1
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Carreira R, Lama-Diaz T, Crugeiras M, Aguado FJ, Sebesta M, Krejci L, Blanco MG. Concurrent D-loop cleavage by Mus81 and Yen1 yields half-crossover precursors. Nucleic Acids Res 2024:gkae453. [PMID: 38832625 DOI: 10.1093/nar/gkae453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 05/05/2024] [Accepted: 05/14/2024] [Indexed: 06/05/2024] Open
Abstract
Homologous recombination involves the formation of branched DNA molecules that may interfere with chromosome segregation. To resolve these persistent joint molecules, cells rely on the activation of structure-selective endonucleases (SSEs) during the late stages of the cell cycle. However, the premature activation of SSEs compromises genome integrity, due to untimely processing of replication and/or recombination intermediates. Here, we used a biochemical approach to show that the budding yeast SSEs Mus81 and Yen1 possess the ability to cleave the central recombination intermediate known as the displacement loop or D-loop. Moreover, we demonstrate that, consistently with previous genetic data, the simultaneous action of Mus81 and Yen1, followed by ligation, is sufficient to recreate the formation of a half-crossover precursor in vitro. Our results provide not only mechanistic explanation for the formation of a half-crossover, but also highlight the critical importance for precise regulation of these SSEs to prevent chromosomal rearrangements.
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Affiliation(s)
- Raquel Carreira
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - Tomas Lama-Diaz
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - Maria Crugeiras
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - F Javier Aguado
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - Marek Sebesta
- Department of Biology and National Centre for Biomolecular Research, Masaryk University, Brno 62500, Czech Republic
| | - Lumir Krejci
- Department of Biology and National Centre for Biomolecular Research, Masaryk University, Brno 62500, Czech Republic
| | - Miguel G Blanco
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
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2
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Frazier MN, Wilson IM, Krahn JM, Butay KJ, Dillard LB, Borgnia MJ, Stanley RE. Flipped over U: structural basis for dsRNA cleavage by the SARS-CoV-2 endoribonuclease. Nucleic Acids Res 2022; 50:8290-8301. [PMID: 35801916 DOI: 10.1093/nar/gkac589] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 01/13/2023] Open
Abstract
Coronaviruses generate double-stranded (ds) RNA intermediates during viral replication that can activate host immune sensors. To evade activation of the host pattern recognition receptor MDA5, coronaviruses employ Nsp15, which is a uridine-specific endoribonuclease. Nsp15 is proposed to associate with the coronavirus replication-transcription complex within double-membrane vesicles to cleave these dsRNA intermediates. How Nsp15 recognizes and processes dsRNA is poorly understood because previous structural studies of Nsp15 have been limited to small single-stranded (ss) RNA substrates. Here we present cryo-EM structures of SARS-CoV-2 Nsp15 bound to a 52nt dsRNA. We observed that the Nsp15 hexamer forms a platform for engaging dsRNA across multiple protomers. The structures, along with site-directed mutagenesis and RNA cleavage assays revealed critical insight into dsRNA recognition and processing. To process dsRNA Nsp15 utilizes a base-flipping mechanism to properly orient the uridine within the active site for cleavage. Our findings show that Nsp15 is a distinctive endoribonuclease that can cleave both ss- and dsRNA effectively.
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Affiliation(s)
- Meredith N Frazier
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Isha M Wilson
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Juno M Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Kevin John Butay
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Lucas B Dillard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
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3
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Sun J, Antczak NM, Gahlon HL, Sturla SJ. Molecular beacons with oxidized bases report on substrate specificity of DNA oxoguanine glycosylases. Chem Sci 2022; 13:4295-4302. [PMID: 35509469 PMCID: PMC9007065 DOI: 10.1039/d1sc05648d] [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: 10/13/2021] [Accepted: 02/15/2022] [Indexed: 11/21/2022] Open
Abstract
DNA glycosylase enzymes recognize and remove structurally distinct modified forms of DNA bases, thereby repairing genomic DNA from chemically induced damage or erasing epigenetic marks. However, these enzymes are often promiscuous, and advanced tools are needed to evaluate and engineer their substrate specificity. Thus, in the present study, we developed a new strategy to rapidly profile the substrate specificity of 8-oxoguanine glycosylases, which cleave biologically relevant oxidized forms of guanine. We monitored the enzymatic excision of fluorophore-labeled oligonucleotides containing synthetic modifications 8-oxoG and FapyG, or G. Using this molecular beacon approach, we identified several hOGG1 mutants with higher specificity for FapyG than 8-oxoG. This approach and the newly synthesized probes will be useful for the characterization of glycosylase substrate specificity and damage excision mechanisms, as well as for evaluating engineered enzymes with altered reactivities.
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Affiliation(s)
- Jingjing Sun
- Department of Health Sciences and Technology, ETH Zürich Zürich 8092 Switzerland
- Department of Biological Engineering, Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Nicole M Antczak
- Department of Health Sciences and Technology, ETH Zürich Zürich 8092 Switzerland
- Department of Chemistry, Skidmore College 815 North Broadway Saratoga Springs NY 12866 USA
| | - Hailey L Gahlon
- Department of Health Sciences and Technology, ETH Zürich Zürich 8092 Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zürich Zürich 8092 Switzerland
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4
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Frazier MN, Dillard LB, Krahn JM, Perera L, Williams JG, Wilson IM, Stewart ZD, Pillon MC, Deterding LJ, Borgnia MJ, Stanley RE. Characterization of SARS2 Nsp15 nuclease activity reveals it's mad about U. Nucleic Acids Res 2021; 49:10136-10149. [PMID: 34403466 PMCID: PMC8385992 DOI: 10.1093/nar/gkab719] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 12/18/2022] Open
Abstract
Nsp15 is a uridine specific endoribonuclease that coronaviruses employ to cleave viral RNA and evade host immune defense systems. Previous structures of Nsp15 from across Coronaviridae revealed that Nsp15 assembles into a homo-hexamer and has a conserved active site similar to RNase A. Beyond a preference for cleaving RNA 3′ of uridines, it is unknown if Nsp15 has any additional substrate preferences. Here, we used cryo-EM to capture structures of Nsp15 bound to RNA in pre- and post-cleavage states. The structures along with molecular dynamics and biochemical assays revealed critical residues involved in substrate specificity, nuclease activity, and oligomerization. Moreover, we determined how the sequence of the RNA substrate dictates cleavage and found that outside of polyU tracts, Nsp15 has a strong preference for purines 3′ of the cleaved uridine. This work advances our understanding of how Nsp15 recognizes and processes viral RNA, and will aid in the development of new anti-viral therapeutics.
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Affiliation(s)
- Meredith N Frazier
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Lucas B Dillard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Juno M Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Jason G Williams
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Isha M Wilson
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Zachary D Stewart
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Monica C Pillon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Leesa J Deterding
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
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5
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De Falco M, Massa F, Rossi M, De Felice M. The Sulfolobus solfataricus RecQ-like DNA helicase Hel112 inhibits the NurA/HerA complex exonuclease activity. Extremophiles 2018; 22:581-589. [PMID: 29488113 DOI: 10.1007/s00792-018-1018-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/21/2018] [Indexed: 02/03/2023]
Abstract
ATPase/Helicases and nucleases play important roles in DNA end-resection, a critical step during homologous recombination repair in all organisms. In hyperthermophilic archaea the exo-endonuclease NurA and the ATPase HerA cooperate with the highly conserved Mre11-Rad50 complex in 3' single-stranded DNA (ssDNA) end processing to coordinate repair of double-stranded DNA breaks. Little is known, however, about the assembly mechanism and activation of the HerA-NurA complex. In this study we demonstrate that the NurA exonuclease activity is inhibited by the Sulfolobus solfataricus RecQ-like Hel112 helicase. Inhibition occurs both in the presence and in the absence of HerA, but is much stronger when NurA is in complex with HerA. In contrast, the endonuclease activity of NurA is not affected by the presence of Hel112. Taken together these results suggest that the functional interaction between NurA/HerA and Hel112 is important for DNA end-resection in archaeal homologous recombination.
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Affiliation(s)
- Mariarosaria De Falco
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, 80131, Naples, Italy.
| | - Federica Massa
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, 80131, Naples, Italy
| | - Mosè Rossi
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, 80131, Naples, Italy
| | - Mariarita De Felice
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, 80131, Naples, Italy.
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6
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Teklemariam TA, Rivera OD, Nelson SW. Kinetic Analysis of the Exonuclease Activity of the Bacteriophage T4 Mre11–Rad50 Complex. Methods Enzymol 2018; 600:135-156. [DOI: 10.1016/bs.mie.2017.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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7
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Ralec C, Henry E, Lemor M, Killelea T, Henneke G. Calcium-driven DNA synthesis by a high-fidelity DNA polymerase. Nucleic Acids Res 2017; 45:12425-12440. [PMID: 29040737 PMCID: PMC5716173 DOI: 10.1093/nar/gkx927] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/04/2017] [Indexed: 11/14/2022] Open
Abstract
Divalent metal ions, usually Mg2+, are required for both DNA synthesis and proofreading functions by DNA polymerases (DNA Pol). Although used as a non-reactive cofactor substitute for binding and crystallographic studies, Ca2+ supports DNA polymerization by only one DNA Pol, Dpo4. Here, we explore whether Ca2+-driven catalysis might apply to high-fidelity (HiFi) family B DNA Pols. The consequences of replacing Mg2+ by Ca2+ on base pairing at the polymerase active site as well as the editing of terminal nucleotides at the exonuclease active site of the archaeal Pyrococcus abyssi DNA Pol (PabPolB) are characterized and compared to other (families B, A, Y, X, D) DNA Pols. Based on primer extension assays, steady-state kinetics and ion-chased experiments, we demonstrate that Ca2+ (and other metal ions) activates DNA synthesis by PabPolB. While showing a slower rate of phosphodiester bond formation, nucleotide selectivity is improved over that of Mg2+. Further mechanistic studies show that the affinities for primer/template are higher in the presence of Ca2+ and reinforced by a correct incoming nucleotide. Conversely, no exonuclease degradation of the terminal nucleotides occurs with Ca2+. Evolutionary and mechanistic insights among DNA Pols are thus discussed.
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Affiliation(s)
- Céline Ralec
- Ifremer, Centre de Brest, LM2E, UMR 6197, Technopole Brest-Iroise, 29280 Plouzané, France.,CNRS, LM2E, UMR 6197, Technopole Brest-Iroise, 29280 Plouzané, France.,Université de Brest Occidentale, UBO, LM2E, UMR 6197, Technopole Brest-Iroise, 29280 Plouzané, France
| | - Etienne Henry
- Ifremer, Centre de Brest, LM2E, UMR 6197, Technopole Brest-Iroise, 29280 Plouzané, France.,CNRS, LM2E, UMR 6197, Technopole Brest-Iroise, 29280 Plouzané, France.,Université de Brest Occidentale, UBO, LM2E, UMR 6197, Technopole Brest-Iroise, 29280 Plouzané, France
| | - Mélanie Lemor
- Ifremer, Centre de Brest, LM2E, UMR 6197, Technopole Brest-Iroise, 29280 Plouzané, France.,CNRS, LM2E, UMR 6197, Technopole Brest-Iroise, 29280 Plouzané, France.,Université de Brest Occidentale, UBO, LM2E, UMR 6197, Technopole Brest-Iroise, 29280 Plouzané, France
| | - Tom Killelea
- Ifremer, Centre de Brest, LM2E, UMR 6197, Technopole Brest-Iroise, 29280 Plouzané, France.,CNRS, LM2E, UMR 6197, Technopole Brest-Iroise, 29280 Plouzané, France.,Université de Brest Occidentale, UBO, LM2E, UMR 6197, Technopole Brest-Iroise, 29280 Plouzané, France
| | - Ghislaine Henneke
- Ifremer, Centre de Brest, LM2E, UMR 6197, Technopole Brest-Iroise, 29280 Plouzané, France.,CNRS, LM2E, UMR 6197, Technopole Brest-Iroise, 29280 Plouzané, France.,Université de Brest Occidentale, UBO, LM2E, UMR 6197, Technopole Brest-Iroise, 29280 Plouzané, France
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8
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Comparative Study of Novel Fluorescent Cyanine Nucleotides: Hybridization Analysis of Labeled PCR Products Using a Biochip. J Fluoresc 2017; 27:2001-2016. [PMID: 28752470 DOI: 10.1007/s10895-017-2139-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 07/18/2017] [Indexed: 01/08/2023]
Abstract
This study investigated the synthesis and substrate properties of Cy5-labeled dUTP derivatives with different substituents, linkers between the dye unit and pyrimidine heterocycle and fluorophore charges. Fluorescently labeled nucleoside triphosphates were studied as substrates using multiplex PCR with Taq and Vent (exo-) DNA polymerases, the typical representatives of the A and B polymerase families. The efficiency of nucleotide incorporation during PCR was assessed with a multi-parameter hybridization analysis using a diagnostic DNA microarray. The hybridization analysis indirectly estimates the incorporation efficiency of dye-labeled nucleotides in multiplex PCR. Our results demonstrated higher efficiencies of substrates with electrically neutral dyes than electropositive and electronegative Cy5 residues.
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9
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Niewoehner O, Jinek M. Structural basis for the endoribonuclease activity of the type III-A CRISPR-associated protein Csm6. RNA (NEW YORK, N.Y.) 2016; 22:318-29. [PMID: 26763118 PMCID: PMC4748810 DOI: 10.1261/rna.054098.115] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/30/2015] [Indexed: 05/14/2023]
Abstract
Prokaryotic CRISPR-Cas systems provide an RNA-guided mechanism for genome defense against mobile genetic elements such as viruses and plasmids. In type III-A CRISPR-Cas systems, the RNA-guided multisubunit Csm effector complex targets both single-stranded RNAs and double-stranded DNAs. In addition to the Csm complex, efficient anti-plasmid immunity mediated by type III-A systems also requires the CRISPR-associated protein Csm6. Here we report the crystal structure of Csm6 from Thermus thermophilus and show that the protein is a ssRNA-specific endoribonuclease. The structure reveals a dimeric architecture generated by interactions involving the N-terminal CARF and C-terminal HEPN domains. HEPN domain dimerization leads to the formation of a composite ribonuclease active site. Consistently, mutations of invariant active site residues impair catalytic activity in vitro. We further show that the ribonuclease activity of Csm6 is conserved across orthologs, suggesting that it plays an important functional role in CRISPR-Cas systems. The dimer interface of the CARF domains features a conserved electropositive pocket that may function as a ligand-binding site for allosteric control of ribonuclease activity. Altogether, our work suggests that Csm6 proteins provide an auxiliary RNA-targeting interference mechanism in type III-A CRISPR-Cas systems that operates in conjunction with the RNA- and DNA-targeting endonuclease activities of the Csm effector complex.
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Affiliation(s)
- Ole Niewoehner
- Department of Biochemistry, University of Zurich, Zurich CH-8057, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich CH-8057, Switzerland
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10
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De Falco M, Catalano F, Rossi M, Ciaramella M, De Felice M. NurA Is Endowed with Endo- and Exonuclease Activities that Are Modulated by HerA: New Insight into Their Role in DNA-End Processing. PLoS One 2015; 10:e0142345. [PMID: 26560692 PMCID: PMC4641729 DOI: 10.1371/journal.pone.0142345] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 10/20/2015] [Indexed: 11/18/2022] Open
Abstract
The nuclease NurA and the ATPase HerA are present in all known thermophilic archaea and cooperate with the highly conserved MRE11/RAD50 proteins to facilitate efficient DNA double-strand break end processing during homologous recombinational repair. However, contradictory results have been reported on the exact activities and mutual dependence of these two enzymes. To understand the functional relationship between these two enzymes we deeply characterized Sulfolobus solfataricus NurA and HerA proteins. We found that NurA is endowed with exo- and endonuclease activities on various DNA substrates, including linear (single-stranded and double stranded) as well as circular molecules (single stranded and supercoiled double-stranded). All these activities are not strictly dependent on the presence of HerA, require divalent ions (preferably Mn2+), and are inhibited by the presence of ATP. The endo- and exonculease activities have distinct requirements: whereas the exonuclease activity on linear DNA fragments is stimulated by HerA and depends on the catalytic D58 residue, the endonuclease activity on circular double-stranded DNA is HerA-independent and is not affected by the D58A mutation. On the basis of our results we propose a mechanism of action of NurA/HerA complex during DNA end processing.
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Affiliation(s)
- Mariarosaria De Falco
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, Naples, 80131, Italy
- * E-mail: (M. De Falco); (M. De Felice)
| | - Federico Catalano
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, Naples, 80131, Italy
| | - Mosè Rossi
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, Naples, 80131, Italy
| | - Maria Ciaramella
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, Naples, 80131, Italy
| | - Mariarita De Felice
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, Naples, 80131, Italy
- * E-mail: (M. De Falco); (M. De Felice)
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11
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Cui X, Wu P, Lai D, Zheng S, Chen Y, Eremin SA, Peng W, Zhao S. Development of a Highly Specific Fluorescence Immunoassay for Detection of Diisobutyl Phthalate in Edible Oil Samples. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:9372-9378. [PMID: 26449794 DOI: 10.1021/acs.jafc.5b03922] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The diisobutyl phthalate (DiBP) hapten containing an amino group was synthesized successfully, and the polyclonal antibody against 4-amino phthalate-bovine serum albumin (BSA) was developed. On the basis of the polyclonal antibody, a rapid and sensitive indirect competitive fluorescence immunoassay (icFIA) has been established to detect DiBP in edible oil samples for the first time. Under the optimized conditions, the quantitative working range of the icFIA was from 10.47 to 357.06 ng/mL (R(2) = 0.991), exhibiting a detection limit of 5.82 ng/mL. In this assay, the specific results showed that other similar phthalates did not significantly interfere with the analysis, with the cross-reactivity less than 1.5%, except for that of DiBAP. Thereafter, DiBP contamination in edible oil samples was detected by icFIA, with the recovery being from 79 to 103%. Furthermore, the reliability of icFIA was validated by gas chromatography-mass spectrometry (GC-MS). Therefore, the developed icFIA is suitable for monitoring DiBP in some edible oil samples.
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Affiliation(s)
- Xiping Cui
- Department of Pharmaceutical Engineering, Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology , Guangzhou, Guangdong 510006, People's Republic of China
| | - Panpan Wu
- Department of Pharmaceutical Engineering, Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology , Guangzhou, Guangdong 510006, People's Republic of China
| | - Dan Lai
- Department of Pharmaceutical Engineering, Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology , Guangzhou, Guangdong 510006, People's Republic of China
| | - Shengwu Zheng
- Department of Pharmaceutical Engineering, Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology , Guangzhou, Guangdong 510006, People's Republic of China
| | - Yingshan Chen
- Department of Pharmaceutical Engineering, Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology , Guangzhou, Guangdong 510006, People's Republic of China
| | - Sergei A Eremin
- Department of Chemical Enzymology, Faculty of Chemistry, M.V. Lomonosov State University , Moscow 119992, Russia
| | - Wei Peng
- School of Public Health, Guangzhou Medical University , Guangzhou, Guangdong 510006, People's Republic of China
| | - Suqing Zhao
- Department of Pharmaceutical Engineering, Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology , Guangzhou, Guangdong 510006, People's Republic of China
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12
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Greenough L, Schermerhorn KM, Mazzola L, Bybee J, Rivizzigno D, Cantin E, Slatko BE, Gardner AF. Adapting capillary gel electrophoresis as a sensitive, high-throughput method to accelerate characterization of nucleic acid metabolic enzymes. Nucleic Acids Res 2015; 44:e15. [PMID: 26365239 PMCID: PMC4737176 DOI: 10.1093/nar/gkv899] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 08/28/2015] [Indexed: 01/26/2023] Open
Abstract
Detailed biochemical characterization of nucleic acid enzymes is fundamental to understanding nucleic acid metabolism, genome replication and repair. We report the development of a rapid, high-throughput fluorescence capillary gel electrophoresis method as an alternative to traditional polyacrylamide gel electrophoresis to characterize nucleic acid metabolic enzymes. The principles of assay design described here can be applied to nearly any enzyme system that acts on a fluorescently labeled oligonucleotide substrate. Herein, we describe several assays using this core capillary gel electrophoresis methodology to accelerate study of nucleic acid enzymes. First, assays were designed to examine DNA polymerase activities including nucleotide incorporation kinetics, strand displacement synthesis and 3′-5′ exonuclease activity. Next, DNA repair activities of DNA ligase, flap endonuclease and RNase H2 were monitored. In addition, a multicolor assay that uses four different fluorescently labeled substrates in a single reaction was implemented to characterize GAN nuclease specificity. Finally, a dual-color fluorescence assay to monitor coupled enzyme reactions during Okazaki fragment maturation is described. These assays serve as a template to guide further technical development for enzyme characterization or nucleoside and non-nucleoside inhibitor screening in a high-throughput manner.
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Affiliation(s)
| | | | | | - Joanna Bybee
- From New England Biolabs, Inc., Ipswich, MA 01938, USA
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