1
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Tessmer I, Margison GP. The DNA Alkyltransferase Family of DNA Repair Proteins: Common Mechanisms, Diverse Functions. Int J Mol Sci 2023; 25:463. [PMID: 38203633 PMCID: PMC10779285 DOI: 10.3390/ijms25010463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
DNA alkyltransferase and alkyltransferase-like family proteins are responsible for the repair of highly mutagenic and cytotoxic O6-alkylguanine and O4-alkylthymine bases in DNA. Their mechanism involves binding to the damaged DNA and flipping the base out of the DNA helix into the active site pocket in the protein. Alkyltransferases then directly and irreversibly transfer the alkyl group from the base to the active site cysteine residue. In contrast, alkyltransferase-like proteins recruit nucleotide excision repair components for O6-alkylguanine elimination. One or more of these proteins are found in all kingdoms of life, and where this has been determined, their overall DNA repair mechanism is strictly conserved between organisms. Nevertheless, between species, subtle as well as more extensive differences that affect target lesion preferences and/or introduce additional protein functions have evolved. Examining these differences and their functional consequences is intricately entwined with understanding the details of their DNA repair mechanism(s) and their biological roles. In this review, we will present and discuss various aspects of the current status of knowledge on this intriguing protein family.
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Affiliation(s)
- Ingrid Tessmer
- Rudolf Virchow Center, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Geoffrey P. Margison
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
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2
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Yin Y, Zhang L. Archaeal DNA alkylation repair conducted by DNA glycosylase and methyltransferase. Appl Microbiol Biotechnol 2023; 107:3131-3142. [PMID: 37036526 DOI: 10.1007/s00253-023-12506-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/25/2023] [Accepted: 03/28/2023] [Indexed: 04/11/2023]
Abstract
Alkylated bases in DNA created in the presence of endogenous and exogenous alkylating agents are either cytotoxic or mutagenic, or both to a cell. Currently, cells have evolved several strategies for repairing alkylated base. One strategy is a base excision repair process triggered by a specific DNA glycosylase that is used for the repair of the cytotoxic 3-methyladenine. Additionally, the cytotoxic and mutagenic O6-methylguanine (O6-meG) is corrected by O6-methylguanine methyltransferase (MGMT) via directly transferring the methyl group in the lesion to a specific cysteine in this protein. Furthermore, oxidative DNA demethylation catalyzed by DNA dioxygenase is utilized for repairing the cytotoxic 3-methylcytosine (3-meC) and 1-methyladenine (1-meA) in a direct reversal manner. As the third domain of life, Archaea possess 3-methyladenine DNA glycosylase II (AlkA) and MGMT, but no DNA dioxygenase homologue responsible for oxidative demethylation. Herein, we summarize recent progress in structural and biochemical properties of archaeal AlkA and MGMT to gain a better understanding of archaeal DNA alkylation repair, focusing on similarities and differences between the proteins from different archaeal species and between these archaeal proteins and their bacterial and eukaryotic relatives. To our knowledge, it is the first review on archaeal DNA alkylation repair conducted by DNA glycosylase and methyltransferase. KEY POINTS: • Archaeal MGMT plays an essential role in the repair of O 6 -meG • Archaeal AlkA can repair 3-meC and 1-meA.
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Affiliation(s)
- Youcheng Yin
- Marine Science & Technology Institute, College of Environmental Science and Engineering, Yangzhou University, Yangzhou City, China
| | - Likui Zhang
- Marine Science & Technology Institute, College of Environmental Science and Engineering, Yangzhou University, Yangzhou City, China.
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3
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Merlo R, Mattossovich R, Genta M, Valenti A, Di Mauro G, Minassi A, Miggiano R, Perugino G. First thermostable CLIP-tag by rational design applied to an archaeal O-alkyl-guanine-DNA-alkyl-transferase. Comput Struct Biotechnol J 2022; 20:5275-5286. [PMID: 36212535 PMCID: PMC9519396 DOI: 10.1016/j.csbj.2022.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 11/30/2022] Open
Abstract
Self-labelling protein tags (SLPs) are resourceful tools that revolutionized sensor imaging, having the versatile ability of being genetically fused with any protein of interest and undergoing activation with alternative probes specifically designed for each variant (namely, SNAP-tag, CLIP-tag and Halo-tag). Commercially available SLPs are highly useful in studying molecular aspects of mesophilic organisms, while they fail in characterizing model organisms that thrive in harsh conditions. By applying an integrated computational and structural approach, we designed a engineered variant of the alkylguanine-DNA-alkyl-transferase (OGT) from the hyper-thermophilic archaeon Saccharolobus solfataricus (SsOGT), with no DNA-binding activity, able to covalently react with O6-benzyl-cytosine (BC-) derivatives, obtaining the first thermostable CLIP-tag, named SsOGT-MC8. The presented construct is able to recognize and to covalently bind BC- substrates with a marked specificity, displaying a very low activity on orthogonal benzyl-guanine (BG-) substrate and showing a remarkable thermal stability that broadens the applicability of SLPs. The rational mutagenesis that, starting from SsOGT, led to the production of SsOGT-MC8 was first evaluated by structural predictions to precisely design the chimeric construct, by mutating specific residues involved in protein stability and substrate recognition. The final construct was further validated by biochemical characterization and X-ray crystallography, allowing us to present here the first structural model of a CLIP-tag establishing the molecular determinants of its activity, as well as proposing a general approach for the rational engineering of any O6-alkylguanine-DNA-alkyl-transferase turning it into a SNAP- and a CLIP-tag variant.
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4
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Kröll S, Rabe KS, Niemeyer CM. An Orthogonal Covalent Connector System for the Efficient Assembly of Enzyme Cascades on DNA Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2105095. [PMID: 34825457 DOI: 10.1002/smll.202105095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/19/2021] [Indexed: 05/06/2023]
Abstract
Combining structural DNA nanotechnology with the virtually unlimited variety of enzymes offers unique opportunities for generating novel biocatalytic devices. However, the immobilization of enzymes is still restricted by a lack of efficient covalent coupling techniques. The rational re-engineering of the genetically fusible SNAP-tag linker is reported here. By replacing five amino acids that alter the electrostatic properties of the SNAP_R5 variant, up to 11-fold increased coupling efficiency with benzylguanine-modified oligonucleotides and DNA origami nanostructures (DON) was achieved, resulting in typical occupancy densities of 75%. The novel SNAP_R5 linker can be combined with the equally efficient Halo-based oligonucleotide binding tag (HOB). Since both linkers exhibit neither cross-reactivity nor non-specific binding, they allowed orthogonal assembly of an enzyme cascade consisting of the stereoselective ketoreductase Gre2p and the cofactor-regenerating isocitrate dehydrogenase on DON. The cascade showed approximately 1.6-fold higher activity in a stereoselective cascade reaction than the corresponding free solubilized enzymes. The connector system presented here and the methods used to validate it represent important tools for further development of DON-based multienzyme systems to investigate mechanistic effects of substrate channeling and compartmentalization relevant for exploitation in biosensing and catalysis.
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Affiliation(s)
- Sandra Kröll
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
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5
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Koirala RP, Pokhrel R, Baral P, Tiwari PB, Chapagain PP, Adhikari NP. Structural insights into the repair mechanism of AGT for methyl-induced DNA damage. Biol Chem 2021; 402:1203-1211. [PMID: 34192828 DOI: 10.1515/hsz-2021-0198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/29/2021] [Indexed: 02/06/2023]
Abstract
Methylation induced DNA base-pairing damage is one of the major causes of cancer. O6-alkylguanine-DNA alkyltransferase (AGT) is considered a demethylation agent of the methylated DNA. Structural investigations with thermodynamic properties of the AGT-DNA complex are still lacking. In this report, we modeled two catalytic states of AGT-DNA interactions and an AGT-DNA covalent complex and explored structural features using molecular dynamics (MD) simulations. We utilized the umbrella sampling method to investigate the changes in the free energy of the interactions in two different AGT-DNA catalytic states, one with methylated GUA in DNA and the other with methylated CYS145 in AGT. These non-covalent complexes represent the pre- and post-repair complexes. Therefore, our study encompasses the process of recognition, complex formation, and separation of the AGT and the damaged (methylated) DNA base. We believe that the use of parameters for the amino acid and nucleotide modifications and for the protein-DNA covalent bond will allow investigations of the DNA repair mechanism as well as the exploration of cancer therapeutics targeting the AGT-DNA complexes at various functional states as well as explorations via stabilization of the complex.
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Affiliation(s)
| | - Rudramani Pokhrel
- Department of Physics, Florida International University, Miami, FL, USA
| | - Prabin Baral
- Department of Physics, Florida International University, Miami, FL, USA
| | | | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
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6
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Wilhelm J, Kühn S, Tarnawski M, Gotthard G, Tünnermann J, Tänzer T, Karpenko J, Mertes N, Xue L, Uhrig U, Reinstein J, Hiblot J, Johnsson K. Kinetic and Structural Characterization of the Self-Labeling Protein Tags HaloTag7, SNAP-tag, and CLIP-tag. Biochemistry 2021; 60:2560-2575. [PMID: 34339177 PMCID: PMC8388125 DOI: 10.1021/acs.biochem.1c00258] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/23/2021] [Indexed: 01/16/2023]
Abstract
The self-labeling protein tags (SLPs) HaloTag7, SNAP-tag, and CLIP-tag allow the covalent labeling of fusion proteins with synthetic molecules for applications in bioimaging and biotechnology. To guide the selection of an SLP-substrate pair and provide guidelines for the design of substrates, we report a systematic and comparative study of the labeling kinetics and substrate specificities of HaloTag7, SNAP-tag, and CLIP-tag. HaloTag7 reaches almost diffusion-limited labeling rate constants with certain rhodamine substrates, which are more than 2 orders of magnitude higher than those of SNAP-tag for the corresponding substrates. SNAP-tag labeling rate constants, however, are less affected by the structure of the label than those of HaloTag7, which vary over 6 orders of magnitude for commonly employed substrates. Determining the crystal structures of HaloTag7 and SNAP-tag labeled with fluorescent substrates allowed us to rationalize their substrate preferences. We also demonstrate how these insights can be exploited to design substrates with improved labeling kinetics.
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Affiliation(s)
- Jonas Wilhelm
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Stefanie Kühn
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Miroslaw Tarnawski
- Protein
Expression and Characterization Facility, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Guillaume Gotthard
- Structural
Biology Group, European Synchrotron Radiation
Facility (ESRF), 38043 Grenoble, France
| | - Jana Tünnermann
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Timo Tänzer
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Julie Karpenko
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Nicole Mertes
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Lin Xue
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Ulrike Uhrig
- Chemical
Biology Core Facility, European Molecular
Biology Laboratory, 69117 Heidelberg, Germany
| | - Jochen Reinstein
- Department
of Biomolecular Mechanisms, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Julien Hiblot
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Kai Johnsson
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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7
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Merlo R, Caprioglio D, Cillo M, Valenti A, Mattossovich R, Morrone C, Massarotti A, Rossi F, Miggiano R, Leonardi A, Minassi A, Perugino G. The SNAP- tag technology revised: an effective chemo-enzymatic approach by using a universal azide-based substrate. J Enzyme Inhib Med Chem 2021; 36:85-97. [PMID: 33121288 PMCID: PMC7599001 DOI: 10.1080/14756366.2020.1841182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
SNAP-tag ® is a powerful technology for the labelling of protein/enzymes by using benzyl-guanine (BG) derivatives as substrates. Although commercially available or ad hoc produced, their synthesis and purification are necessary, increasing time and costs. To address this limitation, here we suggest a revision of this methodology, by performing a chemo-enzymatic approach, by using a BG-substrate containing an azide group appropriately distanced by a spacer from the benzyl ring. The SNAP-tag ® and its relative thermostable version (SsOGT-H5 ) proved to be very active on this substrate. The stability of these tags upon enzymatic reaction makes possible the exposition to the solvent of the azide-moiety linked to the catalytic cysteine, compatible for the subsequent conjugation with DBCO-derivatives by azide-alkyne Huisgen cycloaddition. Our studies propose a strengthening and an improvement in terms of biotechnological applications for this self-labelling protein-tag.
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Affiliation(s)
- Rosa Merlo
- Institute of Biosciences and BioResources, National Research Council of Italy, Naples, Italy
| | - Diego Caprioglio
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Novara, Italy
| | - Michele Cillo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Anna Valenti
- Institute of Biosciences and BioResources, National Research Council of Italy, Naples, Italy
| | - Rosanna Mattossovich
- Institute of Biosciences and BioResources, National Research Council of Italy, Naples, Italy
| | - Castrese Morrone
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Novara, Italy
| | - Alberto Massarotti
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Novara, Italy.,IXTAL srl, Novara, Italy
| | - Franca Rossi
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Novara, Italy
| | - Riccardo Miggiano
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Novara, Italy.,IXTAL srl, Novara, Italy
| | - Antonio Leonardi
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Alberto Minassi
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Novara, Italy
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources, National Research Council of Italy, Naples, Italy
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8
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Farag N, Mattossovich R, Merlo R, Nierzwicki Ł, Palermo G, Porchetta A, Perugino G, Ricci F. Folding-upon-Repair DNA Nanoswitches for Monitoring the Activity of DNA Repair Enzymes. Angew Chem Int Ed Engl 2021; 60:7283-7289. [PMID: 33415794 PMCID: PMC8783695 DOI: 10.1002/anie.202016223] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Indexed: 09/28/2023]
Abstract
We present a new class of DNA-based nanoswitches that, upon enzymatic repair, could undergo a conformational change mechanism leading to a change in fluorescent signal. Such folding-upon-repair DNA nanoswitches are synthetic DNA sequences containing O6 -methyl-guanine (O6 -MeG) nucleobases and labelled with a fluorophore/quencher optical pair. The nanoswitches are rationally designed so that only upon enzymatic demethylation of the O6 -MeG nucleobases they can form stable intramolecular Hoogsteen interactions and fold into an optically active triplex DNA structure. We have first characterized the folding mechanism induced by the enzymatic repair activity through fluorescent experiments and Molecular Dynamics simulations. We then demonstrated that the folding-upon-repair DNA nanoswitches are suitable and specific substrates for different methyltransferase enzymes including the human homologue (hMGMT) and they allow the screening of novel potential methyltransferase inhibitors.
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Affiliation(s)
- Nada Farag
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Rosanna Mattossovich
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Rosa Merlo
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Łukasz Nierzwicki
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
- Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
| | - Alessandro Porchetta
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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9
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Farag N, Mattossovich R, Merlo R, Nierzwicki Ł, Palermo G, Porchetta A, Perugino G, Ricci F. Folding‐upon‐Repair DNA Nanoswitches for Monitoring the Activity of DNA Repair Enzymes. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016223] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Nada Farag
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Rosanna Mattossovich
- Institute of Biosciences and BioResources National Research Council of Italy Via Pietro Castellino 111 80131 Naples Italy
| | - Rosa Merlo
- Institute of Biosciences and BioResources National Research Council of Italy Via Pietro Castellino 111 80131 Naples Italy
| | - Łukasz Nierzwicki
- Department of Bioengineering University of California Riverside 900 University Avenue Riverside CA 52512 USA
| | - Giulia Palermo
- Department of Bioengineering University of California Riverside 900 University Avenue Riverside CA 52512 USA
- Department of Chemistry University of California Riverside 900 University Avenue Riverside CA 52512 USA
| | - Alessandro Porchetta
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources National Research Council of Italy Via Pietro Castellino 111 80131 Naples Italy
| | - Francesco Ricci
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
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10
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Copp W, Wilds CJ. O 6 -Alkylguanine DNA Alkyltransferase Mediated Disassembly of a DNA Tetrahedron. Chemistry 2020; 26:14802-14806. [PMID: 32543755 DOI: 10.1002/chem.202002565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Indexed: 11/05/2022]
Abstract
Tetrahedron DNA structures were formed by the assembly of three-way junction (TWJ) oligonucleotides containing O6 -2'-deoxyguanosine-alkylene-O6 -2'-deoxyguanosine (butylene and heptylene linked) intrastrand cross-links (IaCLs) lacking a phosphodiester group between the 2'-deoxyribose residues. The DNA tetrahedra containing TWJs were shown to undergo an unhooking reaction by the human DNA repair protein O6 -alkylguanine DNA alkyltransferase (hAGT) resulting in structure disassembly. The unhooking reaction of hAGT towards the DNA tetrahedra was observed to be moderate to virtually complete depending on the protein equivalents. DNA tetrahedron structures have been explored as drug delivery platforms that release their payload in response to triggers, such as light, chemical agents or hybridization of release strands. The dismantling of DNA tetrahedron structures by a DNA repair protein contributes to the armamentarium of approaches for drug release employing DNA nanostructures.
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Affiliation(s)
- William Copp
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, H4B 1R6, Canada
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, H4B 1R6, Canada
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11
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O6-alkylguanine-DNA Alkyltransferases in Microbes Living on the Edge: From Stability to Applicability. Int J Mol Sci 2020; 21:ijms21082878. [PMID: 32326075 PMCID: PMC7216122 DOI: 10.3390/ijms21082878] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/09/2020] [Accepted: 04/16/2020] [Indexed: 02/06/2023] Open
Abstract
The genome of living cells is continuously exposed to endogenous and exogenous attacks, and this is particularly amplified at high temperatures. Alkylating agents cause DNA damage, leading to mutations and cell death; for this reason, they also play a central role in chemotherapy treatments. A class of enzymes known as AGTs (alkylguanine-DNA-alkyltransferases) protects the DNA from mutations caused by alkylating agents, in particular in the recognition and repair of alkylated guanines in O6-position. The peculiar irreversible self-alkylation reaction of these enzymes triggered numerous studies, especially on the human homologue, in order to identify effective inhibitors in the fight against cancer. In modern biotechnology, engineered variants of AGTs are developed to be used as protein tags for the attachment of chemical ligands. In the last decade, research on AGTs from (hyper)thermophilic sources proved useful as a model system to clarify numerous phenomena, also common for mesophilic enzymes. This review traces recent progress in this class of thermozymes, emphasizing their usefulness in basic research and their consequent advantages for in vivo and in vitro biotechnological applications.
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12
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Merlo R, Del Prete S, Valenti A, Mattossovich R, Carginale V, Supuran CT, Capasso C, Perugino G. An AGT-based protein-tag system for the labelling and surface immobilization of enzymes on E. coli outer membrane. J Enzyme Inhib Med Chem 2019; 34:490-499. [PMID: 30724623 PMCID: PMC6366409 DOI: 10.1080/14756366.2018.1559161] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 11/28/2018] [Accepted: 12/04/2018] [Indexed: 12/14/2022] Open
Abstract
The use of natural systems, such as outer membrane protein A (OmpA), phosphoporin E (PhoE), ice nucleation protein (INP), etc., has been proved very useful for the surface exposure of proteins on the outer membrane of Gram-negative bacteria. These strategies have the clear advantage of unifying in a one-step the production, the purification and the in vivo immobilisation of proteins/biocatalysts onto a specific biological support. Here, we introduce the novel Anchoring-and-Self-Labelling-protein-tag (ASLtag), which allows the in vivo immobilisation of enzymes on E. coli surface and the labelling of the neosynthesised proteins with the engineered alkylguanine-DNA-alkyl-transferase (H5) from Sulfolobus solfataricus. Our results demonstrated that this tag enhanced the overexpression of thermostable enzymes, such as the carbonic anhydrase (SspCA) from Sulfurihydrogenibium yellowstonense and the β-glycoside hydrolase (SsβGly) from S. solfataricus, without affecting their folding and catalytic activity, proposing a new tool for the improvement in the utilisation of biocatalysts of biotechnological interest.
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Affiliation(s)
- Rosa Merlo
- Department of Biology Agriculture and Food Sciences, Institute of Bioscience and BioResources – National Research Council of Italy, Naples, Italy
| | - Sonia Del Prete
- Department of Biology Agriculture and Food Sciences, Institute of Bioscience and BioResources – National Research Council of Italy, Naples, Italy
| | - Anna Valenti
- Department of Biology Agriculture and Food Sciences, Institute of Bioscience and BioResources – National Research Council of Italy, Naples, Italy
| | - Rosanna Mattossovich
- Department of Biology Agriculture and Food Sciences, Institute of Bioscience and BioResources – National Research Council of Italy, Naples, Italy
| | - Vincenzo Carginale
- Department of Biology Agriculture and Food Sciences, Institute of Bioscience and BioResources – National Research Council of Italy, Naples, Italy
| | - Claudiu T. Supuran
- Neurofarba Department, University of Florence, Polo Scientifico, Sesto Fiorentino Firenze, Italy
| | - Clemente Capasso
- Department of Biology Agriculture and Food Sciences, Institute of Bioscience and BioResources – National Research Council of Italy, Naples, Italy
| | - Giuseppe Perugino
- Department of Biology Agriculture and Food Sciences, Institute of Bioscience and BioResources – National Research Council of Italy, Naples, Italy
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13
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Mattossovich R, Merlo R, Fontana A, d'Ippolito G, Terns MP, Watts EA, Valenti A, Perugino G. A journey down to hell: new thermostable protein-tags for biotechnology at high temperatures. Extremophiles 2019; 24:81-91. [PMID: 31555904 DOI: 10.1007/s00792-019-01134-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/13/2019] [Indexed: 12/14/2022]
Abstract
The specific labelling of proteins in recent years has made use of self-labelling proteins, such as the SNAP-tag® and the Halotag®. These enzymes, by their nature or suitably engineered, have the ability to specifically react with their respective substrates, but covalently retaining a part of them in the catalytic site upon reaction. This led to the synthesis of substrates conjugated with, e.g., fluorophores (proposing them as alternatives to fluorescent proteins), but also with others chemical groups, for numerous biotechnological applications. Recently, a mutant of the OGT from Saccharolobus solfataricus (H5) very stable to high temperatures and in the presence of physical and chemical denaturing agents has been proposed as a thermostable SNAP-tag® for in vivo and in vitro harsh reaction conditions. Here, we show two new thermostable OGTs from Thermotoga neapolitana and Pyrococcus furiosus, which, respectively, display a higher catalytic activity and thermostability respect to H5, proposing them as alternatives for in vivo studies in these extreme model organisms.
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Affiliation(s)
- Rosanna Mattossovich
- Institute of Biosciences and BioResources, National Council of Research of Italy, Via P. Castellino 111, 80131, Naples, Italy
| | - Rosa Merlo
- Institute of Biosciences and BioResources, National Council of Research of Italy, Via P. Castellino 111, 80131, Naples, Italy
| | - Angelo Fontana
- Institute of Biomolecular Chemistry, National Council of Research of Italy, Via Campi Flegrei, 34, 80078, Pozzuoli, NA, Italy
| | - Giuliana d'Ippolito
- Institute of Biomolecular Chemistry, National Council of Research of Italy, Via Campi Flegrei, 34, 80078, Pozzuoli, NA, Italy
| | - Michael P Terns
- Departments of Biochemistry and Molecular Biology, Genetics, and Microbiology, University of Georgia, Athens, GA, USA
| | - Elizabeth A Watts
- Departments of Biochemistry and Molecular Biology, Genetics, and Microbiology, University of Georgia, Athens, GA, USA
| | - Anna Valenti
- Institute of Biosciences and BioResources, National Council of Research of Italy, Via P. Castellino 111, 80131, Naples, Italy
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources, National Council of Research of Italy, Via P. Castellino 111, 80131, Naples, Italy.
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14
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Serpe M, Forenza C, Adamo A, Russo N, Perugino G, Ciaramella M, Valenti A. The DNA Alkylguanine DNA Alkyltransferase-2 (AGT-2) Of Caenorhabditis Elegans Is Involved In Meiosis And Early Development Under Physiological Conditions. Sci Rep 2019; 9:6889. [PMID: 31053748 PMCID: PMC6499797 DOI: 10.1038/s41598-019-43394-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/23/2019] [Indexed: 12/11/2022] Open
Abstract
DNA alkylguanine DNA alkyltransferases (AGTs) are evolutionary conserved proteins that repair alkylation damage in DNA, counteracting the effects of agents inducing such lesions. Over the last years AGTs have raised considerable interest for both the peculiarity of their molecular mechanism and their relevance in cancer biology. AGT knock out mice show increased tumour incidence in response to alkylating agents, and over-expression of the human AGT protein in cancer cells is frequently associated with resistance to alkylating chemotherapy. While all data available point to a function of AGT proteins in the cell response to alkylation lesions, we report for the first time that one of the two AGT paralogs of the model organism C. elegans, called AGT-2, also plays unexpected roles in meiosis and early development under physiological conditions. Our data suggest a role for AGT-2 in conversion of homologous recombination intermediates into post-strand exchange products in meiosis, and show that agt-2 gene down-regulation, or treatment of animals with an AGT inhibitor results in increased number of germ cells that are incompatible with producing viable offspring and are eliminated by apoptosis. These results suggest possible functions for AGTs in cell processes distinct from repair of alkylating damage.
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Affiliation(s)
- Mario Serpe
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, Naples, 80131, Italy
| | - Chiara Forenza
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, Naples, 80131, Italy
| | - Adele Adamo
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, Naples, 80131, Italy
| | - Noemi Russo
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, Naples, 80131, Italy
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, Naples, 80131, Italy
| | - Maria Ciaramella
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, Naples, 80131, Italy
| | - Anna Valenti
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, Naples, 80131, Italy.
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15
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Optimization of an In Vitro Transcription/Translation System Based on Sulfolobus solfataricus Cell Lysate. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2019; 2019:9848253. [PMID: 30886540 PMCID: PMC6388310 DOI: 10.1155/2019/9848253] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 11/05/2018] [Indexed: 11/18/2022]
Abstract
A system is described which permits the efficient synthesis of proteins in vitro at high temperature. It is based on the use of an unfractionated cell lysate (S30) from Sulfolobus solfataricus previously well characterized in our laboratory for translation of pretranscribed mRNAs, and now adapted to perform coupled transcription and translation. The essential element in this expression system is a strong promoter derived from the S. solfataricus 16S/23S rRNA-encoding gene, from which specific mRNAs may be transcribed with high efficiency. The synthesis of two different proteins is reported, including the S. solfataricus DNA-alkylguanine-DNA-alkyl-transferase protein (SsOGT), which is shown to be successfully labeled with appropriate fluorescent substrates and visualized in cell extracts. The simplicity of the experimental procedure and specific activity of the proteins offer a number of possibilities for the study of structure-function relationships of proteins.
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16
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Copp W, O'Flaherty DK, Wilds CJ. Covalent capture of OGT's active site using engineered human-E. coli chimera and intrastrand DNA cross-links. Org Biomol Chem 2018; 16:9053-9058. [PMID: 30430154 DOI: 10.1039/c8ob02453g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
O 6-Alkylguanine DNA alkyltransferases (AGTs) are proteins found in most organisms whose role is to remove alkylation damage from the O6- and O4-positions of 2'-deoxyguanosine (dG) and thymidine (dT), respectively. Variations in active site residues between AGTs from different organisms leads to differences in repair proficiency: The human variant (hAGT) has a proclivity for removal of alkyl groups at the O6-position of guanine and the E. coli OGT protein has activity towards the O4-position of thymine. A chimeric protein (hOGT) that our laboratory has engineered with twenty of the active site residues mutated in hAGT to those found in OGT, exhibited activity towards a broader range of substrates relative to native OGT. Among the substrates that the hOGT protein was found to act upon was interstrand cross-linked DNA connected by an alkylene linkage at the O6-position of dG to the complementary strand. In the present study the activity of hOGT towards DNA containing alkylene intrastrand cross-links (IaCL) at the O6- and O4-positions respectively of dG and dT, which lack a phosphodiester linkage between the connected residues, was evaluated. The hOGT protein exhibited proficiency at removal of an alkylene linkage at the O6-atom of dG but the O4-position of dT was refractory to protein activity. The activity of the chimeric hOGT protein towards these IaCLs to prepare well defined DNA-protein cross-linked conjugates will enable mechanistic and high resolution structural studies to address the differences observed in the repair adeptness of O4-alkylated dT by the OGT protein relative to other AGT variants.
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Affiliation(s)
- William Copp
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B1R6, Canada.
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17
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Rossi F, Morrone C, Massarotti A, Ferraris DM, Valenti A, Perugino G, Miggiano R. Crystal structure of a thermophilic O6-alkylguanine-DNA alkyltransferase-derived self-labeling protein-tag in covalent complex with a fluorescent probe. Biochem Biophys Res Commun 2018; 500:698-703. [DOI: 10.1016/j.bbrc.2018.04.139] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 04/17/2018] [Indexed: 02/07/2023]
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18
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Miggiano R, Valenti A, Rossi F, Rizzi M, Perugino G, Ciaramella M. Every OGT Is Illuminated … by Fluorescent and Synchrotron Lights. Int J Mol Sci 2017; 18:ijms18122613. [PMID: 29206193 PMCID: PMC5751216 DOI: 10.3390/ijms18122613] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 11/28/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022] Open
Abstract
O6-DNA-alkyl-guanine-DNA-alkyl-transferases (OGTs) are evolutionarily conserved, unique proteins that repair alkylation lesions in DNA in a single step reaction. Alkylating agents are environmental pollutants as well as by-products of cellular reactions, but are also very effective chemotherapeutic drugs. OGTs are major players in counteracting the effects of such agents, thus their action in turn affects genome integrity, survival of organisms under challenging conditions and response to chemotherapy. Numerous studies on OGTs from eukaryotes, bacteria and archaea have been reported, highlighting amazing features that make OGTs unique proteins in their reaction mechanism as well as post-reaction fate. This review reports recent functional and structural data on two prokaryotic OGTs, from the pathogenic bacterium Mycobacterium tuberculosis and the hyperthermophilic archaeon Sulfolobus solfataricus, respectively. These studies provided insight in the role of OGTs in the biology of these microorganisms, but also important hints useful to understand the general properties of this class of proteins.
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Affiliation(s)
- Riccardo Miggiano
- DSF-Dipartimento di Scienze del Farmaco, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy.
| | - Anna Valenti
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy.
| | - Franca Rossi
- DSF-Dipartimento di Scienze del Farmaco, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy.
| | - Menico Rizzi
- DSF-Dipartimento di Scienze del Farmaco, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy.
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy.
| | - Maria Ciaramella
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy.
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19
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Visone V, Han W, Perugino G, del Monaco G, She Q, Rossi M, Valenti A, Ciaramella M. In vivo and in vitro protein imaging in thermophilic archaea by exploiting a novel protein tag. PLoS One 2017; 12:e0185791. [PMID: 28973046 PMCID: PMC5626487 DOI: 10.1371/journal.pone.0185791] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/19/2017] [Indexed: 12/25/2022] Open
Abstract
Protein imaging, allowing a wide variety of biological studies both in vitro and in vivo, is of great importance in modern biology. Protein and peptide tags fused to proteins of interest provide the opportunity to elucidate protein location and functions, detect protein-protein interactions, and measure protein activity and kinetics in living cells. Whereas several tags are suitable for protein imaging in mesophilic organisms, the application of this approach to microorganisms living at high temperature has lagged behind. Archaea provide an excellent and unique model for understanding basic cell biology mechanisms. Here, we present the development of a toolkit for protein imaging in the hyperthermophilic archaeon Sulfolobus islandicus. The system relies on a thermostable protein tag (H5) constructed by engineering the alkylguanine-DNA-alkyl-transferase protein of Sulfolobus solfataricus, which can be covalently labeled using a wide range of small molecules. As a suitable host, we constructed, by CRISPR-based genome-editing technology, a S. islandicus mutant strain deleted for the alkylguanine-DNA-alkyl-transferase gene (Δogt). Introduction of a plasmid-borne H5 gene in this strain led to production of a functional H5 protein, which was successfully labeled with appropriate fluorescent molecules and visualized in cell extracts as well as in Δogt live cells. H5 was fused to reverse gyrase, a peculiar thermophile-specific DNA topoisomerase endowed with positive supercoiling activity, and allowed visualization of the enzyme in living cells. To the best of our knowledge, this is the first report of in vivo imaging of any protein of a thermophilic archaeon, filling an important gap in available tools for cell biology studies in these organisms.
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Affiliation(s)
- Valeria Visone
- Institute of Biosciences and Bioresources, National Research Council of Italy, Napoli, Italy
| | - Wenyuan Han
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Giuseppe Perugino
- Institute of Biosciences and Bioresources, National Research Council of Italy, Napoli, Italy
| | - Giovanni del Monaco
- Institute of Biosciences and Bioresources, National Research Council of Italy, Napoli, Italy
| | - Qunxin She
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mosè Rossi
- Institute of Biosciences and Bioresources, National Research Council of Italy, Napoli, Italy
| | - Anna Valenti
- Institute of Biosciences and Bioresources, National Research Council of Italy, Napoli, Italy
- * E-mail: (MC); (AV)
| | - Maria Ciaramella
- Institute of Biosciences and Bioresources, National Research Council of Italy, Napoli, Italy
- * E-mail: (MC); (AV)
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20
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Interdomain interactions rearrangements control the reaction steps of a thermostable DNA alkyltransferase. Biochim Biophys Acta Gen Subj 2016; 1861:86-96. [PMID: 27777086 DOI: 10.1016/j.bbagen.2016.10.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/07/2016] [Accepted: 10/20/2016] [Indexed: 12/18/2022]
Abstract
BACKGROUND Alkylated DNA-protein alkyltransferases (AGTs) are conserved proteins that repair alkylation damage in DNA by using a single-step mechanism leading to irreversible alkylation of the catalytic cysteine in the active site. Trans-alkylation induces inactivation and destabilization of the protein, both in vitro and in vivo, likely triggering conformational changes. A complete picture of structural rearrangements occurring during the reaction cycle is missing, despite considerable interest raised by the peculiarity of AGT reaction, and the contribution of a functional AGT in limiting the efficacy of chemotherapy with alkylating drugs. METHODS As a model for AGTs we have used a thermostable ortholog from the archaeon Sulfolobus solfataricus (SsOGT), performing biochemical, structural, molecular dynamics and in silico analysis of ligand-free, DNA-bound and mutated versions of the protein. RESULTS Conformational changes occurring during lesion recognition and after the reaction, allowed us to identify a novel interaction network contributing to SsOGT stability, which is perturbed when a bulky adduct between the catalytic cysteine and the alkyl group is formed, a mandatory step toward the permanent protein alkylation. CONCLUSIONS Our data highlighted conformational changes and perturbation of intramolecular interaction occurring during lesion recognition and catalysis, confirming our previous hypothesis that coordination between the N- and C-terminal domains of SsOGT is important for protein activity and stability. GENERAL SIGNIFICANCE A general model of structural rearrangements occurring during the reaction cycle of AGTs is proposed. If confirmed, this model might be a starting point to design strategies to modulate AGT activity in therapeutic settings.
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21
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Vettone A, Serpe M, Hidalgo A, Berenguer J, del Monaco G, Valenti A, Rossi M, Ciaramella M, Perugino G. A novel thermostable protein-tag: optimization of the Sulfolobus solfataricus DNA- alkyl-transferase by protein engineering. Extremophiles 2016; 20:1-13. [PMID: 26499124 DOI: 10.1007/s00792-015-0791-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/03/2015] [Indexed: 12/12/2022]
Abstract
In the last decade, a powerful biotechnological tool for the in vivo and in vitro specific labeling of proteins (SNAP-tag™ technology) was proposed as a valid alternative to classical protein-tags (green fluorescent proteins, GFPs). This was made possible by the discovery of the irreversible reaction of the human alkylguanine-DNA-alkyl-transferase (hAGT) in the presence of benzyl-guanine derivatives. However, the mild reaction conditions and the general instability of the mesophilic SNAP-tag™ make this new approach not fully applicable to (hyper-)thermophilic and, in general, extremophilic organisms. Here, we introduce an engineered variant of the thermostable alkylguanine-DNA-alkyl-transferase from the Archaea Sulfolobus solfataricus (SsOGT-H5), which displays a catalytic efficiency comparable to the SNAP-tag™ protein, but showing high intrinsic stability typical of proteins from this organism. The successful heterologous expression obtained in a thermophilic model organism makes SsOGT-H5 a valid candidate as protein-tag for organisms living in extreme environments.
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Affiliation(s)
- Antonella Vettone
- Institute of Biosciences and BioResources, National Council of Research of Italy, Via P. Castellino 111, 80131 Naples, Italy
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22
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Ishino S, Nishi Y, Oda S, Uemori T, Sagara T, Takatsu N, Yamagami T, Shirai T, Ishino Y. Identification of a mismatch-specific endonuclease in hyperthermophilic Archaea. Nucleic Acids Res 2016; 44:2977-86. [PMID: 27001046 PMCID: PMC4838380 DOI: 10.1093/nar/gkw153] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/29/2016] [Indexed: 12/17/2022] Open
Abstract
The common mismatch repair system processed by MutS and MutL and their homologs was identified in Bacteria and Eukarya. However, no evidence of a functional MutS/L homolog has been reported for archaeal organisms, and it is not known whether the mismatch repair system is conserved in Archaea. Here, we describe an endonuclease that cleaves double-stranded DNA containing a mismatched base pair, from the hyperthermophilic archaeon Pyrococcus furiosus The corresponding gene revealed that the activity originates from PF0012, and we named this enzyme Endonuclease MS (EndoMS) as the mismatch-specific Endonuclease. The sequence similarity suggested that EndoMS is the ortholog of NucS isolated from Pyrococcus abyssi, published previously. Biochemical characterizations of the EndoMS homolog from Thermococcus kodakarensis clearly showed that EndoMS specifically cleaves both strands of double-stranded DNA into 5'-protruding forms, with the mismatched base pair in the central position. EndoMS cleaves G/T, G/G, T/T, T/C and A/G mismatches, with a more preference for G/T, G/G and T/T, but has very little or no effect on C/C, A/C and A/A mismatches. The discovery of this endonuclease suggests the existence of a novel mismatch repair process, initiated by the double-strand break generated by the EndoMS endonuclease, in Archaea and some Bacteria.
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Affiliation(s)
- Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
| | - Yuki Nishi
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
| | - Soichiro Oda
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
| | - Takashi Uemori
- Takara Bio Inc., Nojihigashi 7-4-38, Kusatsu, Shiga 525-0058, Japan
| | - Takehiro Sagara
- Takara Bio Inc., Nojihigashi 7-4-38, Kusatsu, Shiga 525-0058, Japan
| | - Nariaki Takatsu
- Takara Bio Inc., Nojihigashi 7-4-38, Kusatsu, Shiga 525-0058, Japan
| | - Takeshi Yamagami
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
| | - Tsuyoshi Shirai
- Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
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23
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Crystal structure of Mycobacterium tuberculosis O6-methylguanine-DNA methyltransferase protein clusters assembled on to damaged DNA. Biochem J 2015; 473:123-33. [PMID: 26512127 DOI: 10.1042/bj20150833] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 10/28/2015] [Indexed: 11/17/2022]
Abstract
Mycobacterium tuberculosis O(6)-methylguanine-DNA methyltransferase (MtOGT) contributes to protect the bacterial GC-rich genome against the pro-mutagenic potential of O(6)-methylated guanine in DNA. Several strains of M. tuberculosis found worldwide encode a point-mutated O(6)-methylguanine-DNA methyltransferase (OGT) variant (MtOGT-R37L), which displays an arginine-to-leucine substitution at position 37 of the poorly functionally characterized N-terminal domain of the protein. Although the impact of this mutation on the MtOGT activity has not yet been proved in vivo, we previously demonstrated that a recombinant MtOGT-R37L variant performs a suboptimal alkylated-DNA repair in vitro, suggesting a direct role for the Arg(37)-bearing region in catalysis. The crystal structure of MtOGT complexed with modified DNA solved in the present study reveals details of the protein-protein and protein-DNA interactions occurring during alkylated-DNA binding, and the protein capability also to host unmodified bases inside the active site, in a fully extrahelical conformation. Our data provide the first experimental picture at the atomic level of a possible mode of assembling three adjacent MtOGT monomers on the same monoalkylated dsDNA molecule, and disclose the conformational flexibility of discrete regions of MtOGT, including the Arg(37)-bearing random coil. This peculiar structural plasticity of MtOGT could be instrumental to proper protein clustering at damaged DNA sites, as well as to protein-DNA complexes disassembling on repair.
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24
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Perugino G, Miggiano R, Serpe M, Vettone A, Valenti A, Lahiri S, Rossi F, Rossi M, Rizzi M, Ciaramella M. Structure-function relationships governing activity and stability of a DNA alkylation damage repair thermostable protein. Nucleic Acids Res 2015; 43:8801-16. [PMID: 26227971 PMCID: PMC4605297 DOI: 10.1093/nar/gkv774] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 07/18/2015] [Indexed: 12/22/2022] Open
Abstract
Alkylated DNA-protein alkyltransferases repair alkylated DNA bases, which are among the most common DNA lesions, and are evolutionary conserved, from prokaryotes to higher eukaryotes. The human ortholog, hAGT, is involved in resistance to alkylating chemotherapy drugs. We report here on the alkylated DNA-protein alkyltransferase, SsOGT, from an archaeal species living at high temperature, a condition that enhances the harmful effect of DNA alkylation. The exceptionally high stability of SsOGT gave us the unique opportunity to perform structural and biochemical analysis of a protein of this class in its post-reaction form. This analysis, along with those performed on SsOGT in its ligand-free and DNA-bound forms, provides insights in the structure-function relationships of the protein before, during and after DNA repair, suggesting a molecular basis for DNA recognition, catalytic activity and protein post-reaction fate, and giving hints on the mechanism of alkylation-induced inactivation of this class of proteins.
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Affiliation(s)
- Giuseppe Perugino
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80125 Naples, Italy
| | - Riccardo Miggiano
- DiSF-Dipartimento di Scienze del Farmaco, University of Piemonte Orientale 'A. Avogadro', Via Bovio 6, 28100 Novara, Italy
| | - Mario Serpe
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80125 Naples, Italy
| | - Antonella Vettone
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80125 Naples, Italy
| | - Anna Valenti
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80125 Naples, Italy
| | - Samarpita Lahiri
- DiSF-Dipartimento di Scienze del Farmaco, University of Piemonte Orientale 'A. Avogadro', Via Bovio 6, 28100 Novara, Italy
| | - Franca Rossi
- DiSF-Dipartimento di Scienze del Farmaco, University of Piemonte Orientale 'A. Avogadro', Via Bovio 6, 28100 Novara, Italy
| | - Mosè Rossi
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80125 Naples, Italy
| | - Menico Rizzi
- DiSF-Dipartimento di Scienze del Farmaco, University of Piemonte Orientale 'A. Avogadro', Via Bovio 6, 28100 Novara, Italy
| | - Maria Ciaramella
- Institute of Biosciences and Bioresources, National Research Council of Italy, Via P. Castellino 111, 80125 Naples, Italy
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25
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Ishino Y, Narumi I. DNA repair in hyperthermophilic and hyperradioresistant microorganisms. Curr Opin Microbiol 2015; 25:103-12. [PMID: 26056771 DOI: 10.1016/j.mib.2015.05.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 04/22/2015] [Accepted: 05/20/2015] [Indexed: 10/23/2022]
Abstract
The genome of a living cell is continuously under attack by exogenous and endogenous genotoxins. Especially, life at high temperature inflicts additional stress on genomic DNA, and very high rates of potentially mutagenic DNA lesions, including deamination, depurination, and oxidation, are expected. However, the spontaneous mutation rates in hyperthermophiles are similar to that in Escherichia coli, and it is interesting to determine how the hyperthermophiles preserve their genomes under such grueling environmental conditions. In addition, organisms with extremely radioresistant phenotypes are targets for investigating special DNA repair mechanisms in extreme environments. Multiple DNA repair mechanisms have evolved in all organisms to ensure genomic stability, by preventing impediments that result in genome destabilizing lesions.
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Affiliation(s)
- Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Fukuoka, Fukuoka 812-8581, Japan.
| | - Issay Narumi
- Radiation Microbiology Laboratory, Department of Life Sciences, Faculty of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura, Gunma 374-0193, Japan
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26
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Couturier M, Bizard AH, Garnier F, Nadal M. Insight into the cellular involvement of the two reverse gyrases from the hyperthermophilic archaeon Sulfolobus solfataricus. BMC Mol Biol 2014; 15:18. [PMID: 25200003 PMCID: PMC4183072 DOI: 10.1186/1471-2199-15-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 08/27/2014] [Indexed: 12/12/2022] Open
Abstract
Background Reverse gyrases are DNA topoisomerases characterized by their unique DNA positive-supercoiling activity. Sulfolobus solfataricus, like most Crenarchaeota, contains two genes each encoding a reverse gyrase. We showed previously that the two genes are differently regulated according to temperature and that the corresponding purified recombinant reverse gyrases have different enzymatic characteristics. These observations suggest a specialization of functions of the two reverse gyrases. As no mutants of the TopR genes could be obtained in Sulfolobales, we used immunodetection techniques to study the function(s) of these proteins in S. solfataricus in vivo. In particular, we investigated whether one or both reverse gyrases are required for the hyperthermophilic lifestyle. Results For the first time the two reverse gyrases of S. solfataricus have been discriminated at the protein level and their respective amounts have been determined in vivo. Actively dividing S. solfataricus cells contain only small amounts of both reverse gyrases, approximately 50 TopR1 and 125 TopR2 molecules per cell at 80°C. S. solfataricus cells are resistant at 45°C for several weeks, but there is neither cell division nor replication initiation; these processes are fully restored upon a return to 80°C. TopR1 is not found after three weeks at 45°C whereas the amount of TopR2 remains constant. Enzymatic assays in vitro indicate that TopR1 is not active at 45°C but that TopR2 exhibits highly positive DNA supercoiling activity at 45°C. Conclusions The two reverse gyrases of S. solfataricus are differently regulated, in terms of protein abundance, in vivo at 80°C and 45°C. TopR2 is present both at high and low temperatures and is therefore presumably required whether cells are dividing or not. By contrast, TopR1 is present only at high temperature where the cell division occurs, suggesting that TopR1 is required for controlling DNA topology associated with cell division activity and/or life at high temperature. Our findings in vitro that TopR1 is able to positively supercoil DNA only at high temperature, and TopR2 is active at both temperatures are consistent with them having different functions within the cells.
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Affiliation(s)
| | | | - Florence Garnier
- Université Versailles St-Quentin, 45 avenue des Etats-Unis, Versailles 78035, France.
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Genome stability: recent insights in the topoisomerase reverse gyrase and thermophilic DNA alkyltransferase. Extremophiles 2014; 18:895-904. [DOI: 10.1007/s00792-014-0662-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/18/2014] [Indexed: 10/24/2022]
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Label-free and rapid colorimetric detection of DNA damage based on self-assembly of a hemin-graphene nanocomposite. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1245-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Pluchon PF, Fouqueau T, Crezé C, Laurent S, Briffotaux J, Hogrel G, Palud A, Henneke G, Godfroy A, Hausner W, Thomm M, Nicolas J, Flament D. An extended network of genomic maintenance in the archaeon Pyrococcus abyssi highlights unexpected associations between eucaryotic homologs. PLoS One 2013; 8:e79707. [PMID: 24244547 PMCID: PMC3820547 DOI: 10.1371/journal.pone.0079707] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 09/24/2013] [Indexed: 11/18/2022] Open
Abstract
In Archaea, the proteins involved in the genetic information processing pathways, including DNA replication, transcription, and translation, share strong similarities with those of eukaryotes. Characterizations of components of the eukaryotic-type replication machinery complex provided many interesting insights into DNA replication in both domains. In contrast, DNA repair processes of hyperthermophilic archaea are less well understood and very little is known about the intertwining between DNA synthesis, repair and recombination pathways. The development of genetic system in hyperthermophilic archaea is still at a modest stage hampering the use of complementary approaches of reverse genetics and biochemistry to elucidate the function of new candidate DNA repair gene. To gain insights into genomic maintenance processes in hyperthermophilic archaea, a protein-interaction network centred on informational processes of Pyrococcus abyssi was generated by affinity purification coupled with mass spectrometry. The network consists of 132 interactions linking 87 proteins. These interactions give insights into the connections of DNA replication with recombination and repair, leading to the discovery of new archaeal components and of associations between eucaryotic homologs. Although this approach did not allow us to clearly delineate new DNA pathways, it provided numerous clues towards the function of new molecular complexes with the potential to better understand genomic maintenance processes in hyperthermophilic archaea. Among others, we found new potential partners of the replication clamp and demonstrated that the single strand DNA binding protein, Replication Protein A, enhances the transcription rate, in vitro, of RNA polymerase. This interaction map provides a valuable tool to explore new aspects of genome integrity in Archaea and also potentially in Eucaryotes.
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Affiliation(s)
- Pierre-François Pluchon
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Thomas Fouqueau
- Lehrstuhl für Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Christophe Crezé
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Sébastien Laurent
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Julien Briffotaux
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Gaëlle Hogrel
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Adeline Palud
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Ghislaine Henneke
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Anne Godfroy
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Winfried Hausner
- Lehrstuhl für Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Michael Thomm
- Lehrstuhl für Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Jacques Nicolas
- IRISA-INRIA, Campus de Beaulieu, Rennes, France
- * E-mail: (DF); (JN)
| | - Didier Flament
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- * E-mail: (DF); (JN)
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Biochemical and structural studies of the Mycobacterium tuberculosis O6-methylguanine methyltransferase and mutated variants. J Bacteriol 2013; 195:2728-36. [PMID: 23564173 DOI: 10.1128/jb.02298-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium tuberculosis displays remarkable genetic stability despite continuous exposure to the hostile environment represented by the host's infected macrophages. Similarly to other organisms, M. tuberculosis possesses multiple systems to counteract the harmful potential of DNA alkylation. In particular, the suicidal enzyme O(6)-methylguanine-DNA methyltransferase (OGT) is responsible for the direct repair of O(6)-alkylguanine in double-stranded DNA and is therefore supposed to play a central role in protecting the mycobacterial genome from the risk of G · C-to-A · T transition mutations. Notably, a number of geographically widely distributed M. tuberculosis strains shows nonsynonymous single-nucleotide polymorphisms in their OGT-encoding gene, leading to amino acid substitutions at position 15 (T15S) or position 37 (R37L) of the N-terminal domain of the corresponding protein. However, the role of these mutations in M. tuberculosis pathogenesis is unknown. We describe here the in vitro characterization of M. tuberculosis OGT (MtOGT) and of two point-mutated versions of the protein mimicking the naturally occurring ones, revealing that both mutated proteins are impaired in their activity as a consequence of their lower affinity for alkylated DNA than the wild-type protein. The analysis of the crystal structures of MtOGT and MtOGT-R37L confirms the high level of structural conservation of members of this protein family and provides clues to an understanding of the molecular bases for the reduced affinity for the natural substrate displayed by mutated MtOGT. Our in vitro results could contribute to validate the inferred participation of mutated OGTs in M. tuberculosis phylogeny and biology.
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Bioinformatic study of the relationship between protein regulation and sequence properties. Genomics 2012; 100:240-4. [PMID: 22800766 DOI: 10.1016/j.ygeno.2012.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Revised: 05/21/2012] [Accepted: 07/03/2012] [Indexed: 11/21/2022]
Abstract
Although protein expression and regulation have been intensively studied, a complete picture of its mechanisms is still to be drawn. Analysis of high-throughput quantitative proteomics data provides a way to better understand protein regulation. Here, we introduce a bioinformatic analysis method to correlate protein regulation with individual amino acid patterns. We compare the amino acid composition between groups of regulated and unregulated proteins and investigate the correlation between codon usage patterns and protein regulation levels in two Sulfolobus species in "biofilm vs planktonic" experiments. The identified amino acids can then be associated with the regulation of specific gene functions. Strikingly, our analysis shows that functional categories of regulated proteins with similar composition and codon usage pattern of specific amino acids behave similarly. This finding can contribute to a better understanding of protein and gene expression regulation and could find applications in gene optimisation.
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