Treatable Intellectual Disability Endeavour in British Columbia, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada; Center for Molecular Medicine and Therapeutics, Child and Family Research Institute, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada; Department of Medical Genetics, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Graham Sinclair
- Treatable Intellectual Disability Endeavour in British Columbia, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada; Biochemical Genetics Laboratory, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3N1, Canada; Department of Pathology & Laboratory Medicine, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Abdul Waheed
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Wyeth W Wasserman
- Treatable Intellectual Disability Endeavour in British Columbia, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada; Center for Molecular Medicine and Therapeutics, Child and Family Research Institute, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada; Department of Medical Genetics, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Sylvia Stockler-Ipsiroglu
- Division of Biochemical Diseases, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3V4, Canada; Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, BC V6H 3V4, Canada; Treatable Intellectual Disability Endeavour in British Columbia, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
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Lietzan AD, St. Maurice M. Functionally diverse biotin-dependent enzymes with oxaloacetate decarboxylase activity. Arch Biochem Biophys 2014; 544:75-86. [DOI: 10.1016/j.abb.2013.10.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 10/15/2013] [Accepted: 10/18/2013] [Indexed: 12/31/2022]
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246
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Menefee AL, Zeczycki TN. Nearly 50 years in the making: defining the catalytic mechanism of the multifunctional enzyme, pyruvate carboxylase. FEBS J 2014; 281:1333-1354. [PMID: 24476417 DOI: 10.1111/febs.12713] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/02/2014] [Accepted: 01/06/2014] [Indexed: 01/04/2023]
Abstract
Numerous steady-state kinetic studies have examined the complex catalytic reaction mechanism of the multifunctional enzyme, pyruvate carboxylase (PC). Through initial velocity, product inhibition, isotopic exchange and alternate substrate experiments, early investigators established that PC catalyzes the MgATP-dependent carboxylation of pyruvate by HCO3 (-) through a nonclassical sequential Bi Bi Uni Uni reaction mechanism. This review surveys previous steady-state kinetic investigations of PC and evaluates the proposed hypotheses concerning the overall catalytic mechanism, nonlinear kinetics and active site coupling in the context of recent structural and mutagenic analyses of this multifunctional enzyme. The determination several PC holoenzyme structures have aided in corroborating the proposed molecular mechanisms by which catalysis occurs and established the inextricable link between the dynamic protein motions and complex kinetic mechanisms associated with PC activity. Unexpectedly, the conclusions drawn from these early steady-state kinetic investigations have consistently proven to be in fundamental agreement with our current understanding of PC catalysis, which is a testament to the overarching sophistication of the methods pioneered by Michaelis and Menten and further developed by Northrop, Cleland and others.
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Affiliation(s)
- Ann L Menefee
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, NC, USA; The East Carolina Diabetes and Obesity Institute, Brody School of Medicine at East Carolina University, Greenville, NC, USA
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247
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Plant amino acid-derived vitamins: biosynthesis and function. Amino Acids 2013; 46:809-24. [PMID: 24368523 DOI: 10.1007/s00726-013-1653-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 12/14/2013] [Indexed: 02/06/2023]
Abstract
Vitamins are essential organic compounds for humans, having lost the ability to de novo synthesize them. Hence, they represent dietary requirements, which are covered by plants as the main dietary source of most vitamins (through food or livestock's feed). Most vitamins synthesized by plants present amino acids as precursors (B1, B2, B3, B5, B7, B9 and E) and are therefore linked to plant nitrogen metabolism. Amino acids play different roles in their biosynthesis and metabolism, either incorporated into the backbone of the vitamin or as amino, sulfur or one-carbon group donors. There is a high natural variation in vitamin contents in crops and its exploitation through breeding, metabolic engineering and agronomic practices can enhance their nutritional quality. While the underlying biochemical roles of vitamins as cosubstrates or cofactors are usually common for most eukaryotes, the impact of vitamins B and E in metabolism and physiology can be quite different on plants and animals. Here, we first aim at giving an overview of the biosynthesis of amino acid-derived vitamins in plants, with a particular focus on how this knowledge can be exploited to increase vitamin contents in crops. Second, we will focus on the functions of these vitamins in both plants and animals (and humans in particular), to unravel common and specific roles for vitamins in evolutionary distant organisms, in which these amino acid-derived vitamins play, however, an essential role.
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248
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Chandrakar B, Jain A, Roy S, Gutlapalli VR, Saraf S, Suppahia A, Verma A, Tiwari A, Yadav M, Nayarisseri A. Molecular modeling of Acetyl-CoA carboxylase (ACC) from Jatropha curcas and virtual screening for identification of inhibitors. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.jopr.2013.07.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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249
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Solitary BioY proteins mediate biotin transport into recombinant Escherichia coli. J Bacteriol 2013; 195:4105-11. [PMID: 23836870 DOI: 10.1128/jb.00350-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Energy-coupling factor (ECF) transporters form a large group of vitamin uptake systems in prokaryotes. They are composed of highly diverse, substrate-specific, transmembrane proteins (S units), a ubiquitous transmembrane protein (T unit), and homo- or hetero-oligomeric ABC ATPases. Biotin transporters represent a special case of ECF-type systems. The majority of the biotin-specific S units (BioY) is known or predicted to interact with T units and ABC ATPases. About one-third of BioY proteins, however, are encoded in organisms lacking any recognizable T unit. This finding raises the question of whether these BioYs function as transporters in a solitary state, a feature ascribed to certain BioYs in the past. To address this question in living cells, an Escherichia coli K-12 derivative deficient in biotin synthesis and devoid of its endogenous high-affinity biotin transporter was constructed as a reference strain. This organism is particularly suited for this purpose because components of ECF transporters do not naturally occur in E. coli K-12. The double mutant was viable in media containing either high levels of biotin or a precursor of the downstream biosynthetic path. Importantly, it was nonviable on trace levels of biotin. Eight solitary bioY genes of proteobacterial origin were individually expressed in the reference strain. Each of the BioYs conferred biotin uptake activity on the recombinants, which was inferred from uptake assays with [(3)H]biotin and growth of the cells on trace levels of biotin. The results underscore that solitary BioY transports biotin across the cytoplasmic membrane.
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250
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Froese DS, Forouhar F, Tran TH, Vollmar M, Kim YS, Lew S, Neely H, Seetharaman J, Shen Y, Xiao R, Acton TB, Everett JK, Cannone G, Puranik S, Savitsky P, Krojer T, Pilka ES, Kiyani W, Lee WH, Marsden BD, von Delft F, Allerston CK, Spagnolo L, Gileadi O, Montelione GT, Oppermann U, Yue WW, Tong L. Crystal structures of malonyl-coenzyme A decarboxylase provide insights into its catalytic mechanism and disease-causing mutations. Structure 2013; 21:1182-92. [PMID: 23791943 PMCID: PMC3701320 DOI: 10.1016/j.str.2013.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 05/09/2013] [Accepted: 05/09/2013] [Indexed: 01/17/2023]
Abstract
Malonyl-coenzyme A decarboxylase (MCD) is found from bacteria to humans, has important roles in regulating fatty acid metabolism and food intake, and is an attractive target for drug discovery. We report here four crystal structures of MCD from human, Rhodopseudomonas palustris, Agrobacterium vitis, and Cupriavidus metallidurans at up to 2.3 Å resolution. The MCD monomer contains an N-terminal helical domain involved in oligomerization and a C-terminal catalytic domain. The four structures exhibit substantial differences in the organization of the helical domains and, consequently, the oligomeric states and intersubunit interfaces. Unexpectedly, the MCD catalytic domain is structurally homologous to those of the GCN5-related N-acetyltransferase superfamily, especially the curacin A polyketide synthase catalytic module, with a conserved His-Ser/Thr dyad important for catalysis. Our structures, along with mutagenesis and kinetic studies, provide a molecular basis for understanding pathogenic mutations and catalysis, as well as a template for structure-based drug design. Structures of human and bacterial MCDs were determined at up to 2.3 Å resolution Distinct tetrameric and dimeric MCD oligomerizations were observed Unexpected homology to the GNAT superfamily gives insights into catalytic mechanism The structures provide the molecular basis for the disease-causing mutations in MCD
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Affiliation(s)
- D Sean Froese
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
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