1
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Dagva O, Thibessard A, Lorenzi JN, Labat V, Piotrowski E, Rouhier N, Myllykallio H, Leblond P, Bertrand C. Correction of non-random mutational biases along a linear bacterial chromosome by the mismatch repair endonuclease NucS. Nucleic Acids Res 2024; 52:5033-5047. [PMID: 38444149 PMCID: PMC11109965 DOI: 10.1093/nar/gkae132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/19/2024] [Accepted: 02/09/2024] [Indexed: 03/07/2024] Open
Abstract
The linear chromosome of Streptomyces exhibits a highly compartmentalized structure with a conserved central region flanked by variable arms. As double strand break (DSB) repair mechanisms play a crucial role in shaping the genome plasticity of Streptomyces, we investigated the role of EndoMS/NucS, a recently characterized endonuclease involved in a non-canonical mismatch repair (MMR) mechanism in archaea and actinobacteria, that singularly corrects mismatches by creating a DSB. We showed that Streptomyces mutants lacking NucS display a marked colonial phenotype and a drastic increase in spontaneous mutation rate. In vitro biochemical assays revealed that NucS cooperates with the replication clamp to efficiently cleave G/T, G/G and T/T mismatched DNA by producing DSBs. These findings are consistent with the transition-shifted mutational spectrum observed in the mutant strains and reveal that NucS-dependent MMR specific task is to eliminate G/T mismatches generated by the DNA polymerase during replication. Interestingly, our data unveil a crescent-shaped distribution of the transition frequency from the replication origin towards the chromosomal ends, shedding light on a possible link between NucS-mediated DSBs and Streptomyces genome evolution.
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Affiliation(s)
- Oyut Dagva
- Université de Lorraine, INRAE, UMR 1128 DynAMic, 54000 Nancy, France
| | | | | | - Victor Labat
- Université de Lorraine, INRAE, UMR 1128 DynAMic, 54000 Nancy, France
| | - Emilie Piotrowski
- Université de Lorraine, INRAE, UMR 1128 DynAMic, 54000 Nancy, France
| | - Nicolas Rouhier
- Université de Lorraine, INRAE, UMR 1136 IAM, 54000 Nancy, France
| | - Hannu Myllykallio
- Ecole Polytechnique, INSERM U696-CNRS UMR 7645 LOB, 91128 Palaiseau, France
| | - Pierre Leblond
- Université de Lorraine, INRAE, UMR 1128 DynAMic, 54000 Nancy, France
| | - Claire Bertrand
- Université de Lorraine, INRAE, UMR 1128 DynAMic, 54000 Nancy, France
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2
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Lestini R, Collien Y, Olivier D, Olivier N, Myllykallio H. BrdU Incorporation and Labeling of Nascent DNA to Investigate Archaeal Replication Using Super-Resolution Imaging. Methods Mol Biol 2022; 2522:419-434. [PMID: 36125768 DOI: 10.1007/978-1-0716-2445-6_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The labeling and specific detection of nascent DNA by the incorporation of thymidine analogs provide crucial information about DNA replication dynamics without requiring the intracellular expression of fluorescent proteins. After cell fixation and permeabilization, specific detection of thymidine analogs by antibodies can be performed using super-resolution imaging techniques. Here we describe a protocol to label nascent DNA using 5'-bromo-2'-deoxyuridine (BrdU) in Haloferax volcanii cells and generate super-resolved images of neo-synthesized DNA foci either by 3D Structured illumination microscopy (3D-SIM) or Stochastic Optical Reconstruction Microscopy (STORM).
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Affiliation(s)
- Roxane Lestini
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645-INSERM U1182, IP Paris, Palaiseau, Cedex, France.
| | - Yoann Collien
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645-INSERM U1182, IP Paris, Palaiseau, Cedex, France
| | - Debora Olivier
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645-INSERM U1182, IP Paris, Palaiseau, Cedex, France
| | - Nicolas Olivier
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645-INSERM U1182, IP Paris, Palaiseau, Cedex, France
| | - Hannu Myllykallio
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645-INSERM U1182, IP Paris, Palaiseau, Cedex, France
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3
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Biteau NG, Roy V, Lambry JC, Becker HF, Myllykallio H, Agrofoglio LA. Synthesis of acyclic nucleoside phosphonates targeting flavin-dependent thymidylate synthase in Mycobacterium tuberculosis. Bioorg Med Chem 2021; 46:116351. [PMID: 34391120 DOI: 10.1016/j.bmc.2021.116351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/16/2021] [Accepted: 07/30/2021] [Indexed: 10/20/2022]
Abstract
Flavin-Dependent Thymidylate Synthase (FDTS) encoded by ThyX gene was discovered as a new class of thymidylate synthase involved in the de novo synthesis of dTMP named only in 30 % of human pathogenic bacteria. This target was pursed for the development of new antibacterial agents against multiresistant pathogens. We have developed a new class of ANPs based on the mimic of two natural's cofactors (dUMP and FAD) as inhibitors against Mycobacterium tuberculosis ThyX. Several synthetic efforts were performed to optimize regioselective N1-alkylation, cross-coupling metathesis and Sonogashira cross-coupling. Compound 19c showed a poor 31.8% inhibitory effect on ThyX at 200 μM.
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Affiliation(s)
| | - Vincent Roy
- ICOA, Univ. Orléans, CNRS UMR 7311, F-45067 Orléans, France.
| | | | - Hubert F Becker
- LOB, INSERM U696-CNRS UMR 7645, Ecole Polytechnique, 91128 Palaiseau, France; Sorbonne Université, Faculté des Sciences et Ingénierie, 75005 Paris, France
| | - Hannu Myllykallio
- LOB, INSERM U696-CNRS UMR 7645, Ecole Polytechnique, 91128 Palaiseau, France
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4
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Croitoru A, Babin M, Myllykallio H, Gondry M, Aleksandrov A. Cyclodipeptide Synthases of the NYH Subfamily Recognize tRNA Using an α-Helix Enriched with Positive Residues. Biochemistry 2020; 60:64-76. [PMID: 33331769 DOI: 10.1021/acs.biochem.0c00761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclodipeptide synthases (CDPSs) perform nonribosomal protein synthesis using two aminoacyl-tRNA substrates to produce cyclodipeptides. At present, there are no structural details of the CDPS:tRNA interaction available. Using AlbC, a CDPS that produces cyclo(l-Phe-l-Phe), the interaction between AlbC and its Phe-tRNA substrate was investigated. Simulations of models of the AlbC:tRNA complex, proposed by rigid-body docking or homology modeling, demonstrated that interactions with residues of an AlbC α-helix, α4, significantly contribute to the free energy of binding of AlbC to tRNA. Individual residue contributions to the tRNA binding free energy of the discovered binding mode explain well the available biochemical data, and the results of in vivo assay experiments performed in this work and guided by simulations. In molecular dynamics simulations, the phenylalanyl group predominantly occupied the two positions observed in the experimental structure of AlbC in the dipeptide intermediate state, suggesting that tRNAs of the first and second substrates interact with AlbC in a similar manner. Overall, given the high degree of sequence and structural similarity among the members of the CDPS NYH protein subfamily, the mechanism of the protein:tRNA interaction is expected to be pertinent to a wide range of proteins interacting with tRNA.
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Affiliation(s)
- Anastasia Croitoru
- Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182), Ecole Polytechnique, Institut polytechnique de Paris, F-91128 Palaiseau, France
| | - Morgan Babin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Hannu Myllykallio
- Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182), Ecole Polytechnique, Institut polytechnique de Paris, F-91128 Palaiseau, France
| | - Muriel Gondry
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Alexey Aleksandrov
- Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182), Ecole Polytechnique, Institut polytechnique de Paris, F-91128 Palaiseau, France
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5
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Myllykallio H, Becker HF, Aleksandrov A. Mechanism of Naphthoquinone Selectivity of Thymidylate Synthase ThyX. Biophys J 2020; 119:2508-2516. [PMID: 33217379 DOI: 10.1016/j.bpj.2020.10.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/23/2020] [Accepted: 10/30/2020] [Indexed: 10/23/2022] Open
Abstract
Naphthoquinones (NQs) are natural and synthetic compounds with a wide range of biological activities commonly attributed to their redox activity and/or chemical reactivity. However, genetic and biochemical experiments have recently demonstrated that 2-hydroxy-NQs (2-OH-NQs) act as highly specific noncovalent inhibitors of the essential bacterial thymidylate synthase ThyX in a cellular context. We used biochemical experiments and molecular dynamics simulations to elucidate the selective inhibition mechanism of NQ inhibitors of ThyX from Mycobacterium tuberculosis (Mtb). Free energy simulations rationalized how ThyX recognizes the natural substrate dUMP in the N3-ionized form using an arginine, Arg199, in Mtb. The results further demonstrated that 2-OH-NQ, similar to dUMP, binds to ThyX in the ionized form, and the strong and selective binding of 2-OH-NQ to ThyX is also explained by electrostatic interactions with Arg199. The stronger binding of the close analog 5F-dUMP to ThyX and its inhibitory properties compared with dUMP were explained by the stronger acidity of the uracil N3 atom. Our results, therefore, revealed that the ionization of 2-OH-NQs drives their biological activities by mimicking the interactions with the natural substrate. Our observations encourage the rational design of optimized ThyX inhibitors that ultimately may serve as antibiotics.
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Affiliation(s)
- Hannu Myllykallio
- Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182), Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France.
| | - Hubert F Becker
- Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182), Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France; Faculté des Sciences et Ingénierie, Sorbonne Université, Paris, France
| | - Alexey Aleksandrov
- Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182), Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France.
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6
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Brázda V, Luo Y, Bartas M, Kaura P, Porubiaková O, Šťastný J, Pečinka P, Verga D, Da Cunha V, Takahashi TS, Forterre P, Myllykallio H, Fojta M, Mergny JL. G-Quadruplexes in the Archaea Domain. Biomolecules 2020; 10:biom10091349. [PMID: 32967357 PMCID: PMC7565180 DOI: 10.3390/biom10091349] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 11/26/2022] Open
Abstract
The importance of unusual DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, G-quadruplexes (G4s) have gained in popularity during the last decade, and their presence and functional relevance at the DNA and RNA level has been demonstrated in a number of viral, bacterial, and eukaryotic genomes, including humans. Here, we performed the first systematic search of G4-forming sequences in all archaeal genomes available in the NCBI database. In this article, we investigate the presence and locations of G-quadruplex forming sequences using the G4Hunter algorithm. G-quadruplex-prone sequences were identified in all archaeal species, with highly significant differences in frequency, from 0.037 to 15.31 potential quadruplex sequences per kb. While G4 forming sequences were extremely abundant in Hadesarchaea archeon (strikingly, more than 50% of the Hadesarchaea archaeon isolate WYZ-LMO6 genome is a potential part of a G4-motif), they were very rare in the Parvarchaeota phylum. The presence of G-quadruplex forming sequences does not follow a random distribution with an over-representation in non-coding RNA, suggesting possible roles for ncRNA regulation. These data illustrate the unique and non-random localization of G-quadruplexes in Archaea.
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Affiliation(s)
- Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Yu Luo
- Institut Curie, CNRS UMR9187, INSERM U1196, Universite Paris Saclay, 91400 Orsay, France
| | - Martin Bartas
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Patrik Kaura
- Faculty of Mechanical Engineering, Brno University of Technology, Technicka 2896/2, 616 69 Brno, Czech Republic
| | - Otilia Porubiaková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Faculty of Chemistry, Brno University of Technology, Purkyňova 464/118, 612 00 Brno, Czech Republic
| | - Jiří Šťastný
- Faculty of Mechanical Engineering, Brno University of Technology, Technicka 2896/2, 616 69 Brno, Czech Republic
- Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Daniela Verga
- Institut Curie, CNRS UMR9187, INSERM U1196, Universite Paris Saclay, 91400 Orsay, France
| | - Violette Da Cunha
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, Université Paris-Saclay, CEDEX, 91198 Gif-sur-Yvette, France
| | - Tomio S Takahashi
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, Université Paris-Saclay, CEDEX, 91198 Gif-sur-Yvette, France
| | - Patrick Forterre
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, Université Paris-Saclay, CEDEX, 91198 Gif-sur-Yvette, France
| | - Hannu Myllykallio
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Miroslav Fojta
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
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7
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Smith CJ, Castanon O, Said K, Volf V, Khoshakhlagh P, Hornick A, Ferreira R, Wu CT, Güell M, Garg S, Ng AHM, Myllykallio H, Church GM. Enabling large-scale genome editing at repetitive elements by reducing DNA nicking. Nucleic Acids Res 2020; 48:5183-5195. [PMID: 32315033 PMCID: PMC7229841 DOI: 10.1093/nar/gkaa239] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/04/2020] [Accepted: 04/01/2020] [Indexed: 12/26/2022] Open
Abstract
To extend the frontier of genome editing and enable editing of repetitive elements of mammalian genomes, we made use of a set of dead-Cas9 base editor (dBE) variants that allow editing at tens of thousands of loci per cell by overcoming the cell death associated with DNA double-strand breaks and single-strand breaks. We used a set of gRNAs targeting repetitive elements-ranging in target copy number from about 32 to 161 000 per cell. dBEs enabled survival after large-scale base editing, allowing targeted mutations at up to ∼13 200 and ∼12 200 loci in 293T and human induced pluripotent stem cells (hiPSCs), respectively, three orders of magnitude greater than previously recorded. These dBEs can overcome current on-target mutation and toxicity barriers that prevent cell survival after large-scale genome engineering.
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Affiliation(s)
- Cory J Smith
- Department of Genetics, Harvard Medical School, Boston, MA, 02115 USA.,Wyss Institute for Biologically Inspired Engineering, Boston, MA, 02115 USA
| | - Oscar Castanon
- Department of Genetics, Harvard Medical School, Boston, MA, 02115 USA.,Wyss Institute for Biologically Inspired Engineering, Boston, MA, 02115 USA.,LOB, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Khaled Said
- Department of Genetics, Harvard Medical School, Boston, MA, 02115 USA.,Wyss Institute for Biologically Inspired Engineering, Boston, MA, 02115 USA
| | - Verena Volf
- Department of Genetics, Harvard Medical School, Boston, MA, 02115 USA.,Wyss Institute for Biologically Inspired Engineering, Boston, MA, 02115 USA.,John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138 USA
| | - Parastoo Khoshakhlagh
- Department of Genetics, Harvard Medical School, Boston, MA, 02115 USA.,Wyss Institute for Biologically Inspired Engineering, Boston, MA, 02115 USA
| | - Amanda Hornick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115 USA.,Wyss Institute for Biologically Inspired Engineering, Boston, MA, 02115 USA
| | - Raphael Ferreira
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Chun-Ting Wu
- Department of Genetics, Harvard Medical School, Boston, MA, 02115 USA.,Wyss Institute for Biologically Inspired Engineering, Boston, MA, 02115 USA
| | - Marc Güell
- Pompeu Fabra University, Barcelona Biomedical Research Park, 08003 Barcelona, Spain
| | - Shilpa Garg
- Department of Genetics, Harvard Medical School, Boston, MA, 02115 USA
| | - Alex H M Ng
- Department of Genetics, Harvard Medical School, Boston, MA, 02115 USA.,Wyss Institute for Biologically Inspired Engineering, Boston, MA, 02115 USA
| | - Hannu Myllykallio
- LOB, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, 02115 USA.,Wyss Institute for Biologically Inspired Engineering, Boston, MA, 02115 USA
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8
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Ishino S, Skouloubris S, Kudo H, l'Hermitte-Stead C, Es-Sadik A, Lambry JC, Ishino Y, Myllykallio H. Activation of the mismatch-specific endonuclease EndoMS/NucS by the replication clamp is required for high fidelity DNA replication. Nucleic Acids Res 2019; 46:6206-6217. [PMID: 29846672 PMCID: PMC6159515 DOI: 10.1093/nar/gky460] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/14/2018] [Indexed: 12/02/2022] Open
Abstract
The mismatch repair (MMR) system, exemplified by the MutS/MutL proteins, is widespread in Bacteria and Eukarya. However, molecular mechanisms how numerous archaea and bacteria lacking the mutS/mutL genes maintain high replication fidelity and genome stability have remained elusive. EndoMS is a recently discovered hyperthermophilic mismatch-specific endonuclease encoded by nucS in Thermococcales. We deleted the nucS from the actinobacterium Corynebacterium glutamicum and demonstrated a drastic increase of spontaneous transition mutations in the nucS deletion strain. The observed spectra of these mutations were consistent with the enzymatic properties of EndoMS in vitro. The robust mismatch-specific endonuclease activity was detected with the purified C. glutamicum EndoMS protein but only in the presence of the β-clamp (DnaN). Our biochemical and genetic data suggest that the frequently occurring G/T mismatch is efficiently repaired by the bacterial EndoMS-β−clamp complex formed via a carboxy-terminal sequence motif of EndoMS proteins. Our study thus has great implications for understanding how the activity of the novel MMR system is coordinated with the replisome and provides new mechanistic insight into genetic diversity and mutational patterns in industrially and clinically (e.g. Mycobacteria) important archaeal and bacterial phyla previously thought to be devoid of the MMR system.
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Affiliation(s)
- Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 8128581, Japan
| | - Stéphane Skouloubris
- Department of Biology, Univ. Paris-Sud, Univ. Paris-Saclay, Orsay F-91405, France.,Laboratory of Optics and Biosciences, CNRS-INSERM-Ecole Polytechnique, 91128 Palaiseau France
| | - Hanae Kudo
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 8128581, Japan
| | | | - Asmae Es-Sadik
- Laboratory of Optics and Biosciences, CNRS-INSERM-Ecole Polytechnique, 91128 Palaiseau France
| | - Jean-Christophe Lambry
- Laboratory of Optics and Biosciences, CNRS-INSERM-Ecole Polytechnique, 91128 Palaiseau France
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 8128581, Japan
| | - Hannu Myllykallio
- Laboratory of Optics and Biosciences, CNRS-INSERM-Ecole Polytechnique, 91128 Palaiseau France
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9
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Becker HF, L'Hermitte-Stead C, Myllykallio H. Diversity of circular RNAs and RNA ligases in archaeal cells. Biochimie 2019; 164:37-44. [PMID: 31212038 DOI: 10.1016/j.biochi.2019.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/13/2019] [Indexed: 01/16/2023]
Abstract
Circular RNAs (circRNAs) differ structurally from other types of RNAs and are resistant against exoribonucleases. Although they have been detected in all domains of life, it remains unclear how circularization affects or changes functions of these ubiquitous nucleic acid circles. The biogenesis of circRNAs has been mostly described as a backsplicing event, but in archaea, where RNA splicing is a rare phenomenon, a second pathway for circRNA formation was described in the cases of rRNAs processing, tRNA intron excision, and Box C/D RNAs formation. At least in some archaeal species, circRNAs are formed by a ligation step catalyzed by an atypic homodimeric RNA ligase belonging to Rnl3 family. In this review, we describe archaeal circRNA transcriptomes obtained using high throughput sequencing technologies on Sulfolobus solfataricus, Pyrococcus abyssi and Nanoarchaeum equitans cells. We will discuss the distribution of circular RNAs among the different RNA categories and present the Rnl3 ligase family implicated in the circularization activity. Special focus is given for the description of phylogenetic distributions, protein structures, and substrate specificities of archaeal RNA ligases.
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Affiliation(s)
- Hubert F Becker
- LOB, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128, Palaiseau, France; Sorbonne Université, Faculté des Sciences et Ingénierie, 75005, Paris, France.
| | | | - Hannu Myllykallio
- LOB, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128, Palaiseau, France
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10
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Modranka J, Li J, Parchina A, Vanmeert M, Dumbre S, Salman M, Myllykallio H, Becker HF, Vanhoutte R, Margamuljana L, Nguyen H, Abu El-Asrar R, Rozenski J, Herdewijn P, De Jonghe S, Lescrinier E. Synthesis and Structure-Activity Relationship Studies of Benzo[b][1,4]oxazin-3(4H)-one Analogues as Inhibitors of Mycobacterial Thymidylate Synthase X. ChemMedChem 2019; 14:645-662. [PMID: 30702807 DOI: 10.1002/cmdc.201800739] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/21/2019] [Indexed: 12/19/2022]
Abstract
Since the discovery of a flavin-dependent thymidylate synthase (ThyX or FDTS) that is absent in humans but crucial for DNA biosynthesis in a diverse group of pathogens, the enzyme has been pursued for the development of new antibacterial agents against Mycobacterium tuberculosis, the causative agent of the widespread infectious disease tuberculosis (TB). In response to a growing need for more effective anti-TB drugs, we have built upon our previous screening efforts and report herein an optimization campaign of a novel series of inhibitors with a unique inhibition profile. The inhibitors display competitive inhibition toward the methylene tetrahydrofolate cofactor of ThyX, enabling us to generate a model of the compounds bound to their target, thus offering insight into their structure-activity relationships.
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Affiliation(s)
- Jakub Modranka
- Medicinal Chemistry, Rega Institute for Medical Science, KU Leuven, Herestraat 49, PO Box 1030, 3000, Leuven, Belgium
| | - Jiahong Li
- Medicinal Chemistry, Rega Institute for Medical Science, KU Leuven, Herestraat 49, PO Box 1030, 3000, Leuven, Belgium
| | - Anastasia Parchina
- Medicinal Chemistry, Rega Institute for Medical Science, KU Leuven, Herestraat 49, PO Box 1030, 3000, Leuven, Belgium
| | - Michiel Vanmeert
- Medicinal Chemistry, Rega Institute for Medical Science, KU Leuven, Herestraat 49, PO Box 1030, 3000, Leuven, Belgium
| | - Shrinivas Dumbre
- Medicinal Chemistry, Rega Institute for Medical Science, KU Leuven, Herestraat 49, PO Box 1030, 3000, Leuven, Belgium
| | - Mayla Salman
- Laboratory of Optics and Biosciences, INSERM U 696-CNRS UMR 7645, Ecole Polytechnique, Route de Saclay, 91128, Palaiseau Cedex, France
| | - Hannu Myllykallio
- Laboratory of Optics and Biosciences, INSERM U 696-CNRS UMR 7645, Ecole Polytechnique, Route de Saclay, 91128, Palaiseau Cedex, France
| | - Hubert F Becker
- Laboratory of Optics and Biosciences, INSERM U 696-CNRS UMR 7645, Ecole Polytechnique, Route de Saclay, 91128, Palaiseau Cedex, France.,Faculté des Sciences et Ingénierie, Sorbonne Université, 4 place Jussieu, 75005, Paris, France
| | - Roeland Vanhoutte
- Present affiliation: Laboratory of Chemical Biology, KU Leuven, O&N I, Herestraat 49, PO Box 802, 3000, Leuven, Belgium
| | - Lia Margamuljana
- Medicinal Chemistry, Rega Institute for Medical Science, KU Leuven, Herestraat 49, PO Box 1030, 3000, Leuven, Belgium
| | - Hoai Nguyen
- Medicinal Chemistry, Rega Institute for Medical Science, KU Leuven, Herestraat 49, PO Box 1030, 3000, Leuven, Belgium
| | - Rania Abu El-Asrar
- Medicinal Chemistry, Rega Institute for Medical Science, KU Leuven, Herestraat 49, PO Box 1030, 3000, Leuven, Belgium
| | - Jef Rozenski
- Medicinal Chemistry, Rega Institute for Medical Science, KU Leuven, Herestraat 49, PO Box 1030, 3000, Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Science, KU Leuven, Herestraat 49, PO Box 1030, 3000, Leuven, Belgium
| | - Steven De Jonghe
- Medicinal Chemistry, Rega Institute for Medical Science, KU Leuven, Herestraat 49, PO Box 1030, 3000, Leuven, Belgium.,Present affiliation: Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49, PO Box 1043, 3000, Leuven, Belgium
| | - Eveline Lescrinier
- Medicinal Chemistry, Rega Institute for Medical Science, KU Leuven, Herestraat 49, PO Box 1030, 3000, Leuven, Belgium
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11
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Sodolescu A, Dian C, Terradot L, Bouzhir-Sima L, Lestini R, Myllykallio H, Skouloubris S, Liebl U. Structural and functional insight into serine hydroxymethyltransferase from Helicobacter pylori. PLoS One 2018; 13:e0208850. [PMID: 30550583 PMCID: PMC6294363 DOI: 10.1371/journal.pone.0208850] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/23/2018] [Indexed: 11/19/2022] Open
Abstract
Serine hydroxymethyltransferase (SHMT), encoded by the glyA gene, is a ubiquitous pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the formation of glycine from serine. The thereby generated 5,10-methylene tetrahydrofolate (MTHF) is a major source of cellular one-carbon units and a key intermediate in thymidylate biosynthesis. While in virtually all eukaryotic and many bacterial systems thymidylate synthase ThyA, SHMT and dihydrofolate reductase (DHFR) are part of the thymidylate/folate cycle, the situation is different in organisms using flavin-dependent thymidylate synthase ThyX. Here the distinct catalytic reaction directly produces tetrahydrofolate (THF) and consequently in most ThyX-containing organisms, DHFR is absent. While the resulting influence on the folate metabolism of ThyX-containing bacteria is not fully understood, the presence of ThyX may provide growth benefits under conditions where the level of reduced folate derivatives is compromised. Interestingly, the third key enzyme implicated in generation of MTHF, serine hydroxymethyltransferase (SHMT), has a universal phylogenetic distribution, but remains understudied in ThyX-containg bacteria. To obtain functional insight into these ThyX-dependent thymidylate/folate cycles, we characterized the predicted SHMT from the ThyX-containing bacterium Helicobacter pylori. Serine hydroxymethyltransferase activity was confirmed by functional genetic complementation of a glyA-inactivated E. coli strain. A H. pylori ΔglyA strain was obtained, but exhibited markedly slowed growth and had lost the virulence factor CagA. Biochemical and spectroscopic evidence indicated formation of a characteristic enzyme-PLP-glycine-folate complex and revealed unexpectedly weak binding affinity of PLP. The three-dimensional structure of the H. pylori SHMT apoprotein was determined at 2.8Ǻ resolution, suggesting a structural basis for the low affinity of the enzyme for its cofactor. Stabilization of the proposed inactive configuration using small molecules has potential to provide a specific way for inhibiting HpSHMT.
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Affiliation(s)
- Andreea Sodolescu
- Laboratory of Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, Université Paris Saclay, Palaiseau, France
| | - Cyril Dian
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris Saclay, Gif-sur-Yvette, France
| | - Laurent Terradot
- UMR 5086 Molecular Microbiology and Structural Biochemistry, Institut de Biologie et Chimie des Protéines, CNRS, Université de Lyon, Lyon, France
| | - Latifa Bouzhir-Sima
- Laboratory of Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, Université Paris Saclay, Palaiseau, France
| | - Roxane Lestini
- Laboratory of Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, Université Paris Saclay, Palaiseau, France
| | - Hannu Myllykallio
- Laboratory of Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, Université Paris Saclay, Palaiseau, France
| | - Stéphane Skouloubris
- Laboratory of Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, Université Paris Saclay, Palaiseau, France
- Department of Biology, Université Paris-Sud, Université Paris Saclay, Orsay, France
| | - Ursula Liebl
- Laboratory of Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, Université Paris Saclay, Palaiseau, France
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Abstract
INTRODUCTION Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) remains the deadliest infectious disease in the world with one-third of the world's population thought to be infected. Over the years, TB mortality rate has been largely reduced; however, this progress has been threatened by the increasing appearance of multidrug-resistant Mtb. Considerable recent efforts have been undertaken to develop new generation antituberculosis drugs. Many of these attempts have relied on in silico approaches, which have emerged recently as powerful tools complementary to biochemical attempts. Areas covered: The authors review the status of pharmaceutical drug development against TB with a special emphasis on computational work. They focus on those studies that have been validated by in vitro and/or in vivo experiments, and thus, that can be considered as successful. The major goals of this review are to present target protein systems, to highlight how in silico efforts compliment experiments, and to aid future drug design endeavors. Expert opinion: Despite having access to all of the gene and protein sequences of Mtb, the search for new optimal treatments against this deadly pathogen are still ongoing. Together with the geometric growth of protein structural and sequence databases, computational methods have become a powerful technique accelerating the successful identification of new ligands.
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Affiliation(s)
- Alexey Aleksandrov
- a Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182) , Ecole Polytechnique , Palaiseau , France
| | - Hannu Myllykallio
- a Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182) , Ecole Polytechnique , Palaiseau , France
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13
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Delpech F, Collien Y, Mahou P, Beaurepaire E, Myllykallio H, Lestini R. Snapshots of archaeal DNA replication and repair in living cells using super-resolution imaging. Nucleic Acids Res 2018; 46:10757-10770. [PMID: 30212908 PMCID: PMC6237752 DOI: 10.1093/nar/gky829] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 09/03/2018] [Accepted: 09/07/2018] [Indexed: 12/17/2022] Open
Abstract
Using the haloarchaeon Haloferax volcanii as a model, we developed nascent DNA labeling and the functional GFP-labeled single-stranded binding protein RPA2 as novel tools to gain new insight into DNA replication and repair in live haloarchaeal cells. Our quantitative fluorescence microscopy data revealed that RPA2 forms distinct replication structures that dynamically responded to replication stress and DNA damaging agents. The number of the RPA2 foci per cell followed a probabilistic Poisson distribution, implying hitherto unnoticed stochastic cell-to-cell variation in haloarchaeal DNA replication and repair processes. The size range of haloarchaeal replication structures is very similar to those observed earlier in eukaryotic cells. The improved lateral resolution of 3D-SIM fluorescence microscopy allowed proposing that inhibition of DNA synthesis results in localized replication foci clustering and facilitated observation of RPA2 complexes brought about by chemical agents creating DNA double-strand breaks. Altogether our in vivo observations are compatible with earlier in vitro studies on archaeal single-stranded DNA binding proteins. Our work thus underlines the great potential of live cell imaging for unraveling the dynamic nature of transient molecular interactions that underpin fundamental molecular processes in the Third domain of life.
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Affiliation(s)
- Floriane Delpech
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645 – INSERM U1182, 91128 Palaiseau Cedex, France
| | - Yoann Collien
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645 – INSERM U1182, 91128 Palaiseau Cedex, France
| | - Pierre Mahou
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645 – INSERM U1182, 91128 Palaiseau Cedex, France
| | - Emmanuel Beaurepaire
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645 – INSERM U1182, 91128 Palaiseau Cedex, France
| | - Hannu Myllykallio
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645 – INSERM U1182, 91128 Palaiseau Cedex, France
| | - Roxane Lestini
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645 – INSERM U1182, 91128 Palaiseau Cedex, France
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14
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Myllykallio H, Sournia P, Heliou A, Liebl U. Unique Features and Anti-microbial Targeting of Folate- and Flavin-Dependent Methyltransferases Required for Accurate Maintenance of Genetic Information. Front Microbiol 2018; 9:918. [PMID: 29867829 PMCID: PMC5954106 DOI: 10.3389/fmicb.2018.00918] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/20/2018] [Indexed: 12/14/2022] Open
Abstract
Comparative genome analyses have led to the discovery and characterization of novel flavin- and folate-dependent methyltransferases that mainly function in DNA precursor synthesis and post-transcriptional RNA modification by forming (ribo) thymidylate and its derivatives. Here we discuss the recent literature on the novel mechanistic features of these enzymes sometimes referred to as “uracil methyltransferases,” albeit we prefer to refer to them as (ribo) thymidylate synthases. These enzyme families attest to the convergent evolution of nucleic acid methylation. Special focus is given to describing the unique characteristics of these flavin- and folate-dependent enzymes that have emerged as new models for studying the non-canonical roles of reduced flavin co-factors (FADH2) in relaying carbon atoms between enzyme substrates. This ancient enzymatic methylation mechanism with a very wide phylogenetic distribution may be more commonly used for biological methylation reactions than previously anticipated. This notion is exemplified by the recent discovery of additional substrates for these enzymes. Moreover, similar reaction mechanisms can be reversed by demethylases, which remove methyl groups e.g., from human histones. Future work is now required to address whether the use of different methyl donors facilitates the regulation of distinct methylation reactions in the cell. It will also be of great interest to address whether the low activity flavin-dependent thymidylate synthases ThyX represent ancestral enzymes that were eventually replaced by the more active thymidylate synthases of the ThyA family to facilitate the maintenance of larger genomes in fast-growing microbes. Moreover, we discuss the recent efforts from several laboratories to identify selective anti-microbial compounds that target flavin-dependent thymidylate synthase ThyX. Altogether we underline how the discovery of the alternative flavoproteins required for methylation of DNA and/or RNA nucleotides, in addition to providing novel targets for antibiotics, has provided new insight into microbial physiology and virulence.
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Affiliation(s)
- Hannu Myllykallio
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université Paris-Saclay, Palaiseau, France
| | - Pierre Sournia
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université Paris-Saclay, Palaiseau, France
| | - Alice Heliou
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université Paris-Saclay, Palaiseau, France.,Laboratoire d'Informatique de l'École Polytechnique, Ecole Polytechnique, Centre National de la Recherche Scientifique, Université Paris-Saclay, Palaiseau, France
| | - Ursula Liebl
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université Paris-Saclay, Palaiseau, France
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15
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Khallef S, Lestini R, Myllykallio H, Houali K. Isolation and identification of two extremely halophilic archaea from sebkhas in the Algerian Sahara. Cell Mol Biol (Noisy-le-grand) 2018. [DOI: 10.14715/cmb/2018.64.4.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In Algeria, many salt lakes are to be found spread from southern Tunisia up to the Atlas Mountains in northern Algeria. Oum Eraneb and Ain El beida sebkhas (salt lakes), are located in the Algerian Sahara. The aim of this study was to explore the diversity of the halobacteria in this type of habitats. The physicochemical properties of these shallow saline environments were examined and compared with other hypersaline and marine ecosystems. Both sites were relatively alkaline with a pH around 8.57- 8.74 and rich in salt at 13% and 16% (w/v) salinity for Oum Eraneb and Ain El beida, respectively, with dominant ions of sodium and chloride. The microbial approach revealed the presence of two halophilic archaea, strains JCM13561 and A33T in both explored sebkhas. Growth occurred between 10 and 25% (w/v) NaCl and the isolates grow optimally at 20% (w/v) NaCl. The pH range for growth was 6 to 9.5 with an optimum at pH 7.5 for the first strain and 7 to 9.5 with an optimum pH at 8.5-9 for the second strain. On the basis of 16S rRNA gene sequence analysis, strains JCM13561 and A33T were most closely related to Halorubrum litoreum and Natronorubrum bangense (99% and 96% similarity, respectively).
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16
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Khallef S, Lestini R, Myllykallio H, Houali K. Isolation and identification of two extremely halophilic archaea from sebkhas in the Algerian Sahara. Cell Mol Biol (Noisy-le-grand) 2018; 64:83-91. [PMID: 29631688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 03/07/2018] [Accepted: 03/12/2018] [Indexed: 06/08/2023]
Abstract
In Algeria, many salt lakes are to be found spread from southern Tunisia up to the Atlas Mountains in northern Algeria. Oum Eraneb and Ain El beida sebkhas (salt lakes), are located in the Algerian Sahara. The aim of this study was to explore the diversity of the halobacteria in this type of habitats. The physicochemical properties of these shallow saline environments were examined and compared with other hypersaline and marine ecosystems. Both sites were relatively alkaline with a pH around 8.57- 8.74 and rich in salt at 13% and 16% (w/v) salinity for Oum Eraneb and Ain El beida, respectively, with dominant ions of sodium and chloride. The microbial approach revealed the presence of two halophilic archaea, strains JCM13561 and A33T in both explored sebkhas. Growth occurred between 10 and 25% (w/v) NaCl and the isolates grow optimally at 20% (w/v) NaCl. The pH range for growth was 6 to 9.5 with an optimum at pH 7.5 for the first strain and 7 to 9.5 with an optimum pH at 8.5-9 for the second strain. On the basis of 16S rRNA gene sequence analysis, strains JCM13561 and A33T were most closely related to Halorubrum litoreum and Natronorubrum bangense (99% and 96% similarity, respectively).
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Affiliation(s)
- Sakina Khallef
- Laboratoire de Bio Ressources Sahariennes. Préservation et valorisation (BRS). Département des Sciences Biologiques, Faculté des Sciences de la Nature et de la Vie, Université Kasdi MERBAH de Ouargla, 30000, Algérie
| | - Roxane Lestini
- Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS UMR7645 - INSERM U696.Université Paris-Saclay, 91 128, Palaiseau Cedex, France
| | - Hannu Myllykallio
- Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS UMR7645 - INSERM U696.Université Paris-Saclay, 91 128, Palaiseau Cedex, France
| | - Karim Houali
- Laboratoire de Biochimie Analytiques et Biotehnologies (LABAB), Faculté des Sciences Biologiques et des Sciences Agronomiques. Université Mouloud MAMMERI de Tizi-Ouzou. Algérie
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17
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Nag L, Sournia P, Myllykallio H, Liebl U, Vos MH. Correction to “Identification of the TyrOH ●+ Radical Cation in the Flavoenzyme TrmFO”. J Am Chem Soc 2017; 139:15554. [DOI: 10.1021/jacs.7b10508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Abstract
Tyrosine (TyrOH) and tryptophan radicals play important roles as intermediates in biochemical charge-transfer reactions. Tryptophanyl radicals have been observed both in their protonated cation form and in their unprotonated neutral form, but to date, tyrosyl radicals have only been observed in their unprotonated form. With a genetically modified form of the flavoenzyme TrmFO as a suitable model system and using ultrafast fluorescence and absorption spectroscopy, we characterize its protonated precursor TyrOH•+, and we show this species to have a distinct visible absorption band and a transition moment that we suggest to lie close to the phenol symmetry axis. TyrOH•+ is formed in ∼1 ps by electron transfer to excited flavin and decays in ∼3 ps by charge recombination. These findings imply that TyrOH oxidation does not necessarily induce its concerted deprotonation. Our results will allow disentangling of photoproduct states in flavoproteins in often-encountered complex situations and more generally are important for understanding redox chains relying on tyrosyl intermediates.
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Affiliation(s)
- Lipsa Nag
- LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau 91128 Cedex, France
| | - Pierre Sournia
- LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau 91128 Cedex, France
| | - Hannu Myllykallio
- LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau 91128 Cedex, France
| | - Ursula Liebl
- LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau 91128 Cedex, France
| | - Marten H Vos
- LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau 91128 Cedex, France
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19
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Becker HF, Héliou A, Djaout K, Lestini R, Regnier M, Myllykallio H. High-throughput sequencing reveals circular substrates for an archaeal RNA ligase. RNA Biol 2017; 14:1075-1085. [PMID: 28277897 DOI: 10.1080/15476286.2017.1302640] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
It is only recently that the abundant presence of circular RNAs (circRNAs) in all kingdoms of Life, including the hyperthermophilic archaeon Pyrococcus abyssi, has emerged. This led us to investigate the physiologic significance of a previously observed weak intramolecular ligation activity of Pab1020 RNA ligase. Here we demonstrate that this enzyme, despite sharing significant sequence similarity with DNA ligases, is indeed an RNA-specific polynucleotide ligase efficiently acting on physiologically significant substrates. Using a combination of RNA immunoprecipitation assays and RNA-seq, our genome-wide studies revealed 133 individual circRNA loci in P. abyssi. The large majority of these loci interacted with Pab1020 in cells and circularization of selected C/D Box and 5S rRNA transcripts was confirmed biochemically. Altogether these studies revealed that Pab1020 is required for RNA circularization. Our results further suggest the functional speciation of an ancestral NTase domain and/or DNA ligase toward RNA ligase activity and prompt for further characterization of the widespread functions of circular RNAs in prokaryotes. Detailed insight into the cellular substrates of Pab1020 may facilitate the development of new biotechnological applications e.g. in ligation of preadenylated adaptors to RNA molecules.
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Affiliation(s)
- Hubert F Becker
- a LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau , France.,b Sorbonne Universités, UPMC Univ Paris 06 , 4 Place Jussieu, Paris , France
| | - Alice Héliou
- a LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau , France.,c LIX, Ecole Polytechnique, CNRS, Université Paris-Saclay, INRIA , Palaiseau , France
| | - Kamel Djaout
- a LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau , France
| | - Roxane Lestini
- a LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau , France
| | - Mireille Regnier
- c LIX, Ecole Polytechnique, CNRS, Université Paris-Saclay, INRIA , Palaiseau , France
| | - Hannu Myllykallio
- a LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau , France
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20
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Skouloubris S, Djaout K, Lamarre I, Lambry JC, Anger K, Briffotaux J, Liebl U, de Reuse H, Myllykallio H. Targeting of Helicobacter pylori thymidylate synthase ThyX by non-mitotoxic hydroxy-naphthoquinones. Open Biol 2016; 5:150015. [PMID: 26040760 PMCID: PMC4632503 DOI: 10.1098/rsob.150015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
ThyX is an essential thymidylate synthase that is mechanistically and structurally unrelated to the functionally analogous human enzyme, thus providing means for selective inhibition of bacterial growth. To identify novel compounds with anti-bacterial activity against the human pathogenic bacterium Helicobacter pylori, based on our earlier biochemical and structural analyses, we designed a series of eighteen 2-hydroxy-1,4-naphthoquinones (2-OH-1,4-NQs) that target HpThyX. Our lead-like molecules markedly inhibited the NADPH oxidation and 2′-deoxythymidine-5′-monophosphate-forming activities of HpThyX enzyme in vitro, with inhibitory constants in the low nanomolar range. The identification of non-cytotoxic and non-mitotoxic 2-OH-1,4-NQ inhibitors permitted testing their in vivo efficacy in a mouse model for H. pylori infections. Despite the widely assumed toxicity of naphthoquinones (NQs), we identified tight-binding ThyX inhibitors that were tolerated in mice and can be associated with a modest effect in reducing the number of colonizing bacteria. Our results thus provide proof-of-concept that targeting ThyX enzymes is a highly feasible strategy for the development of therapies against H. pylori and a high number of other ThyX-dependent pathogenic bacteria. We also demonstrate that chemical reactivity of NQs does not prevent their exploitation as anti-microbial compounds, particularly when mitotoxicity screening is used to prioritize these compounds for further experimentation.
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Affiliation(s)
- Stéphane Skouloubris
- Laboratoire d'Optique et Biosciences, CNRS UMR7645, INSERM U1182, Ecole Polytechnique, Palaiseau 91128, France Department of Biology, Université Paris-Sud, Orsay 91405, France
| | - Kamel Djaout
- Laboratoire d'Optique et Biosciences, CNRS UMR7645, INSERM U1182, Ecole Polytechnique, Palaiseau 91128, France
| | - Isabelle Lamarre
- Laboratoire d'Optique et Biosciences, CNRS UMR7645, INSERM U1182, Ecole Polytechnique, Palaiseau 91128, France
| | - Jean-Christophe Lambry
- Laboratoire d'Optique et Biosciences, CNRS UMR7645, INSERM U1182, Ecole Polytechnique, Palaiseau 91128, France
| | - Karine Anger
- Department of Microbiology, Institut Pasteur, Unité Pathogenèse de Helicobacter, 28 rue du Dr. Roux, Paris 75724, France
| | - Julien Briffotaux
- Laboratoire d'Optique et Biosciences, CNRS UMR7645, INSERM U1182, Ecole Polytechnique, Palaiseau 91128, France
| | - Ursula Liebl
- Laboratoire d'Optique et Biosciences, CNRS UMR7645, INSERM U1182, Ecole Polytechnique, Palaiseau 91128, France
| | - Hilde de Reuse
- Department of Microbiology, Institut Pasteur, Unité Pathogenèse de Helicobacter, 28 rue du Dr. Roux, Paris 75724, France
| | - Hannu Myllykallio
- Laboratoire d'Optique et Biosciences, CNRS UMR7645, INSERM U1182, Ecole Polytechnique, Palaiseau 91128, France
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21
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Garg D, Skouloubris S, Briffotaux J, Myllykallio H, Wade RC. Conservation and Role of Electrostatics in Thymidylate Synthase. Sci Rep 2015; 5:17356. [PMID: 26612036 PMCID: PMC4661567 DOI: 10.1038/srep17356] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 10/28/2015] [Indexed: 11/17/2022] Open
Abstract
Conservation of function across families of orthologous enzymes is generally accompanied by conservation of their active site electrostatic potentials. To study the electrostatic conservation in the highly conserved essential enzyme, thymidylate synthase (TS), we conducted a systematic species-based comparison of the electrostatic potential in the vicinity of its active site. Whereas the electrostatics of the active site of TS are generally well conserved, the TSs from minimal organisms do not conform to the overall trend. Since the genomes of minimal organisms have a high thymidine content compared to other organisms, the observation of non-conserved electrostatics was surprising. Analysis of the symbiotic relationship between minimal organisms and their hosts, and the genetic completeness of the thymidine synthesis pathway suggested that TS from the minimal organism Wigglesworthia glossinidia (W.g.b.) must be active. Four residues in the vicinity of the active site of Escherichia coli TS were mutated individually and simultaneously to mimic the electrostatics of W.g.b TS. The measured activities of the E. coli TS mutants imply that conservation of electrostatics in the region of the active site is important for the activity of TS, and suggest that the W.g.b. TS has the minimal activity necessary to support replication of its reduced genome.
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Affiliation(s)
- Divita Garg
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.,Munich Center for Integrated Protein Science, Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Stephane Skouloubris
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645, INSERM U1182, Université Paris-Saclay, 91128, Palaiseau, France.,Université Paris-Sud, 91405, Orsay, France
| | - Julien Briffotaux
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645, INSERM U1182, Université Paris-Saclay, 91128, Palaiseau, France
| | - Hannu Myllykallio
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645, INSERM U1182, Université Paris-Saclay, 91128, Palaiseau, France
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Baden-Württemberg, Germany
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22
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Salo-Ahen OMH, Tochowicz A, Pozzi C, Cardinale D, Ferrari S, Boum Y, Mangani S, Stroud RM, Saxena P, Myllykallio H, Costi MP, Ponterini G, Wade RC. Hotspots in an obligate homodimeric anticancer target. Structural and functional effects of interfacial mutations in human thymidylate synthase. J Med Chem 2015; 58:3572-81. [PMID: 25798950 DOI: 10.1021/acs.jmedchem.5b00137] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Human thymidylate synthase (hTS), a target for antiproliferative drugs, is an obligate homodimer. Single-point mutations to alanine at the monomer-monomer interface may enable the identification of specific residues that delineate sites for drugs aimed at perturbing the protein-protein interactions critical for activity. We computationally identified putative hotspot residues at the interface and designed mutants to perturb the intersubunit interaction. Dimer dissociation constants measured by a FRET-based assay range from 60 nM for wild-type hTS up to about 1 mM for single-point mutants and agree with computational predictions of the effects of these mutations. Mutations that are remote from the active site retain full or partial activity, although the substrate KM values were generally higher and the dimer was less stable. The lower dimer stability of the mutants can facilitate access to the dimer interface by small molecules and thereby aid the design of inhibitors that bind at the dimer interface.
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Affiliation(s)
- Outi M H Salo-Ahen
- †Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
| | - Anna Tochowicz
- ‡Department of Biochemistry and Biophysics, University of California-San Francisco, San Francisco, California 94158, United States
| | - Cecilia Pozzi
- §Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Daniela Cardinale
- ∥Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Stefania Ferrari
- ∥Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Yap Boum
- ⊥Ecole Polytechnique, CNRS UMR7645, INSERM U696, 91128 Palaiseau, France
| | - Stefano Mangani
- §Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Robert M Stroud
- ‡Department of Biochemistry and Biophysics, University of California-San Francisco, San Francisco, California 94158, United States
| | - Puneet Saxena
- ∥Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Hannu Myllykallio
- ⊥Ecole Polytechnique, CNRS UMR7645, INSERM U696, 91128 Palaiseau, France
| | - Maria Paola Costi
- ∥Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Glauco Ponterini
- ∥Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Rebecca C Wade
- †Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany.,#Center for Molecular Biology, DKFZ-ZMBH Alliance, and Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, 69120 Heidelberg, Germany
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23
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Rezgui R, Lestini R, Kühn J, Fave X, McLeod L, Myllykallio H, Alexandrou A, Bouzigues C. Differential interaction kinetics of a bipolar structure-specific endonuclease with DNA flaps revealed by single-molecule imaging. PLoS One 2014; 9:e113493. [PMID: 25412080 PMCID: PMC4239081 DOI: 10.1371/journal.pone.0113493] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 10/23/2014] [Indexed: 11/18/2022] Open
Abstract
As DNA repair enzymes are essential for preserving genome integrity, understanding their substrate interaction dynamics and the regulation of their catalytic mechanisms is crucial. Using single-molecule imaging, we investigated the association and dissociation kinetics of the bipolar endonuclease NucS from Pyrococcus abyssi (Pab) on 5′ and 3′-flap structures under various experimental conditions. We show that association of the PabNucS with ssDNA flaps is largely controlled by diffusion in the NucS-DNA energy landscape and does not require a free 5′ or 3′ extremity. On the other hand, NucS dissociation is independent of the flap length and thus independent of sliding on the single-stranded portion of the flapped DNA substrates. Our kinetic measurements have revealed previously unnoticed asymmetry in dissociation kinetics from these substrates that is markedly modulated by the replication clamp PCNA. We propose that the replication clamp PCNA enhances the cleavage specificity of NucS proteins by accelerating NucS loading at the ssDNA/dsDNA junctions and by minimizing the nuclease interaction time with its DNA substrate. Our data are also consistent with marked reorganization of ssDNA and nuclease domains occurring during NucS catalysis, and indicate that NucS binds its substrate directly at the ssDNA-dsDNA junction and then threads the ssDNA extremity into the catalytic site. The powerful techniques used here for probing the dynamics of DNA-enzyme binding at the single-molecule have provided new insight regarding substrate specificity of NucS nucleases.
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Affiliation(s)
- Rachid Rezgui
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
| | - Roxane Lestini
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
| | - Joëlle Kühn
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
| | - Xenia Fave
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
| | - Lauren McLeod
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
| | - Hannu Myllykallio
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
| | - Antigoni Alexandrou
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
| | - Cedric Bouzigues
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
- * E-mail:
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24
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Lestini R, Laptenok SP, Kühn J, Hink MA, Schanne-Klein MC, Liebl U, Myllykallio H. Intracellular dynamics of archaeal FANCM homologue Hef in response to halted DNA replication. Nucleic Acids Res 2013; 41:10358-70. [PMID: 24049073 PMCID: PMC3905845 DOI: 10.1093/nar/gkt816] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Hef is an archaeal member of the DNA repair endonuclease XPF (XPF)/Crossover junction endonuclease MUS81 (MUS81)/Fanconi anemia, complementation group M (FANCM) protein family that in eukaryotes participates in the restart of stalled DNA replication forks. To investigate the physiological roles of Hef in maintaining genome stability in living archaeal cells, we studied the localization of Hef–green fluorescent protein fusions by fluorescence microscopy. Our studies revealed that Haloferax volcanii Hef proteins formed specific localization foci under regular growth conditions, the number of which specifically increased in response to replication arrest. Purification of the full-length Hef protein from its native host revealed that it forms a stable homodimer in solution, with a peculiar elongated configuration. Altogether our data indicate that the shape of Hef, significant physicochemical constraints and/or interactions with DNA limit the apparent cytosolic diffusion of halophilic DNA replication/repair complexes, and demonstrate that Hef proteins are dynamically recruited to archaeal eukaryotic-like chromatin to counteract DNA replication stress. We suggest that the evolutionary conserved function of Hef/FANCM proteins is to enhance replication fork stability by directly interacting with collapsed replication forks.
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Affiliation(s)
- Roxane Lestini
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645-INSERM U696, 91128 Palaiseau Cedex, France and Section of Molecular Cytology, Swammerdam Institute for Life Sciences, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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25
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Basta T, Boum Y, Briffotaux J, Becker HF, Lamarre-Jouenne I, Lambry JC, Skouloubris S, Liebl U, Graille M, van Tilbeurgh H, Myllykallio H. Mechanistic and structural basis for inhibition of thymidylate synthase ThyX. Open Biol 2013; 2:120120. [PMID: 23155486 PMCID: PMC3498832 DOI: 10.1098/rsob.120120] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 09/11/2012] [Indexed: 11/12/2022] Open
Abstract
Nature has established two mechanistically and structurally unrelated families of thymidylate synthases that produce de novo thymidylate or dTMP, an essential DNA precursor. Representatives of the alternative flavin-dependent thymidylate synthase family, ThyX, are found in a large number of microbial genomes, but are absent in humans. We have exploited the nucleotide binding pocket of ThyX proteins to identify non-substrate-based tight-binding ThyX inhibitors that inhibited growth of genetically modified Escherichia coli cells dependent on thyX in a manner mimicking a genetic knockout of thymidylate synthase. We also solved the crystal structure of a viral ThyX bound to 2-hydroxy-3-(4-methoxybenzyl)-1,4-naphthoquinone at a resolution of 2.6 Å. This inhibitor was found to bind within the conserved active site of the tetrameric ThyX enzyme, at the interface of two monomers, partially overlapping with the dUMP binding pocket. Our studies provide new chemical tools for investigating the ThyX reaction mechanism and establish a novel mechanistic and structural basis for inhibition of thymidylate synthesis. As essential ThyX proteins are found e.g. in Mycobacterium tuberculosis and Helicobacter pylori, our studies have also potential to pave the way towards the development of new anti-microbial compounds.
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Affiliation(s)
- Tamara Basta
- Laboratoire d'Optique et Biosciences, INSERM U696, CNRS UMR 7645, Ecole Polytechnique, Palaiseau Cedex, Palaiseau 91228, France
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26
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Laptenok SP, Bouzhir-Sima L, Lambry JC, Myllykallio H, Liebl U, Vos MH. Ultrafast real-time visualization of active site flexibility of flavoenzyme thymidylate synthase ThyX. Proc Natl Acad Sci U S A 2013; 110:8924-9. [PMID: 23671075 PMCID: PMC3670337 DOI: 10.1073/pnas.1218729110] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In many bacteria the flavoenzyme thymidylate synthase ThyX produces the DNA nucleotide deoxythymidine monophosphate from dUMP, using methylenetetrahydrofolate as carbon donor and NADPH as hydride donor. Because all three substrates bind in close proximity to the catalytic flavin adenine dinucleotide group, substantial flexibility of the ThyX active site has been hypothesized. Using femtosecond time-resolved fluorescence spectroscopy, we have studied the conformational heterogeneity and the conformational interconversion dynamics in real time in ThyX from the hyperthermophilic bacterium Thermotoga maritima. The dynamics of electron transfer to excited flavin adenine dinucleotide from a neighboring tyrosine residue are used as a sensitive probe of the functional dynamics of the active site. The fluorescence decay spanned a full three orders of magnitude, demonstrating a very wide range of conformations. In particular, at physiological temperatures, multiple angstrom cofactor-residue displacements occur on the picoseconds timescale. These experimental findings are supported by molecular dynamics simulations. Binding of the dUMP substrate abolishes this flexibility and stabilizes the active site in a configuration where dUMP closely interacts with the flavin cofactor and very efficiently quenches fluorescence itself. Our results indicate a dynamic selected-fit mechanism where binding of the first substrate dUMP at high temperature stabilizes the enzyme in a configuration favorable for interaction with the second substrate NADPH, and more generally have important implications for the role of active site flexibility in enzymes interacting with multiple poly-atom substrates and products. Moreover, our data provide the basis for exploring the effect of inhibitor molecules on the active site dynamics of ThyX and other multisubstrate flavoenzymes.
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Affiliation(s)
- Sergey P. Laptenok
- Laboratory for Optics and Biosciences, Centre National de la Recherche Scientifique Ecole Polytechnique, 91128 Palaiseau, France; and
- Institut National de la Santé et de la Recherche Médicale U696, 91128 Palaiseau, France
| | - Latifa Bouzhir-Sima
- Laboratory for Optics and Biosciences, Centre National de la Recherche Scientifique Ecole Polytechnique, 91128 Palaiseau, France; and
- Institut National de la Santé et de la Recherche Médicale U696, 91128 Palaiseau, France
| | - Jean-Christophe Lambry
- Laboratory for Optics and Biosciences, Centre National de la Recherche Scientifique Ecole Polytechnique, 91128 Palaiseau, France; and
- Institut National de la Santé et de la Recherche Médicale U696, 91128 Palaiseau, France
| | - Hannu Myllykallio
- Laboratory for Optics and Biosciences, Centre National de la Recherche Scientifique Ecole Polytechnique, 91128 Palaiseau, France; and
- Institut National de la Santé et de la Recherche Médicale U696, 91128 Palaiseau, France
| | - Ursula Liebl
- Laboratory for Optics and Biosciences, Centre National de la Recherche Scientifique Ecole Polytechnique, 91128 Palaiseau, France; and
- Institut National de la Santé et de la Recherche Médicale U696, 91128 Palaiseau, France
| | - Marten H. Vos
- Laboratory for Optics and Biosciences, Centre National de la Recherche Scientifique Ecole Polytechnique, 91128 Palaiseau, France; and
- Institut National de la Santé et de la Recherche Médicale U696, 91128 Palaiseau, France
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27
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Laptenok SP, Bouzhir-Sima L, Myllykallio H, Liebl U, Vos MH. Configurational fluctuations and flavin-substrate interactions in the flavoenzyme ThyX studied by time- and spectrally resolved fluorescence. EPJ Web of Conferences 2013. [DOI: 10.1051/epjconf/20134107011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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28
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Ligabue A, Marverti G, Liebl U, Myllykallio H. Transcriptional activation and cell cycle block are the keys for 5-fluorouracil induced up-regulation of human thymidylate synthase expression. PLoS One 2012; 7:e47318. [PMID: 23056627 PMCID: PMC3467224 DOI: 10.1371/journal.pone.0047318] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 09/14/2012] [Indexed: 12/27/2022] Open
Abstract
Background 5-fluorouracil, a commonly used chemotherapeutic agent, up-regulates expression of human thymidylate synthase (hTS). Several different regulatory mechanisms have been proposed to mediate this up-regulation in distinct cell lines, but their specific contributions in a single cell line have not been investigated to date. We have established the relative contributions of these previously proposed regulatory mechanisms in the ovarian cancer cell line 2008 and the corresponding cisplatin-resistant and 5-FU cross-resistant-subline C13*. Methodology/Principal Findings Using RNA polymerase II inhibitor DRB treated cell cultures, we showed that 70–80% of up-regulation of hTS results from transcriptional activation of TYMS mRNA. Moreover, we report that 5-FU compromises the cell cycle by blocking the 2008 and C13* cell lines in the S phase. As previous work has established that TYMS mRNA is synthesized in the S and G1 phase and hTS is localized in the nuclei during S and G2-M phase, the observed cell cycle changes are also expected to affect the intracellular regulation of hTS. Our data also suggest that the inhibition of the catalytic activity of hTS and the up-regulation of the hTS protein level are not causally linked, as the inactivated ternary complex, formed by hTS, deoxyuridine monophosphate and methylenetetrahydrofolate, was detected already 3 hours after 5-FU exposure, whereas substantial increase in global TS levels was detected only after 24 hours. Conclusions/Significance Altogether, our data indicate that constitutive TYMS mRNA transcription, cell cycle-induced hTS regulation and hTS enzyme stability are the three key mechanisms responsible for 5-fluorouracil induced up-regulation of human thymidylate synthase expression in the two ovarian cancer cell lines studied. As these three independent regulatory phenomena occur in a precise order, our work provides a feasible rationale for earlier observed synergistic combinations of 5-FU with other drugs and may suggest novel therapeutic strategies.
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Affiliation(s)
- Alessio Ligabue
- INSERM U696, Palaiseau, France
- Laboratoire d'Optique et Biosciences, CNRS, Ecole Polytechnique, Palaiseau, France
| | - Gaetano Marverti
- Dipartimento di Scienze Biomediche, Sezione di Chimica Biologica, University of Modena and Reggio Emilia, Modena, Italy
| | - Ursula Liebl
- INSERM U696, Palaiseau, France
- Laboratoire d'Optique et Biosciences, CNRS, Ecole Polytechnique, Palaiseau, France
| | - Hannu Myllykallio
- INSERM U696, Palaiseau, France
- Laboratoire d'Optique et Biosciences, CNRS, Ecole Polytechnique, Palaiseau, France
- * E-mail:
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29
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Creze C, Ligabue A, Laurent S, Lestini R, Laptenok SP, Khun J, Vos MH, Czjzek M, Myllykallio H, Flament D. Modulation of the Pyrococcus abyssi NucS endonuclease activity by replication clamp at functional and structural levels. J Biol Chem 2012; 287:15648-60. [PMID: 22431731 DOI: 10.1074/jbc.m112.346361] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pyrococcus abyssi NucS is the founding member of a new family of structure-specific DNA endonucleases that interact with the replication clamp proliferating cell nuclear antigen (PCNA). Using a combination of small angle x-ray scattering and surface plasmon resonance analyses, we demonstrate the formation of a stable complex in solution, in which one molecule of the PabNucS homodimer binds to the outside surface of the PabPCNA homotrimer. Using fluorescent labels, PCNA is shown to increase the binding affinity of NucS toward single-strand/double-strand junctions on 5' and 3' flaps, as well as to modulate the cleavage specificity on the branched DNA structures. Our results indicate that the presence of a single major contact between the PabNucS and PabPCNA proteins, together with the complex-induced DNA bending, facilitate conformational flexibility required for specific cleavage at the single-strand/double-strand DNA junction.
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Affiliation(s)
- Christophe Creze
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
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30
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Hamdane D, Argentini M, Cornu D, Myllykallio H, Skouloubris S, Hui-Bon-Hoa G, Golinelli-Pimpaneau B. Insights into folate/FAD-dependent tRNA methyltransferase mechanism: role of two highly conserved cysteines in catalysis. J Biol Chem 2011; 286:36268-80. [PMID: 21846722 DOI: 10.1074/jbc.m111.256966] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The flavoprotein TrmFO methylates specifically the C5 carbon of the highly conserved uridine 54 in tRNAs. Contrary to most methyltransferases, the 1-carbon unit transferred by TrmFO derives from 5,10-methylenetetrahydrofolate and not from S-adenosyl-L-methionine. The enzyme also employs the FAD hydroquinone as a reducing agent of the C5 methylene U54-tRNA intermediate in vitro. By analogy with the catalytic mechanism of thymidylate synthase ThyA, a conserved cysteine located near the FAD isoalloxazine ring was proposed to act as a nucleophile during catalysis. Here, we mutated this residue (Cys-53 in Bacillus subtilis TrmFO) to alanine and investigated its functional role. Biophysical characterization of this variant demonstrated the major structural role of Cys-53 in maintaining both the integrity and plasticity of the flavin binding site. Unexpectedly, gel mobility shift assays showed that, like the wild-type enzyme, the inactive C53A variant was capable of forming a covalent complex with a 5-fluorouridine-containing mini-RNA. This result confirms the existence of a covalent intermediate during catalysis but rules out a nucleophilic role for Cys-53. To identify the actual nucleophile, two other strictly conserved cysteines (Cys-192 and Cys-226) that are relatively far from the active site were replaced with alanine, and a double mutant C53A/C226A was generated. Interestingly, only mutations that target Cys-226 impeded TrmFO from forming a covalent complex and methylating tRNA. Altogether, we propose a revised mechanism for the m(5)U54 modification catalyzed by TrmFO, where Cys-226 attacks the C6 atom of the uridine, and Cys-53 plays the role of the general base abstracting the C5 proton.
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Affiliation(s)
- Djemel Hamdane
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.
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31
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Garg D, Henrich S, Salo-Ahen OMH, Myllykallio H, Costi MP, Wade RC. Novel approaches for targeting thymidylate synthase to overcome the resistance and toxicity of anticancer drugs. J Med Chem 2010; 53:6539-49. [PMID: 20527892 DOI: 10.1021/jm901869w] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Divita Garg
- Molecular and Cellular Modeling Group, Heidelberg Institute of Theoretical Studies gGmbH, Heidelberg, Germany
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32
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Hamdane D, Skouloubris S, Myllykallio H, Golinelli-Pimpaneau B. Expression and purification of untagged and histidine-tagged folate-dependent tRNA:m5U54 methyltransferase from Bacillus subtilis. Protein Expr Purif 2010; 73:83-9. [PMID: 20412857 DOI: 10.1016/j.pep.2010.04.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 04/15/2010] [Accepted: 04/16/2010] [Indexed: 11/30/2022]
Abstract
Folate-dependent tRNA m(5)U methyltransferase TrmFO is a flavoprotein that catalyzes the C(5)-methylation of uridine at position 54 in the TPsiC loop of tRNA in several bacteria. Here we report the cloning and optimization of expression in Escherichia coli BL21 (DE3) of untagged, N-terminus, C-terminus (His)(6)-tagged TrmFO from Bacillus subtilis. Tagged and untagged TrmFO were purified to homogeneity by metal affinity or ion exchange and heparin affinity, respectively, followed by size-exclusion chromatography. The tag did not significantly alter the expression level, flavin content, activity and secondary structure of the protein.
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Affiliation(s)
- Djemel Hamdane
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
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33
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Ren B, Kühn J, Meslet-Cladiere L, Briffotaux J, Norais C, Lavigne R, Flament D, Ladenstein R, Myllykallio H. Structure and function of a novel endonuclease acting on branched DNA substrates. EMBO J 2009; 28:2479-89. [PMID: 19609302 DOI: 10.1038/emboj.2009.192] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Accepted: 06/18/2009] [Indexed: 11/09/2022] Open
Abstract
We show that Pyrococcus abyssi PAB2263 (dubbed NucS (nuclease for ss DNA) is a novel archaeal endonuclease that interacts with the replication clamp PCNA. Structural determination of P. abyssi NucS revealed a two-domain dumbbell-like structure that in overall does not resemble any known protein structure. Biochemical and structural studies indicate that NucS orthologues use a non-catalytic ssDNA-binding domain to regulate the cleavage activity at another site, thus resulting into the specific cleavage at double-stranded DNA (dsDNA)/ssDNA junctions on branched DNA substrates. Both 3' and 5' extremities of the ssDNA can be cleaved at the nuclease channel that is too narrow to accommodate duplex DNA. Altogether, our data suggest that NucS proteins constitute a new family of structure-specific DNA endonucleases that are widely distributed in archaea and in bacteria, including Mycobacterium tuberculosis.
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Affiliation(s)
- Bin Ren
- Center for Structural Biochemistry, Karolinska Institutet, NOVUM, Huddinge, Sweden
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Brooks MA, Meslet-Cladiére L, Graille M, Kuhn J, Blondeau K, Myllykallio H, van Tilbeurgh H. The structure of an archaeal homodimeric ligase which has RNA circularization activity. Protein Sci 2008; 17:1336-45. [PMID: 18511537 DOI: 10.1110/ps.035493.108] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The genome of Pyrococcus abyssi contains two open reading frames encoding proteins which had been previously predicted to be DNA ligases, Pab2002 and Pab1020. We show that while the former is indeed a DNA ligase, Pab1020 had no effect on the substrate deoxyoligo-ribonucleotides tested. Instead, Pab1020 catalyzes the nucleotidylation of oligo-ribonucleotides in an ATP-dependent reaction, suggesting that it is an RNA ligase. We have solved the structure of Pab1020 in complex with the ATP analog AMPPNP by single-wavelength anomalous dispersion (SAD), elucidating a structure with high structural similarity to the catalytic domains of two RNA ligases from the bacteriophage T4. Additional carboxy-terminal domains are also present, and one of these mediates contacts with a second protomer, which is related by noncrystallographic symmetry, generating a homodimeric structure. These C-terminal domains are terminated by short domain swaps which themselves end within 5 A of the active sites of the partner molecules. Additionally, we show that the protein is indeed capable of circularizing RNA molecules in an ATP-dependent reaction. These structural and biochemical results provide an insight into the potential physiological roles of Pab1020.
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Affiliation(s)
- Mark Adrian Brooks
- IBBMC-CNRS, Université de Paris-Sud, CNRS-UMR8619, IFR115, 91405 Orsay, France
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35
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Esra Onen F, Boum Y, Jacquement C, Spanedda MV, Jaber N, Scherman D, Myllykallio H, Herscovici J. Design, synthesis and evaluation of potent thymidylate synthase X inhibitors. Bioorg Med Chem Lett 2008; 18:3628-31. [PMID: 18513963 DOI: 10.1016/j.bmcl.2008.04.080] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Revised: 04/25/2008] [Accepted: 04/25/2008] [Indexed: 10/22/2022]
Abstract
Three synthesized series of compounds based on a thiazolidine core allowed identification of potent inhibitors of thymidylate synthase X. The evaluation of the catalytic activity of the enzyme in the presence of these molecules revealed two distinct classes of compounds that inhibit ThyX with submicromolar concentrations, which could lead, after optimization, to effective inhibitors with potential biomedical interest.
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Affiliation(s)
- F Esra Onen
- Unité de Pharmacologie Chimique et Génétique, Ecole Nationale Supérieure de Chimie de Paris, Paris, France
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36
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Le Breton M, Henneke G, Norais C, Flament D, Myllykallio H, Querellou J, Raffin JP. The heterodimeric primase from the euryarchaeon Pyrococcus abyssi: a multifunctional enzyme for initiation and repair? J Mol Biol 2007; 374:1172-85. [PMID: 17991487 DOI: 10.1016/j.jmb.2007.10.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Revised: 10/02/2007] [Accepted: 10/05/2007] [Indexed: 11/27/2022]
Abstract
We report on the characterization of the DNA primase complex of the hyperthermophilic archaeon Pyrococcus abyssi (Pab). The Pab DNA primase complex is composed of the proteins Pabp41 and Pabp46, which show sequence similarities to the p49 and p58 subunits, respectively, of the eukaryotic polymerase alpha-primase complex. Both subunits were expressed, purified, and characterized. The Pabp41 subunit alone had no RNA synthesis activity but could synthesize long (up to 3 kb) DNA strands. Addition of the Pabp46 subunit increased the rate of DNA synthesis but decreased the length of the DNA fragments synthesized and conferred RNA synthesis capability. Moreover, in our experimental conditions, Pab DNA primase had comparable affinities for ribonucleotides and deoxyribonucleotides, and its activity was dependent on the presence of Mg2+ and Mn2+. Interestingly, Pab DNA primase also displayed DNA polymerase, gap-filling, and strand-displacement activities. Genetic analyses undertaken in Haloferax volcanii suggested that the eukaryotic-type heterodimeric primase is essential for survival in archaeal cells. Our results are in favor of a multifunctional archaeal primase involved in priming and repair.
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Affiliation(s)
- Magali Le Breton
- Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, Ifremer, BP 70, F-29280 Plouzané, France
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Meslet-Cladiére L, Norais C, Kuhn J, Briffotaux J, Sloostra JW, Ferrari E, Hübscher U, Flament D, Myllykallio H. A Novel Proteomic Approach Identifies New Interaction Partners for Proliferating Cell Nuclear Antigen. J Mol Biol 2007; 372:1137-48. [PMID: 17720188 DOI: 10.1016/j.jmb.2007.06.056] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2007] [Revised: 06/14/2007] [Accepted: 06/18/2007] [Indexed: 11/28/2022]
Abstract
During DNA replication and repair, many proteins bind to and dissociate in a highly specific and ordered manner from proliferating cell nuclear antigen (PCNA). We describe a combined approach of in silico searches at the genome level and combinatorial peptide synthesis to investigate the binding properties of hundreds of short PCNA-interacting peptides (PIP-peptides) to archaeal and eukaryal PCNAs. Biological relevance of our combined approach was demonstrated by identification an inactive complex of Pyrococcus abyssi ribonuclease HII with PCNA. Furthermore we show that PIP-peptides interact with PCNA largely in a sequence independent manner. Our experimental approach also identified many so far unidentified PCNA interacting peptides in a number of human proteins.
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Leduc D, Escartin F, Nijhout HF, Reed MC, Liebl U, Skouloubris S, Myllykallio H. Flavin-dependent thymidylate synthase ThyX activity: implications for the folate cycle in bacteria. J Bacteriol 2007; 189:8537-45. [PMID: 17890305 PMCID: PMC2168944 DOI: 10.1128/jb.01380-07] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although flavin-dependent ThyX proteins show thymidylate synthase activity in vitro and functionally complement thyA defects in heterologous systems, direct proof of their cellular functions is missing. Using insertional mutagenesis of Rhodobacter capsulatus thyX, we constructed the first defined thyX inactivation mutant. Phenotypic analyses of the obtained mutant strain confirmed that R. capsulatus ThyX is required for de novo thymidylate synthesis. Full complementation of the R. capsulatus thyX::spec strain to thymidine prototrophy required not only the canonical thymidylate synthase ThyA but also the dihydrofolate reductase FolA. Strikingly, we also found that addition of exogenous methylenetetrahydrofolate transiently inhibited the growth of the different Rhodobacter strains used in this work. To rationalize these experimental results, we used a mathematical model of bacterial folate metabolism. This model suggests that a very low dihydrofolate reductase activity is enough to rescue significant thymidylate synthesis in the presence of ThyX proteins and is in agreement with the notion that intracellular accumulation of folates results in growth inhibition. In addition, our observations suggest that the presence of flavin-dependent thymidylate synthase X provides growth benefits under conditions in which the level of reduced folate derivatives is compromised.
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Affiliation(s)
- Damien Leduc
- INSERM Avenir group, Institut de Génétique et de Microbiologie, CNRS UMR8621, F-91405 Orsay, France
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Ren B, Kuhn J, Meslet-Cladiere L, Myllykallio H, Ladenstein R. Crystallization and preliminary X-ray analysis of a RecB-family nuclease from the archaeon Pyrococcus abyssi. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:406-8. [PMID: 17565182 PMCID: PMC2334999 DOI: 10.1107/s1744309107015278] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Accepted: 03/28/2007] [Indexed: 11/11/2022]
Abstract
Nucleases are required to process and repair DNA damage in living cells. One of the best studied nucleases is the RecB protein, which functions in Escherichia coli as a component of the RecBCD enzyme complex that amends double-strand breaks in DNA. Although archaea do not contain the RecBCD complex, a RecB-like nuclease from Pyrococcus abyssi has been cloned, expressed and purified. The protein was crystallized by the sitting-drop vapour-diffusion method using polyethylene glycol 8000 as the precipitant. The crystals belong to the orthorhombic space group C222(1), with unit-cell parameters a = 81.5, b = 159.8, c = 100.8 A. Self-rotation function and native Patterson map calculations revealed that there is a dimer in the asymmetric unit with its local twofold axis running parallel to the crystallographic twofold screw axis. The crystals diffracted to about 2 A and a complete native data set was collected to 2.65 A resolution.
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Affiliation(s)
- Bin Ren
- Center for Structural Biochemistry, Karolinska Institute, NOVUM, S-141 57 Huddinge, Sweden.
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Norais C, Hawkins M, Hartman AL, Eisen JA, Myllykallio H, Allers T. Genetic and physical mapping of DNA replication origins in Haloferax volcanii. PLoS Genet 2007; 3:e77. [PMID: 17511521 PMCID: PMC1868953 DOI: 10.1371/journal.pgen.0030077] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Accepted: 03/05/2007] [Indexed: 11/18/2022] Open
Abstract
The halophilic archaeon Haloferax volcanii has a multireplicon genome, consisting of a main chromosome, three secondary chromosomes, and a plasmid. Genes for the initiator protein Cdc6/Orc1, which are commonly located adjacent to archaeal origins of DNA replication, are found on all replicons except plasmid pHV2. However, prediction of DNA replication origins in H. volcanii is complicated by the fact that this species has no less than 14 cdc6/orc1 genes. We have used a combination of genetic, biochemical, and bioinformatic approaches to map DNA replication origins in H. volcanii. Five autonomously replicating sequences were found adjacent to cdc6/orc1 genes and replication initiation point mapping was used to confirm that these sequences function as bidirectional DNA replication origins in vivo. Pulsed field gel analyses revealed that cdc6/orc1-associated replication origins are distributed not only on the main chromosome (2.9 Mb) but also on pHV1 (86 kb), pHV3 (442 kb), and pHV4 (690 kb) replicons. Gene inactivation studies indicate that linkage of the initiator gene to the origin is not required for replication initiation, and genetic tests with autonomously replicating plasmids suggest that the origin located on pHV1 and pHV4 may be dominant to the principal chromosomal origin. The replication origins we have identified appear to show a functional hierarchy or differential usage, which might reflect the different replication requirements of their respective chromosomes. We propose that duplication of H. volcanii replication origins was a prerequisite for the multireplicon structure of this genome, and that this might provide a means for chromosome-specific replication control under certain growth conditions. Our observations also suggest that H. volcanii is an ideal organism for studying how replication of four replicons is regulated in the context of the archaeal cell cycle.
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Affiliation(s)
- Cédric Norais
- Institut de Génétique et Microbiologie, Université Paris-Sud, Orsay, France
- CNRS, UMR8621, Orsay, France
| | - Michelle Hawkins
- Institute of Genetics, University of Nottingham, Nottingham, United Kingdom
| | - Amber L Hartman
- Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jonathan A Eisen
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Hannu Myllykallio
- Institut de Génétique et Microbiologie, Université Paris-Sud, Orsay, France
- CNRS, UMR8621, Orsay, France
- * To whom correspondence should be addressed. E-mail: (HM); (TA)
| | - Thorsten Allers
- Institute of Genetics, University of Nottingham, Nottingham, United Kingdom
- * To whom correspondence should be addressed. E-mail: (HM); (TA)
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Urbonavicius J, Brochier-Armanet C, Skouloubris S, Myllykallio H, Grosjean H. In vitro detection of the enzymatic activity of folate-dependent tRNA (Uracil-54,-C5)-methyltransferase: evolutionary implications. Methods Enzymol 2007; 425:103-19. [PMID: 17673080 DOI: 10.1016/s0076-6879(07)25004-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Formation of 5-methyluridine (ribothymidine) at position 54 of the T-psi loop of tRNA is catalyzed by site-specific tRNA methyltransferases (tRNA[uracil-54,C5]-MTases). In eukaryotes and many bacteria, the methyl donor for this reaction is generally S-adenosyl-L-methionine (S-AdoMet). However, in other bacteria, like Enterococcus faecalis and Bacillus subtilis, it was shown that the source of carbon is N(5),N(10)-methylenetetrahydrofolate (CH(2)=THF). Recently we have determined that the Bacillus subtilis gid gene (later renamed to trmFO) encodes the folate-dependent tRNA(uracil-54,C5)-MTase. Here, we describe a procedure for overexpression and purification of this recombinant enzyme, as well as detection of its activity in vitro. Inspection of presently available sequenced genomes reveals that trmFO gene is present in most Firmicutes, in all alpha- and delta-Proteobacteria (except Rickettsiales in which the trmFO gene is missing), Deinococci, Cyanobacteria, Fusobacteria, Thermotogales, Acidobacteria, and in one Actinobacterium. Interestingly, trmFO is never found in genomes containing the gene trmA coding for S-adenosyl-L-methionine-dependent tRNA (uracil-54,C5)-MTase. The phylogenetic analysis of TrmFO sequences suggests an ancient origin of this enzyme in bacteria.
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Graziani S, Bernauer J, Skouloubris S, Graille M, Zhou CZ, Marchand C, Decottignies P, van Tilbeurgh H, Myllykallio H, Liebl U. Catalytic mechanism and structure of viral flavin-dependent thymidylate synthase ThyX. J Biol Chem 2006; 281:24048-57. [PMID: 16707489 DOI: 10.1074/jbc.m600745200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
By using biochemical and structural analyses, we have investigated the catalytic mechanism of the recently discovered flavin-dependent thymidylate synthase ThyX from Paramecium bursaria chlorella virus-1 (PBCV-1). Site-directed mutagenesis experiments have identified several residues implicated in either NADPH oxidation or deprotonation activity of PBCV-1 ThyX. Chemical modification by diethyl pyrocarbonate and mass spectroscopic analyses identified a histidine residue (His53) crucial for NADPH oxidation and located in the vicinity of the redox active N-5 atom of the FAD ring system. Moreover, we observed that the conformation of active site key residues of PBCV-1 ThyX differs from earlier reported ThyX structures, suggesting structural changes during catalysis. Steady-state kinetic analyses support a reaction mechanism where ThyX catalysis proceeds via formation of distinct ternary complexes without formation of a methyl enzyme intermediate.
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Affiliation(s)
- Sébastien Graziani
- CNRS, UMR 7645, Laboratory of Optics and Biosciences, Ecole Polytechnique, 91128 Palaiseau, France
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Abstract
The thyX gene for thymidylate synthase of the Lyme borreliosis (LB) agent Borrelia burgdorferi is located in a 54-kb linear plasmid. In the present study, we identified an orthologous thymidylate synthase gene in the relapsing fever (RF) agent Borrelia hermsii, located it in a 180-kb linear plasmid, and demonstrated its expression. The functions of the B. hermsii and B. burgdorferi thyX gene products were evaluated both in vivo, by complementation of a thymidylate synthase-deficient Escherichia coli mutant, and in vitro, by testing their activities after purification. The B. hermsii thyX gene complemented the thyA mutation in E. coli, and purified B. hermsii ThyX protein catalyzed the conversion of dTMP from dUMP. In contrast, the B. burgdorferi ThyX protein had only weakly detectable activity in vitro, and the B. burgdorferi thyX gene did not provide complementation in vivo. The lack of activity of B. burgdorferi's ThyX protein was associated with the substitution of a cysteine for a highly conserved arginine at position 91. The B. hermsii thyX locus was further distinguished by the downstream presence in the plasmid of orthologues of nrdI, nrdE, and nrdF, which encode the subunits of ribonucleoside diphosphate reductase and which are not present in the LB agents B. burgdorferi and Borrelia garinii. Phylogenetic analysis suggested that the nrdIEF cluster of B. hermsii was acquired by horizontal gene transfer. These findings indicate that Borrelia spp. causing RF have a greater capability for de novo pyrimidine synthesis than those causing LB, thus providing a basis for some of the biological differences between the two groups of pathogens.
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Affiliation(s)
- Jianmin Zhong
- Departments of Microbiology and of Molecular Genetics and Medicine, University of California Irvine, Irvine, CA 92697-4028, USA
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Urbonavičius J, Skouloubris S, Myllykallio H, Grosjean H. Identification of a novel gene encoding a flavin-dependent tRNA:m5U methyltransferase in bacteria--evolutionary implications. Nucleic Acids Res 2005; 33:3955-64. [PMID: 16027442 PMCID: PMC1178002 DOI: 10.1093/nar/gki703] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Formation of 5-methyluridine (ribothymidine) at position 54 of the T-psi loop of tRNA is catalyzed by site-specific tRNA methyltransferases (tRNA:m5U-54 MTase). In all Eukarya and many Gram-negative Bacteria, the methyl donor for this reaction is S-adenosyl-l-methionine (S-AdoMet), while in several Gram-positive Bacteria, the source of carbon is N5, N10-methylenetetrahydrofolate (CH2H4folate). We have identified the gene for Bacillus subtilis tRNA:m5U-54 MTase. The encoded recombinant protein contains tightly bound flavin and is active in Escherichia coli mutant lacking m5U-54 in tRNAs and in vitro using T7 tRNA transcript as substrate. This gene is currently annotated gid in Genome Data Banks and it is here renamed trmFO. TrmFO (Gid) orthologs have also been identified in many other bacterial genomes and comparison of their amino acid sequences reveals that they are phylogenetically distinct from either ThyA or ThyX class of thymidylate synthases, which catalyze folate-dependent formation of deoxyribothymine monophosphate, the universal DNA precursor.
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Affiliation(s)
| | - Stéphane Skouloubris
- INSERM Avenir group, Institute of Genetics and Microbiology, CNRS, University Paris XIOrsay, F-91405, France
| | - Hannu Myllykallio
- INSERM Avenir group, Institute of Genetics and Microbiology, CNRS, University Paris XIOrsay, F-91405, France
| | - Henri Grosjean
- To whom correspondence should be addressed. Tel: +33 1 69823468; Fax: +33 1 69823129;
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Leduc D, Graziani S, Meslet-Cladiere L, Sodolescu A, Liebl U, Myllykallio H. Two distinct pathways for thymidylate (dTMP) synthesis in (hyper)thermophilic Bacteria and Archaea. Biochem Soc Trans 2004; 32:231-5. [PMID: 15046578 DOI: 10.1042/bst0320231] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The hyperthermophilic anaerobic archaeon Pyrococcus abyssi, which lacks thymidine kinase, incorporates label from extracellular uracil, but not from thymidine, into its DNA. This implies that P. abyssi must synthesize dTMP (thymidylate), an essential precursor for DNA synthesis, de novo. However, iterative similarity searches of the three completed Pyrococcus genomes fail to detect candidate genes for canonical thymidylate synthase ThyA, suggesting the presence of alternative pathways for dTMP synthesis. Indeed, by identifying a novel class of flavin-dependent thymidylate synthases, ThyX, we have recently proven that two distinct pathways for de novo synthesis of dTMP are operational in the microbial world. While both thyX and thyA can be found in hyperthermophilic micro-organisms, the phylogenetic distribution of thyX among hyperthermophiles is wider than that of thyA. In this contribution, we discuss the differences in the distinct mechanisms of dTMP synthesis, with a special emphasis on hyperthermophilic micro-organisms.
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Affiliation(s)
- D Leduc
- Institut de Génétique et Microbiologie, Université de Paris-Sud, 91405 Orsay, France
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46
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Graziani S, Xia Y, Gurnon JR, Van Etten JL, Leduc D, Skouloubris S, Myllykallio H, Liebl U. Functional analysis of FAD-dependent thymidylate synthase ThyX from Paramecium bursaria Chlorella virus-1. J Biol Chem 2004; 279:54340-7. [PMID: 15471872 DOI: 10.1074/jbc.m409121200] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sequence analysis of the 330-kb double-stranded DNA genome of Paramecium bursaria chlorella virus-1 revealed an open reading frame A674R that encodes a protein with up to 53% amino acid identity to a recently discovered new class of thymidylate synthases, called ThyX. Unlike the traditional thymidylate synthase, ThyA, that uses methylenetetrahydrofolate (CH(2)H(4)folate) as both a source of the methylene group and the reductant, CH(2)H(4)folate only supplies the methylene group in ThyX-catalyzed reactions. Furthermore, ThyX only catalyzes thymidylate (dTMP) formation in the presence of reduced pyridine nucleotides and oxidized FAD. The distribution and transcription patterns of the a674r gene in Chlorella viruses were examined. The a674r gene was cloned, and the protein was expressed in Escherichia coli. Biochemical characterization of the P. bursaria chlorella virus-1 recombinant ThyX protein indicates that it is more efficient at converting dUMP to dTMP than previously studied ThyX enzymes, thus allowing more detailed mechanistic studies of the enzyme. The ThyX-dUMP complexes with bound FAD function as efficient NAD(P)H oxidases, indicating that dUMP binds to the enzyme prior to NAD(P)H. This oxidation activity is directly linked to FAD reduction. Our results indicate that ThyX-specific inhibitors can be designed that do not affect ThyA enzymes. Finally, a model is proposed for the early stages of ThyX catalysis.
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Affiliation(s)
- Sébastien Graziani
- Laboratory of Optics and Biosciences, INSERM U451-CNRS UMR 7645, Ecole Polytechnique, 91128 Palaiseau Cedex, France
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Leduc D, Graziani S, Lipowski G, Marchand C, Le Maréchal P, Liebl U, Myllykallio H. Functional evidence for active site location of tetrameric thymidylate synthase X at the interphase of three monomers. Proc Natl Acad Sci U S A 2004; 101:7252-7. [PMID: 15123820 PMCID: PMC409905 DOI: 10.1073/pnas.0401365101] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Little is known about the catalytic mechanism of the recently discovered ThyX family of flavin-dependent thymidylate synthases that are required for thymidylate (deoxythymidine 5'-monophosphate) synthesis in a large number of microbial species. Using a combination of site-directed mutagenesis and biochemical measurements, we have identified several residues of the Helicobacter pylori ThyX protein with crucial roles in ThyX catalysis. By providing functional evidence that the active site(s) of homotetrameric ThyX proteins is formed by three different subunits, our findings suggest that ThyX proteins have evolved through multimerization of inactive monomers. Moreover, because the active-site configurations of ThyX proteins, present in many human pathogenic bacteria, and of human thymidylate synthase ThyA are different, our results will aid in the identification of compounds specifically inhibiting microbial growth.
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Affiliation(s)
- Damien Leduc
- Université Paris-Sud, Institut de Génétique et Microbiologie, Centre National de la Recherche Scientifique Unité Mixte de Recherche 8621, F-91405 Orsay Cedex, France
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Armengaud J, Fernandez B, Chaumont V, Rollin-Genetet F, Finet S, Marchetti C, Myllykallio H, Vidaud C, Pellequer JL, Gribaldo S, Forterre P, Gans P. Identification, purification, and characterization of an eukaryotic-like phosphopantetheine adenylyltransferase (coenzyme A biosynthetic pathway) in the hyperthermophilic archaeon Pyrococcus abyssi. J Biol Chem 2003; 278:31078-87. [PMID: 12756245 DOI: 10.1074/jbc.m301891200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although coenzymeA (CoA) is essential in numerous metabolic pathways in all living cells, molecular characterization of the CoA biosynthetic pathway in Archaea remains undocumented. Archaeal genomes contain detectable homologues for only three of the five steps of the CoA biosynthetic pathway characterized in Eukarya and Bacteria. In case of phosphopantetheine adenylyltransferase (PPAT) (EC 2.7.7.3), the putative archaeal enzyme exhibits significant sequence similarity only with its eukaryotic homologs, an unusual situation for a protein involved in a central metabolic pathway. We have overexpressed in Escherichia coli, purified, and characterized this putative PPAT from the hyperthermophilic archaeon Pyrococcus abyssi (PAB0944). Matrix-assisted laser desorption ionization-time of flight mass spectrometry and high performance liquid chromatography measurements are consistent with the presence of a dephospho-CoA (dPCoA) molecule tightly bound to the polypeptide. The protein indeed catalyzes the synthesis of dPCoA from 4'-phosphopantetheine and ATP, as well as the reverse reaction. The presence of dPCoA stabilizes PAB0944, as it induces a shift from 76 to 82 degrees C of the apparent Tm measured by differential scanning microcalorimetry. Potassium glutamate was found to stabilize the protein at 400 mm. The enzyme behaves as a monomeric protein. Although only distantly related, secondary structure prediction indicates that archaeal and eukaryal PPAT belong to the same nucleotidyltransferase superfamily of bacterial PPAT. The existence of operational proteins highly conserved between Archaea and Eukarya involved in a central metabolic pathway challenge evolutionary scenarios in which eukaryal operational proteins are strictly of bacterial origin.
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Affiliation(s)
- Jean Armengaud
- CEA VALRHO, DSV-DIEP, SBTN, Service de Biochimie post-génomique and Toxicologie Nucléaire, 30207 Bagnols-sur-Cèze, France.
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Jolivet E, Matsunaga F, Ishino Y, Forterre P, Prieur D, Myllykallio H. Physiological responses of the hyperthermophilic archaeon "Pyrococcus abyssi" to DNA damage caused by ionizing radiation. J Bacteriol 2003; 185:3958-61. [PMID: 12813090 PMCID: PMC161593 DOI: 10.1128/jb.185.13.3958-3961.2003] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The mechanisms by which hyperthermophilic Archaea, such as "Pyrococcus abyssi" and Pyrococcus furiosus, survive high doses of ionizing gamma irradiation are not thoroughly elucidated. Following gamma-ray irradiation at 2,500 Gy, the restoration of "P. abyssi" chromosomes took place within chromosome fragmentation. DNA synthesis in irradiated "P. abyssi" cells during the DNA repair phase was inhibited in comparison to nonirradiated control cultures, suggesting that DNA damage causes a replication block in this organism. We also found evidence for transient export of damaged DNA out of irradiated "P. abyssi" cells prior to a restart of chromosomal DNA synthesis. Our cell fractionation assays further suggest that "P. abyssi" contains a highly efficient DNA repair system which is continuously ready to repair the DNA damage caused by high temperature and/or ionizing radiation.
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Affiliation(s)
- Edmond Jolivet
- Institut Universitaire Européen de la Mer, Université de Bretagne occidentale, CNRS UMR 6539, Technopôle Brest-Iroise, 29 280 Plouzané, France.
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Abstract
Reduced folate derivatives participate in numerous reactions of bacterial intermediary metabolism. Consequently, the well-characterized enzyme implicated in the formation of tetrahydrofolate--dihydrofolate reductase FolA--was considered to be essential for bacterial growth. However, comparative genomics has revealed several bacterial genome sequences that appear to lack the folA gene. Here, we provide in silico evidence indicating that folA-lacking bacteria use a recently discovered class of flavin-dependent thymidylate synthases for deoxythymidine-5'-monophosphate synthesis, and propose that many bacteria must contain uncharacterized sources for reduced folate molecules that are still waiting to be discovered.
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Affiliation(s)
- Hannu Myllykallio
- Institut de Génétique et Microbiologie CNRS UMR8621, Université de Paris-Sud, Orsay, France.
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