1
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Verma AK, Sharma P, Islam Z, Biswal AK, Tak Y, Sahi C. Arabidopsis Dph4 is an Hsp70 Cochaperone with Iron-Binding Properties. ACS OMEGA 2024; 9:37650-37661. [PMID: 39281955 PMCID: PMC11391554 DOI: 10.1021/acsomega.4c01776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 07/06/2024] [Accepted: 07/30/2024] [Indexed: 09/18/2024]
Abstract
J-domain proteins (JDPs) are obligate cochaperones of Hsp70s with a wide range of functions in protein homeostasis. Although the J-domain is required for the stimulation of Hsp70s ATPase activity, the functional specificity of JDPs is governed by domains or regions other than the J-domain. Jjj3/Dph4, a class III JDP, is required for diphthamide (DPH) biosynthesis in eukaryotes, including yeast and mammals. Dph4 has a conserved N-terminal J-domain and an uncharacterized C-terminal domain containing a signature CSL zinc finger motif. Previously, we showed that the Dph4 ortholog in Arabidopsis thaliana (atDjC13/AtJjj3/AtDph4) could restore DPH biosynthesis in yeast jjj3Δ mutant in a J-domain-dependent manner. Here, we characterize the C-terminal CSL motif of AtDph4 using yeast genetic and biochemical approaches. The CSL motif of AtDph4 is essential for DPH biosynthesis, and like human Dph4, AtDph4 showed distinct iron-binding activity, which is not present in its yeast counterpart. ScDph4 and AtDph4 proteins exhibit distinct iron-binding capabilities, as evidenced by UV-vis spectrophotometry, SEM-EDS (energy-dispersive spectroscopy function on the scanning electron microscope) and electron paramagnetic resonance (EPR) spectra analyses. Collectively, our data suggests that beyond their role as an Hsp70 cochaperone, Dph4 homologues in complex eukaryotes may have iron-binding abilities, indicating a potential role in iron-sulfur cluster assembly and iron homeostasis.
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Affiliation(s)
- Amit Kumar Verma
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas 75390-9096, United States
| | - Priya Sharma
- Department of Botany, Faculty of Science, University of Delhi, Delhi 110007, India
| | - Zeyaul Islam
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
- Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, PO Box 34110 Doha, Qatar
| | - Anup Kumar Biswal
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
| | - Yogesh Tak
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brian Institute, UT Southwestern Medical Center, Dallas, Texas 75390-9096, United States
| | - Chandan Sahi
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
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2
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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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3
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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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4
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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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5
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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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6
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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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7
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Huang R, Zhi N, Yu L, Li Y, Wu X, He J, Zhu H, Qiao J, Liu X, Tian C, Wang J, Dong M. Genetically Encoded Photosensitizer Protein Reduces Iron–Sulfur Clusters of Radical SAM Enzymes. ACS Catal 2023. [DOI: 10.1021/acscatal.2c05143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Rongrong Huang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Ning Zhi
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Lu Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Yaoyang Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xiangyu Wu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jiale He
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Hongji Zhu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jianjun Qiao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xiaohong Liu
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Changlin Tian
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- The First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Joint Center for Biological Analytical Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jiangyun Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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8
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Lindahl PA, Vali SW. Mössbauer-based molecular-level decomposition of the Saccharomyces cerevisiae ironome, and preliminary characterization of isolated nuclei. Metallomics 2022; 14:mfac080. [PMID: 36214417 PMCID: PMC9624242 DOI: 10.1093/mtomcs/mfac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/23/2022] [Indexed: 11/25/2022]
Abstract
One hundred proteins in Saccharomyces cerevisiae are known to contain iron. These proteins are found mainly in mitochondria, cytosol, nuclei, endoplasmic reticula, and vacuoles. Cells also contain non-proteinaceous low-molecular-mass labile iron pools (LFePs). How each molecular iron species interacts on the cellular or systems' level is underdeveloped as doing so would require considering the entire iron content of the cell-the ironome. In this paper, Mössbauer (MB) spectroscopy was used to probe the ironome of yeast. MB spectra of whole cells and isolated organelles were predicted by summing the spectral contribution of each iron-containing species in the cell. Simulations required input from published proteomics and microscopy data, as well as from previous spectroscopic and redox characterization of individual iron-containing proteins. Composite simulations were compared to experimentally determined spectra. Simulated MB spectra of non-proteinaceous iron pools in the cell were assumed to account for major differences between simulated and experimental spectra of whole cells and isolated mitochondria and vacuoles. Nuclei were predicted to contain ∼30 μM iron, mostly in the form of [Fe4S4] clusters. This was experimentally confirmed by isolating nuclei from 57Fe-enriched cells and obtaining the first MB spectra of the organelle. This study provides the first semi-quantitative estimate of all concentrations of iron-containing proteins and non-proteinaceous species in yeast, as well as a novel approach to spectroscopically characterizing LFePs.
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Affiliation(s)
- Paul A Lindahl
- Department of Chemistry, Texas A&M University, College Station, TX,USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station TX,USA
| | - Shaik Waseem Vali
- Department of Chemistry, Texas A&M University, College Station, TX,USA
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9
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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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10
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Yokoyama K, Li D, Pang H. Resolving the Multidecade-Long Mystery in MoaA Radical SAM Enzyme Reveals New Opportunities to Tackle Human Health Problems. ACS BIO & MED CHEM AU 2022; 2:94-108. [PMID: 35480226 PMCID: PMC9026282 DOI: 10.1021/acsbiomedchemau.1c00046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 01/31/2023]
Abstract
![]()
MoaA is one of the
most conserved radical S-adenosyl-l-methionine
(SAM) enzymes, and is found in most organisms in
all three kingdoms of life. MoaA contributes to the biosynthesis of
molybdenum cofactor (Moco), a redox enzyme cofactor used in various
enzymes such as purine and sulfur catabolism in humans and anaerobic
respiration in bacteria. Unlike many other cofactors, in most organisms,
Moco cannot be taken up as a nutrient and requires de novo biosynthesis.
Consequently, Moco biosynthesis has been linked to several human health
problems, such as human Moco deficiency disease and bacterial infections.
Despite
the medical and biological significance, the biosynthetic mechanism
of Moco’s characteristic pyranopterin structure remained elusive
for more than two decades. This transformation requires the actions
of the MoaA radical SAM enzyme and another protein, MoaC. Recently,
MoaA and MoaC functions were elucidated as a radical SAM GTP 3′,8-cyclase
and cyclic pyranopterin monophosphate (cPMP) synthase, respectively.
This finding resolved the key mystery in the field and revealed new
opportunities in studying the enzymology and chemical biology of MoaA
and MoaC to elucidate novel mechanisms in enzyme catalysis or to address
unsolved questions in Moco-related human health problems. Here, we
summarize the recent progress in the functional and mechanistic studies
of MoaA and MoaC and discuss the field’s future directions.
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Affiliation(s)
- Kenichi Yokoyama
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States.,Department of Chemistry, Duke University, Durham, North Carolina 27710, United States
| | - Di Li
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Haoran Pang
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
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11
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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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12
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The B 12-independent glycerol dehydratase activating enzyme from Clostridium butyricum cleaves SAM to produce 5'-deoxyadenosine and not 5'-deoxy-5'-(methylthio)adenosine. J Inorg Biochem 2022; 227:111662. [PMID: 34847521 PMCID: PMC8889718 DOI: 10.1016/j.jinorgbio.2021.111662] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 11/04/2021] [Accepted: 11/04/2021] [Indexed: 02/03/2023]
Abstract
Glycerol dehydratase activating enzyme (GD-AE) is a radical S-adenosyl-l-methionine (SAM) enzyme that installs a catalytically essential amino acid backbone radical onto glycerol dehydratase in bacteria under anaerobic conditions. Although GD-AE is closely homologous to other radical SAM activases that have been shown to cleave the S-C(5') bond of SAM to produce 5'-deoxyadenosine (5'-dAdoH) and methionine, GD-AE from Clostridium butyricum has been reported to instead cleave the S-C(γ) bond of SAM to yield 5'-deoxy-5'-(methylthio)adenosine (MTA). Here we re-investigate the SAM cleavage reaction catalyzed by GD-AE and show that it produces the widely observed 5'-dAdoH, and not the less conventional product MTA.
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13
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Xu B, Liu L, Song G. Functions and Regulation of Translation Elongation Factors. Front Mol Biosci 2022; 8:816398. [PMID: 35127825 PMCID: PMC8807479 DOI: 10.3389/fmolb.2021.816398] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/20/2021] [Indexed: 12/18/2022] Open
Abstract
Translation elongation is a key step of protein synthesis, during which the nascent polypeptide chain extends by one amino acid residue during one elongation cycle. More and more data revealed that the elongation is a key regulatory node for translational control in health and disease. During elongation, elongation factor Tu (EF-Tu, eEF1A in eukaryotes) is used to deliver aminoacyl-tRNA (aa-tRNA) to the A-site of the ribosome, and elongation factor G (EF-G, EF2 in eukaryotes and archaea) is used to facilitate the translocation of the tRNA2-mRNA complex on the ribosome. Other elongation factors, such as EF-Ts/eEF1B, EF-P/eIF5A, EF4, eEF3, SelB/EFsec, TetO/Tet(M), RelA and BipA, have been found to affect the overall rate of elongation. Here, we made a systematic review on the canonical and non-canonical functions and regulation of these elongation factors. In particular, we discussed the close link between translational factors and human diseases, and clarified how post-translational modifications control the activity of translational factors in tumors.
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Affiliation(s)
- Benjin Xu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
- *Correspondence: Benjin Xu, ; Guangtao Song,
| | - Ling Liu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
| | - Guangtao Song
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Benjin Xu, ; Guangtao Song,
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14
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Zhi N, Zhu H, Qiao J, Dong M. Recent progress in radical SAM enzymes: New reactions and mechanisms. CHINESE SCIENCE BULLETIN-CHINESE 2021. [DOI: 10.1360/tb-2021-1067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Feng J, Shaik S, Wang B. Spin‐Regulated Electron Transfer and Exchange‐Enhanced Reactivity in Fe
4
S
4
‐Mediated Redox Reaction of the Dph2 Enzyme During the Biosynthesis of Diphthamide. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jianqiang Feng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Sason Shaik
- Institute of Chemistry The Hebrew University of Jerusalem Jerusalem 9190401 Israel
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
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16
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Feng J, Shaik S, Wang B. Spin-Regulated Electron Transfer and Exchange-Enhanced Reactivity in Fe 4 S 4 -Mediated Redox Reaction of the Dph2 Enzyme During the Biosynthesis of Diphthamide. Angew Chem Int Ed Engl 2021; 60:20430-20436. [PMID: 34302311 DOI: 10.1002/anie.202107008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Indexed: 11/06/2022]
Abstract
The [4Fe-4S]-dependent radical S-adenosylmethionine (SAM) proteins is one of large families of redox enzymes that are able to carry a panoply of challenging transformations. Despite the extensive studies of structure-function relationships of radical SAM (RS) enzymes, the electronic state-dependent reactivity of the [4Fe-4S] cluster in these enzymes remains elusive. Using combined MD simulations and QM/MM calculations, we deciphered the electronic state-dependent reactivity of the [4Fe-4S] cluster in Dph2, a key enzyme involved in the biosynthesis of diphthamide. Our calculations show that the reductive cleavage of the S-C(γ) bond is highly dependent on the electronic structure of [4Fe-4S]. Interestingly, the six electronic states can be classified into a low-energy and a high-energy groups, which are correlated with the net spin of Fe4 atom ligated to SAM. Due to the driving force of Fe4-C(γ) bonding, the net spin on the Fe4 moiety dictate the shift of the opposite spin electron from the Fe1-Fe2-Fe3 block to SAM. Such spin-regulated electron transfer results in the exchange-enhanced reactivity in the lower-energy group compared with those in the higher-energy group. This reactivity principle provides fundamental mechanistic insights into reactivities of [4Fe-4S] cluster in RS enzymes.
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Affiliation(s)
- Jianqiang Feng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
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17
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Abstract
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TYW1 is a radical S-adenosyl-l-methionine
(SAM) enzyme that catalyzes the condensation of pyruvate and N-methylguanosine-containing tRNAPhe, forming
4-demethylwyosine-containing tRNAPhe. Homologues of TYW1
are found in both archaea and eukarya; archaeal homologues consist
of a single domain, while eukaryal homologues contain a flavin binding
domain in addition to the radical SAM domain shared with archaeal
homologues. In this study, TYW1 from Saccharomyces cerevisiae (ScTYW1) was heterologously expressed in Escherichia coli and purified to homogeneity. ScTYW1 is purified with 0.54 ± 0.07 and 4.2 ± 1.9 equiv of
flavin mononucleotide (FMN) and iron, respectively, per mole of protein,
suggesting the protein is ∼50% replete with Fe–S clusters
and FMN. While both NADPH and NADH are sufficient for activity, significantly
more product is observed when used in combination with flavin nucleotides. ScTYW1 is the first example of a radical SAM flavoenzyme
that is active with NAD(P)H alone.
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Affiliation(s)
- Anthony P Young
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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18
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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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19
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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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20
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Przybyla-Toscano J, Boussardon C, Law SR, Rouhier N, Keech O. Gene atlas of iron-containing proteins in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:258-274. [PMID: 33423341 DOI: 10.1111/tpj.15154] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 12/17/2020] [Accepted: 01/04/2021] [Indexed: 05/27/2023]
Abstract
Iron (Fe) is an essential element for the development and physiology of plants, owing to its presence in numerous proteins involved in central biological processes. Here, we established an exhaustive, manually curated inventory of genes encoding Fe-containing proteins in Arabidopsis thaliana, and summarized their subcellular localization, spatiotemporal expression and evolutionary age. We have currently identified 1068 genes encoding potential Fe-containing proteins, including 204 iron-sulfur (Fe-S) proteins, 446 haem proteins and 330 non-Fe-S/non-haem Fe proteins (updates of this atlas are available at https://conf.arabidopsis.org/display/COM/Atlas+of+Fe+containing+proteins). A fourth class, containing 88 genes for which iron binding is uncertain, is indexed as 'unclear'. The proteins are distributed in diverse subcellular compartments with strong differences per category. Interestingly, analysis of the gene age index showed that most genes were acquired early in plant evolutionary history and have progressively gained regulatory elements, to support the complex organ-specific and development-specific functions necessitated by the emergence of terrestrial plants. With this gene atlas, we provide a valuable and updateable tool for the research community that supports the characterization of the molecular actors and mechanisms important for Fe metabolism in plants. This will also help in selecting relevant targets for breeding or biotechnological approaches aiming at Fe biofortification in crops.
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Affiliation(s)
| | - Clément Boussardon
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, S-90187, Sweden
| | - Simon R Law
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, S-90187, Sweden
| | | | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, S-90187, Sweden
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21
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Zhao C, Li Y, Wang C, Chen H. Mechanistic Dichotomy in the Activation of SAM by Radical SAM Enzymes: QM/MM Modeling Deciphers the Determinant. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03384] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Chengxin Zhao
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yao Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
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22
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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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23
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Zrzavy T, Leutmezer F, Kristoferitsch W, Kornek B, Schneider C, Rommer P, Berger T, Zimprich A. Exome-Sequence Analyses of Four Multi-Incident Multiple Sclerosis Families. Genes (Basel) 2020; 11:E988. [PMID: 32854198 PMCID: PMC7563748 DOI: 10.3390/genes11090988] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/14/2020] [Accepted: 08/19/2020] [Indexed: 11/16/2022] Open
Abstract
Multiple sclerosis (MS) is an inflammatory demyelinating disease of the Central Nervous System (CNS). Currently, it is estimated that 30-40% of the phenotypic variability of MS can be explained by genetic factors. However, low susceptibility variants identified through Genome Wide Association Study (GWAS) were calculated to explain about 50% of the heritability. Whether familial high-risk variants also contribute to heritability is a subject of controversy. In the last few years, several familial variants have been nominated, but none of them have been unequivocally confirmed. One reason for this may be that genetic heterogeneity and reduced penetrance are hindering detection. Sequencing a large number of MS families is needed to answer this question. In this study, we performed whole exome sequencing in four multi-case families, of which at least three affected individuals per family were analyzed. We identified a total of 138 rare variants segregating with disease in each of the families. Although no single variant showed convincing evidence for disease causation, some genes seemed particularly interesting based on their biological function. The main aim of this study was to provide a complete list of all rare segregating variants to provide the possibility for other researchers to cross-check familial candidate genes in an unbiased manner.
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Affiliation(s)
- Tobias Zrzavy
- Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria; (T.Z.); (F.L.); (B.K.); (P.R.); (T.B.)
| | - Fritz Leutmezer
- Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria; (T.Z.); (F.L.); (B.K.); (P.R.); (T.B.)
| | - Wolfgang Kristoferitsch
- Karl Landsteiner Institute for Neuroimmunological and Neurodegenerative Disorders, 1090 Vienna, Austria;
| | - Barbara Kornek
- Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria; (T.Z.); (F.L.); (B.K.); (P.R.); (T.B.)
| | - Christine Schneider
- Department of Neurology, University Medical Center Augsburg, 86156 Augsburg, Germany;
| | - Paulus Rommer
- Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria; (T.Z.); (F.L.); (B.K.); (P.R.); (T.B.)
| | - Thomas Berger
- Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria; (T.Z.); (F.L.); (B.K.); (P.R.); (T.B.)
| | - Alexander Zimprich
- Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria; (T.Z.); (F.L.); (B.K.); (P.R.); (T.B.)
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24
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Abstract
Mitochondria are essential in most eukaryotes and are involved in numerous biological functions including ATP production, cofactor biosyntheses, apoptosis, lipid synthesis, and steroid metabolism. Work over the past two decades has uncovered the biogenesis of cellular iron-sulfur (Fe/S) proteins as the essential and minimal function of mitochondria. This process is catalyzed by the bacteria-derived iron-sulfur cluster assembly (ISC) machinery and has been dissected into three major steps: de novo synthesis of a [2Fe-2S] cluster on a scaffold protein; Hsp70 chaperone-mediated trafficking of the cluster and insertion into [2Fe-2S] target apoproteins; and catalytic conversion of the [2Fe-2S] into a [4Fe-4S] cluster and subsequent insertion into recipient apoproteins. ISC components of the first two steps are also required for biogenesis of numerous essential cytosolic and nuclear Fe/S proteins, explaining the essentiality of mitochondria. This review summarizes the molecular mechanisms underlying the ISC protein-mediated maturation of mitochondrial Fe/S proteins and the importance for human disease.
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Affiliation(s)
- Roland Lill
- Institut für Zytobiologie, Philipps-Universität Marburg, 35032 Marburg, Germany;
- SYNMIKRO Zentrum für synthetische Mikrobiologie, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Sven-A Freibert
- Institut für Zytobiologie, Philipps-Universität Marburg, 35032 Marburg, Germany;
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25
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Coding and noncoding somatic mutations in candidate genes in basal cell carcinoma. Sci Rep 2020; 10:8005. [PMID: 32409749 PMCID: PMC7224188 DOI: 10.1038/s41598-020-65057-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 04/26/2020] [Indexed: 12/14/2022] Open
Abstract
Basal cell carcinoma (BCC) represents the most commonly diagnosed human cancer among persons of European ancestry with etiology mainly attributed to sun-exposure. In this study we investigated mutations in coding and flanking regions of PTCH1 and TP53 and noncoding alterations in the TERT and DPH3 promoters in 191 BCC tumors. In addition, we measured CpG methylation within the TERT hypermethylated oncological region (THOR) and transcription levels of the reverse transcriptase subunit. We observed mutations in PTCH1 in 58.6% and TP53 in 31.4% of the tumors. Noncoding mutations in TERT and DPH3 promoters were detected in 59.2% and 38.2% of the tumors, respectively. We observed a statistically significant co-occurrence of mutations at the four investigated loci. While PTCH1 mutations tended to associate with decreased patient age at diagnosis; TP53 mutations were associated with light skin color and increased number of nevi; TERT and DPH3 promoter with history of cutaneous neoplasms in BCC patients. Increased reverse transcriptase subunit expression was observed in tumors with TERT promoter mutations and not with THOR methylation. Our study signifies, in addition to the protein altering mutations in the PTCH1 and TP53 genes, the importance of noncoding mutations in BCC, particularly functional alterations in the TERT promoter.
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26
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Dong M, Dando EE, Kotliar I, Su X, Dzikovski B, Freed JH, Lin H. The asymmetric function of Dph1-Dph2 heterodimer in diphthamide biosynthesis. J Biol Inorg Chem 2019; 24:777-782. [PMID: 31463593 DOI: 10.1007/s00775-019-01702-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/06/2019] [Indexed: 01/12/2023]
Abstract
Diphthamide, the target of diphtheria toxin, is a post-translationally modified histidine residue found in archaeal and eukaryotic translation elongation factor 2 (EF2). In the first step of diphthamide biosynthesis, a [4Fe-4S] cluster-containing radical SAM enzyme, Dph1-Dph2 heterodimer in eukaryotes or Dph2 homodimer in archaea, cleaves S-adenosylmethionine and transfers the 3-amino-3-carboxypropyl group to EF2. It was demonstrated previously that for the archaeal Dph2 homodimer, only one [4Fe-4S] cluster is necessary for the in vitro activity. Here, we demonstrate that for the eukaryotic Dph1-Dph2 heterodimer, the [4Fe-4S] cluster-binding cysteine residues in each subunit are required for diphthamide biosynthesis to occur in vivo. Furthermore, our in vitro reconstitution experiments with Dph1-Dph2 mutants suggested that the Dph1 cluster serves a catalytic role, while the Dph2 cluster facilitates the reduction of the Dph1 cluster by the physiological reducing system Dph3/Cbr1/NADH. Our results reveal the asymmetric functional roles of the Dph1-Dph2 heterodimer and may help to understand how the Fe-S clusters in radical SAM enzymes are reduced in biology.
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Affiliation(s)
- Min Dong
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Emily E Dando
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Ilana Kotliar
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Xiaoyang Su
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Boris Dzikovski
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY, 14853, USA.
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27
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Gumkowski JD, Martinie RJ, Corrigan PS, Pan J, Bauerle MR, Almarei M, Booker SJ, Silakov A, Krebs C, Boal AK. Analysis of RNA Methylation by Phylogenetically Diverse Cfr Radical S-Adenosylmethionine Enzymes Reveals an Iron-Binding Accessory Domain in a Clostridial Enzyme. Biochemistry 2019; 58:3169-3184. [PMID: 31246421 DOI: 10.1021/acs.biochem.9b00197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cfr is a radical S-adenosylmethionine (SAM) RNA methylase linked to multidrug antibiotic resistance in bacterial pathogens. It catalyzes a chemically challenging C-C bond-forming reaction to methylate C8 of A2503 (Escherichia coli numbering) of 23S rRNA during ribosome assembly. The cfr gene has been identified as a mobile genetic element in diverse bacteria and in the genome of select Bacillales and Clostridiales species. Despite the importance of Cfr, few representatives have been purified and characterized in vitro. Here we show that Cfr homologues from Bacillus amyloliquefaciens, Enterococcus faecalis, Paenibacillus lautus, and Clostridioides difficile act as C8 adenine RNA methylases in biochemical assays. C. difficile Cfr contains an additional Cys-rich C-terminal domain that binds a mononuclear Fe2+ ion in a rubredoxin-type Cys4 motif. The C-terminal domain can be truncated with minimal impact on C. difficile Cfr activity, but the rate of turnover is decreased upon disruption of the Fe2+-binding site by Zn2+ substitution or ligand mutation. These findings indicate an important purpose for the observed C-terminal iron in the native fusion protein. Bioinformatic analysis of the C. difficile Cfr Cys-rich domain shows that it is widespread (∼1400 homologues) as a stand-alone gene in pathogenic or commensal Bacilli and Clostridia, with >10% encoded adjacent to a predicted radical SAM RNA methylase. Although the domain is not essential for in vitro C. difficile Cfr activity, the genomic co-occurrence and high abundance in the human microbiome suggest a possible functional role for a specialized rubredoxin in certain radical SAM RNA methylases that are relevant to human health.
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Affiliation(s)
- James D Gumkowski
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Ryan J Martinie
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Patrick S Corrigan
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Juan Pan
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Matthew R Bauerle
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Mohamed Almarei
- Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Squire J Booker
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States.,Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States.,Howard Hughes Medical Institute , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Alexey Silakov
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Carsten Krebs
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States.,Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Amie K Boal
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States.,Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
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28
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Mateus-Seidl R, Stahl S, Dengl S, Birzele F, Herrmuth H, Mayer K, Niederfellner G, Liu XF, Pastan I, Brinkmann U. Interplay between reversible phosphorylation and irreversible ADP-ribosylation of eukaryotic translation elongation factor 2. Biol Chem 2019; 400:501-512. [PMID: 30218597 DOI: 10.1515/hsz-2018-0280] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/11/2018] [Indexed: 11/15/2022]
Abstract
The functionality of eukaryotic translation elongation factor 2 (eEF2) is modulated by phosphorylation, eEF2 is simultaneously the molecular target of ADP-ribosylating toxins. We analyzed the interplay between phosphorylation and diphthamide-dependent ADP-ribosylation. Phosphorylation does not require diphthamide, eEF2 without it still becomes phosphorylated. ADP-ribosylation not only modifies the H715 diphthamide but also inhibits phosphorylation of S595 located in proximity to H715, and stimulates phosphorylation of T56. S595 can be phosphorylated by CDK2 and CDK1 which affects EEF2K-mediated T56-phosphorylation. Thus, ADP-ribosylation and S595-phosphorylation by kinases occur within the same vicinity and both trigger T56-phosphorylation. Diphthamide is surface-accessible permitting access to ADP-ribosylating enzymes, the adjacent S595 side chain extends into the interior. This orientation is incompatible with phosphorylation, neither allowing kinase access nor phosphate attachment. S595 phosphorylation must therefore be accompanied by structural alterations affecting the interface to ADP-ribosylating toxins. In agreement with that, replacement of S595 with Ala, Glu or Asp prevents ADP-ribosylation. Phosphorylation (starvation) as well as ADP-ribosylation (toxins) inhibit protein synthesis, both affect the S595/H715 region of eEF2, both trigger T57-phosphorylation eliciting similar transcriptional responses. Phosphorylation is short lived while ADP-ribosylation is stable. Thus, phosphorylation of the S595/H715 'modifier region' triggers transient interruption of translation while ADP-ribosylation arrests irreversibly.
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Affiliation(s)
- Rita Mateus-Seidl
- Roche Pharma Research and Early Development, Discovery Oncology, Roche Innovation Center Munich, Nonnenwald 2, D-82377 Penzberg, FRG, Germany
| | - Sebastian Stahl
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, D-82377 Penzberg, FRG, Germany
| | - Stefan Dengl
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, D-82377 Penzberg, FRG, Germany
| | - Fabian Birzele
- Roche Pharma Research and Early Development, Pharmaceutical Sciences- Bioinformatics, Roche Innovation Center Basel, Grenzacherstr. 124, CH-4070 Basel, Germany
| | - Hedda Herrmuth
- Roche Pharma Research and Early Development, Discovery Oncology, Roche Innovation Center Munich, Nonnenwald 2, D-82377 Penzberg, FRG, Germany
| | - Klaus Mayer
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, D-82377 Penzberg, FRG, Germany
| | - Gerhard Niederfellner
- Roche Pharma Research and Early Development, Discovery Oncology, Roche Innovation Center Munich, Nonnenwald 2, D-82377 Penzberg, FRG, Germany
| | - Xiu-Fen Liu
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr, Bethesda, MD 20814, USA
| | - Ira Pastan
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr, Bethesda, MD 20814, USA
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, D-82377 Penzberg, FRG, Germany
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29
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Mayer K, Mundigl O, Kettenberger H, Birzele F, Stahl S, Pastan I, Brinkmann U. Diphthamide affects selenoprotein expression: Diphthamide deficiency reduces selenocysteine incorporation, decreases selenite sensitivity and pre-disposes to oxidative stress. Redox Biol 2019; 20:146-156. [PMID: 30312900 PMCID: PMC6180344 DOI: 10.1016/j.redox.2018.09.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/17/2018] [Accepted: 09/24/2018] [Indexed: 12/31/2022] Open
Abstract
The diphthamide modification of translation elongation factor 2 is highly conserved in eukaryotes and archaebacteria. Nevertheless, cells lacking diphthamide can carry out protein synthesis and are viable. We have analyzed the phenotypes of diphthamide deficient cells and found that diphthamide deficiency reduces selenocysteine incorporation into selenoproteins. Additional phenotypes resulting from diphthamide deficiency include altered tRNA-synthetase and selenoprotein transcript levels, hypersensitivity to oxidative stress and increased selenite tolerance. Diphthamide-eEF2 occupies the aminoacyl-tRNA translocation site at which UGA either stalls translation or decodes selenocysteine. Its position is in close proximity and mutually exclusive to the ribosomal binding site of release/recycling factor ABCE1, which harbors a redox-sensitive Fe-S cluster and, like diphthamide, is present in eukaryotes and archaea but not in eubacteria. Involvement of diphthamide in UGA-SECIS decoding may explain deregulated selenoprotein expression and as a consequence oxidative stress, NFkB activation and selenite tolerance in diphthamide deficient cells.
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Affiliation(s)
- Klaus Mayer
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Olaf Mundigl
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Hubert Kettenberger
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Fabian Birzele
- Roche Pharma Research & Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | - Sebastian Stahl
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Ira Pastan
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ulrich Brinkmann
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany.
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30
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Hawer H, Ütkür K, Arend M, Mayer K, Adrian L, Brinkmann U, Schaffrath R. Importance of diphthamide modified EF2 for translational accuracy and competitive cell growth in yeast. PLoS One 2018; 13:e0205870. [PMID: 30335802 PMCID: PMC6193676 DOI: 10.1371/journal.pone.0205870] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/02/2018] [Indexed: 01/23/2023] Open
Abstract
In eukaryotes, the modification of an invariant histidine (His-699 in yeast) residue in translation elongation factor 2 (EF2) with diphthamide involves a conserved pathway encoded by the DPH1-DPH7 gene network. Diphthamide is the target for diphtheria toxin and related lethal ADP ribosylases, which collectively kill cells by inactivating the essential translocase function of EF2 during mRNA translation and protein biosynthesis. Although this notion emphasizes the pathological importance of diphthamide, precisely why cells including our own require EF2 to carry it, is unclear. Mining the synthetic genetic array (SGA) landscape from the budding yeast Saccharomyces cerevisiae has revealed negative interactions between EF2 (EFT1-EFT2) and diphthamide (DPH1-DPH7) gene deletions. In line with these correlations, we confirm in here that loss of diphthamide modification (dphΔ) on EF2 combined with EF2 undersupply (eft2Δ) causes synthetic growth phenotypes in the composite mutant (dphΔ eft2Δ). These reflect negative interference with cell performance under standard as well as thermal and/or chemical stress conditions, cell growth rates and doubling times, competitive fitness, cell viability in the presence of TOR inhibitors (rapamycin, caffeine) and translation indicator drugs (hygromycin, anisomycin). Together with significantly suppressed tolerance towards EF2 inhibition by cytotoxic DPH5 overexpression and increased ribosomal -1 frame-shift errors in mutants lacking modifiable pools of EF2 (dphΔ, dphΔ eft2Δ), our data indicate that diphthamide is important for the fidelity of the EF2 translocation function during mRNA translation.
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Affiliation(s)
- Harmen Hawer
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Koray Ütkür
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Meike Arend
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Klaus Mayer
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center München, Penzberg, Germany
| | - Lorenz Adrian
- AG Geobiochemie, Department Isotopenbiogeochemie, Helmholtz-Zentrum für Umweltforschung GmbH–UFZ, Leipzig, Germany
- Fachgebiet Geobiotechnologie, Technische Universität Berlin, Berlin, Germany
| | - Ulrich Brinkmann
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center München, Penzberg, Germany
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
- * E-mail:
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31
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Hörberg J, Saenz-Mendez P, Eriksson LA. QM/MM Studies of Dph5 - A Promiscuous Methyltransferase in the Eukaryotic Biosynthetic Pathway of Diphthamide. J Chem Inf Model 2018; 58:1406-1414. [PMID: 29927239 DOI: 10.1021/acs.jcim.8b00217] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Eukaryotic diphthine synthase, Dph5, is a promiscuous methyltransferase that catalyzes an extraordinary N, O-tetramethylation of 2-(3-carboxy-3-aminopropyl)-l-histidine (ACP) to yield diphthine methyl ester (DTM). These are intermediates in the biosynthesis of the post-translationally modified histidine residue diphthamide (DTA), a unique and essential residue part of the eukaryotic elongation factor 2 (eEF2). Herein, the promiscuity of Saccharomyces cerevisiae Dph5 has been studied with in silico approaches, including homology modeling to provide the structure of Dph5, protein-protein docking and molecular dynamics to construct the Dph5-eEF2 complex, and quantum mechanics/molecular mechanics (QM/MM) calculations to outline a plausible mechanism. The calculations show that the methylation of ACP follows a typical SN2 mechanism, initiating with a complete methylation (trimethylation) at the N-position, followed by the single O-methylation. For each of the three N-methylation reactions, our calculations support a stepwise mechanism, which first involve proton transfer through a bridging water to a conserved aspartate residue D165, followed by a methyl transfer. Once fully methylated, the trimethyl amino group forms a weak electrostatic interaction with D165, which allows the carboxylate group of diphthine to attain the right orientation for the final methylation step to be accomplished.
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Affiliation(s)
- Johanna Hörberg
- Department of Chemistry and Molecular Biology , University of Gothenburg , 405 30 Göteborg , Sweden
| | - Patricia Saenz-Mendez
- Computational Chemistry and Biology Group, Facultad de Química , Universidad de la República , 11800 Montevideo , Uruguay
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology , University of Gothenburg , 405 30 Göteborg , Sweden
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32
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Yokoyama K, Lilla EA. C-C bond forming radical SAM enzymes involved in the construction of carbon skeletons of cofactors and natural products. Nat Prod Rep 2018; 35:660-694. [PMID: 29633774 PMCID: PMC6051890 DOI: 10.1039/c8np00006a] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to the end of 2017 C-C bond formations are frequently the key steps in cofactor and natural product biosynthesis. Historically, C-C bond formations were thought to proceed by two electron mechanisms, represented by Claisen condensation in fatty acids and polyketide biosynthesis. These types of mechanisms require activated substrates to create a nucleophile and an electrophile. More recently, increasing number of C-C bond formations catalyzed by radical SAM enzymes are being identified. These free radical mediated reactions can proceed between almost any sp3 and sp2 carbon centers, allowing introduction of C-C bonds at unconventional positions in metabolites. Therefore, free radical mediated C-C bond formations are frequently found in the construction of structurally unique and complex metabolites. This review discusses our current understanding of the functions and mechanisms of C-C bond forming radical SAM enzymes and highlights their important roles in the biosynthesis of structurally complex, naturally occurring organic molecules. Mechanistic consideration of C-C bond formation by radical SAM enzymes identifies the significance of three key mechanistic factors: radical initiation, acceptor substrate activation and radical quenching. Understanding the functions and mechanisms of these characteristic enzymes will be important not only in promoting our understanding of radical SAM enzymes, but also for understanding natural product and cofactor biosynthesis.
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Affiliation(s)
- Kenichi Yokoyama
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.
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33
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Dong M, Zhang Y, Lin H. Noncanonical Radical SAM Enzyme Chemistry Learned from Diphthamide Biosynthesis. Biochemistry 2018; 57:3454-3459. [PMID: 29708734 DOI: 10.1021/acs.biochem.8b00287] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Radical S-adenosylmethionine (SAM) enzymes are a superfamily of enzymes that use SAM and reduced [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical to catalyze numerous challenging reactions. We have reported a type of noncanonical radical SAM enzymes in the diphthamide biosynthesis pathway. These enzymes also use SAM and reduced [4Fe-4S] clusters, but generate a 3-amino-3-carboxypropyl (ACP) radical to modify the substrate protein, translation elongation factor 2. The regioselective cleavage of a different C-S bond of the sulfonium center of SAM in these enzymes comparing to canonical radical SAM enzymes is intriguing. Here, we highlight some recent findings in the mechanism of these types of enzymes, showing that the diphthamide biosynthetic radial SAM enzymes bound SAM with a distinct geometry. In this way, the unique iron of the [4Fe-4S] cluster in the enzyme can only attack the carbon on the ACP group to form an organometallic intermediate. The homolysis of the organometallic intermediate releases the ACP radical and generates the EF2 radial.
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Affiliation(s)
- Min Dong
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Yugang Zhang
- 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; Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
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34
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Dong M, Kathiresan V, Fenwick MK, Torelli AT, Zhang Y, Caranto JD, Dzikovski B, Sharma A, Lancaster KM, Freed JH, Ealick SE, Hoffman BM, Lin H. Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis. Science 2018; 359:1247-1250. [PMID: 29590073 DOI: 10.1126/science.aao6595] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 01/30/2018] [Indexed: 12/31/2022]
Abstract
Diphthamide biosynthesis involves a carbon-carbon bond-forming reaction catalyzed by a radical S-adenosylmethionine (SAM) enzyme that cleaves a carbon-sulfur (C-S) bond in SAM to generate a 3-amino-3-carboxypropyl (ACP) radical. Using rapid freezing, we have captured an organometallic intermediate with an iron-carbon (Fe-C) bond between ACP and the enzyme's [4Fe-4S] cluster. In the presence of the substrate protein, elongation factor 2, this intermediate converts to an organic radical, formed by addition of the ACP radical to a histidine side chain. Crystal structures of archaeal diphthamide biosynthetic radical SAM enzymes reveal that the carbon of the SAM C-S bond being cleaved is positioned near the unique cluster Fe, able to react with the cluster. Our results explain how selective C-S bond cleavage is achieved in this radical SAM enzyme.
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Affiliation(s)
- Min Dong
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | - Michael K Fenwick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Andrew T Torelli
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Yang Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jonathan D Caranto
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Boris Dzikovski
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Ajay Sharma
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Steven E Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA.
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA. .,Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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35
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Dong M, Zhang Y, Lin H. Methods for Studying the Radical SAM Enzymes in Diphthamide Biosynthesis. Methods Enzymol 2018; 606:421-438. [PMID: 30097101 DOI: 10.1016/bs.mie.2018.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Diphthamide is a unique posttranslational modification on translation elongation factor 2 (EF2) in archaea and eukaryotes. Biosynthesis of diphthamide was proposed to involve four steps. The first step is a CC bond forming reaction catalyzed by unique radical S-adenosylmethionine (SAM) enzymes. Classical radical SAM enzymes use SAM and [4Fe-4S] clusters to generate a 5'-deoxyadenynal radical and catalyze numerous reactions. Radical SAM enzymes in diphthamide biosynthesis cleave a different CS bond in SAM to generate a 3-amino-3-carboxypropyl radical and modify a histidine residue of substrate protein EF2. Here, we describe our investigations on these unique radical SAM enzymes, including the preparation, characterization, and activity assays we have developed.
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Affiliation(s)
- Min Dong
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States
| | - Yugang Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States
| | - Hening Lin
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY, United States.
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36
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Johansson MJO, Xu F, Byström AS. Elongator-a tRNA modifying complex that promotes efficient translational decoding. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1861:401-408. [PMID: 29170010 DOI: 10.1016/j.bbagrm.2017.11.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 11/19/2017] [Indexed: 12/22/2022]
Abstract
Naturally occurring modifications of the nucleosides in the anticodon region of tRNAs influence their translational decoding properties. Uridines present at the wobble position in eukaryotic cytoplasmic tRNAs often contain a 5-carbamoylmethyl (ncm(5)) or 5-methoxycarbonylmethyl (mcm(5)) side-chain and sometimes also a 2-thio or 2'-O-methyl group. The first step in the formation of the ncm(5) and mcm(5) side-chains requires the conserved six-subunit Elongator complex. Although Elongator has been implicated in several different cellular processes, accumulating evidence suggests that its primary, and possibly only, cellular function is to promote modification of tRNAs. In this review, we discuss the biosynthesis and function of modified wobble uridines in eukaryotic cytoplasmic tRNAs, focusing on the in vivo role of Elongator-dependent modifications in Saccharomyces cerevisiae. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
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Affiliation(s)
| | - Fu Xu
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Anders S Byström
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden.
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37
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Dauden MI, Jaciuk M, Müller CW, Glatt S. Structural asymmetry in the eukaryotic Elongator complex. FEBS Lett 2017; 592:502-515. [DOI: 10.1002/1873-3468.12865] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 09/08/2017] [Accepted: 09/24/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Maria I. Dauden
- Structural and Computational Biology Unit European Molecular Biology Laboratory Heidelberg Germany
| | - Marcin Jaciuk
- Max Planck Research Group at the Malopolska Centre of Biotechnology Jagiellonian University Krakow Poland
| | - Christoph W. Müller
- Structural and Computational Biology Unit European Molecular Biology Laboratory Heidelberg Germany
| | - Sebastian Glatt
- Max Planck Research Group at the Malopolska Centre of Biotechnology Jagiellonian University Krakow Poland
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38
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Elp3 and Dph3 of Schizosaccharomyces pombe mediate cellular stress responses through tRNA LysUUU modifications. Sci Rep 2017; 7:7225. [PMID: 28775286 PMCID: PMC5543170 DOI: 10.1038/s41598-017-07647-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/30/2017] [Indexed: 01/31/2023] Open
Abstract
Efficient protein synthesis in eukaryotes requires diphthamide modification of translation elongation factor eEF2 and wobble uridine modifications of tRNAs. In higher eukaryotes, these processes are important for preventing neurological and developmental defects and cancer. In this study, we used Schizosaccharomyces pombe as a model to analyse mutants defective in eEF2 modification (dph1Δ), in tRNA modifications (elp3Δ), or both (dph3Δ) for sensitivity to cytotoxic agents and thermal stress. The dph3Δ and elp3Δ mutants were sensitive to a range of drugs and had growth defects at low temperature. dph3Δ was epistatic with dph1Δ for sensitivity to hydroxyurea and methyl methanesulfonate, and with elp3Δ for methyl methanesulfonate and growth at 16 °C. The dph1Δ and dph3Δ deletions rescued growth defects of elp3Δ in response to thiabendazole and at 37 °C. Elevated tRNALysUUU levels suppressed the elp3Δ phenotypes and some of the dph3Δ phenotypes, indicating that lack of tRNALysUUU modifications were responsible. Furthermore, we found positive genetic interactions of elp3Δ and dph3Δ with sty1Δ and atf1Δ, indicating that Elp3/Dph3-dependent tRNA modifications are important for efficient biosynthesis of key factors required for accurate responses to cytotoxic stress conditions.
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39
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Evolutionary Conservation and Emerging Functional Diversity of the Cytosolic Hsp70:J Protein Chaperone Network of Arabidopsis thaliana. G3-GENES GENOMES GENETICS 2017; 7:1941-1954. [PMID: 28450372 PMCID: PMC5473770 DOI: 10.1534/g3.117.042291] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Heat shock proteins of 70 kDa (Hsp70s) partner with structurally diverse Hsp40s (J proteins), generating distinct chaperone networks in various cellular compartments that perform myriad housekeeping and stress-associated functions in all organisms. Plants, being sessile, need to constantly maintain their cellular proteostasis in response to external environmental cues. In these situations, the Hsp70:J protein machines may play an important role in fine-tuning cellular protein quality control. Although ubiquitous, the functional specificity and complexity of the plant Hsp70:J protein network has not been studied. Here, we analyzed the J protein network in the cytosol of Arabidopsis thaliana and, using yeast genetics, show that the functional specificities of most plant J proteins in fundamental chaperone functions are conserved across long evolutionary timescales. Detailed phylogenetic and functional analysis revealed that increased number, regulatory differences, and neofunctionalization in J proteins together contribute to the emerging functional diversity and complexity in the Hsp70:J protein network in higher plants. Based on the data presented, we propose that higher plants have orchestrated their "chaperome," especially their J protein complement, according to their specialized cellular and physiological stipulations.
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40
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A mutated dph3 gene causes sensitivity of Schizosaccharomyces pombe cells to cytotoxic agents. Curr Genet 2017; 63:1081-1091. [PMID: 28555368 PMCID: PMC5668335 DOI: 10.1007/s00294-017-0711-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/11/2017] [Accepted: 05/23/2017] [Indexed: 12/11/2022]
Abstract
Dph3 is involved in diphthamide modification of the eukaryotic translation elongation factor eEF2 and in Elongator-mediated modifications of tRNAs, where a 5-methoxycarbonyl-methyl moiety is added to wobble uridines. Lack of such modifications affects protein synthesis due to inaccurate translation of mRNAs at ribosomes. We have discovered that integration of markers at the msh3 locus of Schizosaccharomyces pombe impaired the function of the nearby located dph3 gene. Such integrations rendered cells sensitive to the cytotoxic drugs hydroxyurea and methyl methanesulfonate. We constructed dph3 and msh3 strains with mutated ATG start codons (ATGmut), which allowed investigating drug sensitivity without potential interference by marker insertions. The dph3-ATGmut and a dph3::loxP-ura4-loxM gene disruption strain, but not msh3-ATGmut, turned out to be sensitive to hydroxyurea and methyl methanesulfonate, likewise the strains with cassettes integrated at the msh3 locus. The fungicide sordarin, which inhibits diphthamide modified eEF2 of Saccharomyces cerevisiae, barely affected survival of wild type and msh3Δ S. pombe cells, while the dph3Δ mutant was sensitive. The msh3-ATG mutation, but not dph3Δ or the dph3-ATG mutation caused a defect in mating-type switching, indicating that the ura4 marker at the dph3 locus did not interfere with Msh3 function. We conclude that Dph3 is required for cellular resistance to the fungicide sordarin and to the cytotoxic drugs hydroxyurea and methyl methanesulfonate. This is likely mediated by efficient translation of proteins in response to DNA damage and replication stress.
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41
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Dong M, Horitani M, Dzikovski B, Freed JH, Ealick SE, Hoffman BM, Lin H. Substrate-Dependent Cleavage Site Selection by Unconventional Radical S-Adenosylmethionine Enzymes in Diphthamide Biosynthesis. J Am Chem Soc 2017; 139:5680-5683. [PMID: 28383907 DOI: 10.1021/jacs.7b01712] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
S-Adenosylmethionine (SAM) has a sulfonium ion with three distinct C-S bonds. Conventional radical SAM enzymes use a [4Fe-4S] cluster to cleave homolytically the C5',adenosine-S bond of SAM to generate a 5'-deoxyadenosyl radical, which catalyzes various downstream chemical reactions. Radical SAM enzymes involved in diphthamide biosynthesis, such as Pyrococcus horikoshii Dph2 (PhDph2) and yeast Dph1-Dph2 instead cleave the Cγ,Met-S bond of methionine to generate a 3-amino-3-carboxylpropyl radical. We here show radical SAM enzymes can be tuned to cleave the third C-S bond to the sulfonium sulfur by changing the structure of SAM. With a decarboxyl SAM analogue (dc-SAM), PhDph2 cleaves the Cmethyl-S bond, forming 5'-deoxy-5'-(3-aminopropylthio) adenosine (dAPTA, 1). The methyl cleavage activity, like the cleavage of the other two C-S bonds, is dependent on the presence of a [4Fe-4S]+ cluster. Electron-nuclear double resonance and mass spectroscopy data suggests that mechanistically one of the S atoms in the [4Fe-4S] cluster captures the methyl group from dc-SAM, forming a distinct EPR-active intermediate, which can transfer the methyl group to nucleophiles such as dithiothreitol. This reveals the [4Fe-4S] cluster in a radical SAM enzyme can be tuned to cleave any one of the three bonds to the sulfonium sulfur of SAM or analogues, and is the first demonstration a radical SAM enzyme could switch from an Fe-based one electron transfer reaction to a S-based two electron transfer reaction in a substrate-dependent manner. This study provides an illustration of the versatile reactivity of Fe-S clusters.
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Affiliation(s)
- Min Dong
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Masaki Horitani
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States.,Department of Applied Biochemistry and Food Science, Saga University , Saga 840-8502, Japan
| | - Boris Dzikovski
- 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
| | - Steven E Ealick
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Hening Lin
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
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42
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Mayer K, Schröder A, Schnitger J, Stahl S, Brinkmann U. Influence of DPH1 and DPH5 Protein Variants on the Synthesis of Diphthamide, the Target of ADPRibosylating Toxins. Toxins (Basel) 2017; 9:E78. [PMID: 28245596 PMCID: PMC5371833 DOI: 10.3390/toxins9030078] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 02/20/2017] [Indexed: 01/22/2023] Open
Abstract
The diphthamide on eukaryotic translation elongation factor 2 (eEF2) is the target of ADPribosylating toxins and -derivatives that serve as payloads in targeted tumor therapy. Diphthamide is generated by seven DPH proteins; cells deficient in these (DPHko) lack diphthamide and are toxin-resistant. We have established assays to address the functionality of DPH1 (OVCA1) and DPH5 variants listed in dbSNP and cosmic databases: plasmids encoding wildtype and mutant DPHs were transfected into DPHko cells. Supplementation of DPH1 and DPH5 restores diphthamide synthesis and toxin sensitivity in DPH1ko and DPH5ko cells, respectively. Consequently, the determination of the diphthamide status of cells expressing DPH variants differentiates active and compromised proteins. The DPH1 frameshift variant L96fs* (with Nterminal 96 amino acids, truncated thereafter) and two splice isoforms lacking 80 or 140 amino acids at their N-termini failed to restore DPH1ko deficiency. The DPH1 frameshift variant R312fs* retained some residual activity even though it lacks a large C-terminal portion. DPH1 missense variants R27W and S56F retained activity while S221P had reduced activity, indicated by a decreased capability to restore diphthamide synthesis. The DPH5 nonsense or frameshift variants E60*, W136fs* and R207* (containing intact N-termini with truncations after 60, 136 or 207 amino acids, respectively) were inactive: none compensated the deficiency of DPH5ko cells. In contrast, missense variants D57G, G87R, S123C and Q170H as well as the frequently occurring DPH5 isoform delA212 retained activity. Sensitivity to ADP-ribosylating toxins and tumor-targeted immunotoxins depends on diphthamide which, in turn, requires DPH functionality. Because of that, DPH variants (in particular those that are functionally compromised) may serve as a biomarker and correlate with the efficacy of immunotoxin-based therapies.
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Affiliation(s)
- Klaus Mayer
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, 82377 Penzberg, Germany.
| | - Anna Schröder
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, 82377 Penzberg, Germany.
| | - Jerome Schnitger
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, 82377 Penzberg, Germany.
| | - Sebastian Stahl
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, 82377 Penzberg, Germany.
| | - Ulrich Brinkmann
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, 82377 Penzberg, Germany.
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43
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Abstract
Wobble uridines (U34) are generally modified in all species. U34 modifications can be essential in metazoans but are not required for viability in fungi. In this review, we provide an overview on the types of modifications and how they affect the physico-chemical properties of wobble uridines. We describe the molecular machinery required to introduce these modifications into tRNA posttranscriptionally and discuss how posttranslational regulation may affect the activity of the modifying enzymes. We highlight the activity of anticodon specific RNases that target U34 containing tRNA. Finally, we discuss how defects in wobble uridine modifications lead to phenotypes in different species. Importantly, this review will mainly focus on the cytoplasmic tRNAs of eukaryotes. A recent review has extensively covered their bacterial and mitochondrial counterparts.1
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Affiliation(s)
- Raffael Schaffrath
- a Institut für Biologie, FG Mikrobiologie , Universität Kassel , Germany
| | - Sebastian A Leidel
- b Max Planck Institute for Molecular Biomedicine , Germany.,c Cells-in-Motion Cluster of Excellence , University of Münster , Münster , Germany.,d Medical Faculty , University of Münster , Albert-Schweitzer-Campus 1, Münster , Germany
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44
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Kolaj-Robin O, Séraphin B. Structures and Activities of the Elongator Complex and Its Cofactors. RNA MODIFICATION 2017; 41:117-149. [DOI: 10.1016/bs.enz.2017.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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45
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Lyu Z, Whitman WB. Evolution of the archaeal and mammalian information processing systems: towards an archaeal model for human disease. Cell Mol Life Sci 2017; 74:183-212. [PMID: 27261368 PMCID: PMC11107668 DOI: 10.1007/s00018-016-2286-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 05/05/2016] [Accepted: 05/27/2016] [Indexed: 12/22/2022]
Abstract
Current evolutionary models suggest that Eukaryotes originated from within Archaea instead of being a sister lineage. To test this model of ancient evolution, we review recent studies and compare the three major information processing subsystems of replication, transcription and translation in the Archaea and Eukaryotes. Our hypothesis is that if the Eukaryotes arose within the archaeal radiation, their information processing systems will appear to be one of kind and not wholly original. Within the Eukaryotes, the mammalian or human systems are emphasized because of their importance in understanding health. Biochemical as well as genetic studies provide strong evidence for the functional similarity of archaeal homologs to the mammalian information processing system and their dissimilarity to the bacterial systems. In many independent instances, a simple archaeal system is functionally equivalent to more elaborate eukaryotic homologs, suggesting that evolution of complexity is likely an central feature of the eukaryotic information processing system. Because fewer components are often involved, biochemical characterizations of the archaeal systems are often easier to interpret. Similarly, the archaeal cell provides a genetically and metabolically simpler background, enabling convenient studies on the complex information processing system. Therefore, Archaea could serve as a parsimonious and tractable host for studying human diseases that arise in the information processing systems.
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Affiliation(s)
- Zhe Lyu
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA.
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46
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Denisova E, Heidenreich B, Nagore E, Rachakonda PS, Hosen I, Akrap I, Traves V, García-Casado Z, López-Guerrero JA, Requena C, Sanmartin O, Serra-Guillén C, Llombart B, Guillén C, Ferrando J, Gimeno E, Nordheim A, Hemminki K, Kumar R. Frequent DPH3 promoter mutations in skin cancers. Oncotarget 2016; 6:35922-30. [PMID: 26416425 PMCID: PMC4742151 DOI: 10.18632/oncotarget.5771] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/12/2015] [Indexed: 12/24/2022] Open
Abstract
Recent reports suggested frequent occurrence of cancer associated somatic mutations within regulatory elements of the genome. Based on initial exome sequencing of 21 melanomas, we report frequent somatic mutations in skin cancers in a bidirectional promoter of diphthamide biosynthesis 3 (DPH3) and oxidoreductase NAD-binding domain containing 1 (OXNAD1) genes. The UV-signature mutations occurred at sites adjacent and within a binding motif for E-twenty six/ternary complex factors (Ets/TCF), at -8 and -9 bp from DPH3 transcription start site. Follow up screening of 586 different skin lesions showed that the DPH3 promoter mutations were present in melanocytic nevi (2/114; 2%), melanoma (30/304; 10%), basal cell carcinoma of skin (BCC; 57/137; 42%) and squamous cell carcinoma of skin (SCC; 12/31; 39%). Reporter assays carried out in one melanoma cell line for DPH3 and OXNAD1 orientations showed statistically significant increased promoter activity due to -8/-9CC > TT tandem mutations; although, no effect of the mutations on DPH3 and OXNAD1 transcription in tumors was observed. The results from this study show occurrence of frequent somatic non-coding mutations adjacent to a pre-existing binding site for Ets transcription factors within the directional promoter of DPH3 and OXNAD1 genes in three major skin cancers. The detected mutations displayed typical UV signature; however, the functionality of the mutations remains to be determined.
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Affiliation(s)
- Evgeniya Denisova
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Barbara Heidenreich
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Eduardo Nagore
- Department of Dermatology, Instituto Valenciano de Oncologia, Valencia, Spain
| | | | - Ismail Hosen
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Ivana Akrap
- Interfaculty Institute of Cell Biology, Tuebingen University, and IMPRS ("From Molecules to Organisms"), Tuebingen, Germany
| | - Víctor Traves
- Department of Pathology, Instituto Valenciano de Oncologia, Valencia, Spain
| | - Zaida García-Casado
- Laboratory of Molecular Biology, Instituto Valenciano de Oncologia, Valencia, Spain
| | | | - Celia Requena
- Department of Dermatology, Instituto Valenciano de Oncologia, Valencia, Spain
| | - Onofre Sanmartin
- Department of Dermatology, Instituto Valenciano de Oncologia, Valencia, Spain
| | | | - Beatriz Llombart
- Department of Dermatology, Instituto Valenciano de Oncologia, Valencia, Spain
| | - Carlos Guillén
- Department of Dermatology, Instituto Valenciano de Oncologia, Valencia, Spain
| | - Jose Ferrando
- Departments of Pathology & Dermatology, Hospital Arnau de Vilanova, Valencia, Spain
| | - Enrique Gimeno
- Departments of Pathology & Dermatology, Hospital Arnau de Vilanova, Valencia, Spain
| | - Alfred Nordheim
- Interfaculty Institute of Cell Biology, Tuebingen University, and IMPRS ("From Molecules to Organisms"), Tuebingen, Germany.,German Cancer Consortium (DKTK/DKFZ), Heidelberg, Germany
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany.,Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
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47
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Cbr1 is a Dph3 reductase required for the tRNA wobble uridine modification. Nat Chem Biol 2016; 12:995-997. [PMID: 27694803 PMCID: PMC5110365 DOI: 10.1038/nchembio.2190] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 07/28/2016] [Indexed: 11/28/2022]
Abstract
Diphthamide and the tRNA wobble uridine modifications both require Dph3 (DiPHthamide biosynthesis 3) protein as an electron donor for the iron-sulfur clusters in their biosynthetic enzymes. Here, using a proteomic approach, we identified Saccharomyces cerevisiae cytochrome B5 reductase (Cbr1) as a NADH-dependent reductase for Dph3. The NADH- and Cbr1-dependent reduction of Dph3 may provide a regulatory linkage between cellular metabolic state and protein translation.
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48
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Dong M, Horitani M, Dzikovski B, Pandelia ME, Krebs C, Freed JH, Hoffman BM, Lin H. Organometallic Complex Formed by an Unconventional Radical S-Adenosylmethionine Enzyme. J Am Chem Soc 2016; 138:9755-8. [PMID: 27465315 DOI: 10.1021/jacs.6b04155] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Pyrococcus horikoshii Dph2 (PhDph2) is an unusual radical S-adenosylmethionine (SAM) enzyme involved in the first step of diphthamide biosynthesis. It catalyzes the reaction by cleaving SAM to generate a 3-amino-3-carboxypropyl (ACP) radical. To probe the reaction mechanism, we synthesized a SAM analogue (SAMCA), in which the ACP group of SAM is replaced with a 3-carboxyallyl group. SAMCA is cleaved by PhDph2, yielding a paramagnetic (S = 1/2) species, which is assigned to a complex formed between the reaction product, α-sulfinyl-3-butenoic acid, and the [4Fe-4S] cluster. Electron-nuclear double resonance (ENDOR) measurements with (13)C and (2)H isotopically labeled SAMCA support a π-complex between the C═C double bond of α-sulfinyl-3-butenoic acid and the unique iron of the [4Fe-4S] cluster. This is the first example of a radical SAM-related [4Fe-4S](+) cluster forming an organometallic complex with an alkene, shedding additional light on the mechanism of PhDph2 and expanding our current notions for the reactivity of [4Fe-4S] clusters in radical SAM enzymes.
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Affiliation(s)
- Min Dong
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Masaki Horitani
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Boris Dzikovski
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Maria-Eirini Pandelia
- Department of Biochemistry, Brandeis University , Waltham, Massachusetts 02453, United States
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, 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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49
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Structural basis for tRNA modification by Elp3 from Dehalococcoides mccartyi. Nat Struct Mol Biol 2016; 23:794-802. [PMID: 27455459 PMCID: PMC5018218 DOI: 10.1038/nsmb.3265] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 06/17/2016] [Indexed: 12/11/2022]
Abstract
During translation elongation decoding is based on the recognition of codons by corresponding tRNA anticodon triplets. Molecular mechanisms that regulate global protein synthesis via specific base modifications in tRNA anticodons have recently received increasing attention. The conserved eukaryotic Elongator complex specifically modifies uridines located in the wobble base position of tRNAs. Here, we present the crystal structure of Dehalococcoides mccartyi Elp3 (DmcElp3) at 2.15 Å resolution. Our results reveal the unexpected arrangement of Elp3 lysine acetyl transferase (KAT) and radical S-adenosyl-methionine (SAM) domains that share a large interface to form a composite active site and tRNA binding pocket with an iron sulfur cluster located in the dimerization interface of two DmcElp3 molecules. Structure-guided mutagenesis studies of yeast Elp3 confirm the relevance of our findings for eukaryotic Elp3s and for understanding Elongator’s role in the onset of various neurodegenerative diseases and cancer in humans.
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50
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Karlsborn T, Tükenmez H, Mahmud AKMF, Xu F, Xu H, Byström AS. Elongator, a conserved complex required for wobble uridine modifications in eukaryotes. RNA Biol 2015; 11:1519-28. [PMID: 25607684 DOI: 10.4161/15476286.2014.992276] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Elongator is a 6 subunit protein complex highly conserved in eukaryotes. The role of this complex has been controversial as the pleiotropic phenotypes of Elongator mutants have implicated the complex in several cellular processes. However, in yeast there is convincing evidence that the primary and probably only role of this complex is in formation of the 5-methoxycarbonylmethyl (mcm(5)) and 5-carbamoylmethyl (ncm(5)) side chains on uridines at wobble position in tRNA. In this review we summarize the cellular processes that have been linked to the Elongator complex and discuss its role in tRNA modification and regulation of translation. We also describe additional gene products essential for formation of ncm(5) and mcm(5) side chains at U34 and their influence on Elongator activity.
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Affiliation(s)
- Tony Karlsborn
- a Department of Molecular Biology ; Umeå University; Umeå , Sweden
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