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Auverlot J, Dard A, Sáez-Vásquez J, Reichheld JP. Redox regulation of epigenetic and epitranscriptomic gene regulatory pathways in plants. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4459-4475. [PMID: 38642408 DOI: 10.1093/jxb/erae165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/18/2024] [Indexed: 04/22/2024]
Abstract
Developmental and environmental constraints influence genome expression through complex networks of regulatory mechanisms. Epigenetic modifications and remodelling of chromatin are some of the major actors regulating the dynamic of gene expression. Unravelling the factors relaying environmental signals that induce gene expression reprogramming under stress conditions is an important and fundamental question. Indeed, many enzymes involved in epigenetic and chromatin modifications are regulated by redox pathways, through post-translational modifications of proteins or by modifications of the flux of metabolic intermediates. Such modifications are potential hubs to relay developmental and environmental changes for gene expression reprogramming. In this review, we provide an update on the interaction between major redox mediators, such as reactive oxygen and nitrogen species and antioxidants, and epigenetic changes in plants. We detail how redox status alters post-translational modifications of proteins, intracellular epigenetic and epitranscriptional modifications, and how redox regulation interplays with DNA methylation, histone acetylation and methylation, miRNA biogenesis, and chromatin structure and remodelling to reprogram genome expression under environmental constraints.
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Affiliation(s)
- Juline Auverlot
- Laboratoire Génome et Développement des Plantes, Université Perpignan Via Domitia, F-66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, CNRS, F-66860 Perpignan, France
| | - Avilien Dard
- Laboratoire Génome et Développement des Plantes, Université Perpignan Via Domitia, F-66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, CNRS, F-66860 Perpignan, France
- Centre for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - Julio Sáez-Vásquez
- Laboratoire Génome et Développement des Plantes, Université Perpignan Via Domitia, F-66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, CNRS, F-66860 Perpignan, France
| | - Jean-Philippe Reichheld
- Laboratoire Génome et Développement des Plantes, Université Perpignan Via Domitia, F-66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, CNRS, F-66860 Perpignan, France
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2
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Want K, D'Autréaux B. Mechanism of mitochondrial [2Fe-2S] cluster biosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119811. [PMID: 39128597 DOI: 10.1016/j.bbamcr.2024.119811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 07/13/2024] [Accepted: 08/05/2024] [Indexed: 08/13/2024]
Abstract
Iron‑sulfur (Fe-S) clusters constitute ancient cofactors that accompany a versatile range of fundamental biological reactions across eukaryotes and prokaryotes. Several cellular pathways exist to coordinate iron acquisition and sulfur mobilization towards a scaffold protein during the tightly regulated synthesis of Fe-S clusters. The mechanism of mitochondrial eukaryotic [2Fe-2S] cluster synthesis is coordinated by the Iron-Sulfur Cluster (ISC) machinery and its aberrations herein have strong implications to the field of disease and medicine which is therefore of particular interest. Here, we describe our current knowledge on the step-by-step mechanism leading to the production of mitochondrial [2Fe-2S] clusters while highlighting the recent developments in the field alongside the challenges that are yet to be overcome.
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Affiliation(s)
- Kristian Want
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Benoit D'Autréaux
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
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3
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Sun J, Wu J, Yuan Y, Fan L, Chua WLP, Ling YHS, Balamkundu S, priya D, Suen HCS, de Crécy-Lagard V, Dziergowska A, Dedon PC. tRNA modification profiling reveals epitranscriptome regulatory networks in Pseudomonas aeruginosa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601603. [PMID: 39005467 PMCID: PMC11245014 DOI: 10.1101/2024.07.01.601603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Transfer RNA (tRNA) modifications have emerged as critical posttranscriptional regulators of gene expression affecting diverse biological and disease processes. While there is extensive knowledge about the enzymes installing the dozens of post-transcriptional tRNA modifications - the tRNA epitranscriptome - very little is known about how metabolic, signaling, and other networks integrate to regulate tRNA modification levels. Here we took a comprehensive first step at understanding epitranscriptome regulatory networks by developing a high-throughput tRNA isolation and mass spectrometry-based modification profiling platform and applying it to a Pseudomonas aeruginosa transposon insertion mutant library comprising 5,746 strains. Analysis of >200,000 tRNA modification data points validated the annotations of predicted tRNA modification genes, uncovered novel tRNA-modifying enzymes, and revealed tRNA modification regulatory networks in P. aeruginosa. Platform adaptation for RNA-seq library preparation would complement epitranscriptome studies, while application to human cell and mouse tissue demonstrates its utility for biomarker and drug discovery and development.
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Affiliation(s)
- Jingjing Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602 Singapore
| | - Junzhou Wu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602 Singapore
| | - Yifeng Yuan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611 USA
| | - Leon Fan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Wei Lin Patrina Chua
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602 Singapore
| | - Yan Han Sharon Ling
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602 Singapore
| | | | - Dwija priya
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602 Singapore
| | - Hazel Chay Suen Suen
- Department of Food, Chemical & Biotechnology, Singapore of Institute of Technology, 138683 Singapore
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611 USA
- Genetic Institute, University of Florida, Gainesville, FL 32611 USA
| | | | - Peter C. Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602 Singapore
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4
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Ip JY, Wijaya I, Lee LT, Lim Y, Teoh DEJ, Chan CSC, Cui L, Begley TJ, Dedon PC, Guo H. ROS-induced translational regulation-through spatiotemporal differences in codon recognition-is a key driver of brown adipogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.22.572954. [PMID: 38463965 PMCID: PMC10925207 DOI: 10.1101/2023.12.22.572954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The role of translational regulation in brown adipogenesis is relatively unknown. Localized translation of mRNAs encoding mitochondrial components enables swift mitochondrial responses, but whether this occurs during brown adipogenesis, which involves massive mitochondrial biogenesis, has not been explored. Here, we used ribosome profiling and RNA-Seq, coupled with cellular fractionation, to obtain spatiotemporal insights into translational regulation. During brown adipogenesis, a translation bias towards G/C-ending codons is triggered first in the mitochondrial vicinity by reactive oxygen species (ROS), which later spreads to the rest of the cell. This translation bias is induced through ROS modulating the activity of the tRNA modification enzyme, ELP3. Intriguingly, functionally relevant mRNAs, including those encoding ROS scavengers, benefit from this bias; in so doing, ROS-induced translation bias both fuels differentiation and concurrently minimizes oxidative damage. These ROS-induced changes could enable sustained mitochondrial biogenesis during brown adipogenesis, and explain in part, the molecular basis for ROS hormesis.
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Bou-Nader C, Pecqueur L, de Crécy-Lagard V, Hamdane D. Integrative Approach to Probe Alternative Redox Mechanisms in RNA Modifications. Acc Chem Res 2023; 56:3142-3152. [PMID: 37916403 PMCID: PMC10999249 DOI: 10.1021/acs.accounts.3c00418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
RNA modifications found in most RNAs, particularly in tRNAs and rRNAs, reveal an abundance of chemical alterations of nucleotides. Over 150 distinct RNA modifications are known, emphasizing a remarkable diversity of chemical moieties in RNA molecules. These modifications play pivotal roles in RNA maturation, structural integrity, and the fidelity and efficiency of translation processes. The catalysts responsible for these modifications are RNA-modifying enzymes that use a striking array of chemistries to directly influence the chemical landscape of RNA. This diversity is further underscored by instances where the same modification is introduced by distinct enzymes that use unique catalytic mechanisms and cofactors across different domains of life. This phenomenon of convergent evolution highlights the biological importance of RNA modification and the vast potential within the chemical repertoire for nucleotide alteration. While shared RNA modifications can hint at conserved enzymatic pathways, a major bottleneck is to identify alternative routes within species that possess a modified RNA but are devoid of known RNA-modifying enzymes. To address this challenge, a combination of bioinformatic and experimental strategies proves invaluable in pinpointing new genes responsible for RNA modifications. This integrative approach not only unveils new chemical insights but also serves as a wellspring of inspiration for biocatalytic applications and drug design. In this Account, we present how comparative genomics and genome mining, combined with biomimetic synthetic chemistry, biochemistry, and anaerobic crystallography, can be judiciously implemented to address unprecedented and alternative chemical mechanisms in the world of RNA modification. We illustrate these integrative methodologies through the study of tRNA and rRNA modifications, dihydrouridine, 5-methyluridine, queuosine, 8-methyladenosine, 5-carboxymethylamino-methyluridine, or 5-taurinomethyluridine, each dependent on a diverse array of redox chemistries, often involving organic compounds, organometallic complexes, and metal coenzymes. We explore how vast genome and tRNA databases empower comparative genomic analyses and enable the identification of novel genes that govern RNA modification. Subsequently, we describe how the isolation of a stable reaction intermediate can guide the synthesis of a biomimetic to unveil new enzymatic pathways. We then discuss the usefulness of a biochemical "shunt" strategy to study catalytic mechanisms and to directly visualize reactive intermediates bound within active sites. While we primarily focus on various RNA-modifying enzymes studied in our laboratory, with a particular emphasis on the discovery of a SAM-independent methylation mechanism, the strategies and rationale presented herein are broadly applicable for the identification of new enzymes and the elucidation of their intricate chemistries. This Account offers a comprehensive glimpse into the evolving landscape of RNA modification research and highlights the pivotal role of integrated approaches to identify novel enzymatic pathways.
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Affiliation(s)
- Charles Bou-Nader
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, 32611, USA
- University of Florida, Genetics Institute, Gainesville, Florida, 32610, USA
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
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6
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Mara P, Zhou YL, Teske A, Morono Y, Beaudoin D, Edgcomb V. Microbial gene expression in Guaymas Basin subsurface sediments responds to hydrothermal stress and energy limitation. THE ISME JOURNAL 2023; 17:1907-1919. [PMID: 37658181 PMCID: PMC10579382 DOI: 10.1038/s41396-023-01492-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 09/03/2023]
Abstract
Analyses of gene expression of subsurface bacteria and archaea provide insights into their physiological adaptations to in situ subsurface conditions. We examined patterns of expressed genes in hydrothermally heated subseafloor sediments with distinct geochemical and thermal regimes in Guaymas Basin, Gulf of California, Mexico. RNA recovery and cell counts declined with sediment depth, however, we obtained metatranscriptomes from eight sites at depths spanning between 0.8 and 101.9 m below seafloor. We describe the metabolic potential of sediment microorganisms, and discuss expressed genes involved in tRNA, mRNA, and rRNA modifications that enable physiological flexibility of bacteria and archaea in the hydrothermal subsurface. Microbial taxa in hydrothermally influenced settings like Guaymas Basin may particularly depend on these catalytic RNA functions since they modulate the activity of cells under elevated temperatures and steep geochemical gradients. Expressed genes for DNA repair, protein maintenance and circadian rhythm were also identified. The concerted interaction of many of these genes may be crucial for microorganisms to survive and to thrive in the Guaymas Basin subsurface biosphere.
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Affiliation(s)
- Paraskevi Mara
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Ying-Li Zhou
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Andreas Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Yuki Morono
- Kochi Institute for Core Sample Research, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Monobe, Nankoku, Kochi, Japan
| | - David Beaudoin
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Virginia Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
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7
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Montacié C, Riondet C, Wei L, Darrière T, Weiss A, Pontvianne F, Escande ML, de Bures A, Jobet E, Barbarossa A, Carpentier MC, Aarts MGM, Attina A, Hirtz C, David A, Marchand V, Motorin Y, Curie C, Mari S, Reichheld JP, Sáez-Vásquez J. NICOTIANAMINE SYNTHASE activity affects nucleolar iron accumulation and impacts rDNA silencing and RNA methylation in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4384-4400. [PMID: 37179467 PMCID: PMC10433931 DOI: 10.1093/jxb/erad180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/11/2023] [Indexed: 05/15/2023]
Abstract
In plant cells, a large pool of iron (Fe) is contained in the nucleolus, as well as in chloroplasts and mitochondria. A central determinant for intracellular distribution of Fe is nicotianamine (NA) generated by NICOTIANAMINE SYNTHASE (NAS). Here, we used Arabidopsis thaliana plants with disrupted NAS genes to study the accumulation of nucleolar iron and understand its role in nucleolar functions and more specifically in rRNA gene expression. We found that nas124 triple mutant plants, which contained lower quantities of the iron ligand NA, also contained less iron in the nucleolus. This was concurrent with the expression of normally silenced rRNA genes from nucleolar organizer regions 2 (NOR2). Notably, in nas234 triple mutant plants, which also contained lower quantities of NA, nucleolar iron and rDNA expression were not affected. In contrast, in both nas124 and nas234, specific RNA modifications were differentially regulated in a genotype dependent manner. Taken together, our results highlight the impact of specific NAS activities in RNA gene expression. We discuss the interplay between NA and nucleolar iron with rDNA functional organization and RNA methylation.
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Affiliation(s)
- Charlotte Montacié
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Christophe Riondet
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Lili Wei
- Institut Agro, BPMP, CNRS, INRAE, Université Montpellier, 34060 Montpellier, France
| | - Tommy Darrière
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Alizée Weiss
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Frédéric Pontvianne
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Marie-Line Escande
- Observatoire Océanologique de Banyuls s/ mer, CNRS, 66650 Banyuls-sur-mer, France
- BioPIC Platform of the OOB, 66650 Banyuls-sur-mer, France
| | - Anne de Bures
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Edouard Jobet
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Adrien Barbarossa
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Mark G M Aarts
- Laboratory of Genetics, Wageningen University & Research, 6700AA Wageningen, Netherlands
| | - Aurore Attina
- INSERM, CHU Montpellier, CNRS, IRMB, Université Montpellier, 34090Montpellier, France
| | - Christophe Hirtz
- INSERM, CHU Montpellier, CNRS, IRMB, Université Montpellier, 34090Montpellier, France
| | - Alexandre David
- IGF, CNRS, INSERM, Université Montpellier, 34090Montpellier, France
| | - Virginie Marchand
- Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, CNRS, INSERM, IBSLor (UMS2008/US40), Université de Lorraine, F-54000 Nancy, France
| | - Yuri Motorin
- Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, CNRS, INSERM, IBSLor (UMS2008/US40), Université de Lorraine, F-54000 Nancy, France
- CNRS, IMoPA (UMR 7365), Université de Lorraine, F-54000 Nancy, France
| | - Catherine Curie
- Institut Agro, BPMP, CNRS, INRAE, Université Montpellier, 34060 Montpellier, France
| | - Stéphane Mari
- Institut Agro, BPMP, CNRS, INRAE, Université Montpellier, 34060 Montpellier, France
| | - Jean-Philippe Reichheld
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Julio Sáez-Vásquez
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
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8
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Lee WL, Sinha A, Lam LN, Loo HL, Liang J, Ho P, Cui L, Chan CSC, Begley T, Kline KA, Dedon P. An RNA modification enzyme directly senses reactive oxygen species for translational regulation in Enterococcus faecalis. Nat Commun 2023; 14:4093. [PMID: 37433804 DOI: 10.1038/s41467-023-39790-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 06/27/2023] [Indexed: 07/13/2023] Open
Abstract
Bacteria possess elaborate systems to manage reactive oxygen and nitrogen species (ROS) arising from exposure to the mammalian immune system and environmental stresses. Here we report the discovery of an ROS-sensing RNA-modifying enzyme that regulates translation of stress-response proteins in the gut commensal and opportunistic pathogen Enterococcus faecalis. We analyze the tRNA epitranscriptome of E. faecalis in response to reactive oxygen species (ROS) or sublethal doses of ROS-inducing antibiotics and identify large decreases in N2-methyladenosine (m2A) in both 23 S ribosomal RNA and transfer RNA. This we determine to be due to ROS-mediated inactivation of the Fe-S cluster-containing methyltransferase, RlmN. Genetic knockout of RlmN gives rise to a proteome that mimics the oxidative stress response, with an increase in levels of superoxide dismutase and decrease in virulence proteins. While tRNA modifications were established to be dynamic for fine-tuning translation, here we report the discovery of a dynamically regulated, environmentally responsive rRNA modification. These studies lead to a model in which RlmN serves as a redox-sensitive molecular switch, directly relaying oxidative stress to modulating translation through the rRNA and the tRNA epitranscriptome, adding a different paradigm in which RNA modifications can directly regulate the proteome.
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Affiliation(s)
- Wei Lin Lee
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
| | - Ameya Sinha
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Ling Ning Lam
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL, USA
| | - Hooi Linn Loo
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
| | - Jiaqi Liang
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
- School of Chemistry, Chemical Engineering and Biotechnology, College of Engineering, Nanyang Technological University, Singapore, Singapore
| | - Peiying Ho
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
| | - Liang Cui
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
| | - Cheryl Siew Choo Chan
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
- Critical Analytics for Manufacturing Personalized-Medicine IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
| | - Thomas Begley
- Department of Biological Sciences and The RNA Institute, University at Albany, Albany, NY, USA
| | - Kimberly Ann Kline
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Peter Dedon
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore, Singapore.
- Dept. of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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9
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Monfort B, Want K, Gervason S, D’Autréaux B. Recent Advances in the Elucidation of Frataxin Biochemical Function Open Novel Perspectives for the Treatment of Friedreich’s Ataxia. Front Neurosci 2022; 16:838335. [PMID: 35310092 PMCID: PMC8924461 DOI: 10.3389/fnins.2022.838335] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/28/2022] [Indexed: 12/25/2022] Open
Abstract
Friedreich’s ataxia (FRDA) is the most prevalent autosomic recessive ataxia and is associated with a severe cardiac hypertrophy and less frequently diabetes. It is caused by mutations in the gene encoding frataxin (FXN), a small mitochondrial protein. The primary consequence is a defective expression of FXN, with basal protein levels decreased by 70–98%, which foremost affects the cerebellum, dorsal root ganglia, heart and liver. FXN is a mitochondrial protein involved in iron metabolism but its exact function has remained elusive and highly debated since its discovery. At the cellular level, FRDA is characterized by a general deficit in the biosynthesis of iron-sulfur (Fe-S) clusters and heme, iron accumulation and deposition in mitochondria, and sensitivity to oxidative stress. Based on these phenotypes and the proposed ability of FXN to bind iron, a role as an iron storage protein providing iron for Fe-S cluster and heme biosynthesis was initially proposed. However, this model was challenged by several other studies and it is now widely accepted that FXN functions primarily in Fe-S cluster biosynthesis, with iron accumulation, heme deficiency and oxidative stress sensitivity appearing later on as secondary defects. Nonetheless, the biochemical function of FXN in Fe-S cluster biosynthesis is still debated. Several roles have been proposed for FXN: iron chaperone, gate-keeper of detrimental Fe-S cluster biosynthesis, sulfide production stimulator and sulfur transfer accelerator. A picture is now emerging which points toward a unique function of FXN as an accelerator of a key step of sulfur transfer between two components of the Fe-S cluster biosynthetic complex. These findings should foster the development of new strategies for the treatment of FRDA. We will review here the latest discoveries on the biochemical function of frataxin and the implication for a potential therapeutic treatment of FRDA.
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10
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Freibert SA, Boniecki MT, Stümpfig C, Schulz V, Krapoth N, Winge DR, Mühlenhoff U, Stehling O, Cygler M, Lill R. N-terminal tyrosine of ISCU2 triggers [2Fe-2S] cluster synthesis by ISCU2 dimerization. Nat Commun 2021; 12:6902. [PMID: 34824239 PMCID: PMC8617193 DOI: 10.1038/s41467-021-27122-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 11/03/2021] [Indexed: 12/03/2022] Open
Abstract
Synthesis of iron-sulfur (Fe/S) clusters in living cells requires scaffold proteins for both facile synthesis and subsequent transfer of clusters to target apoproteins. The human mitochondrial ISCU2 scaffold protein is part of the core ISC (iron-sulfur cluster assembly) complex that synthesizes a bridging [2Fe-2S] cluster on dimeric ISCU2. Initial iron and sulfur loading onto monomeric ISCU2 have been elucidated biochemically, yet subsequent [2Fe-2S] cluster formation and dimerization of ISCU2 is mechanistically ill-defined. Our structural, biochemical and cell biological experiments now identify a crucial function of the universally conserved N-terminal Tyr35 of ISCU2 for these late reactions. Mixing two, per se non-functional ISCU2 mutant proteins with oppositely charged Asp35 and Lys35 residues, both bound to different cysteine desulfurase complexes NFS1-ISD11-ACP, restores wild-type ISCU2 maturation demonstrating that ionic forces can replace native Tyr-Tyr interactions during dimerization-induced [2Fe-2S] cluster formation. Our studies define the essential mechanistic role of Tyr35 in the reaction cycle of de novo mitochondrial [2Fe-2S] cluster synthesis. [2Fe-2S] protein cofactors are essential for life and are synthesized on ISCU2 scaffolds. Here, the authors show that hydrophobic interaction of two conserved N-terminal tyrosines induces ISCU2 dimerization and concomitant [2Fe-2S] cluster synthesis.
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Affiliation(s)
- Sven-A Freibert
- Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032, Marburg, Germany.,Core Facility 'Protein Biochemistry and Spectroscopy', Karl-von-Frisch-Str. 14, 35032, Marburg, Germany
| | - Michal T Boniecki
- Department of Biochemistry, Microbiology & Immunology, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, SK, S7N 5E5, Canada
| | - Claudia Stümpfig
- Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032, Marburg, Germany
| | - Vinzent Schulz
- Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032, Marburg, Germany
| | - Nils Krapoth
- Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032, Marburg, Germany
| | - Dennis R Winge
- Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032, Marburg, Germany.,Department of Medicine, University of Utah Health Sciences Center, Salt Lake City, UT, USA
| | - Ulrich Mühlenhoff
- Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032, Marburg, Germany
| | - Oliver Stehling
- Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032, Marburg, Germany.,Core Facility 'Protein Biochemistry and Spectroscopy', Karl-von-Frisch-Str. 14, 35032, Marburg, Germany
| | - Miroslaw Cygler
- Department of Biochemistry, Microbiology & Immunology, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, SK, S7N 5E5, Canada.
| | - Roland Lill
- Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032, Marburg, Germany. .,Core Facility 'Protein Biochemistry and Spectroscopy', Karl-von-Frisch-Str. 14, 35032, Marburg, Germany. .,LOEWE Zentrum für Synthetische Mikrobiologie SynMikro, Hans-Meerwein-Str., 35043, Marburg, Germany.
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11
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Metal utilization in genome-reduced bacteria: Do human mycoplasmas rely on iron? Comput Struct Biotechnol J 2021; 19:5752-5761. [PMID: 34765092 PMCID: PMC8566771 DOI: 10.1016/j.csbj.2021.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 12/04/2022] Open
Abstract
Mycoplasmas are parasitic bacteria with streamlined genomes and complex nutritional requirements. Although iron is vital for almost all organisms, its utilization by mycoplasmas is controversial. Despite its minimalist nature, mycoplasmas can survive and persist within the host, where iron availability is rigorously restricted through nutritional immunity. In this review, we describe the putative iron-enzymes, transporters, and metalloregulators of four relevant human mycoplasmas. This work brings in light critical differences in the mycoplasma-iron interplay. Mycoplasma penetrans, the species with the largest genome (1.36 Mb), shows a more classic repertoire of iron-related proteins, including different enzymes using iron-sulfur clusters as well as iron storage and transport systems. In contrast, the iron requirement is less apparent in the three species with markedly reduced genomes, Mycoplasma genitalium (0.58 Mb), Mycoplasma hominis (0.67 Mb) and Mycoplasma pneumoniae (0.82 Mb), as they exhibit only a few proteins possibly involved in iron homeostasis. The multiple facets of iron metabolism in mycoplasmas illustrate the remarkable evolutive potential of these minimal organisms when facing nutritional immunity and question the dependence of several human-infecting species for iron. Collectively, our data contribute to better understand the unique biology and infective strategies of these successful pathogens.
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Key Words
- ABC, ATP-binding cassette
- ECF transporter
- ECF, energy-coupling factor
- Fur, ferric uptake regulator
- Hrl, histidine-rich lipoprotein
- Iron homeostasis
- Metal acquisition
- Metalloenzyme
- Mge, Mycoplasma genitalium
- Mho, Mycoplasma hominis
- Mollicutes
- Mpe, Mycoplasma penetrans
- Mpn, Mycoplasma pneumonia
- Mycoplasmas
- PDB, protein data bank
- RNR, ribonucleotide reductase
- XRF, X-ray fluorescence
- ZIP, zinc-iron permease
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12
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Chen CH, Chou YT, Yang YW, Lo KY. High-dose copper activates p53-independent apoptosis through the induction of nucleolar stress in human cell lines. Apoptosis 2021; 26:612-627. [PMID: 34708319 DOI: 10.1007/s10495-021-01692-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2021] [Indexed: 12/17/2022]
Abstract
Copper is an essential micronutrient involved in many redox reactions in human cells. However, a high concentration of copper, intake from the environment or abnormal accumulation within cells because of genetic mutation, leads to cell toxicity. This is attributable to oxidative damage, altered gene expression, and functional impairment of the mitochondria. Copper stress also alters the morphology of the nucleolus, but the process has not been fully elucidated. In this study, cells were treated with copper sulfate at 3-9 ppm and examined if a high dose of copper would block ribosome biogenesis. With the incorrect distribution of nucleolar proteins nucleophosmin and fibrillarin to the nucleoplasm, ribosomal RNA (rRNA) processing was impaired; 34S rRNA from an abnormal A2 cut increased, and downstream pre-rRNAs decreased. The under-accumulation of 60S subunits was detected using sucrose gradients. From transcriptome analysis, ribosome synthesis-related genes were misregulated. Blockage in ribosome synthesis under copper-treatment induced nucleolar stress and triggered p53-independent apoptosis pathways. Thus, nucleolar stress is one cause of cell death under copper exposure.
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Affiliation(s)
- Chieh-Hsin Chen
- Department of Agricultural Chemistry, National Taiwan University, 1 Sec. 4, Roosevelt Road, Taipei, 10617, Taiwan
| | - Yi-Ting Chou
- Department of Agricultural Chemistry, National Taiwan University, 1 Sec. 4, Roosevelt Road, Taipei, 10617, Taiwan
| | - Ya-Wen Yang
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Kai-Yin Lo
- Department of Agricultural Chemistry, National Taiwan University, 1 Sec. 4, Roosevelt Road, Taipei, 10617, Taiwan.
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13
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Vallée Y, Youssef-Saliba S. Sulfur Amino Acids: From Prebiotic Chemistry to Biology and Vice Versa. SYNTHESIS-STUTTGART 2021. [DOI: 10.1055/a-1472-7914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractTwo sulfur-containing amino acids are included in the list of the 20 classical protein amino acids. A methionine residue is introduced at the start of the synthesis of all current proteins. Cysteine, thanks to its thiol function, plays an essential role in a very large number of catalytic sites. Here we present what is known about the prebiotic synthesis of these two amino acids and homocysteine, and we discuss their introduction into primitive peptides and more elaborate proteins.1 Introduction2 Sulfur Sources3 Prebiotic Synthesis of Cysteine4 Prebiotic Synthesis of Methionine5 Homocysteine and Its Thiolactone6 Methionine and Cystine in Proteins7 Prebiotic Scenarios Using Sulfur Amino Acids8 Introduction of Cys and Met in the Genetic Code9 Conclusion
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14
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Das AB, Seddon AR, O'Connor KM, Hampton MB. Regulation of the epigenetic landscape by immune cell oxidants. Free Radic Biol Med 2021; 170:131-149. [PMID: 33444713 DOI: 10.1016/j.freeradbiomed.2020.12.453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/21/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022]
Abstract
Excessive production of microbicidal oxidants by neutrophils can damage host tissue. The short-term response of cells to oxidative stress is well understood, but the mechanisms behind long-term consequences require further clarification. Epigenetic pathways mediate cellular adaptation, and are therefore a potential target of oxidative stress. Indeed, there is evidence that many proteins and metabolites involved in epigenetic pathways are redox sensitive. In this review we provide an overview of the epigenetic landscape and discuss the potential for redox regulation. Using this information, we highlight specific examples where neutrophil oxidants react with epigenetic pathway components. We also use published data from redox proteomics to map out known intersections between oxidative stress and epigenetics that may signpost helpful directions for future investigation. Finally, we discuss the role neutrophils play in adaptive pathologies with a focus on tumour initiation and progression. We hope this information will stimulate further discourse on the emerging field of redox epigenomics.
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Affiliation(s)
- Andrew B Das
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Annika R Seddon
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Karina M O'Connor
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Mark B Hampton
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
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15
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Lill R. From the discovery to molecular understanding of cellular iron-sulfur protein biogenesis. Biol Chem 2021; 401:855-876. [PMID: 32229650 DOI: 10.1515/hsz-2020-0117] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/10/2020] [Indexed: 12/23/2022]
Abstract
Protein cofactors often are the business ends of proteins, and are either synthesized inside cells or are taken up from the nutrition. A cofactor that strictly needs to be synthesized by cells is the iron-sulfur (Fe/S) cluster. This evolutionary ancient compound performs numerous biochemical functions including electron transfer, catalysis, sulfur mobilization, regulation and protein stabilization. Since the discovery of eukaryotic Fe/S protein biogenesis two decades ago, more than 30 biogenesis factors have been identified in mitochondria and cytosol. They support the synthesis, trafficking and target-specific insertion of Fe/S clusters. In this review, I first summarize what led to the initial discovery of Fe/S protein biogenesis in yeast. I then discuss the function and localization of Fe/S proteins in (non-green) eukaryotes. The major part of the review provides a detailed synopsis of the three major steps of mitochondrial Fe/S protein biogenesis, i.e. the de novo synthesis of a [2Fe-2S] cluster on a scaffold protein, the Hsp70 chaperone-mediated transfer of the cluster and integration into [2Fe-2S] recipient apoproteins, and the reductive fusion of [2Fe-2S] to [4Fe-4S] clusters and their subsequent assembly into target apoproteins. Finally, I summarize the current knowledge of the mechanisms underlying the maturation of cytosolic and nuclear Fe/S proteins.
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Affiliation(s)
- Roland Lill
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, D-35032 Marburg, Germany.,SYNMIKRO Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Str., D-35043 Marburg, Germany
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16
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The iron chaperone and nucleic acid-binding activities of poly(rC)-binding protein 1 are separable and independently essential. Proc Natl Acad Sci U S A 2021; 118:2104666118. [PMID: 34161287 DOI: 10.1073/pnas.2104666118] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Poly(rC)-binding protein (PCBP1) is a multifunctional adaptor protein that can coordinate single-stranded nucleic acids and iron-glutathione complexes, altering the processing and transfer of these ligands through interactions with other proteins. Multiple phenotypes are ascribed to cells lacking PCBP1, but the relative contribution of RNA, DNA, or iron chaperone activity is not consistently clear. Here, we report the identification of amino acid residues required for iron coordination on each structural domain of PCBP1 and confirm the requirement of iron coordination for binding target proteins BolA2 and ferritin. We further construct PCBP1 variants that lack either nucleic acid- or iron-binding activity and examine their functions in human cells and mouse tissues depleted of endogenous PCBP1. We find that these activities are separable and independently confer essential functions. While iron chaperone activity controls cell cycle progression and suppression of DNA damage, RNA/DNA-binding activity maintains cell viability in both cultured cell and mouse models. The coevolution of RNA/DNA binding and iron chaperone activities on a single protein may prove advantageous for nucleic acid processing that depends on enzymes with iron cofactors.
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17
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Cianciulli Sesso A, Lilić B, Amman F, Wolfinger MT, Sonnleitner E, Bläsi U. Gene Expression Profiling of Pseudomonas aeruginosa Upon Exposure to Colistin and Tobramycin. Front Microbiol 2021; 12:626715. [PMID: 33995291 PMCID: PMC8120321 DOI: 10.3389/fmicb.2021.626715] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/31/2021] [Indexed: 11/22/2022] Open
Abstract
Pseudomonas aeruginosa (Pae) is notorious for its high-level resistance toward clinically used antibiotics. In fact, Pae has rendered most antimicrobials ineffective, leaving polymyxins and aminoglycosides as last resort antibiotics. Although several resistance mechanisms of Pae are known toward these drugs, a profounder knowledge of hitherto unidentified factors and pathways appears crucial to develop novel strategies to increase their efficacy. Here, we have performed for the first time transcriptome analyses and ribosome profiling in parallel with strain PA14 grown in synthetic cystic fibrosis medium upon exposure to polymyxin E (colistin) and tobramycin. This approach did not only confirm known mechanisms involved in colistin and tobramycin susceptibility but revealed also as yet unknown functions/pathways. Colistin treatment resulted primarily in an anti-oxidative stress response and in the de-regulation of the MexT and AlgU regulons, whereas exposure to tobramycin led predominantly to a rewiring of the expression of multiple amino acid catabolic genes, lower tricarboxylic acid (TCA) cycle genes, type II and VI secretion system genes and genes involved in bacterial motility and attachment, which could potentially lead to a decrease in drug uptake. Moreover, we report that the adverse effects of tobramycin on translation are countered with enhanced expression of genes involved in stalled ribosome rescue, tRNA methylation and type II toxin-antitoxin (TA) systems.
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Affiliation(s)
- Anastasia Cianciulli Sesso
- Max Perutz Labs, Vienna Biocenter (VBC), Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Branislav Lilić
- Max Perutz Labs, Vienna Biocenter (VBC), Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Fabian Amman
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Michael T Wolfinger
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.,Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Elisabeth Sonnleitner
- Max Perutz Labs, Vienna Biocenter (VBC), Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Udo Bläsi
- Max Perutz Labs, Vienna Biocenter (VBC), Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
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18
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Systematic Surveys of Iron Homeostasis Mechanisms Reveal Ferritin Superfamily and Nucleotide Surveillance Regulation to be Modified by PINK1 Absence. Cells 2020; 9:cells9102229. [PMID: 33023155 PMCID: PMC7650593 DOI: 10.3390/cells9102229] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/21/2020] [Accepted: 09/29/2020] [Indexed: 12/13/2022] Open
Abstract
Iron deprivation activates mitophagy and extends lifespan in nematodes. In patients suffering from Parkinson’s disease (PD), PINK1-PRKN mutations via deficient mitophagy trigger iron accumulation and reduce lifespan. To evaluate molecular effects of iron chelator drugs as a potential PD therapy, we assessed fibroblasts by global proteome profiles and targeted transcript analyses. In mouse cells, iron shortage decreased protein abundance for iron-binding nucleotide metabolism enzymes (prominently XDH and ferritin homolog RRM2). It also decreased the expression of factors with a role for nucleotide surveillance, which associate with iron-sulfur-clusters (ISC), and are important for growth and survival. This widespread effect included prominently Nthl1-Ppat-Bdh2, but also mitochondrial Glrx5-Nfu1-Bola1, cytosolic Aco1-Abce1-Tyw5, and nuclear Dna2-Elp3-Pold1-Prim2. Incidentally, upregulated Pink1-Prkn levels explained mitophagy induction, the downregulated expression of Slc25a28 suggested it to function in iron export. The impact of PINK1 mutations in mouse and patient cells was pronounced only after iron overload, causing hyperreactive expression of ribosomal surveillance factor Abce1 and of ferritin, despite ferritin translation being repressed by IRP1. This misregulation might be explained by the deficiency of the ISC-biogenesis factor GLRX5. Our systematic survey suggests mitochondrial ISC-biogenesis and post-transcriptional iron regulation to be important in the decision, whether organisms undergo PD pathogenesis or healthy aging.
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19
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Braymer JJ, Freibert SA, Rakwalska-Bange M, Lill R. Mechanistic concepts of iron-sulfur protein biogenesis in Biology. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118863. [PMID: 33007329 DOI: 10.1016/j.bbamcr.2020.118863] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 02/08/2023]
Abstract
Iron-sulfur (Fe/S) proteins are present in virtually all living organisms and are involved in numerous cellular processes such as respiration, photosynthesis, metabolic reactions, nitrogen fixation, radical biochemistry, protein synthesis, antiviral defense, and genome maintenance. Their versatile functions may go back to the proposed role of their Fe/S cofactors in the origin of life as efficient catalysts and electron carriers. More than two decades ago, it was discovered that the in vivo synthesis of cellular Fe/S clusters and their integration into polypeptide chains requires assistance by complex proteinaceous machineries, despite the fact that Fe/S proteins can be assembled chemically in vitro. In prokaryotes, three Fe/S protein biogenesis systems are known; ISC, SUF, and the more specialized NIF. The former two systems have been transferred by endosymbiosis from bacteria to mitochondria and plastids, respectively, of eukaryotes. In their cytosol, eukaryotes use the CIA machinery for the biogenesis of cytosolic and nuclear Fe/S proteins. Despite the structural diversity of the protein constituents of these four machineries, general mechanistic concepts underlie the complex process of Fe/S protein biogenesis. This review provides a comprehensive and comparative overview of the various known biogenesis systems in Biology, and summarizes their common or diverging molecular mechanisms, thereby illustrating both the conservation and diverse adaptions of these four machineries during evolution and under different lifestyles. Knowledge of these fundamental biochemical pathways is not only of basic scientific interest, but is important for the understanding of human 'Fe/S diseases' and can be used in biotechnology.
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Affiliation(s)
- Joseph J Braymer
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, 35032 Marburg, Germany
| | - Sven A Freibert
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, 35032 Marburg, Germany
| | | | - Roland Lill
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, 35032 Marburg, Germany; SYNMIKRO Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35043 Marburg, Germany.
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20
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Karambelkar S, Udupa S, Gowthami VN, Ramachandra SG, Swapna G, Nagaraja V. Emergence of a novel immune-evasion strategy from an ancestral protein fold in bacteriophage Mu. Nucleic Acids Res 2020; 48:5294-5305. [PMID: 32369169 PMCID: PMC7261163 DOI: 10.1093/nar/gkaa319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/17/2020] [Accepted: 04/21/2020] [Indexed: 01/21/2023] Open
Abstract
The broad host range bacteriophage Mu employs a novel 'methylcarbamoyl' modification to protect its DNA from diverse restriction systems of its hosts. The DNA modification is catalyzed by a phage-encoded protein Mom, whose mechanism of action is a mystery. Here, we characterized the co-factor and metal-binding properties of Mom and provide a molecular mechanism to explain 'methylcarbamoyl'ation of DNA by Mom. Computational analyses revealed a conserved GNAT (GCN5-related N-acetyltransferase) fold in Mom. We demonstrate that Mom binds to acetyl CoA and identify the active site. We discovered that Mom is an iron-binding protein, with loss of Fe2+/3+-binding associated with loss of DNA modification activity. The importance of Fe2+/3+ is highlighted by the colocalization of Fe2+/3+ with acetyl CoA within the Mom active site. Puzzlingly, acid-base mechanisms employed by >309,000 GNAT members identified so far, fail to support methylcarbamoylation of adenine using acetyl CoA. In contrast, free-radical chemistry catalyzed by transition metals like Fe2+/3+ can explain the seemingly challenging reaction, accomplished by collaboration between acetyl CoA and Fe2+/3+. Thus, binding to Fe2+/3+, a small but unprecedented step in the evolution of Mom, allows a giant chemical leap from ordinary acetylation to a novel methylcarbamoylation function, while conserving the overall protein architecture.
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Affiliation(s)
- Shweta Karambelkar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Shubha Udupa
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Vykuntham Naga Gowthami
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | | | - Ganduri Swapna
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
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21
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Bimai O, Arragain S, Golinelli-Pimpaneau B. Structure-based mechanistic insights into catalysis by tRNA thiolation enzymes. Curr Opin Struct Biol 2020; 65:69-78. [PMID: 32652441 DOI: 10.1016/j.sbi.2020.06.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/16/2020] [Accepted: 06/04/2020] [Indexed: 12/21/2022]
Abstract
In all domains of life, ribonucleic acid (RNA) maturation includes post-transcriptional chemical modifications of nucleosides. Many sulfur-containing nucleosides have been identified in transfer RNAs (tRNAs), such as the derivatives of 2-thiouridine (s2U), 4-thiouridine (s4U), 2-thiocytidine (s2C), 2-methylthioadenosine (ms2A). These modifications are essential for accurate and efficient translation of the genetic code from messenger RNA (mRNA) for protein synthesis. This review summarizes the recent discoveries concerning the mechanistic and structural characterization of tRNA thiolation enzymes that catalyze the non-redox substitution of oxygen for sulfur in nucleosides. Two mechanisms have been described. One involves persulfide formation on catalytic cysteines, while the other uses a [4Fe-4S] cluster, chelated by three conserved cysteines only, as a sulfur carrier.
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Affiliation(s)
- Ornella Bimai
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris Sciences et Lettres, 11 Place Marcelin Berthelot, 75231 Paris cedex 05, France
| | - Simon Arragain
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris Sciences et Lettres, 11 Place Marcelin Berthelot, 75231 Paris cedex 05, France
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris Sciences et Lettres, 11 Place Marcelin Berthelot, 75231 Paris cedex 05, France.
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22
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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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23
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Ishiguro K, Arai T, Suzuki T. Depletion of S-adenosylmethionine impacts on ribosome biogenesis through hypomodification of a single rRNA methylation. Nucleic Acids Res 2019; 47:4226-4239. [PMID: 30799486 PMCID: PMC6486555 DOI: 10.1093/nar/gkz111] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 02/18/2019] [Indexed: 11/14/2022] Open
Abstract
S-adenosylmethionine (SAM) is an essential metabolite and a methyl group donor in all living organisms. The intracellular SAM concentration is tightly regulated, and depletion causes hypomethylation of substrates, growth defects and pathological consequences. In the emerging field of epitranscriptomics, SAM-dependent RNA methylations play a critical role in gene expression. Herein, we analyzed the methylation status of ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs) in Escherichia coli Δmtn strain in which cellular SAM was down-regulated, and found hypomodification of several methylation sites, including 2′-O-methylation at position 2552 (Um2552) of 23S rRNA. We observed severe growth defect of the Δmtn strain with significant accumulation of 45S ribosomal precursor harboring 23S rRNA with hypomodified Um2552. Strikingly, the growth defect was partially restored by overexpression of rlmE encoding the SAM-dependent methyltransferase responsible for Um2552. Although SAM is involved not only in rRNA methylation but also in various cellular processes, effects on ribosome biogenesis contribute substantially to the observed defects on cell proliferation.
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Affiliation(s)
- Kensuke Ishiguro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Taiga Arai
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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24
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Adusei-Danso F, Khaja FT, DeSantis M, Jeffrey PD, Dubnau E, Demeler B, Neiditch MB, Dubnau D. Structure-Function Studies of the Bacillus subtilis Ric Proteins Identify the Fe-S Cluster-Ligating Residues and Their Roles in Development and RNA Processing. mBio 2019; 10:e01841-19. [PMID: 31530674 PMCID: PMC6751060 DOI: 10.1128/mbio.01841-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 08/26/2019] [Indexed: 01/01/2023] Open
Abstract
In Bacillus subtilis, the RicA (YmcA), RicF (YlbF), and RicT (YaaT) proteins accelerate the phosphorylation of the transcription factor Spo0A, contributing to genetic competence, sporulation, and biofilm formation, and are also essential for the correct maturation of several protein-encoding and riboswitch RNAs. These proteins form a stable complex (RicAFT) that carries two [4Fe-4S]+2 clusters. We show here that the complex is a 1:1:1 heterotrimer, and we present the X-ray crystal structures of a RicAF heterotetramer and of a RicA dimer. We also demonstrate that one of the Fe-S clusters (cluster 1) is ligated by cysteine residues donated exclusively by RicT and can be retained when the RicT monomer is purified by itself. Cluster 2 is ligated by C167 from RicT, by C134 and C146 located near the C terminus of RicF, and by C141 at the C terminus of RicA. These findings imply the following novel arrangement: adjacent RicT residues C166 and 167 ligate clusters 1 and 2, respectively, while cluster 2 is ligated by cysteine residues from RicT, RicA, and RicF. Thus, the two clusters must lie close to one another and at the interface of the RicAFT protomers. We also show that the cluster-ligating cysteine residues, and therefore most likely both Fe-S clusters, are essential for cggR-gapA mRNA maturation, for the regulation of ricF transcript stability, and for several Ric-associated developmental phenotypes, including competence for transformation, biofilm formation, and sporulation. Finally, we present evidence that RicAFT, RicAF, and RicA and the RicT monomer may play distinct regulatory roles in vivoIMPORTANCE The RicA, RicF, and RicT proteins are widely conserved among the firmicute bacteria and play multiple roles in Bacillus subtilis Among the phenotypes associated with the inactivation of these proteins are the inability to be genetically transformed or to form biofilms, a decrease in sporulation frequency, and changes in the stability and maturation of multiple RNA species. Despite their importance, the molecular mechanisms of Ric protein activities have not been elucidated and the roles of the two iron-sulfur clusters on the complex of the three proteins are not understood. To unravel the mechanisms of Ric action, molecular characterization of the complex and of its constituent proteins is essential. This report represents a major step toward understanding the structures of the Ric proteins, the arrangement and roles of the Fe-S clusters, and the phenotypes associated with Ric mutations.
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Affiliation(s)
- Felix Adusei-Danso
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Faisal Tarique Khaja
- Public Health Research Center of New Jersey Medical School, Newark, New Jersey, USA
| | - Micaela DeSantis
- Public Health Research Center of New Jersey Medical School, Newark, New Jersey, USA
| | - Philip D Jeffrey
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Eugenie Dubnau
- Public Health Research Center of New Jersey Medical School, Newark, New Jersey, USA
| | - Borries Demeler
- Department of Chemistry & Biochemistry, The University of Lethbridge, Alberta, Canada
| | - Matthew B Neiditch
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - David Dubnau
- Public Health Research Center of New Jersey Medical School, Newark, New Jersey, USA
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25
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Bennett BD, Gralnick JA. Mechanisms of toxicity by and resistance to ferrous iron in anaerobic systems. Free Radic Biol Med 2019; 140:167-171. [PMID: 31251977 DOI: 10.1016/j.freeradbiomed.2019.06.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 06/13/2019] [Accepted: 06/23/2019] [Indexed: 12/24/2022]
Abstract
Iron is an essential element for nearly all life on Earth, primarily for its value as a redox active cofactor. Iron exists predominantly in two biologically relevant redox states: ferric iron, the oxidized state (Fe3+), and ferrous iron, the reduced state (Fe2+). Fe2+ is well known to facilitate electron transfer reactions that can lead to the generation of reactive oxygen species. Less is known about why iron is toxic to cells in the absence of oxygen, yet this phenomenon is critically important for our understanding of life on early Earth and in iron-rich ecosystems today. In this brief review, we will highlight our current understanding of anaerobic Fe2+ toxicity, focusing on molecular mechanistic studies in several model systems.
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Affiliation(s)
- B D Bennett
- Pacific Biosciences Research Center, University of Hawai‛i at Mānoa, Honolulu, HI, 96813, USA
| | - J A Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota - Twin Cities, St. Paul, MN, 55108, USA.
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26
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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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27
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Saninjuk K, Romsang A, Duang-nkern J, Vattanaviboon P, Mongkolsuk S. Transcriptional regulation of the Pseudomonas aeruginosa iron-sulfur cluster assembly pathway by binding of IscR to multiple sites. PLoS One 2019; 14:e0218385. [PMID: 31251744 PMCID: PMC6599224 DOI: 10.1371/journal.pone.0218385] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/01/2019] [Indexed: 01/06/2023] Open
Abstract
Iron-sulfur ([Fe-S]) cluster proteins have essential functions in many biological processes. [Fe-S] homeostasis is crucial for bacterial survival under a wide range of environmental conditions. IscR is a global transcriptional regulator in Pseudomonas aeruginosa; it has been shown to regulate genes involved in [Fe-S] cluster biosynthesis, iron homeostasis, resistance to oxidants, and pathogenicity. Many aspects of the IscR transcriptional regulatory mechanism differ from those of other well-studied systems. This study demonstrates the mechanisms of IscR Type-1 binding to its target sites that mediate the repression of gene expression at the isc operon, nfuA, and tpx. The analysis of IscR binding to multiple binding sites in the promoter region of the isc operon reveals that IscR first binds to the high-affinity site B followed by binding to the low-affinity site A. The results of in vitro IscR binding assays and in vivo analysis of IscR-mediated repression of gene expression support the role of site B as the primary site, while site A has only a minor role in the efficiency of IscR repression of gene expression. Ligation of an [Fe-S] cluster to IscR is required for the binding of IscR to target sites and in vivo repression and stress-induced gene expression. Analysis of Type-1 sites in many bacteria, including P. aeruginosa, indicates that the first and the last three AT-rich bases were among the most highly conserved bases within all analyzed Type-1 sites. Herein, we first propose the putative sequence of P. aeruginosa IscR Type-1 binding motif as 5'AWWSSYRMNNWWWTNNNWSGGNYWW3'. This can benefit further studies in the identification of novel genes under the IscR regulon and the regulatory mechanism model of P. aeruginosa IscR as it contributes to the roles of an [Fe-S] cluster in several biologically important cellular activities.
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Affiliation(s)
- Kritsakorn Saninjuk
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Adisak Romsang
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Center for Emerging Bacterial Infections, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Jintana Duang-nkern
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| | - Paiboon Vattanaviboon
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
- Program in Applied Biological Sciences: Environmental Health, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology, EHT, Ministry of Education, Bangkok, Thailand
| | - Skorn Mongkolsuk
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Center for Emerging Bacterial Infections, Faculty of Science, Mahidol University, Bangkok, Thailand
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology, EHT, Ministry of Education, Bangkok, Thailand
- * E-mail:
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28
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Tesarova M, Vondrackova A, Stufkova H, Veprekova L, Stranecky V, Berankova K, Hansikova H, Magner M, Galoova N, Honzik T, Vodickova E, Stary J, Zeman J. Sideroblastic anemia associated with multisystem mitochondrial disorders. Pediatr Blood Cancer 2019; 66:e27591. [PMID: 30588737 DOI: 10.1002/pbc.27591] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/18/2018] [Accepted: 11/29/2018] [Indexed: 01/19/2023]
Abstract
BACKGROUND Sideroblastic anemia represents a heterogeneous group of inherited or acquired diseases with disrupted erythroblast iron utilization, ineffective erythropoiesis, and variable systemic iron overload. In a cohort of 421 patients with multisystem mitochondrial diseases, refractory anemia was found in 8 children. RESULTS Five children had sideroblastic anemia with increased numbers of ring sideroblasts >15%. Two of the children had a fatal course of MLASA1 syndrome (mitochondrial myopathy, lactic acidosis, and sideroblastic anemia [SA]) due to a homozygous, 6-kb deletion in the PUS1 gene, part of the six-member family of pseudouridine synthases (pseudouridylases). Large homozygous deletions represent a novel cause of presumed PUS1-loss-of-function phenotype. The other three children with SA had Pearson syndrome (PS) due to mtDNA deletions of 4 to 8 kb; two of these children showed early onset of PS and died due to repeated sepsis; the other child had later onset of PS and survived as the hematological parameters normalized and the disease transitioned to Kearns-Sayre syndrome. In addition, anemia without ring sideroblasts was found in three other patients with mitochondrial disorders, including two children with later onset of PS and one child with failure to thrive, microcephaly, developmental delay, hypertrophic cardiomyopathy, and renal tubular acidosis due to the heterozygous mutations c.610A>G (p.Asn204Asp) and c.674C>T (p.Pro225Leu) in the COX10 gene encoding the cytochrome c oxidase assembly factor. CONCLUSIONS Sideroblastic anemia was found in fewer than 1.2% of patients with multisystem mitochondrial disease, and it was usually associated with an unfavorable prognosis.
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Affiliation(s)
- Marketa Tesarova
- Department of Paediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Alzbeta Vondrackova
- Department of Paediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Hana Stufkova
- Department of Paediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Lenka Veprekova
- Department of Paediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Viktor Stranecky
- Department of Paediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Kamila Berankova
- Department of Paediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Hana Hansikova
- Department of Paediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Martin Magner
- Department of Paediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Natalia Galoova
- Department of Paediatric Oncology and Haematology, Children's University Hospital, Kosice, Slovakia
| | - Tomas Honzik
- Department of Paediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Elena Vodickova
- Department of Haematology, Motol University Hospital, Prague, Czech Republic
| | - Jan Stary
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Jiri Zeman
- Department of Paediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
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29
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Khodour Y, Kaguni LS, Stiban J. Iron-sulfur clusters in nucleic acid metabolism: Varying roles of ancient cofactors. Enzymes 2019; 45:225-256. [PMID: 31627878 DOI: 10.1016/bs.enz.2019.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite their relative simplicity, iron-sulfur clusters have been omnipresent as cofactors in myriad cellular processes such as oxidative phosphorylation and other respiratory pathways. Recent research advances confirm the presence of different clusters in enzymes involved in nucleic acid metabolism. Iron-sulfur clusters can therefore be considered hallmarks of cellular metabolism. Helicases, nucleases, glycosylases, DNA polymerases and transcription factors, among others, incorporate various types of clusters that serve differing roles. In this chapter, we review our current understanding of the identity and functions of iron-sulfur clusters in DNA and RNA metabolizing enzymes, highlighting their importance as regulators of cellular function.
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Affiliation(s)
- Yara Khodour
- Department of Biology and Biochemistry, Birzeit University, West Bank, Palestine
| | - Laurie S Kaguni
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Johnny Stiban
- Department of Biology and Biochemistry, Birzeit University, West Bank, Palestine.
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30
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Mon EE, Wei FY, Ahmad RNR, Yamamoto T, Moroishi T, Tomizawa K. Regulation of mitochondrial iron homeostasis by sideroflexin 2. J Physiol Sci 2018; 69:359-373. [PMID: 30570704 PMCID: PMC6373408 DOI: 10.1007/s12576-018-0652-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/10/2018] [Indexed: 02/08/2023]
Abstract
Mitochondrial iron is indispensable for heme biosynthesis and iron–sulfur cluster assembly. Several mitochondrial transmembrane proteins have been implicated to function in the biosynthesis of heme and iron–sulfur clusters by transporting reaction intermediates. However, several mitochondrial proteins related to iron metabolism remain uncharacterized. Here, we show that human sideroflexin 2 (SFXN2), a member of the SFXN protein family, is involved in mitochondrial iron metabolism. SFXN2 is an evolutionarily conserved protein that localized to mitochondria via its transmembrane domain. SFXN2-knockout (KO) cells had an increased mitochondrial iron content, which was associated with decreases in the heme content and heme-dependent enzyme activities. By contrast, the activities of iron–sulfur cluster-dependent enzymes were unchanged in SFXN2-KO cells. Moreover, abnormal iron metabolism impaired mitochondrial respiration in SFXN2-KO cells and accelerated iron-mediated death of these cells. Our findings demonstrate that SFXN2 functions in mitochondrial iron metabolism by regulating heme biosynthesis.
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Affiliation(s)
- Ei Ei Mon
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Fan-Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo-Ku, Kumamoto, 860-8556, Japan. .,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Kawaguchi, 332-0012, Japan.
| | - Raja Norazireen Raja Ahmad
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Takahiro Yamamoto
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Toshiro Moroishi
- Department of Molecular Enzymology, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan.,Center for Metabolic Regulation of Healthy Aging, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Kawaguchi, 332-0012, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo-Ku, Kumamoto, 860-8556, Japan. .,Center for Metabolic Regulation of Healthy Aging, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan. .,Neutron Therapy Research Center, Okayama University, Okayama, 700-8558, Japan.
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31
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Hori H, Kawamura T, Awai T, Ochi A, Yamagami R, Tomikawa C, Hirata A. Transfer RNA Modification Enzymes from Thermophiles and Their Modified Nucleosides in tRNA. Microorganisms 2018; 6:E110. [PMID: 30347855 PMCID: PMC6313347 DOI: 10.3390/microorganisms6040110] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 12/11/2022] Open
Abstract
To date, numerous modified nucleosides in tRNA as well as tRNA modification enzymes have been identified not only in thermophiles but also in mesophiles. Because most modified nucleosides in tRNA from thermophiles are common to those in tRNA from mesophiles, they are considered to work essentially in steps of protein synthesis at high temperatures. At high temperatures, the structure of unmodified tRNA will be disrupted. Therefore, thermophiles must possess strategies to stabilize tRNA structures. To this end, several thermophile-specific modified nucleosides in tRNA have been identified. Other factors such as RNA-binding proteins and polyamines contribute to the stability of tRNA at high temperatures. Thermus thermophilus, which is an extreme-thermophilic eubacterium, can adapt its protein synthesis system in response to temperature changes via the network of modified nucleosides in tRNA and tRNA modification enzymes. Notably, tRNA modification enzymes from thermophiles are very stable. Therefore, they have been utilized for biochemical and structural studies. In the future, thermostable tRNA modification enzymes may be useful as biotechnology tools and may be utilized for medical science.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Takuya Kawamura
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Takako Awai
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Anna Ochi
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Ryota Yamagami
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Chie Tomikawa
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Akira Hirata
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
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32
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Gallagher PS, Larkin M, Thillainadesan G, Dhakshnamoorthy J, Balachandran V, Xiao H, Wellman C, Chatterjee R, Wheeler D, Grewal SIS. Iron homeostasis regulates facultative heterochromatin assembly in adaptive genome control. Nat Struct Mol Biol 2018; 25:372-383. [PMID: 29686279 PMCID: PMC5936480 DOI: 10.1038/s41594-018-0056-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/09/2018] [Indexed: 01/04/2023]
Abstract
Iron metabolism is critical for sustaining life and maintaining human health. Here, we find that iron homeostasis is linked to facultative heterochromatin assembly and regulation of gene expression during adaptive genome control. We show that the fission yeast Clr4/Suv39h histone methyltransferase is part of a rheostat-like mechanism in which transcriptional upregulation of mRNAs in response to environmental change provides feedback to prevent their uncontrolled expression through heterochromatin assembly. Interestingly, proper iron homeostasis is required, as iron depletion or downregulation of iron transporters causes defects in heterochromatin assembly and unrestrained upregulation of gene expression. Remarkably, an unbiased genetic screen revealed that restoration of iron homeostasis is sufficient to re-establish facultative heterochromatin and proper gene control genome-wide. These results establish a role for iron homeostasis in facultative heterochromatin assembly and reveal a dynamic mechanism for reprogramming the genome in response to environmental changes.
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Affiliation(s)
- Pamela S Gallagher
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Madeline Larkin
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gobi Thillainadesan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jothy Dhakshnamoorthy
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vanivilasini Balachandran
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hua Xiao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christopher Wellman
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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33
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Zohora F, Bidad K, Pourpak Z, Moin M. Biological and Immunological Aspects of Iron Deficiency Anemia in Cancer Development: A Narrative Review. Nutr Cancer 2018; 70:546-556. [PMID: 29697284 DOI: 10.1080/01635581.2018.1460685] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Iron Deficiency Anemia (IDA) is a universal health problem and a risk factor for the development of cancer. IDA changes the microenvironment of the human body by affecting both the biological and immunological systems. It increases DNA damage and genomic instability by different mechanisms. IDA is one of the leading causes of the imbalance between different antioxidant enzymes as well as enzymes involved in DNA damage and DNA repair systems of the body. It can affect the biogenesis/expression of microRNAs. IDA interrupts the oxidative phosphorylation energy metabolism and intestinal Cytochrome-P450 systems. It also disturbs multicellular signaling pathways involved in cell survival and helps in tumor angiogenesis. Moreover, IDA is also responsible for the functional deterioration of innate and adaptive immune systems that lead to immunological dysfunctions against invading pathogens. Genomic instability and immunological dysfunctions are the hallmarks of cancer development. In this review, we will review the evidence linking IDA to increased cancer risk.
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Affiliation(s)
- Fatema Zohora
- a Immunology, Asthma & Allergy Research Institute (IAARI), Tehran University of Medical Sciences (TUMS) , Tehran , Iran
| | - Katayoon Bidad
- a Immunology, Asthma & Allergy Research Institute (IAARI), Tehran University of Medical Sciences (TUMS) , Tehran , Iran
| | - Zahra Pourpak
- a Immunology, Asthma & Allergy Research Institute (IAARI), Tehran University of Medical Sciences (TUMS) , Tehran , Iran
| | - Mostafa Moin
- a Immunology, Asthma & Allergy Research Institute (IAARI), Tehran University of Medical Sciences (TUMS) , Tehran , Iran
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Padgett LR, Lentini JM, Holmes MJ, Stilger KL, Fu D, Sullivan WJ. Elp3 and RlmN: A tale of two mitochondrial tail-anchored radical SAM enzymes in Toxoplasma gondii. PLoS One 2018; 13:e0189688. [PMID: 29293520 PMCID: PMC5749711 DOI: 10.1371/journal.pone.0189688] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/30/2017] [Indexed: 11/19/2022] Open
Abstract
Radical S-adenosylmethionine (rSAM) enzymes use a 5'-deoxyadensyl 5'-radical to methylate a wide array of diverse substrates including proteins, lipids and nucleic acids. One such enzyme, Elongator protein-3 (TgElp3), is an essential protein in Toxoplasma gondii, a protozoan parasite that can cause life-threatening opportunistic disease. Unlike Elp3 homologues which are present in all domains of life, TgElp3 localizes to the outer mitochondrial membrane (OMM) via a tail-anchored trafficking mechanism in Toxoplasma. Intriguingly, we identified a second tail-anchored rSAM domain containing protein (TgRlmN) that also localizes to the OMM. The transmembrane domain (TMD) on Toxoplasma Elp3 and RlmN homologues is required for OMM localization and has not been seen beyond the chromalveolates. Both TgElp3 and TgRlmN contain the canonical rSAM amino acid sequence motif (CxxxCxxC) necessary to form the 4Fe-4S cluster required for tRNA modifications. In E. coli, RlmN is responsible for the 2-methlyadenosine (m2A) synthesis at purine 37 in tRNA while in S. cerevisiae, Elp3 is necessary for the formation of 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) at the wobble tRNA position. To investigate why these two rSAM enzymes localize to the mitochondrion in Toxoplasma, and whether or not TgRlmN and TgElp3 possess tRNA methyltransferase activity, a series of mutational and biochemical studies were performed. Overexpression of either TgElp3 or TgRlmN resulted in a significant parasite replication defect, but overexpression was tolerated if either the TMD or rSAM domain was mutated. Furthermore, we show the first evidence that Toxoplasma tRNAGlu contains the mcm5s2U modification, which is the putative downstream product generated by TgElp3 activity.
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Affiliation(s)
- Leah R. Padgett
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Jenna M. Lentini
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Michael J. Holmes
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Krista L. Stilger
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Dragony Fu
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - William J. Sullivan
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail:
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35
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Wang H, Chen X, Li C, Liu Y, Yang F, Wang C. Sequence-Based Prediction of Cysteine Reactivity Using Machine Learning. Biochemistry 2017; 57:451-460. [DOI: 10.1021/acs.biochem.7b00897] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Haobo Wang
- Synthetic
and Functional Biomolecules Center, Beijing National Laboratory for
Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of Ministry of Education, Peking University, Beijing 100871, China
- Department
of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xuemin Chen
- Synthetic
and Functional Biomolecules Center, Beijing National Laboratory for
Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of Ministry of Education, Peking University, Beijing 100871, China
- Department
of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Can Li
- Department
of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yuan Liu
- Synthetic
and Functional Biomolecules Center, Beijing National Laboratory for
Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of Ministry of Education, Peking University, Beijing 100871, China
- Department
of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
| | - Fan Yang
- Synthetic
and Functional Biomolecules Center, Beijing National Laboratory for
Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of Ministry of Education, Peking University, Beijing 100871, China
- Department
of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chu Wang
- Synthetic
and Functional Biomolecules Center, Beijing National Laboratory for
Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of Ministry of Education, Peking University, Beijing 100871, China
- Department
of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
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Agris PF, Narendran A, Sarachan K, Väre VYP, Eruysal E. The Importance of Being Modified: The Role of RNA Modifications in Translational Fidelity. Enzymes 2017; 41:1-50. [PMID: 28601219 DOI: 10.1016/bs.enz.2017.03.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The posttranscriptional modifications of tRNA's anticodon stem and loop (ASL) domain represent a third level, a third code, to the accuracy and efficiency of translating mRNA codons into the correct amino acid sequence of proteins. Modifications of tRNA's ASL domain are enzymatically synthesized and site specifically located at the anticodon wobble position-34 and 3'-adjacent to the anticodon at position-37. Degeneracy of the 64 Universal Genetic Codes and the limitation in the number of tRNA species require some tRNAs to decode more than one codon. The specific modification chemistries and their impact on the tRNA's ASL structure and dynamics enable one tRNA to decode cognate and "wobble codons" or to expand recognition to synonymous codons, all the while maintaining the translational reading frame. Some modified nucleosides' chemistries prestructure tRNA to read the two codons of a specific amino acid that shares a twofold degenerate codon box, and other chemistries allow a different tRNA to respond to all four codons of a fourfold degenerate codon box. Thus, tRNA ASL modifications are critical and mutations in genes for the modification enzymes and tRNA, the consequences of which is a lack of modification, lead to mistranslation and human disease. By optimizing tRNA anticodon chemistries, structure, and dynamics in all organisms, modifications ensure translational fidelity of mRNA transcripts.
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Affiliation(s)
- Paul F Agris
- The RNA Institute, State University of New York, Albany, NY, United States.
| | - Amithi Narendran
- The RNA Institute, State University of New York, Albany, NY, United States
| | - Kathryn Sarachan
- The RNA Institute, State University of New York, Albany, NY, United States
| | - Ville Y P Väre
- The RNA Institute, State University of New York, Albany, NY, United States
| | - Emily Eruysal
- The RNA Institute, State University of New York, Albany, NY, United States
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Zheng C, Black KA, Dos Santos PC. Diverse Mechanisms of Sulfur Decoration in Bacterial tRNA and Their Cellular Functions. Biomolecules 2017; 7:biom7010033. [PMID: 28327539 PMCID: PMC5372745 DOI: 10.3390/biom7010033] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/10/2017] [Accepted: 03/16/2017] [Indexed: 01/01/2023] Open
Abstract
Sulfur-containing transfer ribonucleic acids (tRNAs) are ubiquitous biomolecules found in all organisms that possess a variety of functions. For decades, their roles in processes such as translation, structural stability, and cellular protection have been elucidated and appreciated. These thionucleosides are found in all types of bacteria; however, their biosynthetic pathways are distinct among different groups of bacteria. Considering that many of the thio-tRNA biosynthetic enzymes are absent in Gram-positive bacteria, recent studies have addressed how sulfur trafficking is regulated in these prokaryotic species. Interestingly, a novel proposal has been given for interplay among thionucleosides and the biosynthesis of other thiocofactors, through participation of shared-enzyme intermediates, the functions of which are impacted by the availability of substrate as well as metabolic demand of thiocofactors. This review describes the occurrence of thio-modifications in bacterial tRNA and current methods for detection of these modifications that have enabled studies on the biosynthesis and functions of S-containing tRNA across bacteria. It provides insight into potential modes of regulation and potential evolutionary events responsible for divergence in sulfur metabolism among prokaryotes.
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Affiliation(s)
- Chenkang Zheng
- Department of Chemistry, Wake Forest University, Winston-Salem, NC 27101, USA.
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Currie MA, Brown G, Wong A, Ohira T, Sugiyama K, Suzuki T, Yakunin AF, Jia Z. Structural and functional characterization of the TYW3/Taw3 class of SAM-dependent methyltransferases. RNA (NEW YORK, N.Y.) 2017; 23:346-354. [PMID: 27932585 PMCID: PMC5311493 DOI: 10.1261/rna.057943.116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/25/2016] [Indexed: 06/01/2023]
Abstract
S-adenosylmethionine (SAM)-dependent methyltransferases regulate a wide range of biological processes through the modification of proteins, nucleic acids, polysaccharides, as well as various metabolites. TYW3/Taw3 is a SAM-dependent methyltransferase responsible for the formation of a tRNA modification known as wybutosine and its derivatives that are required for accurate decoding in protein synthesis. Here, we report the crystal structure of Taw3, a homolog of TYW3 from Sulfolobus solfataricus, which revealed a novel α/β fold. The sequence motif (S/T)xSSCxGR and invariant aspartate and histidine, conserved in TYW3/Taw3, cluster to form the catalytic center. These structural and sequence features indicate that TYW3/Taw3 proteins constitute a distinct class of SAM-dependent methyltransferases. Using site-directed mutagenesis along with in vivo complementation assays combined with mass spectrometry as well as ligand docking and cofactor binding assays, we have identified the active site of TYW3 and residues essential for cofactor binding and methyltransferase activity.
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Affiliation(s)
- Mark A Currie
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Andrew Wong
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Takayuki Ohira
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Kei Sugiyama
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
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Pain D, Dancis A. Roles of Fe-S proteins: from cofactor synthesis to iron homeostasis to protein synthesis. Curr Opin Genet Dev 2016; 38:45-51. [PMID: 27061491 DOI: 10.1016/j.gde.2016.03.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 02/27/2016] [Accepted: 03/09/2016] [Indexed: 12/28/2022]
Abstract
Fe-S cluster assembly is an essential process for all cells. Impairment of Fe-S cluster assembly creates diseases in diverse and surprising ways. In one scenario, the loss of function of lipoic acid synthase, an enzyme with Fe-S cluster cofactor in mitochondria, impairs activity of various lipoamide-dependent enzymes with drastic consequences for metabolism. In a second scenario, the heme biosynthetic pathway in red cell precursors is specifically targeted, and iron homeostasis is perturbed, but lipoic acid synthesis is unaffected. In a third scenario, tRNA modifications arising from action of the cysteine desulfurase and/or Fe-S cluster proteins are lost, which may lead to impaired protein synthesis. These defects can then result in cancer, neurologic dysfunction or type 2 diabetes.
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Affiliation(s)
- Debkumar Pain
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ 07101, USA
| | - Andrew Dancis
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Abstract
Fe-S clusters are critically important cofactors implicated in numerous cellular processes, including respiration, amino acid biosynthesis, cofactor biosynthesis, tRNA modification, DNA repair and regulation of gene expression. In the accompanying manuscript, Tanaka et al. show that reengineering of the isoprenoid biosynthetic pathway in E. coli (to bypass the usage of essential Fe-S cluster proteins by inserting the mevalonate pathway) can offset the indispensability of the Fe-S cluster biosynthetic systems. They show that the resulting Δisc Δsuf double mutants supplemented with mevalonate can grow slowly without detectable Fe-S cluster proteins. This result is astounding and raises interesting questions about what is essential and what is dispensable in the compendium of Fe-S cluster protein functions in this cell.
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Affiliation(s)
- Agostinho G Rocha
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Andrew Dancis
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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Tanaka N, Kanazawa M, Tonosaki K, Yokoyama N, Kuzuyama T, Takahashi Y. Novel features of the ISC machinery revealed by characterization of Escherichia coli mutants that survive without iron-sulfur clusters. Mol Microbiol 2015; 99:835-48. [PMID: 26560204 DOI: 10.1111/mmi.13271] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2015] [Indexed: 01/09/2023]
Abstract
Biological assembly of iron-sulfur (Fe-S) clusters is mediated by complex systems consisting of multiple proteins. Escherichia coli possesses two distinct systems called the ISC and SUF machineries encoded by iscSUA-hscBA-fdx-iscX and sufABCDSE respectively. Deletion of both pathways results in absence of the biosynthetic apparatus for Fe-S clusters, and consequent lethality, which has hampered detailed genetic studies. Here we report that modification of the isoprenoid biosynthetic pathway can offset the indispensability of the Fe-S cluster biosynthetic systems and show that the resulting Δisc Δsuf double mutants can grow without detectable Fe-S cluster-containing proteins. We also constructed a series of mutants in which each isc gene was disrupted in the deletion background of sufABCDSE. Phenotypic analysis of the mutants revealed that Fdx, an essential electron-transfer Fe-S protein in the ISC machinery, is dispensable under anaerobic conditions, which is similar to the situation with IscA. Furthermore, we found that several suppressor mutations in IscU, an Fe-S scaffold protein responsible for the de novo Fe-S cluster assembly, could bypass the essential role of the chaperone system HscA and HscB. These findings pave the way toward a detailed molecular analysis to understand the mechanisms involved in Fe-S cluster biosynthesis.
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Affiliation(s)
- Naoyuki Tanaka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Miaki Kanazawa
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Keitaro Tonosaki
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Nao Yokoyama
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yasuhiro Takahashi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
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Lill R, Dutkiewicz R, Freibert SA, Heidenreich T, Mascarenhas J, Netz DJ, Paul VD, Pierik AJ, Richter N, Stümpfig M, Srinivasan V, Stehling O, Mühlenhoff U. The role of mitochondria and the CIA machinery in the maturation of cytosolic and nuclear iron–sulfur proteins. Eur J Cell Biol 2015; 94:280-91. [DOI: 10.1016/j.ejcb.2015.05.002] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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