1
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Manthei KA, Munson LM, Nandakumar J, Simmons LA. Structural and biochemical characterization of the mitomycin C repair exonuclease MrfB. Nucleic Acids Res 2024; 52:6347-6359. [PMID: 38661211 PMCID: PMC11194089 DOI: 10.1093/nar/gkae308] [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] [Received: 02/18/2024] [Revised: 04/03/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024] Open
Abstract
Mitomycin C (MMC) repair factor A (mrfA) and factor B (mrfB), encode a conserved helicase and exonuclease that repair DNA damage in the soil-dwelling bacterium Bacillus subtilis. Here we have focused on the characterization of MrfB, a DEDDh exonuclease in the DnaQ superfamily. We solved the structure of the exonuclease core of MrfB to a resolution of 2.1 Å, in what appears to be an inactive state. In this conformation, a predicted α-helix containing the catalytic DEDDh residue Asp172 adopts a random coil, which moves Asp172 away from the active site and results in the occupancy of only one of the two catalytic Mg2+ ions. We propose that MrfB resides in this inactive state until it interacts with DNA to become activated. By comparing our structure to an AlphaFold prediction as well as other DnaQ-family structures, we located residues hypothesized to be important for exonuclease function. Using exonuclease assays we show that MrfB is a Mg2+-dependent 3'-5' DNA exonuclease. We show that Leu113 aids in coordinating the 3' end of the DNA substrate, and that a basic loop is important for substrate binding. This work provides insight into the function of a recently discovered bacterial exonuclease important for the repair of MMC-induced DNA adducts.
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Affiliation(s)
- Kelly A Manthei
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lia M Munson
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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2
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Kan Y, Jin Z, Ke Y, Lin D, Yan L, Wu L, He Y. Replicative bypass studies of l-deoxyribonucleosides in Vitro and in E. coli cell. Sci Rep 2022; 12:21183. [PMID: 36476762 PMCID: PMC9729220 DOI: 10.1038/s41598-022-24802-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
L-nucleosides were the most important antiviral lead compounds because they can inhibit viral DNA polymerase and DNA synthesis of many viruses, whereas they may lead to mutations in DNA replication and cause genomic instability. In this study, we reported the replicative bypass of L-deoxynucleosides in recombinant DNA by restriction enzyme-mediated assays to examine their impact on DNA replication in vitro and in E. coli cells. The results showed that a template L-dC inhibited Taq DNA polymerase reaction, whereas it can be bypassed by Vent (exo-) DNA polymerase as well as in cell replication, inserting correct nucleotides opposite L-dC. L-dG can be bypassed by Taq DNA polymerase and in E. coli cells, maintaining insertion of correct incoming nucleotides, and L-dG induced mutagenic replication by Vent (exo-) DNA polymerase. In contrast, L-dA can induced mutagenic replication in vitro and in E. coli cells. MD simulations were performed to investigate how DNA polymerase affected replicative bypass and mutations when D-nucleosides replaced with L-nucleosides. This study will provide a basis for the ability to assess the cytotoxic and mutagenic properties of the L-nucleoside drugs.
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Affiliation(s)
- Yuhe Kan
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China ,grid.411643.50000 0004 1761 0411School of Life Sciences, Inner Mongolia University, Hohhot, 010021 Inner Mongolia People’s Republic of China ,Qilu Pharmaceutical (Inner Mongolia) CO., LTD., Hohhot, 010080 Inner Mongolia People’s Republic of China
| | - Zhaoyang Jin
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Yongqi Ke
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Dao Lin
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Liang Yan
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Li Wu
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China ,grid.11135.370000 0001 2256 9319State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191 People’s Republic of China
| | - Yujian He
- grid.410726.60000 0004 1797 8419School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China ,grid.11135.370000 0001 2256 9319State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191 People’s Republic of China ,grid.410726.60000 0004 1797 8419School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
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3
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Sieg J, Sandmeier CC, Lieske J, Meents A, Lemmen C, Streit WR, Rarey M. Analyzing structural features of proteins from deep-sea organisms. Proteins 2022; 90:1521-1537. [PMID: 35313380 DOI: 10.1002/prot.26337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/10/2022] [Accepted: 03/15/2022] [Indexed: 12/31/2022]
Abstract
Protein adaptations to extreme environmental conditions are drivers in biotechnological process optimization and essential to unravel the molecular limits of life. Most proteins with such desirable adaptations are found in extremophilic organisms inhabiting extreme environments. The deep sea is such an environment and a promising resource that poses multiple extremes on its inhabitants. Conditions like high hydrostatic pressure and high or low temperature are prevalent and many deep-sea organisms tolerate multiple of these extremes. While molecular adaptations to high temperature are comparatively good described, adaptations to other extremes like high pressure are not well-understood yet. To fully unravel the molecular mechanisms of individual adaptations it is probably necessary to disentangle multifactorial adaptations. In this study, we evaluate differences of protein structures from deep-sea organisms and their respective related proteins from nondeep-sea organisms. We created a data collection of 1281 experimental protein structures from 25 deep-sea organisms and paired them with orthologous proteins. We exhaustively evaluate differences between the protein pairs with machine learning and Shapley values to determine characteristic differences in sequence and structure. The results show a reasonable discrimination of deep-sea and nondeep-sea proteins from which we distinguish correlations previously attributed to thermal stability from other signals potentially describing adaptions to high pressure. While some distinct correlations can be observed the overall picture appears intricate.
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Affiliation(s)
- Jochen Sieg
- Universität Hamburg, ZBH - Center for Bioinformatics, Hamburg, Germany
| | | | - Julia Lieske
- Deutsches Elektronen-Synchrotron DESY, Center for Free-Electron Laser Science, Hamburg, Germany
| | - Alke Meents
- Deutsches Elektronen-Synchrotron DESY, Center for Free-Electron Laser Science, Hamburg, Germany
| | | | - Wolfgang R Streit
- Universität Hamburg, Department of Microbiology and Biotechnology, Hamburg, Germany
| | - Matthias Rarey
- Universität Hamburg, ZBH - Center for Bioinformatics, Hamburg, Germany
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4
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Chan KY, Kinghorn AB, Hollenstein M, Tanner JA. Chemical modifications for a next generation of nucleic acid aptamers. Chembiochem 2022; 23:e202200006. [PMID: 35416400 DOI: 10.1002/cbic.202200006] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/11/2022] [Indexed: 11/08/2022]
Abstract
In the past three decades, in vitro systematic evolution of ligands by exponential enrichment (SELEX) has yielded many aptamers for translational applications in both research and clinical settings. Despite their promise as an alternative to antibodies, the low success rate of SELEX (~ 30%) has been a major bottleneck that hampers the further development of aptamers. One hurdle is the lack of chemical diversity in nucleic acids. To address this, the aptamer chemical repertoire has been extended by introducing exotic chemical groups, which provide novel binding functionalities. This review will focus on how modified aptamers can be selected and evolved, with illustration of some successful examples. In particular, unique chemistries are exemplified. Various strategies of incorporating modified building blocks into the standard SELEX protocol are highlighted, with a comparison of the differences between pre-SELEX and post-SELEX modifications. Nucleic acid aptamers with extended functionality evolved from non-natural chemistries will open up new vistas for function and application of nucleic acids.
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Affiliation(s)
- Kwing Yeung Chan
- The University of Hong Kong, School of Biomedical Sciences, HONG KONG
| | | | | | - Julian Alexander Tanner
- The University of Hong Kong, School of Biomedical Sciences, 3/F Laboratory Block, 21 Sassoon Road, 000000, Pokfulam, HONG KONG
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5
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Kimoto M, Soh SHG, Hirao I. Sanger Gap Sequencing for Genetic Alphabet Expansion of DNA. Chembiochem 2020; 21:2287-2296. [DOI: 10.1002/cbic.202000057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/19/2020] [Indexed: 01/03/2023]
Affiliation(s)
- Michiko Kimoto
- Institute of Bioengineering and Nanotechnology, A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
| | - Si Hui Gabriella Soh
- Institute of Bioengineering and Nanotechnology, A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
- Raffles Institution 1 Raffles Institution Lane Singapore 575954 Singapore
| | - Ichiro Hirao
- Institute of Bioengineering and Nanotechnology, A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
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6
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Parkash V, Kulkarni Y, Ter Beek J, Shcherbakova PV, Kamerlin SCL, Johansson E. Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase ε. Nat Commun 2019; 10:373. [PMID: 30670696 PMCID: PMC6342957 DOI: 10.1038/s41467-018-08114-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 12/12/2018] [Indexed: 11/21/2022] Open
Abstract
The most frequently recurring cancer-associated DNA polymerase ε (Pol ε) mutation is a P286R substitution in the exonuclease domain. While originally proposed to increase genome instability by disrupting exonucleolytic proofreading, the P286R variant was later found to be significantly more pathogenic than Pol ε proofreading deficiency per se. The mechanisms underlying its stronger impact remained unclear. Here we report the crystal structure of the yeast orthologue, Pol ε−P301R, complexed with DNA and an incoming dNTP. Structural changes in the protein are confined to the exonuclease domain, with R301 pointing towards the exonuclease site. Molecular dynamics simulations suggest that R301 interferes with DNA binding to the exonuclease site, an outcome not observed with the exonuclease-inactive Pol ε−D290A,E292A variant lacking the catalytic residues. These results reveal a distinct mechanism of exonuclease inactivation by the P301R substitution and a likely basis for its dramatically higher mutagenic and tumorigenic effects. Mutations in the human POLE gene are associated with tumours with high mutational loads. Here the authors provide a structural rationale for the mutagenic activity of the cancer-associated DNA polymerase ε P286R variant.
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Affiliation(s)
- Vimal Parkash
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, SE-90187, Sweden
| | - Yashraj Kulkarni
- Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, S-751 23, Sweden
| | - Josy Ter Beek
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, SE-90187, Sweden
| | - Polina V Shcherbakova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | | | - Erik Johansson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, SE-90187, Sweden.
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7
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Crystal structures of ternary complexes of archaeal B-family DNA polymerases. PLoS One 2017; 12:e0188005. [PMID: 29211756 PMCID: PMC5718519 DOI: 10.1371/journal.pone.0188005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/30/2017] [Indexed: 01/04/2023] Open
Abstract
Archaeal B-family polymerases drive biotechnology by accepting a wide substrate range of chemically modified nucleotides. By now no structural data for archaeal B-family DNA polymerases in a closed, ternary complex are available, which would be the basis for developing next generation nucleotides. We present the ternary crystal structures of KOD and 9°N DNA polymerases complexed with DNA and the incoming dATP. The structures reveal a third metal ion in the active site, which was so far only observed for the eukaryotic B-family DNA polymerase δ and no other B-family DNA polymerase. The structures reveal a wide inner channel and numerous interactions with the template strand that provide space for modifications within the enzyme and may account for the high processivity, respectively. The crystal structures provide insights into the superiority over other DNA polymerases concerning the acceptance of modified nucleotides.
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8
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Xiao Y, Liu Q, Tang X, Yang Z, Wu L, He Y. Mirror-Image Thymidine Discriminates against Incorporation of Deoxyribonucleotide Triphosphate into DNA and Repairs Itself by DNA Polymerases. Bioconjug Chem 2017; 28:2125-2134. [PMID: 28686433 DOI: 10.1021/acs.bioconjchem.7b00301] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
DNA polymerases are known to recognize preferably d-nucleotides over l-nucleotides during DNA synthesis. Here, we report that several general DNA polymerases catalyze polymerization reactions of nucleotides directed by the DNA template containing an l-thymidine (l-T). The results display that the 5'-3' primer extension of natural nucleotides get to the end at chiral modification site with Taq and Phanta Max DNA polymerases, but the primer extension proceeds to the end of the template catalyzed by Deep Vent (exo-), Vent (exo-), and Therminator DNA polymerases. Furthermore, templating l-nucleoside displays a lag in the deoxyribonucleotide triphosphate (dNTP) incorporation rates relative to natural template by kinetics analysis, and polymerase chain reactions were inhibited with the DNA template containing two or three consecutive l-Ts. Most interestingly, no single base mutation or mismatch mixture corresponding to the location of l-T in the template was found, which is physiologically significant because they provide a theoretical basis on the involvement of DNA polymerase in the effective repair of l-T that may lead to cytotoxicity.
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Affiliation(s)
- Yating Xiao
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences , Beijing 100049, China
| | - Qingju Liu
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences , Beijing 100049, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Li Wu
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences , Beijing 100049, China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Yujian He
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences , Beijing 100049, China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
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9
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Betz K, Kimoto M, Diederichs K, Hirao I, Marx A. Strukturelle Studie zur Erweiterung des genetischen Codes durch ein artifizielles Nucleobasenpaar. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704190] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Karin Betz
- Fachbereiche Chemie und Biologie und Konstanz Research School Chemical Biology Universität Konstanz Universitätsstraße 10 78464 Konstanz Deutschland
| | - Michiko Kimoto
- Institute of Bioengineering and Nanotechnology 31 Biopolis Way, The Nanos, #09-01 138669 Singapore Singapur
- RIKEN Center for Life Science Technologies 1–7 22 Suehiro-cho, Tsurumi-ku, Yokohama Kanagawa 230-0045 Japan
| | - Kay Diederichs
- Fachbereiche Chemie und Biologie und Konstanz Research School Chemical Biology Universität Konstanz Universitätsstraße 10 78464 Konstanz Deutschland
| | - Ichiro Hirao
- Institute of Bioengineering and Nanotechnology 31 Biopolis Way, The Nanos, #09-01 138669 Singapore Singapur
- RIKEN Center for Life Science Technologies 1–7 22 Suehiro-cho, Tsurumi-ku, Yokohama Kanagawa 230-0045 Japan
| | - Andreas Marx
- Fachbereiche Chemie und Biologie und Konstanz Research School Chemical Biology Universität Konstanz Universitätsstraße 10 78464 Konstanz Deutschland
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10
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Betz K, Kimoto M, Diederichs K, Hirao I, Marx A. Structural Basis for Expansion of the Genetic Alphabet with an Artificial Nucleobase Pair. Angew Chem Int Ed Engl 2017; 56:12000-12003. [DOI: 10.1002/anie.201704190] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Karin Betz
- Departments of Chemistry and Biology and Konstanz Research School Chemical Biology Universität Konstanz Universitätsstrasse 10 78464 Konstanz Germany
| | - Michiko Kimoto
- Institute of Bioengineering and Nanotechnology 31 Biopolis Way, The Nanos, #09-01 138669 Singapore Singapore
- RIKEN Center for Life Science Technologies 1–7 22 Suehiro-cho, Tsurumi-ku, Yokohama Kanagawa 230-0045 Japan
| | - Kay Diederichs
- Departments of Chemistry and Biology and Konstanz Research School Chemical Biology Universität Konstanz Universitätsstrasse 10 78464 Konstanz Germany
| | - Ichiro Hirao
- Institute of Bioengineering and Nanotechnology 31 Biopolis Way, The Nanos, #09-01 138669 Singapore Singapore
- RIKEN Center for Life Science Technologies 1–7 22 Suehiro-cho, Tsurumi-ku, Yokohama Kanagawa 230-0045 Japan
| | - Andreas Marx
- Departments of Chemistry and Biology and Konstanz Research School Chemical Biology Universität Konstanz Universitätsstrasse 10 78464 Konstanz Germany
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