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Iverson TM, Singh PK, Cecchini G. An evolving view of Complex II - non-canonical complexes, megacomplexes, respiration, signaling, and beyond. J Biol Chem 2023; 299:104761. [PMID: 37119852 DOI: 10.1016/j.jbc.2023.104761] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/20/2023] [Accepted: 04/22/2023] [Indexed: 05/01/2023] Open
Abstract
Mitochondrial Complex II is traditionally studied for its participation in two key respiratory processes: the electron transport chain and the Krebs cycle. There is now a rich body of literature explaining how Complex II contributes to respiration. However, more recent research shows that not all of the pathologies associated with altered Complex II activity clearly correlate with this respiratory role. Complex II activity has now been shown to be necessary for a range of biological processes peripherally-related to respiration, including metabolic control, inflammation, and cell fate. Integration of findings from multiple types of studies suggests that Complex II both participates in respiration and controls multiple succinate-dependent signal transduction pathways. Thus, the emerging view is that the true biological function of Complex II is well beyond respiration. This review uses a semi-chronological approach to highlight major paradigm shifts that occurred over time. Special emphasis is given to the more recently identified functions of Complex II and its subunits because these findings have infused new directions into an established field.
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Affiliation(s)
- T M Iverson
- Departments of Pharmacology, Vanderbilt University, Nashville, TN 37232; Departments of Biochemistry, Vanderbilt University, Nashville, TN 37232; Departments of Center for Structural Biology, Vanderbilt University, Nashville, TN 37232; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232.
| | - Prashant K Singh
- Departments of Pharmacology, Vanderbilt University, Nashville, TN 37232; Departments of Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - Gary Cecchini
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA 94121; Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158.
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2
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Komeyama M, Kanno K, Mino H, Yasuno Y, Shinada T, Ito T, Hemmi H. A [4Fe-4S] cluster resides at the active center of phosphomevalonate dehydratase, a key enzyme in the archaeal modified mevalonate pathway. Front Microbiol 2023; 14:1150353. [PMID: 36992929 PMCID: PMC10040528 DOI: 10.3389/fmicb.2023.1150353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 02/22/2023] [Indexed: 03/15/2023] Open
Abstract
The recent discovery of the archaeal modified mevalonate pathway revealed that the fundamental units for isoprenoid biosynthesis (isopentenyl diphosphate and dimethylallyl diphosphate) are biosynthesized via a specific intermediate, trans-anhydromevalonate phosphate. In this biosynthetic pathway, which is unique to archaea, the formation of trans-anhydromevalonate phosphate from (R)-mevalonate 5-phosphate is catalyzed by a key enzyme, phosphomevalonate dehydratase. This archaea-specific enzyme belongs to the aconitase X family within the aconitase superfamily, along with bacterial homologs involved in hydroxyproline metabolism. Although an iron–sulfur cluster is thought to exist in phosphomevalonate dehydratase and is believed to be responsible for the catalytic mechanism of the enzyme, the structure and role of this cluster have not been well characterized. Here, we reconstructed the iron–sulfur cluster of phosphomevalonate dehydratase from the hyperthermophilic archaeon Aeropyrum pernix to perform biochemical characterization and kinetic analysis of the enzyme. Electron paramagnetic resonance, iron quantification, and mutagenic studies of the enzyme demonstrated that three conserved cysteine residues coordinate a [4Fe-4S] cluster—as is typical in aconitase superfamily hydratases/dehydratases, in contrast to bacterial aconitase X-family enzymes, which have been reported to harbor a [2Fe-2S] cluster.
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Affiliation(s)
- Mutsumi Komeyama
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Kohsuke Kanno
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Hiroyuki Mino
- Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Yoko Yasuno
- Graduate School of Science, Osaka Metropolitan University, Sugimoto, Osaka, Japan
| | - Tetsuro Shinada
- Graduate School of Science, Osaka Metropolitan University, Sugimoto, Osaka, Japan
| | - Tomokazu Ito
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Hisashi Hemmi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
- *Correspondence: Hisashi Hemmi,
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3
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Hevler JF, Albanese P, Cabrera-Orefice A, Potter A, Jankevics A, Misic J, Scheltema RA, Brandt U, Arnold S, Heck AJR. MRPS36 provides a structural link in the eukaryotic 2-oxoglutarate dehydrogenase complex. Open Biol 2023; 13:220363. [PMID: 36854377 PMCID: PMC9974300 DOI: 10.1098/rsob.220363] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
The tricarboxylic acid cycle is the central pathway of energy production in eukaryotic cells and plays a key part in aerobic respiration throughout all kingdoms of life. One of the pivotal enzymes in this cycle is 2-oxoglutarate dehydrogenase complex (OGDHC), which generates NADH by oxidative decarboxylation of 2-oxoglutarate to succinyl-CoA. OGDHC is a megadalton protein complex originally thought to be assembled from three catalytically active subunits (E1o, E2o, E3). In fungi and animals, however, the protein MRPS36 has more recently been proposed as a putative additional component. Based on extensive cross-linking mass spectrometry data supported by phylogenetic analyses, we provide evidence that MRPS36 is an important member of the eukaryotic OGDHC, with no prokaryotic orthologues. Comparative sequence analysis and computational structure predictions reveal that, in contrast with bacteria and archaea, eukaryotic E2o does not contain the peripheral subunit-binding domain (PSBD), for which we propose that MRPS36 evolved as an E3 adaptor protein, functionally replacing the PSBD. We further provide a refined structural model of the complete eukaryotic OGDHC of approximately 3.45 MDa with novel mechanistic insights.
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Affiliation(s)
- Johannes F. Hevler
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Pascal Albanese
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alfredo Cabrera-Orefice
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Alisa Potter
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Andris Jankevics
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Jelena Misic
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Richard A. Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ulrich Brandt
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Susanne Arnold
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
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4
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Activation of unsaturated small molecules by bio-relevant multinuclear metal-sulfur clusters. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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5
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Rutledge HL, Field MJ, Rittle J, Green MT, Akif Tezcan F. Role of Serine Coordination in the Structural and Functional Protection of the Nitrogenase P-Cluster. J Am Chem Soc 2022; 144:22101-22112. [PMID: 36445204 PMCID: PMC9957664 DOI: 10.1021/jacs.2c09480] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Nitrogenase catalyzes the multielectron reduction of dinitrogen to ammonia. Electron transfer in the catalytic protein (MoFeP) proceeds through a unique [8Fe-7S] cluster (P-cluster) to the active site (FeMoco). In the reduced, all-ferrous (PN) state, the P-cluster is coordinated by six cysteine residues. Upon two-electron oxidation to the P2+ state, the P-cluster undergoes conformational changes in which a highly conserved oxygen-based residue (a Ser or a Tyr) and a backbone amide additionally ligate the cluster. Previous studies of Azotobacter vinelandii (Av) MoFeP revealed that when the oxygen-based residue, βSer188, was mutated to a noncoordinating residue, Ala, the P-cluster became redox-labile and reversibly lost two of its eight Fe centers. Surprisingly, the Av strain with a MoFeP variant that lacked the serine ligand (Av βSer188Ala MoFeP) displayed the same diazotrophic growth and in vitro enzyme turnover rates as wild-type Av MoFeP, calling into question the necessity of this conserved ligand for nitrogenase function. Based on these observations, we hypothesized that βSer188 plays a role in protecting the P-cluster under nonideal conditions. Here, we investigated the protective role of βSer188 both in vivo and in vitro by characterizing the ability of Av βSer188Ala cells to grow under suboptimal conditions (high oxidative stress or Fe limitation) and by determining the tendency of βSer188Ala MoFeP to be mismetallated in vitro. Our results demonstrate that βSer188 (1) increases Av cell survival upon exposure to oxidative stress in the form of hydrogen peroxide, (2) is necessary for efficient Av diazotrophic growth under Fe-limiting conditions, and (3) may protect the P-cluster from metal exchange in vitro. Taken together, our findings suggest a structural adaptation of nitrogenase to protect the P-cluster via Ser ligation, which is a previously unidentified functional role of the Ser residue in redox proteins and adds to the expanding functional roles of non-Cys ligands to FeS clusters.
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Affiliation(s)
- Hannah L. Rutledge
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Mackenzie J. Field
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Jonathan Rittle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Michael T. Green
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States.,Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States.,Corresponding Author:
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6
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Rohaun SK, Imlay JA. The vulnerability of radical SAM enzymes to oxidants and soft metals. Redox Biol 2022; 57:102495. [PMID: 36240621 PMCID: PMC9576991 DOI: 10.1016/j.redox.2022.102495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/30/2022] Open
Abstract
Radical S-adenosylmethionine enzymes (RSEs) drive diverse biological processes by catalyzing chemically difficult reactions. Each of these enzymes uses a solvent-exposed [4Fe-4S] cluster to coordinate and cleave its SAM co-reactant. This cluster is destroyed during oxic handling, forcing investigators to work with these enzymes under anoxic conditions. Analogous substrate-binding [4Fe-4S] clusters in dehydratases are similarly sensitive to oxygen in vitro; they are also extremely vulnerable to reactive oxygen species (ROS) in vitro and in vivo. These observations suggested that ROS might similarly poison RSEs. This conjecture received apparent support by the observation that when E. coli experiences hydrogen peroxide stress, it induces a cluster-free isozyme of the RSE HemN. In the present study, surprisingly, the purified RSEs viperin and HemN proved quite resistant to peroxide and superoxide in vitro. Furthermore, pathways that require RSEs remained active inside E. coli cells that were acutely stressed by hydrogen peroxide and superoxide. Viperin, but not HemN, was gradually poisoned by molecular oxygen in vitro, forming an apparent [3Fe-4S]+ form that was readily reactivated. The modest rate of damage, and the known ability of cells to repair [3Fe-4S]+ clusters, suggest why these RSEs remain functional inside fully aerated organisms. In contrast, copper(I) damaged HemN and viperin in vitro as readily as it did fumarase, a known target of copper toxicity inside E. coli. Excess intracellular copper also impaired RSE-dependent biosynthetic processes. These data indicate that RSEs may be targets of copper stress but not of reactive oxygen species.
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Affiliation(s)
| | - James A Imlay
- Department of Microbiology, University of Illinois, Urbana, IL, 61801, USA.
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7
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Cho Y, Kim G, Park J. Mitochondrial aconitase 1 regulates age-related memory impairment via autophagy/mitophagy-mediated neural plasticity in middle-aged flies. Aging Cell 2021; 20:e13520. [PMID: 34799973 PMCID: PMC8672789 DOI: 10.1111/acel.13520] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/06/2021] [Accepted: 11/03/2021] [Indexed: 01/24/2023] Open
Abstract
Age‐related memory impairment (AMI) occurs in many species, including humans. The underlying mechanisms are not fully understood. In wild‐type Drosophila (w1118), AMI appears in the form of a decrease in learning (3‐min memory) from middle age (30 days after eclosion [DAE]). We performed in vivo, DNA microarray, and behavioral screen studies to identify genes controlling both lifespan and AMI and selected mitochondrial Acon1 (mAcon1). mAcon1 expression in the head of w1118 decreased with age. Neuronal overexpression of mAcon1 extended its lifespan and improved AMI. Neuronal or mushroom body expression of mAcon1 regulated the learning of young (10 DAE) and middle‐aged flies. Interestingly, acetyl‐CoA and citrate levels increased in the heads of middle‐aged and neuronal mAcon1 knockdown flies. Acetyl‐CoA, as a cellular energy sensor, is related to autophagy. Autophagy activity and efficacy determined by the positive and negative changes in the expression levels of Atg8a‐II and p62 were proportional to the expression level of mAcon1. Levels of the presynaptic active zone scaffold protein Bruchpilot were inversely proportional to neuronal mAcon1 levels in the whole brain. Furthermore, mAcon1 overexpression in Kenyon cells induced mitophagy labeled with mt‐Keima and improved learning ability. Both processes were blocked by pink1 knockdown. Taken together, our results imply that the regulation of learning and AMI by mAcon1 occurs via autophagy/mitophagy‐mediated neural plasticity.
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Affiliation(s)
- Yun‐Ho Cho
- Department of Physiology Korea University College of Medicine Seoul Republic of Korea
| | - Gye‐Hyeong Kim
- Department of Physiology Korea University College of Medicine Seoul Republic of Korea
| | - Joong‐Jean Park
- Department of Physiology Korea University College of Medicine Seoul Republic of Korea
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8
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Shorthouse D, Hall MWJ, Hall BA. Computational Saturation Screen Reveals the Landscape of Mutations in Human Fumarate Hydratase. J Chem Inf Model 2021; 61:1970-1980. [DOI: 10.1021/acs.jcim.1c00063] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- David Shorthouse
- Department of Medical Physics and Biomedical Engineering, UCL, London WC1E 6BT, U.K
| | - Michael W. J. Hall
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, U.K
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, U.K
| | - Benjamin A. Hall
- Department of Medical Physics and Biomedical Engineering, UCL, London WC1E 6BT, U.K
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9
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Kemp MT, Lewandowski EM, Chen Y. Low barrier hydrogen bonds in protein structure and function. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2021; 1869:140557. [PMID: 33148530 PMCID: PMC7736181 DOI: 10.1016/j.bbapap.2020.140557] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/17/2020] [Accepted: 10/22/2020] [Indexed: 01/05/2023]
Abstract
Low-barrier hydrogen bonds (LBHBs) are a special type of short hydrogen bond (HB) that is characterized by the equal sharing of a hydrogen atom. The existence and catalytic role of LBHBs in proteins has been intensely contested. Advancements in X-ray and neutron diffraction methods has revealed delocalized hydrogen atoms involved in potential LBHBs in a number of proteins, while also demonstrating that short HBs are not necessarily LBHBs. More importantly, a series of experiments on ketosteroid isomerase (KSI) have suggested that LBHBs are significantly stronger than standard HBs in the protein microenvironment in terms of enthalpy, but not free energy. The discrepancy between the enthalpy and free energy of LBHBs offers clues to the challenges, and potential solutions, of the LBHB debate, where the unique strength of LBHBs plays a special role in the kinetic processes of enzyme function and structure, together with other molecular forces in a pre-organized environment.
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Affiliation(s)
- M Trent Kemp
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Eric M Lewandowski
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States.
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10
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Haploinsufficiency due to a novel ACO2 deletion causes mitochondrial dysfunction in fibroblasts from a patient with dominant optic nerve atrophy. Sci Rep 2020; 10:16736. [PMID: 33028849 PMCID: PMC7541502 DOI: 10.1038/s41598-020-73557-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 09/02/2020] [Indexed: 01/20/2023] Open
Abstract
ACO2 is a mitochondrial protein, which is critically involved in the function of the tricarboxylic acid cycle (TCA), the maintenance of iron homeostasis, oxidative stress defense and the integrity of mitochondrial DNA (mtDNA). Mutations in the ACO2 gene were identified in patients suffering from a broad range of symptoms, including optic nerve atrophy, cortical atrophy, cerebellar atrophy, hypotonia, seizures and intellectual disabilities. In the present study, we identified a heterozygous 51 bp deletion (c.1699_1749del51) in ACO2 in a family with autosomal dominant inherited isolated optic atrophy. A complementation assay using aco1-deficient yeast revealed a growth defect for the mutant ACO2 variant substantiating a pathogenic effect of the deletion. We used patient-derived fibroblasts to characterize cellular phenotypes and found a decrease of ACO2 protein levels, while ACO2 enzyme activity was not affected compared to two age- and gender-matched control lines. Several parameters of mitochondrial function, including mitochondrial morphology, mitochondrial membrane potential or mitochondrial superoxide production, were not changed under baseline conditions. However, basal respiration, maximal respiration, and spare respiratory capacity were reduced in mutant cells. Furthermore, we observed a reduction of mtDNA copy number and reduced mtDNA transcription levels in ACO2-mutant fibroblasts. Inducing oxidative stress led to an increased susceptibility for cell death in ACO2-mutant fibroblasts compared to controls. Our study reveals that a monoallelic mutation in ACO2 is sufficient to promote mitochondrial dysfunction and increased vulnerability to oxidative stress as main drivers of cell death related to optic nerve atrophy.
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11
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da Veiga Moreira J, Schwartz L, Jolicoeur M. Targeting Mitochondrial Singlet Oxygen Dynamics Offers New Perspectives for Effective Metabolic Therapies of Cancer. Front Oncol 2020; 10:573399. [PMID: 33042846 PMCID: PMC7530255 DOI: 10.3389/fonc.2020.573399] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/13/2020] [Indexed: 11/13/2022] Open
Abstract
The occurrence of mitochondrial respiration has allowed evolution toward more complex and advanced life forms. However, its dysfunction is now also seen as the most probable cause of one of the biggest scourges in human health, cancer. Conventional cancer treatments such as chemotherapy, which mainly focus on disrupting the cell division process, have shown being effective in the attenuation of various cancers but also showing significant limits as well as serious sides effects. Indeed, the idea that cancer is a metabolic disease with mitochondria as the central site of the pathology is now emerging, and we provide here a review supporting this "novel" hypothesis re-actualizing past century Otto Warburg's thoughts. Our conclusion, while integrating literature, is that mitochondrial activity and, in particular, the activity of cytochrome c oxidase, complex IV of the ETC, plays a fundamental role in the effectiveness or non-effectiveness of chemotherapy, immunotherapy and probably radiotherapy treatments. We therefore propose that cancer cells mitochondrial singlet oxygen (1O2) dynamics may be an efficient target for metabolic therapy development.
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Affiliation(s)
- Jorgelindo da Veiga Moreira
- Research Laboratory in Applied Metabolic Engineering, Department of Chemical Engineering, Polytechnique Montréal, Montréal, QC, Canada
| | | | - Mario Jolicoeur
- Research Laboratory in Applied Metabolic Engineering, Department of Chemical Engineering, Polytechnique Montréal, Montréal, QC, Canada
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12
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Abstract
We propose a new model for prochirality that satisfies all known examples: the prochiral plane. This plane contains the prochiral carbon and defines two separate faces for chemical modification. We extend this to enzyme catalysis, replacing the "three point attachment" hypothesis and its variants. Once a prochiral substrate is fixed on an enzyme surface, the asymmetry of the enzyme provides reactants exclusively on one side of the prochiral plane, producing an enantiomerically pure chiral product. The aconitase reaction is detailed as an example, using molecular modeling and its known enzymatic mechanism. We show that the prochiral substrate for this enzyme is not citrate, but rather cis-aconitate. The number of interaction points of cis-aconitate is not relevant to prochirality, but rather to substrate specificity. A second detailed example is the enzyme fumarase; here the substrate fumarate has only two binding sites, but is nonetheless fixed onto the enzyme and has a defined prochiral plane. We also provide a literature survey of more prochiral substrates, all of which have sp2 hybridized carbon and contain a prochiral plane. An example of a prochiral unnatural substrate for sphingosine kinase 2, fingolimod, has an sp3 hybridized prochiral carbon and also contains a prochiral plane. Finally, we provide an intuitive example of a prochiral physical object, a coffee cup, interacting with one hand and lip.
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Affiliation(s)
- Raymond S Ochs
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY, 11439, USA.
| | - Tanaji T Talele
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY, 11439, USA
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13
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Wachnowsky C, Hendricks AL, Wesley NA, Ferguson C, Fidai I, Cowan JA. Understanding the Mechanism of [4Fe-4S] Cluster Assembly on Eukaryotic Mitochondrial and Cytosolic Aconitase. Inorg Chem 2019; 58:13686-13695. [PMID: 31436962 DOI: 10.1021/acs.inorgchem.9b01278] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Iron-sulfur (Fe-S) clusters are common prosthetic groups that are found within a variety of proteins responsible for functions that include electron transfer, regulation of gene expression, and substrate binding and activation. Acquisition of a [4Fe-4S] cluster is essential for the functionality of many such roles, and dysfunctions in Fe-S cluster synthesis and trafficking often result in human disease, such as multiple mitochondrial dysfunctions syndrome. While the topic of [2Fe-2S] cluster biosynthesis and trafficking has been relatively well studied, the understanding of such processes involving [4Fe-4S] centers is less developed. Herein, we focus on the mechanism of the assembly of [4Fe-4S] clusters on two members of the aconitase family, differing also in organelle placement (mitochondrion and cytosol) and biochemical function. Two mechanistic models are evaluated by a combination of kinetic and spectroscopic models, namely, a consecutive model (I), in which two [2Fe-2S] clusters are sequentially delivered to the target, and a prereaction equilibrium model (II), in which a [4Fe-4S] cluster transiently forms on a donor protein before transfer to the target. The paper also addresses the issue of cluster nuclearity for functionally active forms of ISCU, NFU, and ISCA trafficking proteins, each of which has been postulated to exist in both [2Fe-2S] and [4Fe-4S] bound states. By the application of kinetic assays and electron paramagnetic resonance spectroscopy to examine delivery pathways from a variety of potential [2Fe-2S] donor proteins to eukaryotic forms of both aconitase and iron regulatory protein, we conclude that a consecutive model following the delivery of [2Fe-2S] clusters from NFU1 is the most likely mechanism for these target proteins.
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Affiliation(s)
- Christine Wachnowsky
- Department of Chemistry and Biochemistry , The Ohio State University , 100 West 18th Avenue , Columbus , Ohio 43210 , United States.,The Ohio State Biochemistry Program , The Ohio State University , 484 West 12th Avenue , Columbus , Ohio 43210 , United States
| | - Amber L Hendricks
- Department of Chemistry and Biochemistry , The Ohio State University , 100 West 18th Avenue , Columbus , Ohio 43210 , United States
| | - Nathaniel A Wesley
- Department of Chemistry and Biochemistry , The Ohio State University , 100 West 18th Avenue , Columbus , Ohio 43210 , United States
| | - Connor Ferguson
- Department of Chemistry and Biochemistry , The Ohio State University , 100 West 18th Avenue , Columbus , Ohio 43210 , United States
| | - Insiya Fidai
- Department of Chemistry and Biochemistry , The Ohio State University , 100 West 18th Avenue , Columbus , Ohio 43210 , United States.,The Biophysics Graduate Program , The Ohio State University , 484 West 12th Avenue , Columbus , Ohio 43210 , United States
| | - J A Cowan
- Department of Chemistry and Biochemistry , The Ohio State University , 100 West 18th Avenue , Columbus , Ohio 43210 , United States.,The Ohio State Biochemistry Program , The Ohio State University , 484 West 12th Avenue , Columbus , Ohio 43210 , United States.,The Biophysics Graduate Program , The Ohio State University , 484 West 12th Avenue , Columbus , Ohio 43210 , United States
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14
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Imlay JA, Sethu R, Rohaun SK. Evolutionary adaptations that enable enzymes to tolerate oxidative stress. Free Radic Biol Med 2019; 140:4-13. [PMID: 30735836 PMCID: PMC6684875 DOI: 10.1016/j.freeradbiomed.2019.01.048] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 01/31/2019] [Indexed: 10/27/2022]
Abstract
Biochemical mechanisms emerged and were integrated into the metabolic plan of cellular life long before molecular oxygen accumulated in the biosphere. When oxygen levels finaly rose, they threatened specific types of enzymes: those that use organic radicals as catalysts, and those that depend upon iron centers. Nature has found ways to ensure that such enzymes are still used by contemporary organisms. In some cases they are restricted to microbes that reside in anoxic habitats, but in others they manage to function inside aerobic cells. In the latter case, it is frequently true that the ancestral enzyme has been modified to fend off poisoning. In this review we survey a range of protein adaptations that permit radical-based and low-potential iron chemistry to succeed in oxic environments. In many cases, accessory domains shield the vulnerable radical or metal center from oxygen. In others, the structures of iron cofactors evolved to less oxidizable forms, or alternative metals replaced iron altogether. The overarching view is that some classes of biochemical mechanism are intrinsically incompatible with the presence of oxygen. The structural modification of target enzymes is an under-recognized response to this problem.
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Affiliation(s)
- James A Imlay
- Department of Microbiology, University of Illinois, 601 S. Goodwin Ave, Urbana, IL, 61801, USA.
| | - Ramakrishnan Sethu
- Department of Microbiology, University of Illinois, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Sanjay Kumar Rohaun
- Department of Microbiology, University of Illinois, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
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15
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Bashiri G, Grove TL, Hegde SS, Lagautriere T, Gerfen GJ, Almo SC, Squire CJ, Blanchard JS, Baker EN. The active site of the Mycobacterium tuberculosis branched-chain amino acid biosynthesis enzyme dihydroxyacid dehydratase contains a 2Fe-2S cluster. J Biol Chem 2019; 294:13158-13170. [PMID: 31315931 DOI: 10.1074/jbc.ra119.009498] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/15/2019] [Indexed: 01/17/2023] Open
Abstract
Iron-sulfur clusters are protein cofactors with an ancient evolutionary origin. These clusters are best known for their roles in redox proteins such as ferredoxins, but some iron-sulfur clusters have nonredox roles in the active sites of enzymes. Such clusters are often prone to oxidative degradation, making the enzymes difficult to characterize. Here we report a structural and functional characterization of dihydroxyacid dehydratase (DHAD) from Mycobacterium tuberculosis (Mtb), an essential enzyme in the biosynthesis of branched-chain amino acids. Conducting this analysis under fully anaerobic conditions, we solved the DHAD crystal structure, at 1.88 Å resolution, revealing a 2Fe-2S cluster in which one iron ligand is a potentially exchangeable water molecule or hydroxide. UV and EPR spectroscopy both suggested that the substrate binds directly to the cluster or very close to it. Kinetic analysis implicated two ionizable groups in the catalytic mechanism, which we postulate to be Ser-491 and the iron-bound water/hydroxide. Site-directed mutagenesis showed that Ser-491 is essential for activity, and substrate docking indicated that this residue is perfectly placed for proton abstraction. We found that a bound Mg2+ ion 6.5 Å from the 2Fe-2S cluster plays a key role in substrate binding. We also identified a putative entry channel that enables access to the cluster and show that Mtb-DHAD is inhibited by a recently discovered herbicide, aspterric acid, that, given the essentiality of DHAD for Mtb survival, is a potential lead compound for the design of novel anti-TB drugs.
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Affiliation(s)
- Ghader Bashiri
- Maurice Wilkins Center for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Tyler L Grove
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10805
| | - Subray S Hegde
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10805
| | - Thomas Lagautriere
- Maurice Wilkins Center for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Gary J Gerfen
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10805
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10805
| | - Christopher J Squire
- Maurice Wilkins Center for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - John S Blanchard
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10805
| | - Edward N Baker
- Maurice Wilkins Center for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand.
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16
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Fukada M, Yamada K, Eda S, Inoue K, Ohba C, Matsumoto N, Saitsu H, Nakayama A. Identification of novel compound heterozygous mutations in ACO2 in a patient with progressive cerebral and cerebellar atrophy. Mol Genet Genomic Med 2019; 7:e00698. [PMID: 31106992 PMCID: PMC6625133 DOI: 10.1002/mgg3.698] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 01/29/2019] [Accepted: 04/08/2019] [Indexed: 01/24/2023] Open
Abstract
Background The tricarboxylic acid (TCA) cycle is a sequence of catabolic reactions within the mitochondrial matrix, and is a central pathway for cellular energy metabolism. Genetic defects affecting the TCA cycle are known to cause severe multisystem disorders. Methods We performed whole exome sequencing of genomic DNA of a patient with progressive cerebellar and cerebral atrophy, hypotonia, ataxia, seizure disorder, developmental delay, ophthalmological abnormalities and hearing loss. We also performed biochemical studies using patient fibroblasts. Results We identified new compound heterozygous mutations (c.1534G > A, p.Asp512Asn and c.1997G > C, p.Gly666Ala) in ACO2, which encodes aconitase 2, a component of the TCA cycle. In patient fibroblasts, the aconitase activity was reduced to 15% of that of the control, and the aconitase 2 level decreased to 36% of that of the control. As such a decrease in aconitase 2 in patient fibroblasts was partially restored by proteasome inhibition, mutant aconitase 2 was suggested to be relatively unstable and rapidly degraded after being synthesized. In addition, the activity of the father‐derived variant of aconitase 2 (p.Gly666Ala), which had a mutation near the active center, was 55% of that of wild‐type. Conclusion The marked reduction of aconitase activity in patient fibroblasts was due to the combination of decreased aconitase 2 amount and activity due to mutations. Reduced aconitase activity directly suppresses the TCA cycle, resulting in mitochondrial dysfunction, which may lead to symptoms similar to those observed in mitochondrial diseases.
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Affiliation(s)
- Masahide Fukada
- Department of Embryology, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Japan
| | - Keitaro Yamada
- Department of Pediatric Neurology, Aichi Prefectural Colony Central Hospital, Aichi Human Service Center, Kasugai, Japan
| | - Shima Eda
- Department of Embryology, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Japan
| | - Ken Inoue
- Department of Mental Retardation and Birth Defect Research, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Chihiro Ohba
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Atsuo Nakayama
- Department of Embryology, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Japan.,Department of Neurochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
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17
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Khodour Y, Kaguni LS, Stiban J. Iron-sulfur clusters in nucleic acid metabolism: Varying roles of ancient cofactors. Enzymes 2019; 45:225-256. [PMID: 31627878 DOI: 10.1016/bs.enz.2019.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite their relative simplicity, iron-sulfur clusters have been omnipresent as cofactors in myriad cellular processes such as oxidative phosphorylation and other respiratory pathways. Recent research advances confirm the presence of different clusters in enzymes involved in nucleic acid metabolism. Iron-sulfur clusters can therefore be considered hallmarks of cellular metabolism. Helicases, nucleases, glycosylases, DNA polymerases and transcription factors, among others, incorporate various types of clusters that serve differing roles. In this chapter, we review our current understanding of the identity and functions of iron-sulfur clusters in DNA and RNA metabolizing enzymes, highlighting their importance as regulators of cellular function.
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Affiliation(s)
- Yara Khodour
- Department of Biology and Biochemistry, Birzeit University, West Bank, Palestine
| | - Laurie S Kaguni
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Johnny Stiban
- Department of Biology and Biochemistry, Birzeit University, West Bank, Palestine.
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18
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Maione V, Cantini F, Severi M, Banci L. Investigating the role of the human CIA2A-CIAO1 complex in the maturation of aconitase. Biochim Biophys Acta Gen Subj 2018; 1862:1980-1987. [DOI: 10.1016/j.bbagen.2018.05.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 05/15/2018] [Accepted: 05/24/2018] [Indexed: 02/08/2023]
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19
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Srivastava S, Gubbels CS, Dies K, Fulton A, Yu T, Sahin M. Increased Survival and Partly Preserved Cognition in a Patient With ACO2-Related Disease Secondary to a Novel Variant. J Child Neurol 2017; 32:840-845. [PMID: 28545339 PMCID: PMC5515684 DOI: 10.1177/0883073817711527] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
ACO2 encodes aconitase 2, catalyzing the second step of the tricarboxylic acid. To date, there are only 6 reported families with 5 unique ACO2 mutations. Affected individuals can develop intellectual disability, epilepsy, brain atrophy, hypotonia, ataxia, optic atrophy, and retinal degeneration. Here, we report an 18-year-old boy with a novel ACO2 variant discovered on whole-exome sequencing. He presented with childhood-onset ataxia, impaired self-help skills comparable to severe-profound intellectual disability, intractable epilepsy, cerebellar atrophy, peripheral neuropathy, optic atrophy, and pigmentary retinopathy. His variant is the sixth unique ACO2 mutation. In addition, compared to mild cases (isolated optic atrophy) and severe cases (infantile death), our patient may be moderately affected, evident by increased survival and some preserved cognition (ability to speak full sentences and follow commands), which is a novel presentation. This case expands the disease spectrum to include increased survival with partly spared cognition.
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Affiliation(s)
- Siddharth Srivastava
- 1 Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Cynthia S Gubbels
- 2 Division of Genetics & Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,3 Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kira Dies
- 1 Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anne Fulton
- 4 Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Timothy Yu
- 2 Division of Genetics & Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,3 Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mustafa Sahin
- 1 Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
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20
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Rahman MM, Andberg M, Thangaraj SK, Parkkinen T, Penttilä M, Jänis J, Koivula A, Rouvinen J, Hakulinen N. The Crystal Structure of a Bacterial l-Arabinonate Dehydratase Contains a [2Fe-2S] Cluster. ACS Chem Biol 2017; 12:1919-1927. [PMID: 28574691 DOI: 10.1021/acschembio.7b00304] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a novel crystal structure of the IlvD/EDD family enzyme, l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT, EC 4.2.1.25), which catalyzes the conversion of l-arabinonate to 2-dehydro-3-deoxy-l-arabinonate. The enzyme is a tetramer consisting of a dimer of dimers, where each monomer is composed of two domains. The active site contains a catalytically important [2Fe-2S] cluster and Mg2+ ion and is buried between two domains, and also at the dimer interface. The active site Lys129 was found to be carbamylated. Ser480 and Thr482 were shown to be essential residues for catalysis, and the S480A mutant structure showed an unexpected open conformation in which the active site was more accessible for the substrate. This structure showed the partial binding of l-arabinonate, which allowed us to suggest that the alkoxide ion form of the Ser480 side chain functions as a base and the [2Fe-2S] cluster functions as a Lewis acid in the elimination reaction.
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Affiliation(s)
- Mohammad Mubinur Rahman
- Department
of Chemistry, University of Eastern Finland, P.O. Box 111, FIN-80101 Joensuu, Finland
| | - Martina Andberg
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FIN-02044 VTT, Espoo, Finland
| | - Senthil Kumar Thangaraj
- Department
of Chemistry, University of Eastern Finland, P.O. Box 111, FIN-80101 Joensuu, Finland
| | - Tarja Parkkinen
- Department
of Chemistry, University of Eastern Finland, P.O. Box 111, FIN-80101 Joensuu, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FIN-02044 VTT, Espoo, Finland
| | - Janne Jänis
- Department
of Chemistry, University of Eastern Finland, P.O. Box 111, FIN-80101 Joensuu, Finland
| | - Anu Koivula
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FIN-02044 VTT, Espoo, Finland
| | - Juha Rouvinen
- Department
of Chemistry, University of Eastern Finland, P.O. Box 111, FIN-80101 Joensuu, Finland
| | - Nina Hakulinen
- Department
of Chemistry, University of Eastern Finland, P.O. Box 111, FIN-80101 Joensuu, Finland
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21
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Stiban J, So M, Kaguni LS. Iron-Sulfur Clusters in Mitochondrial Metabolism: Multifaceted Roles of a Simple Cofactor. BIOCHEMISTRY (MOSCOW) 2017; 81:1066-1080. [PMID: 27908232 DOI: 10.1134/s0006297916100059] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Iron-sulfur metabolism is essential for cellular function and is a key process in mitochondria. In this review, we focus on the structure and assembly of mitochondrial iron-sulfur clusters and their roles in various metabolic processes that occur in mitochondria. Iron-sulfur clusters are crucial in mitochondrial respiration, in which they are required for the assembly, stability, and function of respiratory complexes I, II, and III. They also serve important functions in the citric acid cycle, DNA metabolism, and apoptosis. Whereas the identification of iron-sulfur containing proteins and their roles in numerous aspects of cellular function has been a long-standing research area, that in mitochondria is comparatively recent, and it is likely that their roles within mitochondria have been only partially revealed. We review the status of the field and provide examples of other cellular iron-sulfur proteins to highlight their multifarious roles.
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Affiliation(s)
- Johnny Stiban
- Birzeit University, Department of Biology and Biochemistry, West Bank Birzeit, 627, Palestine.
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22
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Crystal structure of an Fe-S cluster-containing fumarate hydratase enzyme from Leishmania major reveals a unique protein fold. Proc Natl Acad Sci U S A 2016; 113:9804-9. [PMID: 27528683 DOI: 10.1073/pnas.1605031113] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Fumarate hydratases (FHs) are essential metabolic enzymes grouped into two classes. Here, we present the crystal structure of a class I FH, the cytosolic FH from Leishmania major, which reveals a previously undiscovered protein fold that coordinates a catalytically essential [4Fe-4S] cluster. Our 2.05 Å resolution data further reveal a dimeric architecture for this FH that resembles a heart, with each lobe comprised of two domains that are arranged around the active site. Besides the active site, where the substrate S-malate is bound bidentate to the unique iron of the [4Fe-4S] cluster, other binding pockets are found near the dimeric enzyme interface, some of which are occupied by malonate, shown here to be a weak inhibitor of this enzyme. Taken together, these data provide a framework both for investigations of the class I FH catalytic mechanism and for drug design aimed at fighting neglected tropical diseases.
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23
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Xu XL, Grant GA. Mutagenic and chemical analyses provide new insight into enzyme activation and mechanism of the type 2 iron-sulfur l-serine dehydratase from Legionella pneumophila. Arch Biochem Biophys 2016; 596:108-17. [PMID: 26971469 DOI: 10.1016/j.abb.2016.03.007] [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: 12/15/2015] [Revised: 02/18/2016] [Accepted: 03/05/2016] [Indexed: 11/28/2022]
Abstract
The crystal structure of the Type 2 l-serine dehydratase from Legionella pneumophila (lpLSD), revealed a "tail-in-mouth" configuration where the C-terminal residue acts as an intrinsic competitive inhibitor. This pre-catalytic structure undergoes an activation step prior to catalytic turnover. Mutagenic analysis of residues at or near the active site cleft is consistent with stabilization of substrate binding by many of the same residues that interact with the C-terminal cysteine and highlight the critical role of certain tail residues in activity. pH-rate profiles show that a residue with pK of 5.9 must be deprotonated and a residue with a pK of 8.5 must be protonated for activity. This supports an earlier suggestion that His 61 is the likely catalytic base. An additional residue with a pK of 8.5-9 increases cooperativity when it is deprotonated. This investigation also demonstrates that the Fe-S dehydratases convert the enamine/imine intermediates of the catalytic reaction to products on the enzyme prior to release. This is in contrast to pyridoxyl 5' phosphate based dehydratases that release an enamine/imine intermediate into solution, which then hydrolyzes to produce the ketoamine product.
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Affiliation(s)
- Xiao Lan Xu
- Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8103, St. Louis, MO 63110, USA
| | - Gregory A Grant
- Developmental Biology, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8103, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8103, St. Louis, MO 63110, USA.
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24
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Abstract
The ancestors of Escherichia coli and Salmonella ultimately evolved to thrive in air-saturated liquids, in which oxygen levels reach 210 μM at 37°C. However, in 1976 Brown and colleagues reported that some sensitivity persists: growth defects still become apparent when hyperoxia is imposed on cultures of E. coli. This residual vulnerability was important in that it raised the prospect that normal levels of oxygen might also injure bacteria, albeit at reduced rates that are not overtly toxic. The intent of this article is both to describe the threat that molecular oxygen poses for bacteria and to detail what we currently understand about the strategies by which E. coli and Salmonella defend themselves against it. E. coli mutants that lack either superoxide dismutases or catalases and peroxidases exhibit a variety of growth defects. These phenotypes constitute the best evidence that aerobic cells continually generate intracellular superoxide and hydrogen peroxide at potentially lethal doses. Superoxide has reduction potentials that allow it to serve in vitro as either a weak univalent reductant or a stronger univalent oxidant. The addition of micromolar hydrogen peroxide to lab media will immediately block the growth of most cells, and protracted exposure will result in the loss of viability. The need for inducible antioxidant systems seems especially obvious for enteric bacteria, which move quickly from the anaerobic gut to fully aerobic surface waters or even to ROS-perfused phagolysosomes. E. coli and Salmonella have provided two paradigmatic models of oxidative-stress responses: the SoxRS and OxyR systems.
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25
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Tröße C, Kongshaug H, Dondrup M, Nilsen F. Characterisation of iron regulatory protein 1A and 1B in the blood-feeding copepod Lepeophtheirus salmonis. Exp Parasitol 2015; 157:1-11. [DOI: 10.1016/j.exppara.2015.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 04/21/2015] [Accepted: 06/15/2015] [Indexed: 11/29/2022]
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26
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Statistical survey of the buried waters in the Protein Data Bank. Amino Acids 2015; 48:193-202. [PMID: 26315961 DOI: 10.1007/s00726-015-2064-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 07/29/2015] [Indexed: 12/18/2022]
Abstract
The structures of buried water molecules were studied in an ensemble of high-quality and non-redundant protein crystal structures. Buried water molecules were clustered and classified in lake-like clusters, which are completely isolated from the bulk solvent, and bay-like clusters, which are in contact with the bulk solvent through a surface water molecule. Buried water molecules are extremely common: lake-like clusters are found in 89 % of the protein crystal structures and bay-like clusters in 93 %. Clusters with only one water molecule are much more common than larger clusters. Both cluster types incline to be surrounded by loop residues, and to a minor extent by residues in extended secondary structure. Helical residues on the contrary do not tend to surround clusters of buried water molecules. One buried water molecule is found every 30-50 amino acid residues, depending on the secondary structures that are more abundant in the protein. Both main- and side-chain atoms are in contact with buried waters; they form four hydrogen bonds with the first water and 1-1.5 additional hydrogen bond for each additional water in the cluster. Consequently, buried water molecules appear to be firmly packed and rigid like the protein atoms. In this regard, it is remarkable to observe that prolines often surround water molecules buried in the protein interior. Interestingly, clusters of buried water molecules tend to be just beneath the protein surface. Moreover, water molecules tend to form a one-dimensional wire rather than more compact arrangements. This agrees with recent evidence of the mechanisms of solvent exchange between internal cavities and bulk solvent.
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27
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Yan Y, Grant GA, Gross ML. Hydrogen-Deuterium Exchange Mass Spectrometry Reveals Unique Conformational and Chemical Transformations Occurring upon [4Fe-4S] Cluster Binding in the Type 2 L-Serine Dehydratase from Legionella pneumophila. Biochemistry 2015; 54:5322-8. [PMID: 26266572 DOI: 10.1021/acs.biochem.5b00761] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The type 2 L-serine dehydratase from Legionella pneumophila (lpLSD) contains a [4Fe-4S](2+) cluster that acts as a Lewis acid to extract the hydroxyl group of L-serine during the dehydration reaction. Surprisingly, the crystal structure shows that all four of the iron atoms in the cluster are coordinated with protein cysteinyl residues and that the cluster is buried and not exposed to solvent. If the crystal structure of lpLSD accurately reflects the structure in solution, then substantial rearrangement at the active site is necessary for the substrate to enter. Furthermore, repair of the oxidized protein when the cluster has degraded would presumably entail exposure of the buried cysteine ligands. Thus, the conformation required for the substrate to enter may be similar to those required for a new cluster to enter the active site. To address this, hydrogen-deuterium exchange combined with mass spectrometry (HDX MS) was used to probe the conformational changes that occur upon oxidative degradation of the Fe-S cluster. The regions that show the most significant differential HDX are adjacent to the cluster location in the holoenzyme or connect regions that are adjacent to the cluster. The observed decrease in flexibility upon cluster binding provides direct evidence that the "tail-in-mouth" conformation observed in the crystal structure also occurs in solution and that the C-terminal peptide is coordinated to the [4Fe-4S] cluster in a precatalytic conformation. This observation is consistent with the requirement of an activation step prior to catalysis and the unusually high level of resistance to oxygen-induced cluster degradation. Furthermore, peptide mapping of the apo form under nonreducing conditions revealed the formation of disulfide bonds between C396 and C485 and possibly between C343 and C385. These observations provide a picture of how the cluster loci are stabilized and poised to receive the cluster in the apo form and the requirement for a reduction step during cluster formation.
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Affiliation(s)
- Yuetian Yan
- Department of Chemistry, Washington University , One Brookings Drive, Box 1134, St. Louis, Missouri 63130, United States
| | - Gregory A Grant
- Department of Developmental Biology and Department of Medicine, Washington University School of Medicine , 660 South Euclid Avenue, Box 8103, St. Louis, Missouri 63110, United States
| | - Michael L Gross
- Department of Chemistry, Washington University , One Brookings Drive, Box 1134, St. Louis, Missouri 63130, United States
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28
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Wu F, Minteer S. Krebs Cycle Metabolon: Structural Evidence of Substrate Channeling Revealed by Cross-Linking and Mass Spectrometry. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409336] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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29
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Wu F, Minteer S. Krebs Cycle Metabolon: Structural Evidence of Substrate Channeling Revealed by Cross-Linking and Mass Spectrometry. Angew Chem Int Ed Engl 2014; 54:1851-4. [DOI: 10.1002/anie.201409336] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Indexed: 11/12/2022]
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30
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Cherrier MV, Chan A, Darnault C, Reichmann D, Amara P, Ollagnier de Choudens S, Fontecilla-Camps JC. The Crystal Structure of Fe4S4 Quinolinate Synthase Unravels an Enzymatic Dehydration Mechanism That Uses Tyrosine and a Hydrolase-Type Triad. J Am Chem Soc 2014; 136:5253-6. [DOI: 10.1021/ja501431b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mickaël V. Cherrier
- Metalloproteins
Unit, Institut de Biologie Structurale, Commissariat à l’Energie
Atomique−Centre National de la Recherche Scientifique, Université Grenoble-Alpes, 6 rue Jules Horowitz, 38000 Grenoble, France
- UMR
5086, BMSSI, CNRS, Université Lyon 1, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, F-69367 Lyon, France
| | - Alice Chan
- Université Grenoble-Alpes, iRTSV-LCBM-Biocatalyse;
CNRS, IRTSV-LCBM-Biocatalyse; CEA, iRTSV-LCBM-Biocatalyse, 38000 Grenoble, France
| | - Claudine Darnault
- Metalloproteins
Unit, Institut de Biologie Structurale, Commissariat à l’Energie
Atomique−Centre National de la Recherche Scientifique, Université Grenoble-Alpes, 6 rue Jules Horowitz, 38000 Grenoble, France
| | - Debora Reichmann
- Université Grenoble-Alpes, iRTSV-LCBM-Biocatalyse;
CNRS, IRTSV-LCBM-Biocatalyse; CEA, iRTSV-LCBM-Biocatalyse, 38000 Grenoble, France
| | - Patricia Amara
- Metalloproteins
Unit, Institut de Biologie Structurale, Commissariat à l’Energie
Atomique−Centre National de la Recherche Scientifique, Université Grenoble-Alpes, 6 rue Jules Horowitz, 38000 Grenoble, France
| | - Sandrine Ollagnier de Choudens
- Université Grenoble-Alpes, iRTSV-LCBM-Biocatalyse;
CNRS, IRTSV-LCBM-Biocatalyse; CEA, iRTSV-LCBM-Biocatalyse, 38000 Grenoble, France
| | - Juan C. Fontecilla-Camps
- Metalloproteins
Unit, Institut de Biologie Structurale, Commissariat à l’Energie
Atomique−Centre National de la Recherche Scientifique, Université Grenoble-Alpes, 6 rue Jules Horowitz, 38000 Grenoble, France
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Lee EH, Lee K, Hwang KY. Structural characterization and comparison of the large subunits of IPM isomerase and homoaconitase from Methanococcus jannaschii. ACTA ACUST UNITED AC 2014; 70:922-31. [PMID: 24699638 DOI: 10.1107/s1399004713033762] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 12/13/2013] [Indexed: 11/10/2022]
Abstract
The aconitase family of proteins includes three classes of hydro-lyase enzymes: aconitases, homoaconitases and isopropylmalate (IPM) isomerases. They have a common Fe-S cluster-binding site and catalyze the isomerization of specific substrates by sequential dehydration and hydration. The archaeon Methanococcus jannaschii contains two aconitase family proteins, IPM isomerase and homoaconitase, which have 50% sequence identity. These two enzymes are heterodimeric proteins composed of large and small subunits encoded by separate genes. Although structures have been reported for the small subunits of the two enzymes, the first structures of oxidized and reduced forms of the large subunit of IPM isomerase (ox-MJ0499 and red-MJ0499, respectively) from M. jannaschii are reported here at 1.8 and 2.7 Å resolution, respectively, together with the structure of the large subunit of homoaconitase (MJ1003) at 2.5 Å resolution. The structures of both proteins have unbound Fe-S clusters and contain a fourth cysteine in the active site. The active site of MJ1003 is homologous to that of aconitase, whereas MJ0499 has significant structural distortion at the active site compared with aconitase. In addition, significant large conformational changes were observed in the active site of red-MJ0499 when compared with ox-MJ0499. The active sites of the two proteins adopt two different states before changing to the Fe-S cluster-bound `activated' state observed in aconitase. MJ1003 has an `open' active site, which forms an active pocket for the cluster, while ox-MJ0499 has a `closed' active site, with four cysteines in disulfide bonds. These data will be helpful in understanding the biochemical mechanism of clustering of the Fe-S protein family.
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Affiliation(s)
- Eun Hye Lee
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong-5, Seongbuk-gu, Seoul 136-701, Republic of Korea
| | - Kitaik Lee
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong-5, Seongbuk-gu, Seoul 136-701, Republic of Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong-5, Seongbuk-gu, Seoul 136-701, Republic of Korea
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Beilschmidt LK, Puccio HM. Mammalian Fe-S cluster biogenesis and its implication in disease. Biochimie 2014; 100:48-60. [PMID: 24440636 DOI: 10.1016/j.biochi.2014.01.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 01/07/2014] [Indexed: 10/25/2022]
Abstract
Iron-sulfur (Fe-S) clusters are inorganic cofactors that are ubiquitous and essential. Due to their chemical versatility, Fe-S clusters are implicated in a wide range of protein functions including mitochondrial respiration and DNA repair. Composed of iron and sulfur, they are sensible to oxygen and their biogenesis requires a highly conserved protein machinery that facilitates assembly of the cluster as well as its insertion into apoproteins. Mitochondria are the central cellular compartment for Fe-S cluster biogenesis in eukaryotic cells and the importance of proper function of this biogenesis for life is highlighted by a constantly increasing number of human genetic diseases that are associated with dysfunction of this Fe-S cluster biogenesis pathway. Although these disorders are rare and appear dissimilar, common aspects are found among them. This review will give an overview on what is known on mammalian Fe-S cluster biogenesis today, by putting it into the context of what is known from studies from lower model organisms, and focuses on the associated diseases, by drawing attention to the respective mutations. Finally, it outlines the importance of adequate cellular and murine models to uncover not only each protein function, but to resolve their role and requirement throughout the mammalian organism.
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Affiliation(s)
- Lena K Beilschmidt
- Translational Medicine and Neurogenetics, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Illkirch, France; Inserm, U596, Illkirch, France; CNRS, UMR7104, Illkirch, France; Université de Strasbourg, Strasbourg, France; Collège de France, Chaire de génétique humaine, Illkirch, France
| | - Hélène M Puccio
- Translational Medicine and Neurogenetics, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Illkirch, France; Inserm, U596, Illkirch, France; CNRS, UMR7104, Illkirch, France; Université de Strasbourg, Strasbourg, France; Collège de France, Chaire de génétique humaine, Illkirch, France.
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33
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Zheng A, Chang W, Hou S, Zhang S, Cai H, Chen G, Lou R, Liu G. Unraveling molecular mechanistic differences in liver metabolism between lean and fat lines of Pekin duck (Anas platyrhynchos domestica): a proteomic study. J Proteomics 2014; 98:271-88. [PMID: 24412807 DOI: 10.1016/j.jprot.2013.12.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 12/18/2013] [Accepted: 12/22/2013] [Indexed: 11/18/2022]
Abstract
UNLABELLED Duck is one of the major poultry meat sources for human consumption. To satisfy different eating habits, lean and fat strains of Pekin ducks have been developed. The objective of this study was to determine the molecular mechanistic differences in liver metabolism between two duck strains. The liver proteome of the Pekin duck lines was compared on days 1, 14, 28, and 42 posthatching using 2-DE based proteomics. There was a different abundance of 76 proteins in the livers of the two duck lines. Fat ducks strongly expressed proteins related to pathways of glycolysis, ATP synthesis, and protein catabolism, suggesting enhanced fat deposition rather than protein retention. In contrast, highly expressed proteins in lean ducks improved protein anabolism and reduced protein catabolism, resulting in an enhancement of lean meat deposition. Along with the decrease in fat deposition, the immune system of the lean duck strain may be enhanced by enhanced expression of proteins involved in stress response, immune defense, and antioxidant functions. These results indicate that selection pressure has shaped the two duck lines differently resulting in different liver metabolic capacities. These observed variations between the two strains at the molecular level are matched with physiological changes in growth performance and meat production. This information may have beneficial impacts in areas such as genetic modification through the manipulation of target proteins or genes in specific pathways to improve the efficiency of duck meat production. BIOLOGICAL SIGNIFICANCE The objective of this study was to unravel molecular mechanistic differences in liver metabolism between lean and fat Pekin duck (Anas platyrhynchos domestica) strains. There was a different abundance of 76 proteins in the livers of the two duck lines. Enhanced protein expression in the fat ducks related to pathways of glycolysis, ATP synthesis and protein catabolism suggesting increased fat deposition rather than protein retention. In contrast, highly expressed proteins in the lean ducks facilitated protein deposition by increasing protein anabolism and reducing protein catabolism to enhance the lean meat percentage. Along with the decrease of fat deposition, the immunity of lean duck appeared to be enhanced by increased expression of proteins involved in stress response, defense and antioxidant function. This study provides potential target proteins or genes for further functional analysis and genetic manipulation to increase the efficiency of duck meat production and help satisfy the global demand for poultry meat.
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Affiliation(s)
- Aijuan Zheng
- Feed Research Institute, Key Laboratory of Feed Biotechnology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenhuan Chang
- Feed Research Institute, Key Laboratory of Feed Biotechnology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuisheng Hou
- Institute of Animal Sciences, State Key Laboratory of Animal Nutrition, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Shu Zhang
- Feed Research Institute, Key Laboratory of Feed Biotechnology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huiyi Cai
- Feed Research Institute, Key Laboratory of Feed Biotechnology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guilan Chen
- Feed Research Institute, Key Laboratory of Feed Biotechnology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ruiying Lou
- Feed Research Institute, Key Laboratory of Feed Biotechnology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guohua Liu
- Feed Research Institute, Key Laboratory of Feed Biotechnology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Terada T, Hirabayashi K, Liu D, Nakamura T, Wakimoto T, Matsumoto T, Tatsumi K. [3:1] Site-Differentiated [4Fe–4S] Clusters Having One Carboxylate and Three Thiolates. Inorg Chem 2013; 52:11997-2004. [DOI: 10.1021/ic4017596] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tamaki Terada
- Department of Chemistry,
Graduate School of Science, ‡Institute of Transformative Bio-Molecules (WPI-ITbM), and §Research Center
for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Kiyohisa Hirabayashi
- Department of Chemistry,
Graduate School of Science, ‡Institute of Transformative Bio-Molecules (WPI-ITbM), and §Research Center
for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Dong Liu
- Department of Chemistry,
Graduate School of Science, ‡Institute of Transformative Bio-Molecules (WPI-ITbM), and §Research Center
for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tomohiko Nakamura
- Department of Chemistry,
Graduate School of Science, ‡Institute of Transformative Bio-Molecules (WPI-ITbM), and §Research Center
for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takuya Wakimoto
- Department of Chemistry,
Graduate School of Science, ‡Institute of Transformative Bio-Molecules (WPI-ITbM), and §Research Center
for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tsuyoshi Matsumoto
- Department of Chemistry,
Graduate School of Science, ‡Institute of Transformative Bio-Molecules (WPI-ITbM), and §Research Center
for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Kazuyuki Tatsumi
- Department of Chemistry,
Graduate School of Science, ‡Institute of Transformative Bio-Molecules (WPI-ITbM), and §Research Center
for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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35
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Wu F, Minteer SD. Fluorescence Characterization of Co-immobilization-Induced Multi-Enzyme Aggregation in a Polymer Matrix Using Förster Resonance Energy Transfer (FRET): Toward the Metabolon Biomimic. Biomacromolecules 2013; 14:2739-49. [DOI: 10.1021/bm400569k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Fei Wu
- Departments of Chemistry
and Materials Science and
Engineering, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Shelley D. Minteer
- Departments of Chemistry
and Materials Science and
Engineering, University of Utah, Salt Lake
City, Utah 84112, United States
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36
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Esposito G, Vos M, Vilain S, Swerts J, De Sousa Valadas J, Van Meensel S, Schaap O, Verstreken P. Aconitase causes iron toxicity in Drosophila pink1 mutants. PLoS Genet 2013; 9:e1003478. [PMID: 23637640 PMCID: PMC3636082 DOI: 10.1371/journal.pgen.1003478] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 03/12/2013] [Indexed: 12/21/2022] Open
Abstract
The PTEN-induced kinase 1 (PINK1) is a mitochondrial kinase, and pink1 mutations cause early onset Parkinson's disease (PD) in humans. Loss of pink1 in Drosophila leads to defects in mitochondrial function, and genetic data suggest that another PD-related gene product, Parkin, acts with pink1 to regulate the clearance of dysfunctional mitochondria (mitophagy). Consequently, pink1 mutants show an accumulation of morphologically abnormal mitochondria, but it is unclear if other factors are involved in pink1 function in vivo and contribute to the mitochondrial morphological defects seen in specific cell types in pink1 mutants. To explore the molecular mechanisms of pink1 function, we performed a genetic modifier screen in Drosophila and identified aconitase (acon) as a dominant suppressor of pink1. Acon localizes to mitochondria and harbors a labile iron-sulfur [4Fe-4S] cluster that can scavenge superoxide to release hydrogen peroxide and iron that combine to produce hydroxyl radicals. Using Acon enzymatic mutants, and expression of mitoferritin that scavenges free iron, we show that [4Fe-4S] cluster inactivation, as a result of increased superoxide in pink1 mutants, results in oxidative stress and mitochondrial swelling. We show that [4Fe-4S] inactivation acts downstream of pink1 in a pathway that affects mitochondrial morphology, but acts independently of parkin. Thus our data indicate that superoxide-dependent [4Fe-4S] inactivation defines a potential pathogenic cascade that acts independent of mitophagy and links iron toxicity to mitochondrial failure in a PD–relevant model. In this work we provide mechanistic insight linking together two of the earliest observations in Parkinson's disease: the excessive build-up of iron in diseased substantia nigra neurons and mitochondrial dysfunction particularly increased reactive oxygen species production at the level of Complex I. We identify aconitase mutants as strong genetic suppressors of Parkinson-related pink1 mutant phenotypes, both at the organismal and at the cellular/mitochondrial level. We show that the mitochondrial dysfunction in pink1 mutants that includes Complex I dysfunction results in superoxide-dependent inactivation of the Aconitase iron-sulfur cluster, leading to the release of iron and peroxide that combine to produce hydroxyl radicals and mitochondrial failure. Consequently, scavenging free iron using expression of mitoferritin or decreasing the levels of aconitase both rescue pink1 mutants; while increased wild-type Aconitase, but not a mutant that does not harbor an iron-sulfur cluster, results in severe mitochondrial defects. Given that reduced electron transport chain activity, increased oxidative stress, and natural iron build-up in the substantia nigra are common factors in sporadic and familial forms of Parkinson's disease, we believe that oxidative inactivation of Aconitase may represent an important pathogenic cascade underlying neuronal dysfunction in Parkinson's disease.
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Affiliation(s)
- Giovanni Esposito
- VIB Center for the Biology of Disease, Leuven, Belgium
- KU Leuven, Center for Human Genetics and Leuven Research Institute for Neuroscience and Disease (LIND), Leuven, Belgium
| | - Melissa Vos
- VIB Center for the Biology of Disease, Leuven, Belgium
- KU Leuven, Center for Human Genetics and Leuven Research Institute for Neuroscience and Disease (LIND), Leuven, Belgium
| | - Sven Vilain
- VIB Center for the Biology of Disease, Leuven, Belgium
- KU Leuven, Center for Human Genetics and Leuven Research Institute for Neuroscience and Disease (LIND), Leuven, Belgium
| | - Jef Swerts
- VIB Center for the Biology of Disease, Leuven, Belgium
- KU Leuven, Center for Human Genetics and Leuven Research Institute for Neuroscience and Disease (LIND), Leuven, Belgium
| | - Jorge De Sousa Valadas
- VIB Center for the Biology of Disease, Leuven, Belgium
- KU Leuven, Center for Human Genetics and Leuven Research Institute for Neuroscience and Disease (LIND), Leuven, Belgium
| | - Stefanie Van Meensel
- VIB Center for the Biology of Disease, Leuven, Belgium
- KU Leuven, Center for Human Genetics and Leuven Research Institute for Neuroscience and Disease (LIND), Leuven, Belgium
| | - Onno Schaap
- VIB Center for the Biology of Disease, Leuven, Belgium
- KU Leuven, Center for Human Genetics and Leuven Research Institute for Neuroscience and Disease (LIND), Leuven, Belgium
| | - Patrik Verstreken
- VIB Center for the Biology of Disease, Leuven, Belgium
- KU Leuven, Center for Human Genetics and Leuven Research Institute for Neuroscience and Disease (LIND), Leuven, Belgium
- * E-mail:
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37
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Liu Q, Simpson DC, Gronert S. Carbonylation of mitochondrial aconitase with 4-hydroxy-2-(E)-nonenal: localization and relative reactivity of addition sites. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1144-54. [PMID: 23518448 DOI: 10.1016/j.bbapap.2013.03.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/30/2013] [Accepted: 03/07/2013] [Indexed: 12/30/2022]
Abstract
Mass spectrometry was used to investigate the effects of exposing mitochondrial aconitase (ACO2) to the membrane lipid peroxidation product, 4-hydroxy-2-(E)-nonenal (HNE). ACO2 was selected for this study because (1) it is known to be inactivated by HNE, (2) elevated concentrations of HNE-adducted ACO2 have been associated with disease states, (3) extensive structural information is available, and (4) the iron-sulfur cluster in ACO2 offers a critical target for HNE adduction. The aim of this study was to relate the inactivation of ACO2 by HNE to structural features. Initially, Western blotting and an enzyme activity assay were used to assess aggregate effects and then gel electrophoresis, in-gel digestion, and tandem mass spectrometry (MS/MS) were used to identify HNE addition sites. HNE addition reaction rates were determined for the most significant sites using the iTRAQ approach. The most reactive sites were Cys(358), Cys(421), and Cys(424), the three iron-sulfur cluster-coordinating cysteines, Cys(99), the closest non-ligated cysteine to the cluster, and Cys(565), which is located in the cleft leading to the active site. Interestingly, both enzyme activity assay and iTRAQ relative abundance plots appeared to be trending toward horizontal asymptotes, rather than completion.
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Affiliation(s)
- Qingyuan Liu
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, USA
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38
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Fazius F, Shelest E, Gebhardt P, Brock M. The fungal α-aminoadipate pathway for lysine biosynthesis requires two enzymes of the aconitase family for the isomerization of homocitrate to homoisocitrate. Mol Microbiol 2012; 86:1508-30. [PMID: 23106124 PMCID: PMC3556520 DOI: 10.1111/mmi.12076] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2012] [Indexed: 11/30/2022]
Abstract
Fungi produce α-aminoadipate, a precursor for penicillin and lysine via the α-aminoadipate pathway. Despite the biotechnological importance of this pathway, the essential isomerization of homocitrate via homoaconitate to homoisocitrate has hardly been studied. Therefore, we analysed the role of homoaconitases and aconitases in this isomerization. Although we confirmed an essential contribution of homoaconitases from Saccharomyces cerevisiae and Aspergillus fumigatus, these enzymes only catalysed the interconversion between homoaconitate and homoisocitrate. In contrast, aconitases from fungi and the thermophilic bacterium Thermus thermophilus converted homocitrate to homoaconitate. Additionally, a single aconitase appears essential for energy metabolism, glutamate and lysine biosynthesis in respirating filamentous fungi, but not in the fermenting yeast S. cerevisiae that possesses two contributing aconitases. While yeast Aco1p is essential for the citric acid cycle and, thus, for glutamate synthesis, Aco2p specifically and exclusively contributes to lysine biosynthesis. In contrast, Aco2p homologues present in filamentous fungi were transcribed, but enzymatically inactive, revealed no altered phenotype when deleted and did not complement yeast aconitase mutants. From these results we conclude that the essential requirement of filamentous fungi for respiration versus the preference of yeasts for fermentation may have directed the evolution of aconitases contributing to energy metabolism and lysine biosynthesis.
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Affiliation(s)
- Felicitas Fazius
- Microbial Biochemistry and Physiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Beutenbergstr. 11a, 07745 Jena, Germany
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39
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Michta E, Schad K, Blin K, Ort-Winklbauer R, Röttig M, Kohlbacher O, Wohlleben W, Schinko E, Mast Y. The bifunctional role of aconitase in Streptomyces viridochromogenes Tü494. Environ Microbiol 2012; 14:3203-19. [PMID: 23116164 DOI: 10.1111/1462-2920.12006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 09/24/2012] [Indexed: 12/01/2022]
Abstract
In many organisms, aconitases have dual functions; they serve as enzymes in the tricarboxylic acid cycle and as regulators of iron metabolism. In this study we defined the role of the aconitase AcnA in Streptomyces viridochromogenes Tü494, the producer of the herbicide phosphinothricyl-alanyl-alanine, also known as phosphinothricin tripeptide or bialaphos. A mutant in which the aconitase gene acnA was disrupted showed severe defects in morphology and physiology, as it was unable to form any aerial mycelium, spores nor phosphinothricin tripeptide. AcnA belongs to the iron regulatory proteins (IRPs). In addition to its catalytic function, AcnA plays a regulatory role by binding to iron responsive elements (IREs) located on the untranslated region of certain mRNAs. A mutation preventing the formation of the [4Fe-4S] cluster of AcnA eliminated its catalytic activity, but did not inhibit RNA-binding ability. In silico analysis of the S. viridochromogenes genome revealed several IRE-like structures. One structure is located upstream of recA, which is involved in the bacterial SOS response, and another one was identified upstream of ftsZ, which is required for the onset of sporulation in streptomycetes. The functionality of different IRE structures was proven with gel shift assays and specific IRE consensus sequences were defined. Furthermore, RecA was shown to be upregulated on post-transcriptional level under oxidative stress conditions in the wild-type strain but not in the acnA mutant, suggesting a regulatory role of AcnA in oxidative stress response.
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Affiliation(s)
- Ewelina Michta
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin (IMIT), Mikrobiologie/Biotechnologie, Fakultät für Biologie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
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40
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Py B, Gerez C, Angelini S, Planel R, Vinella D, Loiseau L, Talla E, Brochier-Armanet C, Garcia Serres R, Latour JM, Ollagnier-de Choudens S, Fontecave M, Barras F. Molecular organization, biochemical function, cellular role and evolution of NfuA, an atypical Fe-S carrier. Mol Microbiol 2012; 86:155-71. [PMID: 22966982 DOI: 10.1111/j.1365-2958.2012.08181.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biosynthesis of iron-sulphur (Fe-S) proteins is catalysed by multi-protein systems, ISC and SUF. However, 'non-ISC, non-SUF' Fe-S biosynthesis factors have been described, both in prokaryotes and eukaryotes. Here we report in vitro and in vivo investigations of such a 'non-ISC, non SUF' component, the Nfu proteins. Phylogenomic analysis allowed us to define four subfamilies. Escherichia coli NfuA is within subfamily II. Most members of this subfamily have a Nfu domain fused to a 'degenerate' A-type carrier domain (ATC*) lacking Fe-S cluster co-ordinating Cys ligands. The Nfu domain binds a [4Fe-4S] cluster while the ATC* domain interacts with NuoG (a complex I subunit) and aconitase B (AcnB). In vitro, holo-NfuA promotes maturation of AcnB. In vivo, NfuA is necessary for full activity of complex I under aerobic growth conditions, and of AcnB in the presence of superoxide. NfuA receives Fe-S clusters from IscU/HscBA and SufBCD scaffolds and eventually transfers them to the ATCs IscA and SufA. This study provides significant information on one of the Fe-S biogenesis factors that has been often used as a building block by ISC and/or SUF synthesizing organisms, including bacteria, plants and animals.
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Affiliation(s)
- Béatrice Py
- Laboratoire de Chimie Bactérienne, UMR 7283 Aix-Marseille Université-CNRS, Institut de Microbiologie de la Méditerranée, 31 Chemin Joseph Aiguier, 13009 Marseille, France
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Chen JQ, Russo J. Dysregulation of glucose transport, glycolysis, TCA cycle and glutaminolysis by oncogenes and tumor suppressors in cancer cells. Biochim Biophys Acta Rev Cancer 2012; 1826:370-84. [PMID: 22750268 DOI: 10.1016/j.bbcan.2012.06.004] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 06/16/2012] [Accepted: 06/18/2012] [Indexed: 12/19/2022]
Abstract
A common set of functional characteristics of cancer cells is that cancer cells consume a large amount of glucose, maintain high rate of glycolysis and convert a majority of glucose into lactic acid even in the presence of oxygen compared to that of normal cells (Warburg's Effects). In addition, cancer cells exhibit substantial alterations in several energy metabolism pathways including glucose transport, tricarboxylic acid (TCA) cycle, glutaminolysis, mitochondrial respiratory chain oxidative phosphorylation and pentose phosphate pathway (PPP). In the present work, we focused on reviewing the current knowledge about the dysregulation of the proteins/enzymes involved in the key regulatory steps of glucose transport, glycolysis, TCA cycle and glutaminolysis by several oncogenes including c-Myc and hypoxia inducible factor-1 (HIF-1) and tumor suppressor, p53, in cancer cells. The dysregulation of glucose transport and energy metabolism pathways by oncogenes and lost functions of the tumor suppressors have been implicated as important biomarkers for cancer detection and as valuable targets for the development of new anticancer therapies.
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Affiliation(s)
- Jin-Qiang Chen
- Breast Cancer Research Laboratory, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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42
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Ohki Y, Tanifuji K, Yamada N, Imada M, Tajima T, Tatsumi K. Synthetic analogues of [Fe4S4(Cys)3(His)] in hydrogenases and [Fe4S4(Cys)4] in HiPIP derived from all-ferric [Fe4S4{N(SiMe3)2}4]. Proc Natl Acad Sci U S A 2011; 108:12635-40. [PMID: 21768339 PMCID: PMC3150945 DOI: 10.1073/pnas.1106472108] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The all-ferric [Fe(4)S(4)](4+) cluster [Fe(4)S(4){N(SiMe(3))(2)}(4)] 1 and its one-electron reduced form [1](-) serve as convenient precursors for the synthesis of 31-site differentiated [Fe(4)S(4)] clusters and high-potential iron-sulfur protein (HiPIP) model clusters. The reaction of 1 with four equivalents (equiv) of the bulky thiol HSDmp (Dmp = 2,6-(mesityl)(2)C(6)H(3), mesityl = 2,4,6-Me(3)C(6)H(2)) followed by treatment with tetrahydrofuran (THF) resulted in the isolation of [Fe(4)S(4)(SDmp)(3)(THF)(3)] 2. Cluster 2 contains an octahedral iron atom with three THF ligands, and its Fe(S)(3)(O)(3) coordination environment is relevant to that in the active site of substrate-bound aconitase. An analogous reaction of [1](-) with four equiv of HSDmp gave [Fe(4)S(4)(SDmp)(4)](-) 3, which models the oxidized form of HiPIP. The THF ligands in 2 can be replaced by tetramethyl-imidazole (Me(4)Im) to give [Fe(4)S(4)(SDmp)(3)(Me(4)Im)] 4 modeling the [Fe(4)S(4)(Cys)(3)(His)] cluster in hydrogenases, and its one-electron reduced form [4](-) was synthesized from the reaction of 3 with Me(4)Im. The reversible redox couple between 3 and [3](-) was observed at E(1/2) = -820 mV vs. Ag/Ag(+), and the corresponding reversible couple for 4 and [4](-) is positively shifted by +440 mV. The cyclic voltammogram of 3 also exhibited a reversible oxidation couple, which indicates generation of the all-ferric [Fe(4)S(4)](4+) cluster, [Fe(4)S(4)(SDmp)(4)].
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Affiliation(s)
- Yasuhiro Ohki
- Department of Chemistry, Graduate School of Science and Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Kazuki Tanifuji
- Department of Chemistry, Graduate School of Science and Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Norihiro Yamada
- Department of Chemistry, Graduate School of Science and Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Motosuke Imada
- Department of Chemistry, Graduate School of Science and Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tomoyuki Tajima
- Department of Chemistry, Graduate School of Science and Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Kazuyuki Tatsumi
- Department of Chemistry, Graduate School of Science and Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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Gu M, Imlay JA. The SoxRS response of Escherichia coli is directly activated by redox-cycling drugs rather than by superoxide. Mol Microbiol 2011; 79:1136-50. [PMID: 21226770 DOI: 10.1111/j.1365-2958.2010.07520.x] [Citation(s) in RCA: 177] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
When Escherichia coli is exposed to redox-cycling drugs, its SoxR transcription factor is activated by oxidation of its [2Fe-2S] cluster. In aerobic cells these drugs generate superoxide, and because superoxide dismutase (SOD) is a member of the SoxRS regulon, superoxide was initially thought to be the activator of SoxR. Its many-gene regulon was therefore believed to comprise a defence against superoxide stress. However, we found that abundant superoxide did not effectively activate SoxR in an SOD⁻ mutant, that overproduced SOD could not suppress activation by redox-cycling drugs, and that redox-cycling drugs were able to activate SoxR in anaerobic cells as long as alternative respiratory acceptors were provided. Thus superoxide is not the signal that SoxR senses. Indeed, redox-cycling drugs directly oxidized the cluster of purified SoxR in vitro, while superoxide did not. Redox-cycling drugs are excreted by both bacteria and plants. Their toxicity does not require superoxide, as they poisoned E. coli under anaerobic conditions, in part by oxidizing dehydratase iron-sulfur clusters. Under these conditions SoxRS induction was protective. Thus it is physiologically appropriate that the SoxR protein directly senses redox-cycling drugs rather than superoxide.
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Affiliation(s)
- Mianzhi Gu
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
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45
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Jeyakanthan J, Drevland RM, Gayathri DR, Velmurugan D, Shinkai A, Kuramitsu S, Yokoyama S, Graham DE. Substrate Specificity Determinants of the Methanogen Homoaconitase Enzyme: Structure and Function of the Small Subunit,. Biochemistry 2010; 49:2687-96. [DOI: 10.1021/bi901766z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jeyaraman Jeyakanthan
- Life Science Group, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu Science Park, Hsinch 30076, Taiwan
| | - Randy M. Drevland
- Chemistry and Biochemistry Department, The University of Texas at Austin, Austin, Texas 78712
| | - Dasara Raju Gayathri
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India
| | - Devadasan Velmurugan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India
| | - Akeo Shinkai
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Seiki Kuramitsu
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - David E. Graham
- Chemistry and Biochemistry Department, The University of Texas at Austin, Austin, Texas 78712
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
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Cleland W. The low-barrier hydrogen bond in enzymic catalysis. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2010. [DOI: 10.1016/s0065-3160(08)44001-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Miller C, Pettee B, Zhang C, Pabst M, McLean J, Anderson A. Copper and cadmium: responses inPseudomonas putidaKT2440. Lett Appl Microbiol 2009; 49:775-83. [DOI: 10.1111/j.1472-765x.2009.02741.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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48
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Schinko E, Schad K, Eys S, Keller U, Wohlleben W. Phosphinothricin-tripeptide biosynthesis: an original version of bacterial secondary metabolism? PHYTOCHEMISTRY 2009; 70:1787-1800. [PMID: 19878959 DOI: 10.1016/j.phytochem.2009.09.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Revised: 09/03/2009] [Accepted: 09/04/2009] [Indexed: 05/28/2023]
Abstract
Streptomyces viridochromogenes Tü494 produces the herbicide phosphinothricyl-alanyl-alanine (phosphinothricin-tripeptide=PTT; bialaphos). Its bioactive moiety phosphinothricin competitively inhibits bacterial and plant glutamine synthetases. The biosynthesis of PTT includes the synthesis of the unusual amino acid N-acetyl-demethyl-phosphinothricin and a three step condensation via non-ribosomal peptide synthetases. Two characteristics within the PTT biosynthesis make it suitable to study the evolution of secondary metabolism biosynthesis. First, PTT biosynthesis represents the only known system where all peptide synthetase modules are located on separate proteins. This 'single enzyme system' might be an archetype of the multimodular and multienzymatic non-ribosomal peptide synthetases in evolutionary terms. The second interesting feature of PTT biosynthesis is the pathway-specific aconitase Pmi that is involved in the supply of N-acetyl-demethyl-phosphinothricin. Pmi is highly similar to the tricarboxylic acid aconitase AcnA. They share 64% identity at the DNA level and both belong to the Iron-Regulatory-Protein/AcnA family. Despite their high sequence similarity, AcnA and Pmi catalyze different reactions and are not able to substitute for each other. Thus, the enzyme pair AcnA/Pmi presents an example of the evolution of a secondary metabolite-specific enzyme from a primary metabolism enzyme.
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Affiliation(s)
- Eva Schinko
- Mikrobiologie/Biotechnologie, Eberhard-Karls-Universität Tübingen, Tübingen, Germany
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The iron-sulfur clusters of dehydratases are primary intracellular targets of copper toxicity. Proc Natl Acad Sci U S A 2009; 106:8344-9. [PMID: 19416816 DOI: 10.1073/pnas.0812808106] [Citation(s) in RCA: 736] [Impact Index Per Article: 49.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Excess copper is poisonous to all forms of life, and copper overloading is responsible for several human pathologic processes. The primary mechanisms of toxicity are unknown. In this study, mutants of Escherichia coli that lack copper homeostatic systems (copA cueO cus) were used to identify intracellular targets and to test the hypothesis that toxicity involves the action of reactive oxygen species. Low micromolar levels of copper were sufficient to inhibit the growth of both WT and mutant strains. The addition of branched-chain amino acids restored growth, indicating that copper blocks their biosynthesis. Indeed, copper treatment rapidly inactivated isopropylmalate dehydratase, an iron-sulfur cluster enzyme in this pathway. Other enzymes in this iron-sulfur dehydratase family were similarly affected. Inactivation did not require oxygen, in vivo or with purified enzyme. Damage occurred concomitant with the displacement of iron atoms from the solvent-exposed cluster, suggesting that Cu(I) damages these proteins by liganding to the coordinating sulfur atoms. Copper efflux by dedicated export systems, chelation by glutathione, and cluster repair by assembly systems all enhance the resistance of cells to this metal.
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Knockdown of proteins involved in iron metabolism limits tick reproduction and development. Proc Natl Acad Sci U S A 2009; 106:1033-8. [PMID: 19171899 DOI: 10.1073/pnas.0807961106] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ticks are among the most important vectors of a wide range of human and animal diseases. During blood feeding, ticks are exposed to an enormous amount of free iron that must be appropriately used and detoxified. However, the mechanism of iron metabolism in ticks is poorly understood. Here, we show that ticks possess a complex system that efficiently utilizes, stores and transports non-heme iron within the tick body. We have characterized a new secreted ferritin (FER2) and an iron regulatory protein (IRP1) from the sheep tick, Ixodes ricinus, and have demonstrated their relationship to a previously described tick intracellular ferritin (FER1). By using RNA interference-mediated gene silencing in the tick, we show that synthesis of FER1, but not of FER2, is subject to IRP1-mediated translational control. Further, we find that depletion of FER2 from the tick plasma leads to a loss of FER1 expression in the salivary glands and ovaries that normally follows blood ingestion. We therefore suggest that secreted FER2 functions as the primary transporter of non-heme iron between the tick gut and the peripheral tissues. Silencing of the fer1, fer2, and irp1 genes by RNAi has an adverse impact on hatching rate and decreases postbloodmeal weight in tick females. Importantly, knockdown of fer2 dramatically impairs the ability of ticks to feed, thus making FER2 a promising candidate for development of an efficient anti-tick vaccine.
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