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Piccirilli F, Vondracek H, Silvestrini L, Parisse P, Spinozzi F, Vaccari L, Toma A, Aglieri V, Casalis L, Piccionello AP, Mariani P, Birarda G, Ortore MG. Dimeric and monomeric conformation of SARS-CoV-2 main protease: New technical approaches based on IR radiation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 322:124772. [PMID: 39003826 DOI: 10.1016/j.saa.2024.124772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/11/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024]
Abstract
The main proteases Mpro are a group of highly conserved cysteine hydrolases in β-coronaviruses. They have been demonstrated to play an unavoidable role in viral replication, and consequently they have been suggested as key targets for treating coronavirus-caused infectious diseases, mainly from the COVID-19 epidemic. Since the most functional form for Mpro enzymatic activity is associated to its homodimer, compounds inhibiting dimerization should also inhibit catalytic activity. We show how PIR-SEIRA (Plasmonic Internal Reflection-Surface Enhanced InfraRed Absorption) spectroscopy can be a noteworthy technique to study proteins subtle structural variations associated to inhibitor binding. Nanoantennas arrays can selectively confine and enhance electromagnetic field via localized plasmonic resonances, thus promoting ultrasensitive detection of biomolecules in close proximity of nanoantenna arrays and enabling the effective investigation of protein monolayers. By adopting this approach, reflection measurements conducted under back illumination of nanoantennas allow to probe anchored protein monolayers, with minimum contribution of environmental buffer molecules. PIR-SEIRA spectroscopy on Mpro was carried out by ad hoc designed devices, resonating in the spectral region of Amide I and Amide II bands. We evaluated here the structure of anchored monomers and dimers in different buffered environment and in presence of a newly designed Mpro inhibitor. Experimental results show that dimerization is not associated to relevant backbone rearrangements of the protein at secondary structure level, and even if the compound inhibits the dimerization, it is not effective at breaking preformed dimers.
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Affiliation(s)
| | - Hendrik Vondracek
- Elettra-Synchrotron Trieste S.C.p.A., Strada Statale 14, Basovizza, Trieste, I-34149, Italy
| | - Lucia Silvestrini
- Department of Life and Environmental Sciences, Marche Polytechnic University, via brecce bianche, Ancona, I-60131, Italy
| | - Pietro Parisse
- Elettra-Synchrotron Trieste S.C.p.A., Strada Statale 14, Basovizza, Trieste, I-34149, Italy; CNR - Istituto Officina dei Materiali, s.s. 14 km 163.5 in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Francesco Spinozzi
- Department of Life and Environmental Sciences, Marche Polytechnic University, via brecce bianche, Ancona, I-60131, Italy
| | - Lisa Vaccari
- Elettra-Synchrotron Trieste S.C.p.A., Strada Statale 14, Basovizza, Trieste, I-34149, Italy
| | - Andrea Toma
- Fondazione Istituto Italiano di Tecnologia, via Morego 30, Genova, I- 16163, Italy
| | - Vincenzo Aglieri
- Fondazione Istituto Italiano di Tecnologia, via Morego 30, Genova, I- 16163, Italy
| | - Loredana Casalis
- Elettra-Synchrotron Trieste S.C.p.A., Strada Statale 14, Basovizza, Trieste, I-34149, Italy
| | - Antonio Palumbo Piccionello
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, viale delle scienze, Palermo, I-90133, Italy
| | - Paolo Mariani
- Department of Life and Environmental Sciences, Marche Polytechnic University, via brecce bianche, Ancona, I-60131, Italy
| | - Giovanni Birarda
- Elettra-Synchrotron Trieste S.C.p.A., Strada Statale 14, Basovizza, Trieste, I-34149, Italy.
| | - Maria Grazia Ortore
- Department of Life and Environmental Sciences, Marche Polytechnic University, via brecce bianche, Ancona, I-60131, Italy.
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2
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Antony P, Baby B, Ali A, Vijayan R, Al Jasmi F. Interaction of Glutathione with MMACHC Arginine-Rich Pocket Variants Associated with Cobalamin C Disease: Insights from Molecular Modeling. Biomedicines 2023; 11:3217. [PMID: 38137438 PMCID: PMC10740964 DOI: 10.3390/biomedicines11123217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/20/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Methylmalonic aciduria and homocystinuria type C protein (MMACHC) is required by the body to metabolize cobalamin (Cbl). Due to its complex structure and cofactor forms, Cbl passes through an extensive series of absorptive and processing steps before being delivered to mitochondrial methyl malonyl-CoA mutase and cytosolic methionine synthase. Depending on the cofactor attached, MMACHC performs either flavin-dependent reductive decyanation or glutathione (GSH)-dependent dealkylation. The alkyl groups of Cbl have to be removed in the presence of GSH to produce intermediates that can later be converted into active cofactor forms. Pathogenic mutations in the GSH binding site, such as R161Q, R161G, R206P, R206W, and R206Q, have been reported to cause Cbl diseases. The impact of these variations on MMACHC's structure and how it affects GSH and Cbl binding at the molecular level is poorly understood. To better understand the molecular basis of this interaction, mutant structures involving the MMACHC-MeCbl-GSH complex were generated using in silico site-directed point mutations and explored using molecular dynamics (MD) simulations. The results revealed that mutations in the key arginine residues disrupt GSH binding by breaking the interactions and reducing the free energy of binding of GSH. Specifically, variations at position 206 appeared to produce weaker GSH binding. The lowered binding affinity for GSH in the variant structures could impact metabolic pathways involving Cbl and its trafficking.
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Affiliation(s)
- Priya Antony
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Bincy Baby
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Amanat Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Ranjit Vijayan
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- The Big Data Analytics Center, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Fatma Al Jasmi
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Department of Pediatrics, Tawam Hospital, Al Ain P.O. Box 15258, United Arab Emirates
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3
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Paz D, Pinales BE, Castellanos BS, Perez I, Gil CB, Madrigal LJ, Reyes-Nava NG, Castro VL, Sloan JL, Quintana AM. Abnormal chondrocyte development in a zebrafish model of cblC syndrome restored by an MMACHC cobalamin binding mutant. Differentiation 2023; 131:74-81. [PMID: 37167860 DOI: 10.1016/j.diff.2023.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/10/2023] [Accepted: 04/24/2023] [Indexed: 05/13/2023]
Abstract
Variants in the MMACHC gene cause combined methylmalonic acidemia and homocystinuria cblC type, the most common inborn error of intracellular cobalamin (vitamin B12) metabolism. cblC is associated with neurodevelopmental, hematological, ocular, and biochemical abnormalities. In a subset of patients, mild craniofacial dysmorphia has also been described. Mouse models of Mmachc deletion are embryonic lethal but cause severe craniofacial phenotypes such as facial clefts. MMACHC encodes an enzyme required for cobalamin processing and variants in this gene result in the accumulation of two metabolites: methylmalonic acid (MMA) and homocysteine (HC). Interestingly, other inborn errors of cobalamin metabolism, such as cblX syndrome, are associated with mild facial phenotypes. However, the presence and severity of MMA and HC accumulation in cblX syndrome is not consistent with the presence or absence of facial phenotypes. Thus, the mechanisms by which mutations in MMACHC cause craniofacial defects are yet to be completely elucidated. Here we have characterized the craniofacial phenotypes in a zebrafish model of cblC (hg13) and performed restoration experiments with either a wildtype or a cobalamin binding deficient MMACHC protein. Homozygous mutants did not display gross morphological defects in facial development but did have abnormal chondrocyte nuclear organization and an increase in the average number of neighboring cell contacts, both phenotypes were fully penetrant. Abnormal chondrocyte nuclear organization was not associated with defects in the localization of neural crest specific markers, sox10 (RFP transgene) or barx1. Both nuclear angles and the number of neighboring cell contacts were fully restored by wildtype MMACHC and a cobalamin binding deficient variant of the MMACHC protein. Collectively, these data suggest that mutation of MMACHC causes mild to moderate craniofacial phenotypes that are independent of cobalamin binding.
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Affiliation(s)
- David Paz
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Briana E Pinales
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Barbara S Castellanos
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Isaiah Perez
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Claudia B Gil
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Lourdes Jimenez Madrigal
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Nayeli G Reyes-Nava
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Victoria L Castro
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Jennifer L Sloan
- Metabolic Medicine Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anita M Quintana
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX, 79968, USA.
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4
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McCorvie TJ, Ferreira D, Yue WW, Froese DS. The complex machinery of human cobalamin metabolism. J Inherit Metab Dis 2023; 46:406-420. [PMID: 36680553 DOI: 10.1002/jimd.12593] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/22/2023]
Abstract
Vitamin B12 (cobalamin, Cbl) is required as a cofactor by two human enzymes, 5-methyltetrahydrofolate-homocysteine methyltransferase (MTR) and methylmalonyl-CoA mutase (MMUT). Within the body, a vast array of transporters, enzymes and chaperones are required for the generation and delivery of these cofactor forms. How they perform these functions is dictated by the structure and interactions of the proteins involved, the molecular bases of which are only now being elucidated. In this review, we highlight recent insights into human Cbl metabolism and address open questions in the field by employing a protein structure and interactome based perspective. We discuss how three very similar proteins-haptocorrin, intrinsic factor and transcobalamin-exploit slight structural differences and unique ligand receptor interactions to effect selective Cbl absorption and internalisation. We describe recent advances in the understanding of how endocytosed Cbl is transported across the lysosomal membrane and the implications of the recently solved ABCD4 structure. We detail how MMACHC and MMADHC cooperate to modify and target cytosolic Cbl to the client enzymes MTR and MMUT using ingenious modifications to an ancient nitroreductase fold, and how MTR and MMUT link with their accessory enzymes to sustainably harness the supernucleophilic potential of Cbl. Finally, we provide an outlook on how future studies may combine structural and interactome based approaches and incorporate knowledge of post-translational modifications to bring further insights.
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Affiliation(s)
- Thomas J McCorvie
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Douglas Ferreira
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wyatt W Yue
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Zürich, Switzerland
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5
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Paz D, Pinales BE, Castellanos BS, Perez I, Gil CB, Madrigal LJ, Reyes-Nava NG, Castro VL, Sloan JL, Quintana AM. Abnormal chondrocyte intercalation in a zebrafish model of cblC syndrome restored by an MMACHC cobalamin binding mutant. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.20.524982. [PMID: 36711998 PMCID: PMC9882310 DOI: 10.1101/2023.01.20.524982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Variants in the MMACHC gene cause combined methylmalonic acidemia and homocystinuria cblC type, the most common inborn error of intracellular cobalamin (vitamin B12) metabolism. cblC is associated with neurodevelopmental, hematological, ocular, and biochemical abnormalities. In a subset of patients, mild craniofacial dysmorphia has also been described. Mouse models of Mmachc deletion are embryonic lethal but cause severe craniofacial phenotypes such as facial clefts. MMACHC encodes an enzyme required for cobalamin processing and variants in this gene result in the accumulation of two metabolites: methylmalonic acid (MMA) and homocysteine (HC). Interestingly, other inborn errors of cobalamin metabolism, such as cblX syndrome, are associated with mild facial phenotypes. However, the presence and severity of MMA and HC accumulation in cblX syndrome is not consistent with the presence or absence of facial phenotypes. Thus, the mechanisms by which mutation of MMACHC cause craniofacial defects have not been completely elucidated. Here we have characterized the craniofacial phenotypes in a zebrafish model of cblC ( hg13 ) and performed restoration experiments with either wildtype or a cobalamin binding deficient MMACHC protein. Homozygous mutants did not display gross morphological defects in facial development, but did have abnormal chondrocyte intercalation, which was fully penetrant. Abnormal chondrocyte intercalation was not associated with defects in the expression/localization of neural crest specific markers, sox10 or barx1 . Most importantly, chondrocyte organization was fully restored by wildtype MMACHC and a cobalamin binding deficient variant of MMACHC protein. Collectively, these data suggest that mutation of MMACHC causes mild to moderate craniofacial phenotypes that are independent of cobalamin binding.
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Affiliation(s)
- David Paz
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968 USA
| | - Briana E Pinales
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968 USA
| | - Barbara S Castellanos
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968 USA
| | - Isaiah Perez
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968 USA
| | - Claudia B Gil
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968 USA
| | - Lourdes Jimenez Madrigal
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968 USA
| | - Nayeli G Reyes-Nava
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968 USA
| | - Victoria L Castro
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968 USA
| | - Jennifer L Sloan
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968 USA
| | - Anita M Quintana
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968 USA
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6
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Esser AJ, Mukherjee S, Dereven‘kov IA, Makarov SV, Jacobsen DW, Spiekerkoetter U, Hannibal L. Versatile Enzymology and Heterogeneous Phenotypes in Cobalamin Complementation Type C Disease. iScience 2022; 25:104981. [PMID: 36105582 PMCID: PMC9464900 DOI: 10.1016/j.isci.2022.104981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Nutritional deficiency and genetic errors that impair the transport, absorption, and utilization of vitamin B12 (B12) lead to hematological and neurological manifestations. The cblC disease (cobalamin complementation type C) is an autosomal recessive disorder caused by mutations and epi-mutations in the MMACHC gene and the most common inborn error of B12 metabolism. Pathogenic mutations in MMACHC disrupt enzymatic processing of B12, an indispensable step before micronutrient utilization by the two B12-dependent enzymes methionine synthase (MS) and methylmalonyl-CoA mutase (MUT). As a result, patients with cblC disease exhibit plasma elevation of homocysteine (Hcy, substrate of MS) and methylmalonic acid (MMA, degradation product of methylmalonyl-CoA, substrate of MUT). The cblC disorder manifests early in childhood or in late adulthood with heterogeneous multi-organ involvement. This review covers current knowledge on the cblC disease, structure–function relationships of the MMACHC protein, the genotypic and phenotypic spectra in humans, experimental disease models, and promising therapies.
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7
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Passantino R, Mangione MR, Ortore MG, Costa MA, Provenzano A, Amenitsch H, Sabbatella R, Alfano C, Martorana V, Vilasi S. Investigation on a MMACHC mutant from cblC disease: The c.394C>T variant. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140793. [PMID: 35618206 DOI: 10.1016/j.bbapap.2022.140793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
The cblC disease is an inborn disorder of the vitamin B12 (cobalamin, Cbl) metabolism characterized by methylmalonic aciduria and homocystinuria. The clinical consequences of this disease are devastating and, even when early treated with current therapies, the affected children manifest symptoms involving vision, growth, and learning. The illness is caused by mutations in the gene codifying for MMACHC, a 282aa protein that transports and transforms the different Cbl forms. Here we present data on the structural properties of the truncated protein p.R132X resulting from the c.394C > T mutation that, along with c.271dupA and c.331C > T, is among the most common mutations in cblC. Although missing part of the Cbl binding domain, p.R132X is associated to late-onset symptoms and, therefore, it is supposed to retain residual function. However, to our knowledge structural-functional studies on c.394C > T mutant aimed at verifying this hypothesis are still lacking. By using a biophysical approach including Circular Dichroism, fluorescence, Small Angle X-ray Scattering, and Molecular Dynamics, we show that the mutant protein MMACHC-R132X retains secondary structure elements and remains compact in solution, partly preserving its binding affinity for Cbl. Insights on the fragile stability of MMACHC-R132X-Cbl are provided.
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Affiliation(s)
- Rosa Passantino
- Biophysics Institute, National Research Council, Palermo 90143, Italy
| | | | - Maria Grazia Ortore
- Dept. Life and Environmental Sciences, Marche Polytechnic University, Ancona 60131, Italy
| | | | | | | | | | | | | | - Silvia Vilasi
- Biophysics Institute, National Research Council, Palermo 90143, Italy.
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Kiessling E, Peters F, Ebner LJ, Merolla L, Samardzija M, Baumgartner MR, Grimm C, Froese DS. HIF1 and DROSHA are involved in MMACHC repression in hypoxia. Biochim Biophys Acta Gen Subj 2022; 1866:130175. [DOI: 10.1016/j.bbagen.2022.130175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/03/2022] [Accepted: 05/23/2022] [Indexed: 11/25/2022]
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Structural Study of the Complex of cblC Methylmalonic Aciduria and Homocystinuria-Related Protein MMACHC with Cyanocobalamin. CRYSTALS 2022. [DOI: 10.3390/cryst12040468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
MMACHC is an essential protein for the body to metabolise vitamin B12, and its deficiency will cause cblC-type methylmalonic aciduria and homocystinuria. MMACHC can interact with cyanocobalamin (a type of vitamin B12) cofactor and plays an important role in targeting cyanocobalamin to the enzyme of interest. In this paper, the GST-tag fusion-tagged MMACHC protein was successfully expressed by Escherichia coli (E. coli) low-temperature induction, and the high-purity MMACHC protein was successfully purified by affinity chromatography and gel filtration. Further, the crystal structure of MMACHC and cyanocobalamin complex was obtained with a resolution of 1.93 Å using X-ray diffraction. By analysing the complex structure of MMACHC and cyanocobalamin, we revealed the reasons for the diversity of MMACHC substrates and explained the reasons for the differences in disease conditions caused by different MMACHC site mutations. The acquisition of the complex structure of MMACHC and cyanocobalamin will play a significant role in promoting research on the metabolic pathway of vitamin B12.
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Hannibal L, Jacobsen DW. Intracellular processing of vitamin B 12 by MMACHC (CblC). VITAMINS AND HORMONES 2022; 119:275-298. [PMID: 35337623 DOI: 10.1016/bs.vh.2022.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Vitamin B12 (cobalamin, Cbl, B12) is a water-soluble micronutrient synthesized exclusively by a group of microorganisms. Human beings are unable to make B12 and thus obtain the vitamin via intake of animal products, fermented plant-based foods or supplements. Vitamin B12 obtained from the diet comprises three major chemical forms, namely hydroxocobalamin (HOCbl), methylcobalamin (MeCbl) and adenosylcobalamin (AdoCbl). The most common form of B12 present in supplements is cyanocobalamin (CNCbl). Yet, these chemical forms cannot be utilized directly as they come, but instead, they undergo chemical processing by the MMACHC protein, also known as CblC. Processing of dietary B12 by CblC involves removal of the upper-axial ligand (beta-ligand) yielding the one-electron reduced intermediate cob(II)alamin. Newly formed cob(II)alamin undergoes trafficking and delivery to the two B12-dependent enzymes, cytosolic methionine synthase (MS) and mitochondrial methylmalonyl-CoA mutase (MUT). The catalytic cycles of MS and MUT incorporate cob(II)alamin as a precursor to regenerate the coenzyme forms MeCbl and AdoCbl, respectively. Mutations and epimutations in the MMACHC gene result in cblC disease, the most common inborn error of B12 metabolism, which manifests with combined homocystinuria and methylmalonic aciduria. Elevation of metabolites homocysteine and methylmalonic acid occurs because the lack of an active CblC blocks formation of the indispensable precursor cob(II)alamin that is necessary to activate MS and MUT. Thus, in patients with cblC disease, vitamin B12 is absorbed and present in circulation in normal to high concentrations, yet, cells are unable to make use of it. Mutations in seemingly unrelated genes that modify MMACHC gene expression also result in clinical phenotypes that resemble cblC disease. We review current knowledge on structural and functional aspects of intracellular processing of vitamin B12 by the versatile protein CblC, its partners and possible regulators.
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Affiliation(s)
- Luciana Hannibal
- Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany.
| | - Donald W Jacobsen
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
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Ruetz M, Koutmos M, Kräutler B. Antivitamins B 12: Synthesis and application as inhibitory ligand of the B 12-tailoring enzyme CblC. Methods Enzymol 2022; 668:157-178. [PMID: 35589193 DOI: 10.1016/bs.mie.2021.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Antivitamins B12 are non-natural corrinoids that have been designed to counteract the metabolic effects of vitamin B12 and related cobalamins (Cbls) in humans and other mammals. A basic structure- and reactivity-based concept typifies antivitamins B12 as close structural mimics of vitamin B12 that are not transformed by the cellular metabolism into organometallic B12-cofactors. Antivitamins B12 have the correct structure for efficient take-up and transport via the natural mammalian pathway for cobalamin assimilation. Thus they can be delivered to every cell in the body, where they are proposed to target and inhibit the Cbl tailoring enzyme CblC. Antivitamins B12 may be specifically inert Cbls or isostructural Cbl-analogues that carry a metal centre other than a cobalt-ion. The syntheses of two antivitamins B12 are detailed here, as are biochemical and crystallographic studies that provide insights into the crucial binding interactions of Cbl-based antivitamins B12 with the human B12-tailoring enzyme CblC. This key enzyme binds genuine antivitamins B12 as inert substrate mimics and enzyme inhibitors, effectively repressing the metabolic generation of the B12-cofactors. Hence, antivitamins B12 induce the diagnostic symptoms of (functional) B12-deficiency, as observed in healthy laboratory mice.
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Affiliation(s)
- Markus Ruetz
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Markos Koutmos
- Department of Chemistry, Program in Biophysics, Program in Chemical Biology, University of Michigan, Ann Arbor, MI, United States.
| | - Bernhard Kräutler
- Institute of Organic Chemistry and Center of Molecular Biosciences, University of Innsbruck, Innsbruck, Austria.
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12
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Chern T, Achilleos A, Tong X, Hill MC, Saltzman AB, Reineke LC, Chaudhury A, Dasgupta SK, Redhead Y, Watkins D, Neilson JR, Thiagarajan P, Green JBA, Malovannaya A, Martin JF, Rosenblatt DS, Poché RA. Mutations in Hcfc1 and Ronin result in an inborn error of cobalamin metabolism and ribosomopathy. Nat Commun 2022; 13:134. [PMID: 35013307 PMCID: PMC8748873 DOI: 10.1038/s41467-021-27759-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 12/13/2021] [Indexed: 12/26/2022] Open
Abstract
Combined methylmalonic acidemia and homocystinuria (cblC) is the most common inborn error of intracellular cobalamin metabolism and due to mutations in Methylmalonic Aciduria type C and Homocystinuria (MMACHC). Recently, mutations in the transcriptional regulators HCFC1 and RONIN (THAP11) were shown to result in cellular phenocopies of cblC. Since HCFC1/RONIN jointly regulate MMACHC, patients with mutations in these factors suffer from reduced MMACHC expression and exhibit a cblC-like disease. However, additional de-regulated genes and the resulting pathophysiology is unknown. Therefore, we have generated mouse models of this disease. In addition to exhibiting loss of Mmachc, metabolic perturbations, and developmental defects previously observed in cblC, we uncovered reduced expression of target genes that encode ribosome protein subunits. We also identified specific phenotypes that we ascribe to deregulation of ribosome biogenesis impacting normal translation during development. These findings identify HCFC1/RONIN as transcriptional regulators of ribosome biogenesis during development and their mutation results in complex syndromes exhibiting aspects of both cblC and ribosomopathies. Combined methylmalonic acidemia (MMA) and hyperhomocysteinemias are inborn errors of vitamin B12 metabolism, and mutations in the transcriptional regulators HCFC1 and RONIN (THAP11) underlie some forms of these disorders. Here the authors generated mouse models of a human syndrome due to mutations in RONIN (THAP11) and HCFC1, and show that this syndrome is both an inborn error of vitamin B12 metabolism and displays some features of ribosomopathy.
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Affiliation(s)
- Tiffany Chern
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Graduate Program in Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Annita Achilleos
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Basic and Clinical Sciences, University of Nicosia Medical School, Nicosia, Cyprus.
| | - Xuefei Tong
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Matthew C Hill
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Alexander B Saltzman
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lucas C Reineke
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arindam Chaudhury
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Swapan K Dasgupta
- Department of Pathology, Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, 77030, USA
| | - Yushi Redhead
- The Francis Crick Institute, London, NW1 1AT, UK.,Centre for Craniofacial Biology and Regeneration, King's College London, London, SE1 9RT, UK
| | - David Watkins
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, Montreal, QC, Canada.,Division of Medical Biochemistry, Department of Specialized Medicine, McGill University Health Centre, Montreal, QC, Canada
| | - Joel R Neilson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Graduate Program in Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Development, Disease Models and Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Perumal Thiagarajan
- Department of Pathology, Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jeremy B A Green
- Centre for Craniofacial Biology and Regeneration, King's College London, London, SE1 9RT, UK
| | - Anna Malovannaya
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James F Martin
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Graduate Program in Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Development, Disease Models and Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Heart Institute, Houston, TX, 77030, USA
| | - David S Rosenblatt
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, Montreal, QC, Canada.,Division of Medical Biochemistry, Department of Specialized Medicine, McGill University Health Centre, Montreal, QC, Canada.,Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Ross A Poché
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Graduate Program in Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Development, Disease Models and Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX, 77030, USA.
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13
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Guéant JL, Guéant-Rodriguez RM, Kosgei VJ, Coelho D. Causes and consequences of impaired methionine synthase activity in acquired and inherited disorders of vitamin B 12 metabolism. Crit Rev Biochem Mol Biol 2021; 57:133-155. [PMID: 34608838 DOI: 10.1080/10409238.2021.1979459] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Methyl-Cobalamin (Cbl) derives from dietary vitamin B12 and acts as a cofactor of methionine synthase (MS) in mammals. MS encoded by MTR catalyzes the remethylation of homocysteine to generate methionine and tetrahydrofolate, which fuel methionine and cytoplasmic folate cycles, respectively. Methionine is the precursor of S-adenosyl methionine (SAM), the universal methyl donor of transmethylation reactions. Impaired MS activity results from inadequate dietary intake or malabsorption of B12 and inborn errors of Cbl metabolism (IECM). The mechanisms at the origin of the high variability of clinical presentation of impaired MS activity are classically considered as the consequence of the disruption of the folate cycle and related synthesis of purines and pyrimidines and the decreased synthesis of endogenous methionine and SAM. For one decade, data on cellular and animal models of B12 deficiency and IECM have highlighted other key pathomechanisms, including altered interactome of MS with methionine synthase reductase, MMACHC, and MMADHC, endoplasmic reticulum stress, altered cell signaling, and genomic/epigenomic dysregulations. Decreased MS activity increases catalytic protein phosphatase 2A (PP2A) and produces imbalanced phosphorylation/methylation of nucleocytoplasmic RNA binding proteins, including ELAVL1/HuR protein, with subsequent nuclear sequestration of mRNAs and dramatic alteration of gene expression, including SIRT1. Decreased SAM and SIRT1 activity induce ER stress through impaired SIRT1-deacetylation of HSF1 and hypomethylation/hyperacetylation of peroxisome proliferator-activated receptor-γ coactivator-1α (PGC1α), which deactivate nuclear receptors and lead to impaired energy metabolism and neuroplasticity. The reversibility of these pathomechanisms by SIRT1 agonists opens promising perspectives in the treatment of IECM outcomes resistant to conventional supplementation therapies.
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Affiliation(s)
- Jean-Louis Guéant
- UMR Inserm 1256 N-GERE (Nutrition, Génetique et Exposition aux Risques Environmentaux), Université de Lorraine, Vandoeuvre-lès-Nancy, France.,Departments of Digestive Diseases and Molecular Medicine and National Center of Inborn Errors of Metabolism, University Hospital Center, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Rosa-Maria Guéant-Rodriguez
- UMR Inserm 1256 N-GERE (Nutrition, Génetique et Exposition aux Risques Environmentaux), Université de Lorraine, Vandoeuvre-lès-Nancy, France.,Departments of Digestive Diseases and Molecular Medicine and National Center of Inborn Errors of Metabolism, University Hospital Center, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Viola J Kosgei
- UMR Inserm 1256 N-GERE (Nutrition, Génetique et Exposition aux Risques Environmentaux), Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - David Coelho
- UMR Inserm 1256 N-GERE (Nutrition, Génetique et Exposition aux Risques Environmentaux), Université de Lorraine, Vandoeuvre-lès-Nancy, France
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14
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Cavicchi C, Oussalah A, Falliano S, Ferri L, Gozzini A, Gasperini S, Motta S, Rigoldi M, Parenti G, Tummolo A, Meli C, Menni F, Furlan F, Daniotti M, Malvagia S, la Marca G, Chery C, Morange PE, Tregouet D, Donati MA, Guerrini R, Guéant JL, Morrone A. PRDX1 gene-related epi-cblC disease is a common type of inborn error of cobalamin metabolism with mono- or bi-allelic MMACHC epimutations. Clin Epigenetics 2021; 13:137. [PMID: 34215320 PMCID: PMC8254308 DOI: 10.1186/s13148-021-01117-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/16/2021] [Indexed: 12/21/2022] Open
Abstract
Background The role of epigenetics in inborn errors of metabolism (IEMs) is poorly investigated. Epigenetic changes can contribute to clinical heterogeneity of affected patients but could also be underestimated determining factors in the occurrence of IEMs. An epigenetic cause of IEMs has been recently described for the autosomal recessive methylmalonic aciduria and homocystinuria, cblC type (cblC disease), and it has been named epi-cblC. Epi-cblC has been reported in association with compound heterozygosity for a genetic variant and an epimutation at the MMACHC locus, which is secondary to a splicing variant (c.515-1G > T or c.515-2A > T) at the adjacent PRDX1 gene. Both these variants cause aberrant antisense transcription and cis-hypermethylation of the MMACHC gene promotor with subsequent silencing. Until now, only nine epi-cblC patients have been reported. Methods We report clinical/biochemical assessment, MMACHC/PRDX1 gene sequencing and genome-wide DNA methylation profiling in 11 cblC patients who had an inconclusive MMACHC gene testing. We also compare clinical phenotype of epi-cblC patients with that of canonical cblC patients. Results All patients turned out to have the epi-cblC disease. One patient had a bi-allelic MMACHC epimutation due to the homozygous PRDX1:c.515-1G > T variant transmitted by both parents. We found that the bi-allelic epimutation produces the complete silencing of MMACHC in the patient’s fibroblasts. The remaining ten patients had a mono-allelic MMACHC epimutation, due to the heterozygous PRDX1:c.515-1G > T, in association with a mono-allelic MMACHC genetic variant. Epi-cblC disease has accounted for about 13% of cblC cases diagnosed by newborn screening in the Tuscany and Umbria regions since November 2001. Comparative analysis showed that clinical phenotype of epi-cblC patients is similar to that of canonical cblC patients. Conclusions We provide evidence that epi-cblC is an underestimated cause of inborn errors of cobalamin metabolism and describe the first instance of epi-cblC due to a bi-allelic MMACHC epimutation. MMACHC epimutation/PRDX1 mutation analyses should be part of routine genetic testing for all patients presenting with a metabolic phenotype that combines methylmalonic aciduria and homocystinuria. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01117-2.
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Affiliation(s)
- Catia Cavicchi
- Molecular and Cell Biology Laboratory of Neurometabolic Diseases, Paediatric Neurology Unit and Laboratories, Meyer Children's Hospital, Viale Pieraccini 24, 50139, Florence, Italy
| | - Abderrahim Oussalah
- INSERM, UMR_S1256 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), Nancy, France
| | - Silvia Falliano
- Molecular and Cell Biology Laboratory of Neurometabolic Diseases, Paediatric Neurology Unit and Laboratories, Meyer Children's Hospital, Viale Pieraccini 24, 50139, Florence, Italy
| | - Lorenzo Ferri
- Molecular and Cell Biology Laboratory of Neurometabolic Diseases, Paediatric Neurology Unit and Laboratories, Meyer Children's Hospital, Viale Pieraccini 24, 50139, Florence, Italy
| | - Alessia Gozzini
- Molecular and Cell Biology Laboratory of Neurometabolic Diseases, Paediatric Neurology Unit and Laboratories, Meyer Children's Hospital, Viale Pieraccini 24, 50139, Florence, Italy
| | - Serena Gasperini
- Rare Metabolic Disease Unit, Department of Paediatrics, Fondazione MBBM, Monza, Italy
| | - Serena Motta
- Rare Metabolic Disease Unit, Department of Paediatrics, Fondazione MBBM, Monza, Italy
| | - Miriam Rigoldi
- Mario Negri Institute for Pharmacological Research IRCCS, Bergamo, Italy
| | | | - Albina Tummolo
- Metabolic Disease Unit, Giovanni XXIII Hospital, Bari, Italy
| | - Concetta Meli
- Metabolic Disease Unit, G. Rodolico Hospital, Catania, Italy
| | - Francesca Menni
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Paediatric Highly Intensive Care Unit, Milan, Italy
| | - Francesca Furlan
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Paediatric Highly Intensive Care Unit, Milan, Italy
| | - Marta Daniotti
- Metabolic and Muscular Unit, Meyer Children's Hospital, Florence, Italy
| | - Sabrina Malvagia
- Newborn Screening, Biochemistry and Pharmacology Laboratory, Meyer Children's Hospital, Florence, Italy
| | - Giancarlo la Marca
- Newborn Screening, Biochemistry and Pharmacology Laboratory, Meyer Children's Hospital, Florence, Italy.,Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Céline Chery
- INSERM, UMR_S1256 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), Nancy, France
| | | | - David Tregouet
- INSERM, UMR_S937, ICAN Institute, Université Pierre et Marie Curie, Paris, France
| | | | - Renzo Guerrini
- Molecular and Cell Biology Laboratory of Neurometabolic Diseases, Paediatric Neurology Unit and Laboratories, Meyer Children's Hospital, Viale Pieraccini 24, 50139, Florence, Italy.,Department of NEUROFARBA, University of Florence, Florence, Italy
| | - Jean-Louis Guéant
- INSERM, UMR_S1256 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), Nancy, France
| | - Amelia Morrone
- Molecular and Cell Biology Laboratory of Neurometabolic Diseases, Paediatric Neurology Unit and Laboratories, Meyer Children's Hospital, Viale Pieraccini 24, 50139, Florence, Italy. .,Department of NEUROFARBA, University of Florence, Florence, Italy.
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15
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Kiessling E, Nötzli S, Todorova V, Forny M, Baumgartner MR, Samardzija M, Krijt J, Kožich V, Grimm C, Froese DS. Absence of MMACHC in peripheral retinal cells does not lead to an ocular phenotype in mice. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166201. [PMID: 34147638 DOI: 10.1016/j.bbadis.2021.166201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/25/2021] [Accepted: 06/08/2021] [Indexed: 01/10/2023]
Abstract
Combined methylmalonic aciduria with homocystinuria (cblC type) is a rare disease caused by mutations in the MMACHC gene. MMACHC encodes an enzyme crucial for intracellular vitamin B12 metabolism, leading to the accumulation of toxic metabolites e.g. methylmalonic acid (MMA) and homocysteine (Hcy), and secondary disturbances in folate and one-carbon metabolism when not fully functional. Patients with cblC deficiency often present in the neonatal or early childhood period with a severe multisystem pathology, which comprises a broad spectrum of treatment-resistant ophthalmological phenotypes, including retinal degeneration, impaired vision, and vascular changes. To examine the potential function of MMACHC in the retina and how its loss may impact disease, we performed gene expression studies in human and mouse, which showed that local expression of MMACHC in the retina and retinal pigment epithelium is relatively stable over time. To study whether functional MMACHC is required for retinal function and tissue integrity, we generated a transgenic mouse lacking Mmachc expression in cells of the peripheral retina. Characterization of this mouse revealed accumulation of cblC disease related metabolites, including MMA and the folate-dependent purine synthesis intermediates AICA-riboside and SAICA-riboside in the retina. Nevertheless, fundus appearance, morphology, vasculature, and cellular composition of the retina, as well as ocular function, remained normal in mice up to 6 or 12 months of age. Our data indicates that peripheral retinal neurons do not require intrinsic expression of Mmachc for survival and function and questions whether a local MMACHC deficiency is responsible for the retinal phenotypes in patients.
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Affiliation(s)
- Eva Kiessling
- Lab for Retinal Cell Biology, Dept. Ophthalmology, University Hospital Zurich, University of Zürich, Switzerland
| | - Sarah Nötzli
- Lab for Retinal Cell Biology, Dept. Ophthalmology, University Hospital Zurich, University of Zürich, Switzerland
| | - Vyara Todorova
- Lab for Retinal Cell Biology, Dept. Ophthalmology, University Hospital Zurich, University of Zürich, Switzerland
| | - Merima Forny
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Switzerland
| | - Matthias R Baumgartner
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Switzerland
| | - Marijana Samardzija
- Lab for Retinal Cell Biology, Dept. Ophthalmology, University Hospital Zurich, University of Zürich, Switzerland
| | - Jakub Krijt
- Dept. of Pediatrics and Inherited Metabolic Disorders, Charles University-First Faculty of Medicine and General University Hospital, Prague, Czech Republic
| | - Viktor Kožich
- Dept. of Pediatrics and Inherited Metabolic Disorders, Charles University-First Faculty of Medicine and General University Hospital, Prague, Czech Republic
| | - Christian Grimm
- Lab for Retinal Cell Biology, Dept. Ophthalmology, University Hospital Zurich, University of Zürich, Switzerland.
| | - D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Switzerland.
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16
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Banerjee R, Gouda H, Pillay S. Redox-Linked Coordination Chemistry Directs Vitamin B 12 Trafficking. Acc Chem Res 2021; 54:2003-2013. [PMID: 33797888 DOI: 10.1021/acs.accounts.1c00083] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Metals are partners for an estimated one-third of the proteome and vary in complexity from mononuclear centers to organometallic cofactors. Vitamin B12 or cobalamin represents the epitome of this complexity and is the product of an assembly line comprising some 30 enzymes. Unable to biosynthesize cobalamin, mammals rely on dietary provision of this essential cofactor, which is needed by just two enzymes, one each in the cytoplasm (methionine synthase) and the mitochondrion (methylmalonyl-CoA mutase). Brilliant clinical genetics studies on patients with inborn errors of cobalamin metabolism spanning several decades had identified at least seven genetic loci in addition to the two encoding B12 enzymes. While cells are known to house a cadre of chaperones dedicated to metal trafficking pathways that contain metal reactivity and confer targeting specificity, the seemingly supernumerary chaperones in the B12 pathway had raised obvious questions as to the rationale for their existence.With the discovery of the genes underlying cobalamin disorders, our laboratory has been at the forefront of ascribing functions to B12 chaperones and elucidating the intricate redox-linked coordination chemistry and protein-linked cofactor conformational dynamics that orchestrate the processing and translocation of cargo along the trafficking pathway. These studies have uncovered novel chemistry that exploits the innate chemical versatility of alkylcobalamins, i.e., the ability to form and dismantle the cobalt-carbon bond using homolytic or heterolytic chemistry. In addition, they have revealed the practical utility of the dimethylbenzimidazole tail, an appendage unique to cobalamins and absent in the structural cousins, porphyrin, chlorin, and corphin, as an instrument for facilitating cofactor transfer between active sites.In this Account, we navigate the chemistry of the B12 trafficking pathway from its point of entry into cells, through lysosomes, and into the cytoplasm, where incoming cobalamin derivatives with a diversity of upper ligands are denuded by the β-ligand transferase activity of CblC to the common cob(II)alamin intermediate. The broad reaction and lax substrate specificity of CblC also enables conversion of cyanocobalamin (technically, vitamin B12, i.e., the form of the cofactor in one-a-day supplements), to cob(II)alamin. CblD then hitches up with CblC via a unique Co-sulfur bond to cob(II)alamin at a bifurcation point, leading to the cytoplasmic methylcobalamin or mitochondrial 5'-deoxyadenosylcobalamin branch. Mutations at loci upstream of the junction point typically affect both branches, leading to homocystinuria and methylmalonic aciduria, whereas mutations in downstream loci lead to one or the other disease. Elucidation of the biochemical penalties associated with individual mutations is providing molecular insights into the clinical data and, in some instances, identifying which cobalamin derivative(s) might be therapeutically beneficial.Our studies on B12 trafficking are revealing strategies for cofactor sequestration and mobilization from low- to high-affinity and low- to high-coordination-number sites, which in turn are regulated by protein dynamics that constructs ergonomic cofactor binding pockets. While these B12 lessons might be broadly relevant to other metal trafficking pathways, much remains to be learned. This Account concludes by identifying some of the major gaps and challenges that are needed to complete our understanding of B12 trafficking.
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Affiliation(s)
- Ruma Banerjee
- Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Harsha Gouda
- Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Shubhadra Pillay
- Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
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17
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Wingert V, Mukherjee S, Esser AJ, Behringer S, Tanimowo S, Klenzendorf M, Derevenkov IA, Makarov SV, Jacobsen DW, Spiekerkoetter U, Hannibal L. Thiolatocobalamins repair the activity of pathogenic variants of the human cobalamin processing enzyme CblC. Biochimie 2020; 183:108-125. [PMID: 33190793 DOI: 10.1016/j.biochi.2020.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/08/2020] [Accepted: 10/19/2020] [Indexed: 01/08/2023]
Abstract
Thiolatocobalamins are a class of cobalamins comprised of naturally occurring and synthetic ligands. Glutathionylcobalamin (GSCbl) occurs naturally in mammalian cells, and also as an intermediate in the glutathione-dependent dealkylation of methylcobalamin (MeCbl) to form cob(I)alamin by pure recombinant CblC from C. elegans. Glutathione-driven deglutathionylation of GSCbl was demonstrated both in mammalian as well as in C. elegans CblC. Dethiolation is orders of magnitude faster than dealkylation of Co-C bonded cobalamins, which motivated us to investigate two synthetic thiolatocobalamins as substrates to repair the enzymatic activity of pathogenic CblC variants in humans. We report the synthesis and kinetic characterization of cysteaminylcobalamin (CyaCbl) and 2-mercaptopropionylglycinocobalamin (MpgCbl). Both CyaCbl and MpgCbl were obtained in high purity (90-95%) and yield (78-85%). UV-visible spectral properties agreed with those reported for other thiolatocobalamins with absorbance maxima observed at 372 nm and 532 nm. Both CyaCbl and MpgCbl bound to wild type human recombinant CblC inducing spectral blue-shifts characteristic of the respective base-on to base-off transitions. Addition of excess glutathione (GSH) resulted in rapid elimination of the β-ligand to give aquacobalamin (H2OCbl) as the reaction product under aerobic conditions. Further, CyaCbl and MpgCbl underwent spontaneous dethiolation thereby repairing the loss of activity of pathogenic variants of human CblC, namely R161G and R161Q. We posit that thiolatocobalamins could be exploited therapeutically for the treatment of inborn errors of metabolism that impair processing of dietary and supplemental cobalamin forms. While these disorders are targets for newborn screening in some countries, there is currently no effective treatment available to patients.
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Affiliation(s)
- Victoria Wingert
- Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center - University of Freiburg, 79106, Freiburg, Germany
| | - Srijan Mukherjee
- Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center - University of Freiburg, 79106, Freiburg, Germany
| | - Anna J Esser
- Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center - University of Freiburg, 79106, Freiburg, Germany
| | - Sidney Behringer
- Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center - University of Freiburg, 79106, Freiburg, Germany
| | - Segun Tanimowo
- Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center - University of Freiburg, 79106, Freiburg, Germany
| | - Melissa Klenzendorf
- Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center - University of Freiburg, 79106, Freiburg, Germany; Faculty of Biology, University of Freiburg Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Ilia A Derevenkov
- Department of Food Chemistry, Ivanovo State University of Chemistry and Technology, Ivanovo, Russian Federation
| | - Sergei V Makarov
- Department of Food Chemistry, Ivanovo State University of Chemistry and Technology, Ivanovo, Russian Federation
| | - Donald W Jacobsen
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, USA
| | - Ute Spiekerkoetter
- Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center - University of Freiburg, 79106, Freiburg, Germany
| | - Luciana Hannibal
- Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center - University of Freiburg, 79106, Freiburg, Germany.
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18
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Li Z, Mascarenhas R, Twahir UT, Kallon A, Deb A, Yaw M, Penner-Hahn J, Koutmos M, Warncke K, Banerjee R. An Interprotein Co-S Coordination Complex in the B 12-Trafficking Pathway. J Am Chem Soc 2020; 142:16334-16345. [PMID: 32871076 DOI: 10.1021/jacs.0c06590] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The CblC and CblD chaperones are involved in early steps in the cobalamin trafficking pathway. Cobalamin derivatives entering the cytoplasm are converted by CblC to a common cob(II)alamin intermediate via glutathione-dependent alkyltransferase or reductive elimination activities. Cob(II)alamin is subsequently converted to one of two biologically active alkylcobalamins by downstream chaperones. The function of CblD has been elusive although it is known to form a complex with CblC under certain conditions. Here, we report that CblD provides a sulfur ligand to cob(II)alamin bound to CblC, forming an interprotein coordination complex that rapidly oxidizes to thiolato-cob(III)alamin. Cysteine scanning mutagenesis and EPR spectroscopy identified Cys-261 on CblD as the sulfur donor. The unusual interprotein Co-S bond was characterized by X-ray absorption spectroscopy and visualized in the crystal structure of the human CblD thiolato-cob(III)alamin complex. Our study provides insights into how cobalamin coordination chemistry could be utilized for cofactor translocation in the trafficking pathway.
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Affiliation(s)
- Zhu Li
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600, United States
| | - Romila Mascarenhas
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600, United States
| | - Umar T Twahir
- Department of Physics, Emory University, Atlanta, Georgia 30322-2430, United States
| | - Albert Kallon
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600, United States
| | - Aniruddha Deb
- Departments of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Madeline Yaw
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600, United States
| | - James Penner-Hahn
- Departments of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Markos Koutmos
- Departments of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kurt Warncke
- Department of Physics, Emory University, Atlanta, Georgia 30322-2430, United States
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600, United States
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19
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Chern T, Achilleos A, Tong X, Hsu CW, Wong L, Poché RA. Mouse models to study the pathophysiology of combined methylmalonic acidemia and homocystinuria, cblC type. Dev Biol 2020; 468:1-13. [PMID: 32941884 DOI: 10.1016/j.ydbio.2020.09.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 09/08/2020] [Accepted: 09/09/2020] [Indexed: 02/06/2023]
Abstract
Combined methylmalonic acidemia and homocystinuria, cblC type, is the most common inherited disorder of cobalamin metabolism and is characterized by severe fetal developmental defects primarily impacting the central nervous system, hematopoietic system, and heart. CblC was previously shown to be due to mutations in the MMACHC gene, which encodes a protein thought to function in intracellular cobalamin trafficking and biosynthesis of adenosylcobalamin (AdoCbl) and methylcobalamin (MeCbl). These coenzymes are required for the production of succinyl-CoA and methionine, respectively. However, it is currently unclear whether additional roles for MMACHC exist outside of cobalamin metabolism. Furthermore, due to a lack of sufficient animal models, the exact pathophysiology of cblC remains unknown. Here, we report the generation and characterization of two new mouse models to study the role of MMACHC in vivo. CRISPR/Cas9 genome editing was used to develop a Mmachc floxed allele (Mmachcflox/flox), which we validated as a conditional null. For a gain-of-function approach, we generated a transgenic mouse line that over-expresses functional Mmachc (Mmachc-OE+/tg) capable of rescuing Mmachc homozygous mutant lethality. Surprisingly, our data also suggest that these mice may exhibit a partially penetrant maternal-effect rescue, which might have implications for in utero therapeutic interventions to treat cblC. Both the Mmachcflox/flox and Mmachc-OE+/tg mouse models will be valuable resources for understanding the biological roles of MMACHC in a variety of tissue contexts and allow for deeper understanding of the pathophysiology of cblC.
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Affiliation(s)
- Tiffany Chern
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA; Graduate Program in Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Annita Achilleos
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xuefei Tong
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Leeyean Wong
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ross A Poché
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA; Graduate Program in Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA; Development, Disease Models and Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA; Genetics and Genomics Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA.
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20
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Castro VL, Quintana AM. The role of HCFC1 in syndromic and non-syndromic intellectual disability. ACTA ACUST UNITED AC 2020; 8. [PMID: 34164576 DOI: 10.18103/mra.v8i6.2122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mutations in the HCFC1 gene are associated with cases of syndromic (cblX) and non-syndromic intellectual disability. Syndromic individuals present with severe neurological defects including intractable epilepsy, facial dysmorphia, and intellectual disability. Non-syndromic individuals have also been described and implicate a role for HCFC1 during brain development. The penetrance of phenotypes and the presence of an overall syndrome is associated with the location of the mutation within the HCFC1 protein. Thus, one could hypothesize that the positioning of HCFC1 mutations lead to different neurological phenotypes that include but are not restricted to intellectual disability. The HCFC1 protein is comprised of multiple domains that function in cellular proliferation/metabolism. Several reports of HCFC1 disease variants have been identified, but a comprehensive review of each variant and its associated phenotypes has not yet been compiled. Here we perform a detailed review of HCFC1 function, model systems, variant location, and accompanying phenotypes to highlight current knowledge and the future status of the field.
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Affiliation(s)
- Victoria L Castro
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968
| | - Anita M Quintana
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968
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21
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Froese DS, Fowler B, Baumgartner MR. Vitamin B 12 , folate, and the methionine remethylation cycle-biochemistry, pathways, and regulation. J Inherit Metab Dis 2019; 42:673-685. [PMID: 30693532 DOI: 10.1002/jimd.12009] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/27/2018] [Accepted: 10/19/2018] [Indexed: 12/16/2022]
Abstract
Vitamin B12 (cobalamin, Cbl) is a nutrient essential to human health. Due to its complex structure and dual cofactor forms, Cbl undergoes a complicated series of absorptive and processing steps before serving as cofactor for the enzymes methylmalonyl-CoA mutase and methionine synthase. Methylmalonyl-CoA mutase is required for the catabolism of certain (branched-chain) amino acids into an anaplerotic substrate in the mitochondrion, and dysfunction of the enzyme itself or in production of its cofactor adenosyl-Cbl result in an inability to successfully undergo protein catabolism with concomitant mitochondrial energy disruption. Methionine synthase catalyzes the methyl-Cbl dependent (re)methylation of homocysteine to methionine within the methionine cycle; a reaction required to produce this essential amino acid and generate S-adenosylmethionine, the most important cellular methyl-donor. Disruption of methionine synthase has wide-ranging implications for all methylation-dependent reactions, including epigenetic modification, but also for the intracellular folate pathway, since methionine synthase uses 5-methyltetrahydrofolate as a one-carbon donor. Folate-bound one-carbon units are also required for deoxythymidine monophosphate and de novo purine synthesis; therefore, the flow of single carbon units to each of these pathways must be regulated based on cellular needs. This review provides an overview on Cbl metabolism with a brief description of absorption and intracellular metabolic pathways. It also provides a description of folate-mediated one-carbon metabolism and its intersection with Cbl at the methionine cycle. Finally, a summary of recent advances in understanding of how both pathways are regulated is presented.
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Affiliation(s)
- D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Brian Fowler
- Division of Metabolism and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Matthias R Baumgartner
- Division of Metabolism and Children's Research Center, University Children's Hospital, Zurich, Switzerland
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22
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Lemoine M, Grangé S, Guerrot D. [Kidney disease in cobalamin C deficiency]. Nephrol Ther 2019; 15:201-214. [PMID: 31130431 DOI: 10.1016/j.nephro.2019.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 03/06/2019] [Indexed: 12/23/2022]
Abstract
Cobalamin C deficiency (cblC) is the most common inborn error of vitamin B12 metabolism. This autosomal recessive disease is due to mutations in MMACHC gene, encoding a cyanocobalamin decyanase. It leads to hyperhomocysteinemia associated with hypomethioninemia and methylmalonic aciduria. Two distinct phenotypes have been described : early-onset forms occur before the age of one year and are characterized by a severe multisystem disease associating failure to thrive to neurological and ophthalmological manifestations. They are opposed to late-onset forms, less severe and heterogeneous. CblC deficiency-associated kidney lesions remain poorly defined. Thirty-eight cases have been described. Age at initial presentation varied from a few days to 28 years. Most of the patients presented renal thrombotic microangiopathy (TMA) associated with acute renal failure, and 21 patients presented typical lesions of renal thrombotic microangiopathy on kidney biopsy. Prognosis was poor, leading to death in the absence of treatment, and related to the severity of renal lesions in the early-onset forms. Late-onset disease had better prognosis and most of patients were weaned off dialysis after treatment initiation. We suggest that all the patients with renal TMA be screened for cobalamin metabolism disorder, regardless of age and even in the absence of neurological symptoms, to rapidly initiate the appropriate treatment.
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Affiliation(s)
- Mathilde Lemoine
- Service de néphrologie, dialyse et transplantation, CHU de Rouen, 1, rue de Germont, 76031 Rouen, France.
| | - Steven Grangé
- Service de réanimation médicale, CHU de Rouen, 1, rue de Germont, 76031 Rouen, France
| | - Dominique Guerrot
- Service de néphrologie, dialyse et transplantation, CHU de Rouen, 1, rue de Germont, 76031 Rouen, France; Inserm U1096, UFR médecine pharmacie, 22, boulevard Gambetta, 76183 Rouen, France
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23
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McDonald MK, Fritz JA, Jia D, Scheuchner D, Snyder FF, Stanislaus A, Curle J, Li L, Stabler SP, Allen RH, Mains PE, Gravel RA. Identification of ABC transporters acting in vitamin B 12 metabolism in Caenorhabditis elegans. Mol Genet Metab 2017; 122:160-171. [PMID: 29153845 DOI: 10.1016/j.ymgme.2017.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 11/10/2017] [Accepted: 11/10/2017] [Indexed: 01/19/2023]
Abstract
Vitamin B12 (cobalamin, Cbl) is a micronutrient essential to human health. Cbl is not utilized as is but must go through complex subcellular and metabolic processing to generate two cofactor forms: methyl-Cbl for methionine synthase, a cytosolic enzyme; and adenosyl-Cbl for methylmalonyl-CoA mutase, a mitochondrial enzyme. Some 10-12 human genes have been identified responsible for the intracellular conversion of Cbl to cofactor forms, including genes that code for ATP-binding cassette (ABC) transporters acting at the lysosomal and plasma membranes. However, the gene for mitochondrial uptake is not known. We hypothesized that ABC transporters should be candidates for other uptake and efflux functions, including mitochondrial transport, and set out to screen ABC transporter mutants for blocks in Cbl utilization using the nematode roundworm Caenorhabditis elegans. Thirty-seven mutant ABC transporters were screened for the excretion of methylmalonic acid (MMA), which should result from loss of Cbl transport into the mitochondria. One mutant, wht-6, showed elevated MMA excretion and reduced [14C]-propionate incorporation, pointing to a functional block in methylmalonyl-CoA mutase. In contrast, the wht-6 mutant appeared to have a normal cytosolic pathway based on analysis of cystathionine excretion, suggesting that cytosolic methionine synthase was functioning properly. Further, the MMA excretion in wht-6 could be partially reversed by including vitamin B12 in the assay medium. The human ortholog of wht-6 is a member of the G family of ABC transporters. We propose wht-6 as a candidate for the transport of Cbl into mitochondria and suggest that a member of the corresponding ABCG family of ABC transporters has this role in humans. Our ABC transporter screen also revealed that mrp-1 and mrp-2 mutants excreted lower MMA than wild type, suggesting they were concentrating intracellular Cbl, consistent with the cellular efflux defect proposed for the mammalian MRP1 ABC transporter.
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Affiliation(s)
- Megan K McDonald
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, T2N 4N1, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, T2N 4N1, Canada
| | - Julie-Anne Fritz
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, T2N 4N1, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, T2N 4N1, Canada
| | - Dongxin Jia
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, T2N 4N1, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, T2N 4N1, Canada
| | - Deborah Scheuchner
- Department of Medical Genetics, University of Calgary, Calgary, T2N 4N1, Canada
| | - Floyd F Snyder
- Department of Medical Genetics, University of Calgary, Calgary, T2N 4N1, Canada
| | - Avalyn Stanislaus
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Jared Curle
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Sally P Stabler
- Division of Hematology, University of Colorado Denver, Aurora, CO, USA
| | - Robert H Allen
- Division of Hematology, University of Colorado Denver, Aurora, CO, USA
| | - Paul E Mains
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, T2N 4N1, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, T2N 4N1, Canada
| | - Roy A Gravel
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, T2N 4N1, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, T2N 4N1, Canada.
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24
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Almannai M, Marom R, Divin K, Scaglia F, Sutton VR, Craigen WJ, Lee B, Burrage LC, Graham BH. Milder clinical and biochemical phenotypes associated with the c.482G>A (p.Arg161Gln) pathogenic variant in cobalamin C disease: Implications for management and screening. Mol Genet Metab 2017; 122:60-66. [PMID: 28693988 PMCID: PMC5612879 DOI: 10.1016/j.ymgme.2017.06.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/24/2017] [Accepted: 06/25/2017] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Cobalamin C disease is a multisystemic disease with variable manifestations and age of onset. Genotype-phenotype correlations are well-recognized in this disorder. Here, we present a large cohort of individuals with cobalamin C disease, several of whom are heterozygous for the c.482G>A pathogenic variant (p.Arg161Gln). We compared clinical characteristics of individuals with this pathogenic variant to those who do not have this variant. To our knowledge, this study represents the largest single cohort of individuals with the c.482G>A (p.Arg161Gln) pathogenic variant. METHODS A retrospective chart review of 27 individuals from 21 families with cobalamin C disease who are followed at our facility was conducted. RESULTS 13 individuals (48%) are compound heterozygous with the c.482G>A (p.Arg161Gln) on one allele and a second pathogenic variant on the other allele. Individuals with the c.482G>A (p.Arg161Gln) pathogenic variant had later onset of symptoms and easier metabolic control. Moreover, they had milder biochemical abnormalities at presentation which likely contributed to the observation that 4 individuals (31%) in this group were missed by newborn screening. CONCLUSION The c.482G>A (p.Arg161Gln) pathogenic variant is associated with milder disease. These individuals may not receive a timely diagnosis as they may not be identified on newborn screening or because of unrecognized, late onset symptoms. Despite the milder presentation, significant complications can occur, especially if treatment is delayed.
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Affiliation(s)
- Mohammed Almannai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Texas Children's Hospital, Houston, TX, USA
| | - Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Texas Children's Hospital, Houston, TX, USA
| | - Kristian Divin
- Department of Molecular and Human Genetics, Texas Children's Hospital, Houston, TX, USA
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Texas Children's Hospital, Houston, TX, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Texas Children's Hospital, Houston, TX, USA
| | - William J Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Texas Children's Hospital, Houston, TX, USA
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Texas Children's Hospital, Houston, TX, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Texas Children's Hospital, Houston, TX, USA.
| | - Brett H Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Texas Children's Hospital, Houston, TX, USA.
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25
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Ruetz M, Shanmuganathan A, Gherasim C, Karasik A, Salchner R, Kieninger C, Wurst K, Banerjee R, Koutmos M, Kräutler B. Inhibierung des humanen B12-verarbeitenden Enzyms CblC durch Antivitamine B12- Kristallstruktur des inaktiven ternären Komplexes mit dem Kosubstrat Glutathion. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701583] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Markus Ruetz
- Institut für Organische Chemie und Zentrum für Molekulare, Biowissenschaften; Universität Innsbruck; 6020 Innsbruck Österreich
- University of Michigan Medical School; Ann Arbor MI 48109-0600 USA
| | | | - Carmen Gherasim
- University of Michigan Medical School; Ann Arbor MI 48109-0600 USA
- Department of Pathology; University of Utah School of Medicine; Salt Lake City UT USA
| | - Agnes Karasik
- Department of Biochemistry; Uniformed Services University of the Health Sciences; Bethesda MD 28104 USA
| | - Robert Salchner
- Institut für Organische Chemie und Zentrum für Molekulare, Biowissenschaften; Universität Innsbruck; 6020 Innsbruck Österreich
- Watercryst GmbH & Co; Kematen Österreich
| | - Christoph Kieninger
- Institut für Organische Chemie und Zentrum für Molekulare, Biowissenschaften; Universität Innsbruck; 6020 Innsbruck Österreich
| | - Klaus Wurst
- Institut für Allgemeine, Anorganische Chemie und Theoretische Chemie; Universität Innsbruck; Österreich
| | - Ruma Banerjee
- University of Michigan Medical School; Ann Arbor MI 48109-0600 USA
| | - Markos Koutmos
- Department of Biochemistry; Uniformed Services University of the Health Sciences; Bethesda MD 28104 USA
| | - Bernhard Kräutler
- Institut für Organische Chemie und Zentrum für Molekulare, Biowissenschaften; Universität Innsbruck; 6020 Innsbruck Österreich
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26
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Ruetz M, Shanmuganathan A, Gherasim C, Karasik A, Salchner R, Kieninger C, Wurst K, Banerjee R, Koutmos M, Kräutler B. Antivitamin B 12 Inhibition of the Human B 12 -Processing Enzyme CblC: Crystal Structure of an Inactive Ternary Complex with Glutathione as the Cosubstrate. Angew Chem Int Ed Engl 2017; 56:7387-7392. [PMID: 28544088 DOI: 10.1002/anie.201701583] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Indexed: 02/06/2023]
Abstract
B12 antivitamins are important and robust tools for investigating the biological roles of vitamin B12 . Here, the potential antivitamin B12 2,4-difluorophenylethynylcobalamin (F2PhEtyCbl) was prepared, and its 3D structure was studied in solution and in the crystal. Chemically inert F2PhEtyCbl resisted thermolysis of its Co-C bond at 100 °C, was stable in bright daylight, and also remained intact upon prolonged storage in aqueous solution at room temperature. It binds to the human B12 -processing enzyme CblC with high affinity (KD =130 nm) in the presence of the cosubstrate glutathione (GSH). F2PhEtyCbl withstood tailoring by CblC, and it also stabilized the ternary complex with GSH. The crystal structure of this inactivated assembly provides first insight into the binding interactions between an antivitamin B12 and CblC, as well as into the organization of GSH and a base-off cobalamin in the active site of this enzyme.
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Affiliation(s)
- Markus Ruetz
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020, Innsbruck, Austria.,University of Michigan Medical School, Ann Arbor, USA
| | | | - Carmen Gherasim
- University of Michigan Medical School, Ann Arbor, USA.,Current address: Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Agnes Karasik
- Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, USA
| | - Robert Salchner
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020, Innsbruck, Austria.,Current address: Watercryst GmbH & Co, Kematen, Austria
| | - Christoph Kieninger
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020, Innsbruck, Austria
| | - Klaus Wurst
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Austria
| | - Ruma Banerjee
- University of Michigan Medical School, Ann Arbor, USA
| | - Markos Koutmos
- Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, USA
| | - Bernhard Kräutler
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020, Innsbruck, Austria
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27
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Li Z, Shanmuganathan A, Ruetz M, Yamada K, Lesniak NA, Kräutler B, Brunold TC, Koutmos M, Banerjee R. Coordination chemistry controls the thiol oxidase activity of the B 12-trafficking protein CblC. J Biol Chem 2017; 292:9733-9744. [PMID: 28442570 DOI: 10.1074/jbc.m117.788554] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 04/20/2017] [Indexed: 01/20/2023] Open
Abstract
The cobalamin or B12 cofactor supports sulfur and one-carbon metabolism and the catabolism of odd-chain fatty acids, branched-chain amino acids, and cholesterol. CblC is a B12-processing enzyme involved in an early cytoplasmic step in the cofactor-trafficking pathway. It catalyzes the glutathione (GSH)-dependent dealkylation of alkylcobalamins and the reductive decyanation of cyanocobalamin. CblC from Caenorhabditis elegans (ceCblC) also exhibits a robust thiol oxidase activity, converting reduced GSH to oxidized GSSG with concomitant scrubbing of ambient dissolved O2 The mechanism of thiol oxidation catalyzed by ceCblC is not known. In this study, we demonstrate that novel coordination chemistry accessible to ceCblC-bound cobalamin supports its thiol oxidase activity via a glutathionyl-cobalamin intermediate. Deglutathionylation of glutathionyl-cobalamin by a second molecule of GSH yields GSSG. The crystal structure of ceCblC provides insights into how architectural differences at the α- and β-faces of cobalamin promote the thiol oxidase activity of ceCblC but mute it in wild-type human CblC. The R161G and R161Q mutations in human CblC unmask its latent thiol oxidase activity and are correlated with increased cellular oxidative stress disease. In summary, we have uncovered key architectural features in the cobalamin-binding pocket that support unusual cob(II)alamin coordination chemistry and enable the thiol oxidase activity of ceCblC.
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Affiliation(s)
- Zhu Li
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Aranganathan Shanmuganathan
- the Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814
| | - Markus Ruetz
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Kazuhiro Yamada
- the Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814
| | - Nicholas A Lesniak
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Bernhard Kräutler
- the Institute of Organic Chemistry and Centre of Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria, and
| | - Thomas C Brunold
- the Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Markos Koutmos
- the Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814
| | - Ruma Banerjee
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600,
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28
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Pan C, Weng J, Wang W. Conformational Dynamics and Protein-Substrate Interaction of ABC Transporter BtuCD at the Occluded State Revealed by Molecular Dynamics Simulations. Biochemistry 2016; 55:6897-6907. [PMID: 27951660 DOI: 10.1021/acs.biochem.6b00386] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
ATP-binding cassette (ABC) transporters are ubiquitous in all three kingdoms of life and are implicated in many clinically relevant physiological processes. They couple the energy released by ATP hydrolysis to facilitate substrate translocation across cell membranes. The crystal structures of type II ABC importers have revealed their unique transmembrane domain architecture consisting of 10 transmembrane helices and their structurally conserved nucleotide-binding domains among all ABC transporters. However, molecular details of the interactions between the importers and their substrate remain largely elusive. Taking vitamin B12 importer BtuCD as an exemplar of type II importers, we investigated the dynamics of its occluded state and the detailed protein-substrate interactions using molecular dynamics simulation. Our trajectories show that the importer accommodates the substrate through a nonspecific binding mode as the substrate undergoes evident vertical and tilt motions inside the translocation cavity. Extensive hydrogen bond and hydrophobic interactions were observed between the substrate and the importer; however, most of these interactions are weak, with <38% occurrence. The presence of substrate leads to enlargement of the translocation cavity, especially at its cytoplasmic end, which may activate cytoplasmic regions and probably facilitate the transportation. The perturbations caused by periplasmic binding protein and nucleotides were also investigated. The study provides deeper insight into the translocation mechanism of BtuCD.
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Affiliation(s)
- Chao Pan
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University , Shanghai, P. R. China
| | - Jingwei Weng
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University , Shanghai, P. R. China
| | - Wenning Wang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University , Shanghai, P. R. China
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29
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Dowling DP, Miles ZD, Köhrer C, Maiocco SJ, Elliott SJ, Bandarian V, Drennan CL. Molecular basis of cobalamin-dependent RNA modification. Nucleic Acids Res 2016; 44:9965-9976. [PMID: 27638883 PMCID: PMC5175355 DOI: 10.1093/nar/gkw806] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 08/30/2016] [Accepted: 09/03/2016] [Indexed: 12/22/2022] Open
Abstract
Queuosine (Q) was discovered in the wobble position of a transfer RNA (tRNA) 47 years ago, yet the final biosynthetic enzyme responsible for Q-maturation, epoxyqueuosine (oQ) reductase (QueG), was only recently identified. QueG is a cobalamin (Cbl)-dependent, [4Fe-4S] cluster-containing protein that produces the hypermodified nucleoside Q in situ on four tRNAs. To understand how QueG is able to perform epoxide reduction, an unprecedented reaction for a Cbl-dependent enzyme, we have determined a series of high resolution structures of QueG from Bacillus subtilis. Our structure of QueG bound to a tRNATyr anticodon stem loop shows how this enzyme uses a HEAT-like domain to recognize the appropriate anticodons and position the hypermodified nucleoside into the enzyme active site. We find Q bound directly above the Cbl, consistent with a reaction mechanism that involves the formation of a covalent Cbl-tRNA intermediate. Using protein film electrochemistry, we show that two [4Fe-4S] clusters adjacent to the Cbl have redox potentials in the range expected for Cbl reduction, suggesting how Cbl can be activated for nucleophilic attack on oQ. Together, these structural and electrochemical data inform our understanding of Cbl dependent nucleic acid modification.
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Affiliation(s)
- Daniel P Dowling
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zachary D Miles
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Caroline Köhrer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Sean J Elliott
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Catherine L Drennan
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA .,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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30
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Yue WW. From structural biology to designing therapy for inborn errors of metabolism. J Inherit Metab Dis 2016; 39:489-98. [PMID: 27240455 PMCID: PMC4920855 DOI: 10.1007/s10545-016-9923-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/09/2016] [Accepted: 02/11/2016] [Indexed: 12/11/2022]
Abstract
At the SSIEM Symposium in Istanbul 2010, I presented an overview of protein structural approaches in the study of inborn errors of metabolism (Yue and Oppermann 2011). Five years on, the field is going strong with new protein structures, uncovered catalytic functions and novel chemical matters for metabolic enzymes, setting the stage for the next generation of drug discovery. This article aims to update on recent advances and lessons learnt on inborn errors of metabolism via the protein-centric approach, citing examples of work from my group, collaborators and co-workers that cover diverse pathways of transsulfuration, cobalamin and glycogen metabolism. Taking into consideration that many inborn errors of metabolism result in the loss of enzyme function, this presentation aims to outline three key principles that guide the design of small molecule therapy in this technically challenging field: (1) integrating structural, biochemical and cell-based data to evaluate the wide spectrum of mutation-driven enzyme defects in stability, catalysis and protein-protein interaction; (2) studying multi-domain proteins and multi-protein complexes as examples from nature, to learn how enzymes are activated by small molecules; (3) surveying different regions of the enzyme, away from its active site, that can be targeted for the design of allosteric activators and inhibitors.
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Affiliation(s)
- Wyatt W Yue
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK.
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Brooks BP, Thompson AH, Sloan JL, Manoli I, Carrillo-Carrasco N, Zein WM, Venditti CP. Ophthalmic Manifestations and Long-Term Visual Outcomes in Patients with Cobalamin C Deficiency. Ophthalmology 2016; 123:571-82. [PMID: 26825575 DOI: 10.1016/j.ophtha.2015.10.041] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 09/25/2015] [Accepted: 10/25/2015] [Indexed: 01/07/2023] Open
Abstract
PURPOSE To explore the ocular manifestations of cobalamin C (cblC) deficiency, an inborn error of intracellular vitamin B12 metabolism. DESIGN Retrospective, observational case series. PARTICIPANTS Twenty-five cblC patients underwent clinical and ophthalmic examination at the National Institutes of Health between August 2004 and September 2012. Patient ages ranged from 2 to 27 years at last ophthalmic visit, and follow-up ranged from 0 to 83 months (median, 37 months; range, 13-83 months) over a total of 69 visits. METHODS Best-corrected visual acuity, slit-lamp biomicroscopy, dilated fundus examination, wide-field photography, fundus autofluorescence imaging, sedated electroretinography, optical coherence tomography, genetics and metabolite assessment. MAIN OUTCOME MEASURES Visual acuity and presence and degree of retinal degeneration and optic nerve pallor. RESULTS Nystagmus (64%), strabismus (52%), macular degeneration (72%), optic nerve pallor (68%), and vascular changes (64%) were present. c.271dupA (p.R91KfsX14) homozygous patients (n = 14) showed early and extensive macular degeneration. Electroretinography showed that scotopic and photopic responses were reduced and delayed, but were preserved remarkably in some patients despite severe degeneration. Optical coherence tomography images through the central macular lesion of a patient with severe retinal degeneration showed extreme thinning, some preservation of retinal lamination, and nearly complete loss of the outer nuclear layer. Despite hyperhomocysteinemia, no patients exhibited lens dislocation. CONCLUSIONS This longitudinal study reports ocular outcomes in the largest group of patients with cblC deficiency systematically examined at a single center over an extended period. Differences in progression and severity of macular degeneration, optic nerve pallor, and vascular attenuation between homozygous c.271dupA (p.R91KfsX14) patients and compound heterozygotes were noted. The pace and chronicity of ophthalmic manifestations lacked strict correlation to metabolic status as measured during visits. Prenatal or early treatment, or both, may have mitigated ocular disease, leading to better functional acuity, but patients still progressed to severe macular degeneration. The effects of prenatal or early treatment, or both, in siblings; the manifestation of severe disease in infancy; the presence of comorbid developmental abnormalities; and the possible laminar structural defect noted in many patients are findings showing that cblC deficiency displays a developmental as well as a degenerative ocular phenotype.
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Affiliation(s)
- Brian P Brooks
- National Eye Institute, Ophthalmic Genetics and Visual Function Branch, National Institutes of Health, Bethesda, Maryland; National Human Genome Research Institute, Genetics and Molecular Biology Branch, National Institutes of Health, Bethesda, Maryland.
| | - Amy H Thompson
- National Eye Institute, Ophthalmic Genetics and Visual Function Branch, National Institutes of Health, Bethesda, Maryland
| | - Jennifer L Sloan
- National Human Genome Research Institute, Genetics and Molecular Biology Branch, National Institutes of Health, Bethesda, Maryland
| | - Irini Manoli
- National Human Genome Research Institute, Genetics and Molecular Biology Branch, National Institutes of Health, Bethesda, Maryland
| | - Nuria Carrillo-Carrasco
- National Center for Advancing Translational Sciences, Therapeutics for Rare and Neglected Diseases, National Institutes of Health, Bethesda, Maryland
| | - Wadih M Zein
- National Eye Institute, Ophthalmic Genetics and Visual Function Branch, National Institutes of Health, Bethesda, Maryland
| | - Charles P Venditti
- National Human Genome Research Institute, Genetics and Molecular Biology Branch, National Institutes of Health, Bethesda, Maryland
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Yamada K, Gherasim C, Banerjee R, Koutmos M. Structure of Human B12 Trafficking Protein CblD Reveals Molecular Mimicry and Identifies a New Subfamily of Nitro-FMN Reductases. J Biol Chem 2015; 290:29155-66. [PMID: 26364851 PMCID: PMC4705922 DOI: 10.1074/jbc.m115.682435] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Indexed: 01/07/2023] Open
Abstract
In mammals, B12 (or cobalamin) is an essential cofactor required by methionine synthase and methylmalonyl-CoA mutase. A complex intracellular pathway supports the assimilation of cobalamin into its active cofactor forms and delivery to its target enzymes. MMADHC (the methylmalonic aciduria and homocystinuria type D protein), commonly referred to as CblD, is a key chaperone involved in intracellular cobalamin trafficking, and mutations in CblD cause methylmalonic aciduria and/or homocystinuria. Herein, we report the first crystal structure of the globular C-terminal domain of human CblD, which is sufficient for its interaction with MMADHC (the methylmalonic aciduria and homocystinuria type C protein), or CblC, and for supporting the cytoplasmic cobalamin trafficking pathway. CblD contains an α+β fold that is structurally reminiscent of the nitro-FMN reductase superfamily. Two of the closest structural relatives of CblD are CblC, a multifunctional enzyme important for cobalamin trafficking, and the activation domain of methionine synthase. CblD, CblC, and the activation domain of methionine synthase share several distinguishing features and, together with two recently described corrinoid-dependent reductive dehalogenases, constitute a new subclass within the nitro-FMN reductase superfamily. We demonstrate that CblD enhances oxidation of cob(II)alamin bound to CblC and that disease-causing mutations in CblD impair the kinetics of this reaction. The striking structural similarity of CblD to CblC, believed to be contiguous in the cobalamin trafficking pathway, suggests the co-option of molecular mimicry as a strategy for achieving its function.
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Affiliation(s)
- Kazuhiro Yamada
- From the Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814 and
| | - Carmen Gherasim
- the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600
| | - Ruma Banerjee
- the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600, To whom correspondence may be addressed. Tel.: 734-615-5238; E-mail:
| | - Markos Koutmos
- From the Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814 and , To whom correspondence may be addressed. Tel.: 301-295-9419; E-mail:
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Froese DS, Kopec J, Fitzpatrick F, Schuller M, McCorvie TJ, Chalk R, Plessl T, Fettelschoss V, Fowler B, Baumgartner MR, Yue WW. Structural Insights into the MMACHC-MMADHC Protein Complex Involved in Vitamin B12 Trafficking. J Biol Chem 2015; 290:29167-77. [PMID: 26483544 PMCID: PMC4705923 DOI: 10.1074/jbc.m115.683268] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Indexed: 11/06/2022] Open
Abstract
Conversion of vitamin B12 (cobalamin, Cbl) into the cofactor forms methyl-Cbl (MeCbl) and adenosyl-Cbl (AdoCbl) is required for the function of two crucial enzymes, mitochondrial methylmalonyl-CoA mutase and cytosolic methionine synthase, respectively. The intracellular proteins MMACHC and MMADHC play important roles in processing and targeting the Cbl cofactor to its destination enzymes, and recent evidence suggests that they may interact while performing these essential trafficking functions. To better understand the molecular basis of this interaction, we have mapped the crucial protein regions required, indicate that Cbl is likely processed by MMACHC prior to interaction with MMADHC, and identify patient mutations on both proteins that interfere with complex formation, via different mechanisms. We further report the crystal structure of the MMADHC C-terminal region at 2.2 Å resolution, revealing a modified nitroreductase fold with surprising homology to MMACHC despite their poor sequence conservation. Because MMADHC demonstrates no known enzymatic activity, we propose it as the first protein known to repurpose the nitroreductase fold solely for protein-protein interaction. Using small angle x-ray scattering, we reveal the MMACHC-MMADHC complex as a 1:1 heterodimer and provide a structural model of this interaction, where the interaction region overlaps with the MMACHC-Cbl binding site. Together, our findings provide novel structural evidence and mechanistic insight into an essential biological process, whereby an intracellular "trafficking chaperone" highly specific for a trace element cofactor functions via protein-protein interaction, which is disrupted by inherited disease mutations.
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Affiliation(s)
- D Sean Froese
- From the Division of Metabolism and Children's Research Center, University Children's, Hospital, CH-8032 Zurich, Switzerland, radiz - Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, CH-8032 Zurich, Switzerland
| | - Jolanta Kopec
- the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom, and
| | - Fiona Fitzpatrick
- the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom, and
| | - Marion Schuller
- the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom, and
| | - Thomas J McCorvie
- the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom, and
| | - Rod Chalk
- the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom, and
| | - Tanja Plessl
- From the Division of Metabolism and Children's Research Center, University Children's, Hospital, CH-8032 Zurich, Switzerland
| | - Victoria Fettelschoss
- From the Division of Metabolism and Children's Research Center, University Children's, Hospital, CH-8032 Zurich, Switzerland
| | - Brian Fowler
- From the Division of Metabolism and Children's Research Center, University Children's, Hospital, CH-8032 Zurich, Switzerland
| | - Matthias R Baumgartner
- From the Division of Metabolism and Children's Research Center, University Children's, Hospital, CH-8032 Zurich, Switzerland, radiz - Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, CH-8032 Zurich, Switzerland, the Zurich Center for Integrative Human Physiology, University of Zurich, 8057 Zurich, Switzerland
| | - Wyatt W Yue
- the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom, and
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34
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Gherasim C, Ruetz M, Li Z, Hudolin S, Banerjee R. Pathogenic mutations differentially affect the catalytic activities of the human B12-processing chaperone CblC and increase futile redox cycling. J Biol Chem 2015; 290:11393-402. [PMID: 25809485 DOI: 10.1074/jbc.m115.637132] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Indexed: 11/06/2022] Open
Abstract
Human CblC catalyzes the elimination of the upper axial ligand in cobalamin or B12 derivatives entering the cell from circulation. This processing step is critical for assimilation of dietary cobalamin into the active cofactor forms that support the B12-dependent enzymes, methionine synthase and methylmalonyl-CoA mutase. Using a modified nitroreductase scaffold tailored to bind cobalamin and glutathione, CblC exhibits versatility in the mechanism by which it removes cyano versus alkyl ligands in cobalamin. In this study, we have characterized the effects of two pathogenic missense mutations at the same residue, R161G and R161Q, which are associated with early and late onset of the CblC disorder, respectively. We find that the R161Q and R161G CblC mutants display lower protein stability and decreased dealkylation but not decyanation activity, suggesting that cyanocobalamin might be therapeutically useful for patients carrying mutations at Arg-161. The mutant proteins also exhibit impaired glutathione binding. In the presence of physiologically relevant glutathione concentrations, stabilization of the cob(II)alamin derivative is observed, which occurs at the expense of increased oxidation of glutathione. Futile redox cycling, which is suppressed in wild-type human CblC, explains the reported increase in oxidative stress levels associated with the CblC disorder.
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Affiliation(s)
- Carmen Gherasim
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Markus Ruetz
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Zhu Li
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Stephanie Hudolin
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Ruma Banerjee
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
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35
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Bommer M, Kunze C, Fesseler J, Schubert T, Diekert G, Dobbek H. Structural basis for organohalide respiration. Science 2014; 346:455-8. [DOI: 10.1126/science.1258118] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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36
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Li Z, Gherasim C, Lesniak NA, Banerjee R. Glutathione-dependent one-electron transfer reactions catalyzed by a B₁₂ trafficking protein. J Biol Chem 2014; 289:16487-97. [PMID: 24742678 DOI: 10.1074/jbc.m114.567339] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CblC is involved in an early step in cytoplasmic cobalamin processing following entry of the cofactor into the cytoplasm. CblC converts the cobalamin cargo arriving from the lysosome to a common cob(II)alamin intermediate, which can be subsequently converted to the biologically active forms. Human CblC exhibits glutathione (GSH)-dependent alkyltransferase activity and flavin-dependent reductive decyanation activity with cyanocobalamin (CNCbl). In this study, we discovered two new GSH-dependent activities associated with the Caenorhabditis elegans CblC for generating cob(II)alamin: decyanation of CNCbl and reduction of aquocobalamin (OH2Cbl). We subsequently found that human CblC also catalyzes GSH-dependent decyanation of CNCbl and reduction of OH2Cbl, albeit efficiently only under anaerobic conditions. The air sensitivity of the human enzyme suggests interception by oxygen during the single-electron transfer step from GSH to CNCbl. These newly discovered GSH-dependent single-electron transfer reactions expand the repertoire of catalytic activities supported by CblC, a versatile B12-processing enzyme.
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Affiliation(s)
- Zhu Li
- From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600
| | - Carmen Gherasim
- From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600
| | - Nicholas A Lesniak
- From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600
| | - Ruma Banerjee
- From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600
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37
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Joseph DDA, Jiao W, Kessans SA, Parker EJ. Substrate-mediated control of the conformation of an ancillary domain delivers a competent catalytic site for N-acetylneuraminic acid synthase. Proteins 2014; 82:2054-66. [PMID: 24633984 DOI: 10.1002/prot.24558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 02/14/2014] [Accepted: 03/04/2014] [Indexed: 12/19/2022]
Abstract
N-Acetylneuraminic acid (NANA) is the most common naturally occurring sialic acid and plays a key role in the pathogenesis of a select number of neuroinvasive bacteria such as Neisseria meningitidis. NANA is synthesized in prokaryotes via a condensation reaction between phosphoenolpyruvate and N-acetylmannosamine. This reaction is catalyzed by a domain swapped, homodimeric enzyme, N-acetylneuraminic acid synthase (NANAS). NANAS comprises two distinct domains; an N-terminal catalytic (β/α)8 barrel linked to a C-terminal antifreeze protein-like (AFPL) domain. We have investigated the role of the AFPL domain by characterizing a truncated variant of NmeNANAS, which was discovered to be soluble yet inactive. Analytical ultracentrifugation and analytical size exclusion were used to probe the quaternary state of the NmeNANAS truncation, and revealed that loss of the AFPL domain destabilizes the dimeric form of the enzyme. The results from this study thereby demonstrate that the AFPL domain plays a critical role for both the catalytic function and quaternary structure stability of NANAS. Small angle X-ray scattering, molecular dynamics simulations, and amino acid substitutions expose a complex hydrogen-bonding relay, which links the roles of the catalytic and AFPL domains across subunit boundaries.
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Affiliation(s)
- Dmitri D A Joseph
- Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
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38
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Hannibal L, DiBello PM, Jacobsen DW. Proteomics of vitamin B12 processing. Clin Chem Lab Med 2013; 51:477-88. [PMID: 23241609 DOI: 10.1515/cclm-2012-0568] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 10/23/2012] [Indexed: 12/18/2022]
Abstract
The causes of cobalamin (B12, Cbl) deficiency are multifactorial. Whether nutritional due to poor dietary intake, or functional due to impairments in absorption or intracellular processing and trafficking events, the major symptoms of Cbl deficiency include megaloblastic anemia, neurological deterioration and in extreme cases, failure to thrive and death. The common biomarkers of Cbl deficiency (hyperhomocysteinemia and methylmalonic acidemia) are extremely valuable diagnostic indicators of the condition, but little is known about the changes that occur at the protein level. A mechanistic explanation bridging the physiological changes associated with functional B12 deficiency with its intracellular processers and carriers is lacking. In this article, we will cover the effects of B12 deficiency in a cblC-disrupted background (also referred to as MMACHC) as a model of functional Cbl deficiency. As will be shown, major protein changes involve the cytoskeleton, the neurological system as well as signaling and detoxification pathways. Supplementation of cultured MMACHC-mutant cells with hydroxocobalamin (HOCbl) failed to restore these variants to the normal phenotype, suggesting that a defective Cbl processing pathway produces irreversible changes at the protein level.
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Affiliation(s)
- Luciana Hannibal
- Department of Pathobiology (NC2 – 104), Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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39
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Jeong J, Park J, Lee DY, Kim J. C-terminal truncation of a bovine B(12) trafficking chaperone enhances the sensitivity of the glutathione-regulated thermostability. BMB Rep 2013; 46:169-74. [PMID: 23527861 PMCID: PMC4133868 DOI: 10.5483/bmbrep.2013.46.3.158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human B12 trafficking chaperone hCblC is well conserved in mammals and non-mammalian eukaryotes. However, the C-terminal ∼40 amino acids of hCblC vary significantly and are predicted to be deleted by alternative splicing of the encoding gene. In this study, we examined the thermostability of the bovine CblC truncated at the C-terminal variable region (t-bCblC) and its regulation by glutathione. t-bCblC is highly thermolabile (Tm = ∼42℃) similar to the full-length protein (f-bCblC). However, t-bCblC is stabilized to a greater extent than f-bCblC by binding of reduced glutathione (GSH) with increased sensitivity to GSH. In addition, binding of oxidized glutathione (GSSG) destabilizes t-bCblC to a greater extent and with increased sensitivity as compared to f-bCblC. These results indicate that t-bCblC is a more sensitive form to be regulated by glutathione than the full-length form of the protein. [BMB Reports 2013; 46(3): 169-174]
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Affiliation(s)
- Jinju Jeong
- School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Korea
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40
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Fofou-Caillierez MB, Mrabet NT, Chéry C, Dreumont N, Flayac J, Pupavac M, Paoli J, Alberto JM, Coelho D, Camadro JM, Feillet F, Watkins D, Fowler B, Rosenblatt DS, Guéant JL. Interaction between methionine synthase isoforms and MMACHC: characterization in cblG-variant, cblG and cblC inherited causes of megaloblastic anaemia. Hum Mol Genet 2013; 22:4591-601. [DOI: 10.1093/hmg/ddt308] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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41
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Backe PH, Ytre-Arne M, Røhr AK, Brodtkorb E, Fowler B, Rootwelt H, Bjørås M, Mørkrid L. Novel Deletion Mutation Identified in a Patient with Late-Onset Combined Methylmalonic Acidemia and Homocystinuria, cblC Type. JIMD Rep 2013; 11:79-85. [PMID: 23580368 DOI: 10.1007/8904_2013_225] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 03/12/2013] [Accepted: 03/14/2013] [Indexed: 01/04/2023] Open
Abstract
Combined methylmalonic aciduria and homocystinuria, cblC type (MMACHC), is the most common inborn error of cellular vitamin B12 metabolism and is caused by mutations in the MMACHC gene. This metabolic disease results in impaired intracellular synthesis of adenosylcobalamin and methylcobalamin, coenzymes for the methylmalonyl-CoA mutase and methionine synthase enzymes, respectively. The inability to produce normal levels of these two coenzymes leads to increased concentrations of methylmalonic acid and homocysteine in plasma and urine, together with normal or decreased concentration of methionine in plasma. Here, we report a novel homozygous deletion mutation (NM_015506.2:c.392_394del) resulting in an in-frame deletion of amino acid Gln131 and late-onset disease in a 23-year-old male. The patient presented with sensory and motoric disabilities, urine and fecal incontinence, and light cognitive impairment. There was an excessive urinary excretion of methylmalonic acid and greatly elevated plasma homocysteine. The clinical symptoms and the laboratory abnormalities responded partly to treatment with hydroxycobalamin, folinic acid, methionine, and betaine. Studies on patient fibroblasts together with spectroscopic activity assays on recombinant MMACHC protein reveal that Gln131 is crucial in order to maintain enzyme activity. Furthermore, structural analyses show that Gln131 is one of only two residues making hydrogen bonds to the tail of cobalamin. Circular dichroism spectroscopy indicates that the 3D structure of the deletion mutant is folded but perturbed compared to the wild-type protein.
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Affiliation(s)
- Paul Hoff Backe
- Department of Microbiology, Oslo University Hospital and University of Oslo, 4950, 0424, Oslo, Nydalen, Norway,
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Gherasim C, Lofgren M, Banerjee R. Navigating the B(12) road: assimilation, delivery, and disorders of cobalamin. J Biol Chem 2013; 288:13186-93. [PMID: 23539619 DOI: 10.1074/jbc.r113.458810] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The reactivity of the cobalt-carbon bond in cobalamins is the key to their chemical versatility, supporting both methyl transfer and isomerization reactions. During evolution of higher eukaryotes that utilize vitamin B12, the high reactivity of the cofactor coupled with its low abundance pressured development of an efficient system for uptake, assimilation, and delivery of the cofactor to client B12-dependent enzymes. Although most proteins suspected to be involved in B12 trafficking were discovered by 2009, the recent identification of a new protein reveals that the quest for elucidating the intracellular B12 highway is still far from complete. Herein, we review the biochemistry of cobalamin trafficking.
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Affiliation(s)
- Carmen Gherasim
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, MI 48109-0600, USA
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