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Ütkür K, Mayer K, Liu S, Brinkmann U, Schaffrath R. Functional Integrity of Radical SAM Enzyme Dph1•Dph2 Requires Non-Canonical Cofactor Motifs with Tandem Cysteines. Biomolecules 2024; 14:470. [PMID: 38672486 PMCID: PMC11048331 DOI: 10.3390/biom14040470] [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] [Received: 03/24/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
The Dph1•Dph2 heterodimer from yeast is a radical SAM (RS) enzyme that generates the 3-amino-3-carboxy-propyl (ACP) precursor for diphthamide, a clinically relevant modification on eukaryotic elongation factor 2 (eEF2). ACP formation requires SAM cleavage and atypical Cys-bound Fe-S clusters in each Dph1 and Dph2 subunit. Intriguingly, the first Cys residue in each motif is found next to another ill-defined cysteine that we show is conserved across eukaryotes. As judged from structural modeling, the orientation of these tandem cysteine motifs (TCMs) suggests a candidate Fe-S cluster ligand role. Hence, we generated, by site-directed DPH1 and DPH2 mutagenesis, Dph1•Dph2 variants with cysteines from each TCM replaced individually or in combination by serines. Assays diagnostic for diphthamide formation in vivo reveal that while single substitutions in the TCM of Dph2 cause mild defects, double mutations almost entirely inactivate the RS enzyme. Based on enhanced Dph1 and Dph2 subunit instability in response to cycloheximide chases, the variants with Cys substitutions in their cofactor motifs are particularly prone to protein degradation. In sum, we identify a fourth functionally cooperative Cys residue within the Fe-S motif of Dph2 and show that the Cys-based cofactor binding motifs in Dph1 and Dph2 are critical for the structural integrity of the dimeric RS enzyme in vivo.
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Affiliation(s)
- Koray Ütkür
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany;
| | - Klaus Mayer
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany; (K.M.); (U.B.)
| | - Shihui Liu
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA;
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany; (K.M.); (U.B.)
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany;
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Schaffrath R, Brinkmann U. Diphthamide - a conserved modification of eEF2 with clinical relevance. Trends Mol Med 2024; 30:164-177. [PMID: 38097404 DOI: 10.1016/j.molmed.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 02/17/2024]
Abstract
Diphthamide, a complex modification on eukaryotic translation elongation factor 2 (eEF2), assures reading-frame fidelity during translation. Diphthamide and enzymes for its synthesis are conserved in eukaryotes and archaea. Originally identified as target for diphtheria toxin (DT) in humans, its clinical relevance now proves to be broader than the link to pathogenic bacteria. Diphthamide synthesis enzymes (DPH1 and DPH3) are associated with cancer, and DPH gene mutations can cause diphthamide deficiency syndrome (DDS). Finally, new analyses provide evidence that diphthamide may restrict propagation of viruses including SARS-CoV-2 and HIV-1, and that DPH enzymes are targeted by viruses for degradation to overcome this restriction. This review describes how diphthamide is synthesized and functions in translation, and covers its clinical relevance in human development, cancer, and infectious diseases.
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Affiliation(s)
- Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany.
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany.
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3
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Ütkür K, Schmidt S, Mayer K, Klassen R, Brinkmann U, Schaffrath R. DPH1 Gene Mutations Identify a Candidate SAM Pocket in Radical Enzyme Dph1•Dph2 for Diphthamide Synthesis on EF2. Biomolecules 2023; 13:1655. [PMID: 38002337 PMCID: PMC10669111 DOI: 10.3390/biom13111655] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
In eukaryotes, the Dph1•Dph2 dimer is a non-canonical radical SAM enzyme. Using iron-sulfur (FeS) clusters, it cleaves the cosubstrate S-adenosyl-methionine (SAM) to form a 3-amino-3-carboxy-propyl (ACP) radical for the synthesis of diphthamide. The latter decorates a histidine residue on elongation factor 2 (EF2) conserved from archaea to yeast and humans and is important for accurate mRNA translation and protein synthesis. Guided by evidence from archaeal orthologues, we searched for a putative SAM-binding pocket in Dph1•Dph2 from Saccharomyces cerevisiae. We predict an SAM-binding pocket near the FeS cluster domain that is conserved across eukaryotes in Dph1 but not Dph2. Site-directed DPH1 mutagenesis and functional characterization through assay diagnostics for the loss of diphthamide reveal that the SAM pocket is essential for synthesis of the décor on EF2 in vivo. Further evidence from structural modeling suggests particularly critical residues close to the methionine moiety of SAM. Presumably, they facilitate a geometry specific for SAM cleavage and ACP radical formation that distinguishes Dph1•Dph2 from classical radical SAM enzymes, which generate canonical 5'-deoxyadenosyl (dAdo) radicals.
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Affiliation(s)
- Koray Ütkür
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany; (K.Ü.); (S.S.); (R.K.)
| | - Sarina Schmidt
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany; (K.Ü.); (S.S.); (R.K.)
| | - Klaus Mayer
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany; (K.M.); (U.B.)
| | - Roland Klassen
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany; (K.Ü.); (S.S.); (R.K.)
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany; (K.M.); (U.B.)
| | - Raffael Schaffrath
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany; (K.M.); (U.B.)
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Arend M, Ütkür K, Hawer H, Mayer K, Ranjan N, Adrian L, Brinkmann U, Schaffrath R. Yeast gene KTI13 (alias DPH8) operates in the initiation step of diphthamide synthesis on elongation factor 2. MICROBIAL CELL (GRAZ, AUSTRIA) 2023; 10:195-203. [PMID: 37662670 PMCID: PMC10468694 DOI: 10.15698/mic2023.09.804] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023]
Abstract
In yeast, Elongator-dependent tRNA modifications are regulated by the Kti11•Kti13 dimer and hijacked for cell killing by zymocin, a tRNase ribotoxin. Kti11 (alias Dph3) also controls modification of elongation factor 2 (EF2) with diphthamide, the target for lethal ADP-ribosylation by diphtheria toxin (DT). Diphthamide formation on EF2 involves four biosynthetic steps encoded by the DPH1-DPH7 network and an ill-defined KTI13 function. On further examining the latter gene in yeast, we found that kti13Δ null-mutants maintain unmodified EF2 able to escape ADP-ribosylation by DT and to survive EF2 inhibition by sordarin, a diphthamide-dependent antifungal. Consistently, mass spectrometry shows kti13Δ cells are blocked in proper formation of amino-carboxyl-propyl-EF2, the first diphthamide pathway intermediate. Thus, apart from their common function in tRNA modification, both Kti11/Dph3 and Kti13 share roles in the initiation step of EF2 modification. We suggest an alias KTI13/DPH8 nomenclature indicating dual-functionality analogous to KTI11/DPH3.
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Affiliation(s)
- Meike Arend
- Institute of Biology, Division of Microbiology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Koray Ütkür
- Institute of Biology, Division of Microbiology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Harmen Hawer
- Institute of Biology, Division of Microbiology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Klaus Mayer
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center München, Nonnenwald 2, 82377 Penzberg, Germany
| | - Namit Ranjan
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Lorenz Adrian
- Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - Ulrich Brinkmann
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center München, Nonnenwald 2, 82377 Penzberg, Germany
| | - Raffael Schaffrath
- Institute of Biology, Division of Microbiology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
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5
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Ütkür K, Mayer K, Khan M, Manivannan T, Schaffrath R, Brinkmann U. DPH1 and DPH2 variants that confer susceptibility to diphthamide deficiency syndrome in human cells and yeast models. Dis Model Mech 2023; 16:dmm050207. [PMID: 37675463 PMCID: PMC10538292 DOI: 10.1242/dmm.050207] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/21/2023] [Indexed: 09/08/2023] Open
Abstract
The autosomal-recessive diphthamide deficiency syndrome presents as intellectual disability with developmental abnormalities, seizures, craniofacial and additional morphological phenotypes. It is caused by reduced activity of proteins that synthesize diphthamide on human translation elongation factor 2. Diphthamide synthesis requires seven proteins (DPH1-DPH7), with clinical deficiency described for DPH1, DPH2 and DPH5. A limited set of variant alleles from syndromic patients has been functionally analyzed, but databases (gnomAD) list additional so far uncharacterized variants in human DPH1 and DPH2. Because DPH enzymes are conserved among eukaryotes, their functionality can be assessed in yeast and mammalian cells. Our experimental assessment of known and uncharacterized DPH1 and DPH2 missense alleles showed that six variants are tolerated despite inter-species conservation. Ten additional human DPH1 (G113R, A114T, H132P, H132R, S136R, C137F, L138P, Y152C, S221P, H240R) and two DPH2 (H105P, C341Y) variants showed reduced functionality and hence are deficiency-susceptibility alleles. Some variants locate close to the active enzyme center and may affect catalysis, while others may impact on enzyme activation. In sum, our study has identified functionally compromised alleles of DPH1 and DPH2 genes that likely cause diphthamide deficiency syndrome.
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Affiliation(s)
- Koray Ütkür
- Institut für Biologie,Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany
| | - Klaus Mayer
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany
| | - Maliha Khan
- Institut für Biologie,Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany
| | - Thirishika Manivannan
- Institut für Biologie,Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany
| | - Raffael Schaffrath
- Institut für Biologie,Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany
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Dou X, Sun Q, Xu G, Liu Y, Zhang C, Wang B, Lu Y, Guo Z, Su L, Huo T, Zhao X, Wang C, Yu Z, Song S, Zhang L, Liu Z, Lai L, Jiao N. Discovery of 2-(furan-2-ylmethylene)hydrazine-1-carbothioamide derivatives as novel inhibitors of SARS-CoV-2 main protease. Eur J Med Chem 2022; 238:114508. [PMID: 35688005 PMCID: PMC9162962 DOI: 10.1016/j.ejmech.2022.114508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 11/30/2022]
Abstract
The COVID-19 posed a serious threat to human life and health, and SARS-CoV-2 Mpro has been considered as an attractive drug target for the treatment of COVID-19. Herein, we report 2-(furan-2-ylmethylene)hydrazine-1-carbothioamide derivatives as novel inhibitors of SARS-CoV-2 Mpro developed by in-house library screening and biological evaluation. Similarity search led to the identification of compound F8–S43 with the enzymatic IC50 value of 10.76 μM. Further structure-based drug design and synthetic optimization uncovered compounds F8–B6 and F8–B22 as novel non-peptidomimetic inhibitors of Mpro with IC50 values of 1.57 μM and 1.55 μM, respectively. Moreover, enzymatic kinetic assay and mass spectrometry demonstrated that F8–B6 was a reversible covalent inhibitor of Mpro. Besides, F8–B6 showed low cytotoxicity with CC50 values of more than 100 μM in Vero and MDCK cells. Overall, these novel SARS-CoV-2 Mpro non-peptidomimetic inhibitors provide a useful starting point for further structural optimization.
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Affiliation(s)
- Xiaodong Dou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Qi Sun
- BNLMS, Peking-Tsinghua Center for Life Sciences at College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Guofeng Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Yameng Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Caifang Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Bingding Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Yangbin Lu
- BNLMS, Peking-Tsinghua Center for Life Sciences at College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Zheng Guo
- BNLMS, Peking-Tsinghua Center for Life Sciences at College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Lingyu Su
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Tongyu Huo
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Xinyi Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Chen Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Zhongtian Yu
- BNLMS, Peking-Tsinghua Center for Life Sciences at College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Song Song
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Zhenming Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Luhua Lai
- BNLMS, Peking-Tsinghua Center for Life Sciences at College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China; Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
| | - Ning Jiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.
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7
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Zhang H, Quintana J, Ütkür K, Adrian L, Hawer H, Mayer K, Gong X, Castanedo L, Schulten A, Janina N, Peters M, Wirtz M, Brinkmann U, Schaffrath R, Krämer U. Translational fidelity and growth of Arabidopsis require stress-sensitive diphthamide biosynthesis. Nat Commun 2022; 13:4009. [PMID: 35817801 PMCID: PMC9273596 DOI: 10.1038/s41467-022-31712-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/30/2022] [Indexed: 11/09/2022] Open
Abstract
Diphthamide, a post-translationally modified histidine residue of eukaryotic TRANSLATION ELONGATION FACTOR2 (eEF2), is the human host cell-sensitizing target of diphtheria toxin. Diphthamide biosynthesis depends on the 4Fe-4S-cluster protein Dph1 catalyzing the first committed step, as well as Dph2 to Dph7, in yeast and mammals. Here we show that diphthamide modification of eEF2 is conserved in Arabidopsis thaliana and requires AtDPH1. Ribosomal -1 frameshifting-error rates are increased in Arabidopsis dph1 mutants, similar to yeast and mice. Compared to the wild type, shorter roots and smaller rosettes of dph1 mutants result from fewer formed cells. TARGET OF RAPAMYCIN (TOR) kinase activity is attenuated, and autophagy is activated, in dph1 mutants. Under abiotic stress diphthamide-unmodified eEF2 accumulates in wild-type seedlings, most strongly upon heavy metal excess, which is conserved in human cells. In summary, our results suggest that diphthamide contributes to the functionality of the translational machinery monitored by plants to regulate growth.
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Affiliation(s)
- Hongliang Zhang
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitaetsstrasse 150, Box 44 ND3/30, 44801, Bochum, Germany
| | - Julia Quintana
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitaetsstrasse 150, Box 44 ND3/30, 44801, Bochum, Germany
| | - Koray Ütkür
- Microbiology, Institute for Biology, University of Kassel, 34132, Kassel, Germany
| | - Lorenz Adrian
- Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, 13355, Berlin, Germany
| | - Harmen Hawer
- Microbiology, Institute for Biology, University of Kassel, 34132, Kassel, Germany
| | - Klaus Mayer
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Munich, 82377, Penzberg, Germany
| | - Xiaodi Gong
- Centre for Organismal Studies (COS), University of Heidelberg, 69120, Heidelberg, Germany
| | - Leonardo Castanedo
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitaetsstrasse 150, Box 44 ND3/30, 44801, Bochum, Germany
| | - Anna Schulten
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitaetsstrasse 150, Box 44 ND3/30, 44801, Bochum, Germany
| | - Nadežda Janina
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitaetsstrasse 150, Box 44 ND3/30, 44801, Bochum, Germany
| | - Marcus Peters
- Molecular Immunology, Medical Faculty, Ruhr University Bochum, 44801, Bochum, Germany
| | - Markus Wirtz
- Centre for Organismal Studies (COS), University of Heidelberg, 69120, Heidelberg, Germany
| | - Ulrich Brinkmann
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Munich, 82377, Penzberg, Germany
| | - Raffael Schaffrath
- Microbiology, Institute for Biology, University of Kassel, 34132, Kassel, Germany
| | - Ute Krämer
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitaetsstrasse 150, Box 44 ND3/30, 44801, Bochum, Germany.
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8
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Iron–sulfur clusters as inhibitors and catalysts of viral replication. Nat Chem 2022; 14:253-266. [DOI: 10.1038/s41557-021-00882-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/15/2021] [Indexed: 12/11/2022]
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9
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Zhang Y, Su D, Dzikovski B, Majer SH, Coleman R, Chandrasekaran S, Fenwick MK, Crane BR, Lancaster KM, Freed JH, Lin H. Dph3 Enables Aerobic Diphthamide Biosynthesis by Donating One Iron Atom to Transform a [3Fe-4S] to a [4Fe-4S] Cluster in Dph1-Dph2. J Am Chem Soc 2021; 143:9314-9319. [PMID: 34154323 PMCID: PMC8251694 DOI: 10.1021/jacs.1c03956] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
All radical S-adenosylmethionine (radical-SAM) enzymes, including the noncanonical radical-SAM enzyme diphthamide biosynthetic enzyme Dph1-Dph2, require at least one [4Fe-4S](Cys)3 cluster for activity. It is well-known in the radical-SAM enzyme community that the [4Fe-4S](Cys)3 cluster is extremely air-sensitive and requires strict anaerobic conditions to reconstitute activity in vitro. Thus, how such enzymes function in vivo in the presence of oxygen in aerobic organisms is an interesting question. Working on yeast Dph1-Dph2, we found that consistent with the known oxygen sensitivity, the [4Fe-4S] cluster is easily degraded into a [3Fe-4S] cluster. Remarkably, the small iron-containing protein Dph3 donates one Fe atom to convert the [3Fe-4S] cluster in Dph1-Dph2 to a functional [4Fe-4S] cluster during the radical-SAM enzyme catalytic cycle. This mechanism to maintain radical-SAM enzyme activity in aerobic environments is likely general, and Dph3-like proteins may exist to keep other radical-SAM enzymes functional in aerobic environments.
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Affiliation(s)
- Yugang Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Dan Su
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Boris Dzikovski
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Sean H Majer
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Rachael Coleman
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Siddarth Chandrasekaran
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Michael K Fenwick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States.,Howard Hughes Medical Institute, Cornell University, Ithaca, New York 14853, United States
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10
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Iron in Translation: From the Beginning to the End. Microorganisms 2021; 9:microorganisms9051058. [PMID: 34068342 PMCID: PMC8153317 DOI: 10.3390/microorganisms9051058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 12/16/2022] Open
Abstract
Iron is an essential element for all eukaryotes, since it acts as a cofactor for many enzymes involved in basic cellular functions, including translation. While the mammalian iron-regulatory protein/iron-responsive element (IRP/IRE) system arose as one of the first examples of translational regulation in higher eukaryotes, little is known about the contribution of iron itself to the different stages of eukaryotic translation. In the yeast Saccharomyces cerevisiae, iron deficiency provokes a global impairment of translation at the initiation step, which is mediated by the Gcn2-eIF2α pathway, while the post-transcriptional regulator Cth2 specifically represses the translation of a subgroup of iron-related transcripts. In addition, several steps of the translation process depend on iron-containing enzymes, including particular modifications of translation elongation factors and transfer RNAs (tRNAs), and translation termination by the ATP-binding cassette family member Rli1 (ABCE1 in humans) and the prolyl hydroxylase Tpa1. The influence of these modifications and their correlation with codon bias in the dynamic control of protein biosynthesis, mainly in response to stress, is emerging as an interesting focus of research. Taking S. cerevisiae as a model, we hereby discuss the relevance of iron in the control of global and specific translation steps.
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11
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Hou L, Xie J, Wu Y, Wang J, Duan A, Ao Y, Liu X, Yu X, Yan H, Perreault J, Li S. Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics. BMC Genomics 2021; 22:164. [PMID: 33750298 PMCID: PMC7941889 DOI: 10.1186/s12864-021-07474-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/24/2021] [Indexed: 11/12/2022] Open
Abstract
Background Only 1.5% of the human genome encodes proteins, while large part of the remaining encodes noncoding RNAs (ncRNA). Many ncRNAs form structures and perform many important functions. Accurately identifying structured ncRNAs in the human genome and discovering their biological functions remain a major challenge. Results Here, we have established a pipeline (CM-line) with the following features for analyzing the large genomes of humans and other animals. First, we selected species with larger genetic distances to facilitate the discovery of covariations and compatible mutations. Second, we used CMfinder, which can generate useful alignments even with low sequence conservation. Third, we removed repetitive sequences and known structured ncRNAs to reduce the workload of CMfinder. Fourth, we used Infernal to find more representatives and refine the structure. We reported 11 classes of structured ncRNA candidates with significant covariations in humans. Functional analysis showed that these ncRNAs may have variable functions. Some may regulate circadian clock genes through poly (A) signals (PAS); some may regulate the elongation factor (EEF1A) and the T-cell receptor signaling pathway by cooperating with RNA binding proteins. Conclusions By searching for important features of RNA structure from large genomes, the CM-line has revealed the existence of a variety of novel structured ncRNAs. Functional analysis suggests that some newly discovered ncRNA motifs may have biological functions. The pipeline we have established for the discovery of structured ncRNAs and the identification of their functions can also be applied to analyze other large genomes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07474-9.
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Affiliation(s)
- Lijuan Hou
- Medical School, Molecular Medicine Engineering and Research Center of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Jin Xie
- Medical School, Molecular Medicine Engineering and Research Center of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Yaoyao Wu
- Medical School, Molecular Medicine Engineering and Research Center of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Jiaojiao Wang
- Medical School, Molecular Medicine Engineering and Research Center of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Anqi Duan
- Medical School, Molecular Medicine Engineering and Research Center of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Yaqi Ao
- Medical School, Molecular Medicine Engineering and Research Center of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Xuejiao Liu
- Medical School, Molecular Medicine Engineering and Research Center of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Xinmei Yu
- Medical School, Molecular Medicine Engineering and Research Center of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Hui Yan
- Medical School, Molecular Medicine Engineering and Research Center of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Jonathan Perreault
- INRS - Institut Armand-Frappier, 531 boul des Prairies, Laval, Québec, H7V1B7, Canada
| | - Sanshu Li
- Medical School, Molecular Medicine Engineering and Research Center of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China.
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Hawer H, Mendelsohn BA, Mayer K, Kung A, Malhotra A, Tuupanen S, Schleit J, Brinkmann U, Schaffrath R. Diphthamide-deficiency syndrome: a novel human developmental disorder and ribosomopathy. Eur J Hum Genet 2020; 28:1497-1508. [PMID: 32576952 PMCID: PMC7575589 DOI: 10.1038/s41431-020-0668-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/06/2020] [Accepted: 05/28/2020] [Indexed: 02/06/2023] Open
Abstract
We describe a novel type of ribosomopathy that is defined by deficiency in diphthamidylation of translation elongation factor 2. The ribosomopathy was identified by correlating phenotypes and biochemical properties of previously described patients with diphthamide biosynthesis gene 1 (DPH1) deficiencies with a new patient that carried inactivating mutations in both alleles of the human diphthamide biosynthesis gene 2 (DPH2). The human DPH1 syndrome is an autosomal recessive disorder associated with developmental delay, abnormal head circumference (microcephaly or macrocephaly), short stature, and congenital heart disease. It is defined by variants with reduced functionality of the DPH1 gene observed so far predominantly in consanguineous homozygous patients carrying identical mutant alleles of DPH1. Here we report a child with a very similar phenotype carrying biallelic variants of the human DPH2. The gene products DPH1 and DPH2 are components of a heterodimeric enzyme complex that mediates the first step of the posttranslational diphthamide modification on the nonredundant eukaryotic translation elongation factor 2 (eEF2). Diphthamide deficiency was shown to reduce the accuracy of ribosomal protein biosynthesis. Both DPH2 variants described here severely impair diphthamide biosynthesis as demonstrated in human and yeast cells. This is the first report of a patient carrying compound heterozygous DPH2 loss-of-function variants with a DPH1 syndrome-like phenotype and implicates diphthamide deficiency as the root cause of this patient's clinical phenotype as well as of DPH1-syndrome. These findings define "diphthamide-deficiency syndrome" as a special ribosomopathy due to reduced functionality of components of the cellular machinery for eEF2-diphthamide synthesis.
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Affiliation(s)
- Harmen Hawer
- Fachgebiet Mikrobiologie, Institut für Biologie, Universität Kassel, D-34132, Kassel, Hessen, Germany
| | | | - Klaus Mayer
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Munich, D-82377, Penzberg, Bavaria, Germany
| | - Ann Kung
- Kaiser Permanente Oakland Medical Center, Oakland, CA, 94611, USA
| | - Amit Malhotra
- Kaiser Permanente Oakland Medical Center, Oakland, CA, 94611, USA
| | - Sari Tuupanen
- Blueprint Genetics Oy, Keilaranta 16 A-B, 02150, Espoo, Finland
| | | | - Ulrich Brinkmann
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Munich, D-82377, Penzberg, Bavaria, Germany.
| | - Raffael Schaffrath
- Fachgebiet Mikrobiologie, Institut für Biologie, Universität Kassel, D-34132, Kassel, Hessen, Germany
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13
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Que L. In celebration of Joan Broderick, 2019 recipient of the Alfred Bader Award in Bioorganic or Bioinorganic Chemistry. J Biol Inorg Chem 2019. [DOI: 10.1007/s00775-019-01715-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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