2017

Publications 2017

(1) Salinas-Giegé, T.; Cavaiuolo, M.; Cognat, V.; Ubrig, E.; Remacle, C.; Duchêne, A.-M.; Vallon, O.; Maréchal-Drouard, L. Polycytidylation of Mitochondrial MRNAs in Chlamydomonas Reinhardtii. Nucleic Acids Res. 2017, 45 (22), 12963–12973 https://doi.org/10.1093/nar/gkx903.

(2) Vakirlis, N. N.; Hebert, A. S.; Opulente, D. A.; Achaz, G.; Hittinger, C. T.; Fischer, G.; Coon, J. J.; Lafontaine, I. A Molecular Portrait of de Novo Genes in Yeasts. Mol. Biol. Evol. 2017 https://doi.org/10.1093/molbev/msx315.

(3) Puvanendran, D.; Cece, Q.; Picard, M. Reconstitution of the Activity of RND Efflux Pumps: A “Bottom-up” Approach. Res. Microbiol. 2017 https://doi.org/10.1016/j.resmic.2017.11.004.

(4) Dumas, L.; Zito, F.; Blangy, S.; Auroy, P.; Johnson, X.; Peltier, G.; Alric, J. A Stromal Region of Cytochrome B6f Subunit IV Is Involved in the Activation of the Stt7 Kinase in Chlamydomonas. PNAS 2017, 201713343 https://doi.org/10.1073/pnas.1713343114.

(5) Cavaiuolo, M.; Kuras, R.; Wollman, F.-A.; Choquet, Y.; Vallon, O. Small RNA Profiling in Chlamydomonas: Insights into Chloroplast RNA Metabolism. Nucleic Acids Res. 2017, 45 (18), 10783–10799 https://doi.org/10.1093/nar/gkx668.

(6) Jagodnik, J.; Chiaruttini, C.; Guillier, M. Stem-Loop Structures within MRNA Coding Sequences Activate Translation Initiation and Mediate Control by Small Regulatory RNAs. Molecular Cell 2017 https://doi.org/10.1016/j.molcel.2017.08.015.

(7) Ma, M.; Li de La Sierra Gallay, I.; Lazar, N.; Pellegrini, O.; Lepault, J.; Condon, C.; Durand, D.; van Tilbeurgh, H. Trz1, the Long Form RNase Z from Yeast, Forms a Stable Heterohexamer with Endonuclease Nuc1 and Mutarotase. Biochem. J. 2017 https://doi.org/10.1042/BCJ20170435.

(8) Jabrani, A.; Makamte, S.; Moreau, E.; Gharbi, Y.; Plessis, A.; Bruzzone, L.; Sanial, M.; Biou, V. Biophysical Characterisation of the Novel Zinc Binding Property in Suppressor of Fused. Scientific Reports 2017, 7 (1), 11139 https://doi.org/10.1038/s41598-017-11203-2.

(9) Boniello, G.; Tribet, C.; Marie, E.; Croquette, V.; Zanchi, D. Rolling and Ageing in T-Ramp Soft Adhesion. arXiv:1709.02971 [cond-mat] 2017.

(10) De Vecchis, D.; Cavellini, L.; Baaden, M.; Hénin, J.; Cohen, M. M.; Taly, A. A Membrane-Inserted Structural Model of the Yeast Mitofusin Fzo1. Sci Rep 2017, 7 (1), 10217 https://doi.org/10.1038/s41598-017-10687-2.

(11) Danilowicz, C.; Hermans, L.; Coljee, V.; Prévost, C.; Prentiss, M. ATP Hydrolysis Provides Functions That Promote Rejection of Pairings between Different Copies of Long Repeated Sequences. Nucleic Acids Res 2017, 45 (14), 8448–8462 https://doi.org/10.1093/nar/gkx582.

(12) Katava, M.; Stirnemann, G.; Zanatta, M.; Capaccioli, S.; Pachetti, M.; Ngai, K. L.; Sterpone, F.; Paciaroni, A. Critical Structural Fluctuations of Proteins upon Thermal Unfolding Challenge the Lindemann Criterion. Proc. Natl. Acad. Sci. U.S.A. 2017 https://doi.org/10.1073/pnas.1707357114.

(13) Bou-Nader, C.; Cornu, D.; Guerineau, V.; Fogeron, T.; Fontecave, M.; Hamdane, D. Enzyme Activation with a Synthetic Catalytic Co-Enzyme Intermediate: Nucleotide Methylation by Flavoenzymes. Angew. Chem. Int. Ed. Engl. 2017 https://doi.org/10.1002/anie.201706219.

(14) Pérez-Pérez, M. E.; Mauriès, A.; Maes, A.; Tourasse, N. J.; Hamon, M.; Lemaire, S. D.; Marchand, C. H. The Deep Thioredoxome in Chlamydomonas Reinhardtii: New Insights into Redox Regulation. Mol Plant 2017, 10 (8), 1107–1125 https://doi.org/10.1016/j.molp.2017.07.009.

(15) Rahaman, O.; Kalimeri, M.; Katava, M.; Paciaroni, A.; Sterpone, F. Configurational Disorder of Water Hydrogen-Bond Network at the Protein Dynamical Transition. J Phys Chem B 2017, 121 (28), 6792–6798 https://doi.org/10.1021/acs.jpcb.7b03888.

(16) Joyet, P.; Mokhtari, A.; Riboulet-Bisson, E.; Blancato, V. S.; Espariz, M.; Magni, C.; Hartke, A.; Deutscher, J.; Sauvageot, N. Enzymes Required for Maltodextrin Catabolism in Enterococcus Faecalis Exhibit Novel Activities. Appl. Environ. Microbiol. 2017, 83 (13), e00038-17 https://doi.org/10.1128/AEM.00038-17.

(17) Caserta, G.; Pecqueur, L.; Adamska-Venkatesh, A.; Papini, C.; Roy, S.; Artero, V.; Atta, M.; Reijerse, E.; Lubitz, W.; Fontecave, M. Structural and Functional Characterization of the Hydrogenase-Maturation HydF Protein. Nat. Chem. Biol. 2017, 13 (7), 779–784 https://doi.org/10.1038/nchembio.2385.

(18) Graf, M.; Bonetti, D.; Lockhart, A.; Serhal, K.; Kellner, V.; Maicher, A.; Jolivet, P.; Teixeira, M. T.; Luke, B. Telomere Length Determines TERRA and R-Loop Regulation through the Cell Cycle. Cell 2017, 170 (1), 72–85.e14 https://doi.org/10.1016/j.cell.2017.06.006.

(19) Arragain, S.; Bimai, O.; Legrand, P.; Caillat, S.; Ravanat, J.-L.; Touati, N.; Binet, L.; Atta, M.; Fontecave, M.; Golinelli-Pimpaneau, B. Nonredox Thiolation in TRNA Occurring via Sulfur Activation by a [4Fe-4S] Cluster. PNAS 2017, 201700902 https://doi.org/10.1073/pnas.1700902114.

(20) Mazur, A. K. Weak Nanoscale Chaos and Anomalous Relaxation in DNA. Phys. Rev. E 2017, 95 (6), 062417 https://doi.org/10.1103/PhysRevE.95.062417.

(21) Mazzanti, L.; Doutreligne, S.; Gageat, C.; Derreumaux, P.; Taly, A.; Baaden, M.; Pasquali, S. What Can Human-Guided Simulations Bring to RNA Folding? Biophys. J. 2017 https://doi.org/10.1016/j.bpj.2017.05.047.

(22) Man, V. H.; Nguyen, P. H.; Derreumaux, P. High-Resolution Structures of the Amyloid-β 1-42 Dimers from the Comparison of Four Atomistic Force Fields. J Phys Chem B 2017, 121 (24), 5977–5987 https://doi.org/10.1021/acs.jpcb.7b04689.

(23) Aroua, S.; Todorova, T. K.; Mougel, V.; Hommes, P.; Reissig, H.-U.; Fontecave, M. New Cobalt-Bisterpyridyl Catalysts for Hydrogen Evolution Reaction. ChemCatChem 2017, 9 (12), 2099–2105 https://doi.org/10.1002/cctc.201700428.

(24) Nawrocki, W.; Bailleul, B.; Cardol, P.; Rappaport, F.; Wollman, F.-A.; Joliot, P. Cyclic Electron Flow in Chlamydomonas Reinhardtii. bioRxiv 2017, 153288 https://doi.org/10.1101/153288.

(25) Dautant, A.; Meyer, P.; Georgescauld, F. Hydrogen/Deuterium Exchange Mass Spectrometry Reveals Mechanistic Details of Activation of Nucleoside Diphosphate Kinases by Oligomerization. Biochemistry 2017, 56 (23), 2886–2896 https://doi.org/10.1021/acs.biochem.7b00282.

(26) Cavellini, L.; Meurisse, J.; Findinier, J.; Erpapazoglou, Z.; Belgareh-Touze, N.; Weissman, A. M.; Cohen, M. M. An Ubiquitin-Dependent Balance between Mitofusin Turnover and Fatty Acids Desaturation Regulates Mitochondrial Fusion. Nat. Commun. 2017, 8, 15832 https://doi.org/10.1038/ncomms15832.

(27) Doig, A. J.; Del Castillo-Frias, M. P.; Berthoumieu, O.; Tarus, B.; Nasica-Labouze, J.; Sterpone, F.; Nguyen, P. H.; Hooper, N. M.; Faller, P.; Derreumaux, P. Why Is Research on Amyloid-β Failing to Give New Drugs for Alzheimer’s Disease? ACS Chem Neurosci 2017 https://doi.org/10.1021/acschemneuro.7b00188.

(28) Ma, M.; Li de la Sierra-Gallay, I.; Lazar, N.; Pellegrini, O.; Durand, D.; Marchfelder, A.; Condon, C.; van Tilbeurgh, H. The Crystal Structure of Trz1, the Long Form RNase Z from Yeast. Nucleic Acids Res. 2017, 45 (10), 6209–6216 https://doi.org/10.1093/nar/gkx216.

(29) Raj-Kumar, P.-K.; Vallon, O.; Liang, C. In Silico Analysis of the Sequence Features Responsible for Alternatively Spliced Introns in the Model Green Alga Chlamydomonas Reinhardtii. Plant Mol. Biol. 2017, 94 (3), 253–265 https://doi.org/10.1007/s11103-017-0605-9.

(30) Loiseau, L.; Fyfe, C.; Aussel, L.; Hajj Chehade, M.; Hernández, S. B.; Faivre, B.; Hamdane, D.; Mellot-Draznieks, C.; Rascalou, B.; Pelosi, L.; Velours, C.; Cornu, D.; Lombard, M.; Casadesús, J.; Pierrel, F.; Fontecave, M.; Barras, F. The UbiK Protein Is an Accessory Factor Necessary for Bacterial Ubiquinone (UQ) Biosynthesis and Forms a Complex with the UQ Biogenesis Factor UbiJ. J. Biol. Chem. 2017 https://doi.org/10.1074/jbc.M117.789164.

(31) Lev, B.; Murail, S.; Poitevin, F.; Cromer, B. A.; Baaden, M.; Delarue, M.; Allen, T. W. String Method Solution of the Gating Pathways for a Pentameric Ligand-Gated Ion Channel. Proc. Natl. Acad. Sci. U.S.A. 2017, 114 (21), E4158–E4167 https://doi.org/10.1073/pnas.1617567114.

(32) Colloc’h, N.; Sacquin-Mora, S.; Avella, G.; Dhaussy, A.-C.; Prangé, T.; Vallone, B.; Girard, E. Determinants of Neuroglobin Plasticity Highlighted by Joint Coarse-Grained Simulations and High Pressure Crystallography. Sci Rep 2017, 7 (1), 1858 https://doi.org/10.1038/s41598-017-02097-1.

(33) Longatte, G.; Rappaport, F.; Wollman, F.-A.; Guille-Collignon, M.; Lemaitre, F. Electrochemical Harvesting of Photosynthetic Electrons from Unicellular Algae Population at the Preparative Scale by Using 2,6-Dichlorobenzoquinone. Electrochim. Acta 2017, 236, 327–332 https://doi.org/10.1016/j.electacta.2017.03.124.

(34) Fu, H.-Y.; Picot, D.; Choquet, Y.; Longatte, G.; Sayegh, A.; Delacotte, J.; Guille-Collignon, M.; Lemaître, F.; Rappaport, F.; Wollman, F.-A. Redesigning the QA Binding Site of Photosystem II Allows Reduction of Exogenous Quinones. Nat Commun 2017, 8, 15274 https://doi.org/10.1038/ncomms15274.

(35) Leroy, M.; Piton, J.; Gilet, L.; Pellegrini, O.; Proux, C.; Coppée, J.-Y.; Figaro, S.; Condon, C. Rae1/YacP, a New Endoribonuclease Involved in Ribosome-Dependent MRNA Decay in Bacillus Subtilis. EMBO J. 2017, 36 (9), 1167–1181 https://doi.org/10.15252/embj.201796540.

(36) Sauvageot, N.; Mokhtari, A.; Joyet, P.; Budin-Verneuil, A.; Blancato, V. S.; Repizo, G. D.; Henry, C.; Pikis, A.; Thompson, J.; Magni, C.; Hartke, A.; Deutscher, J. Enterococcus Faecalis Uses a Phosphotransferase System Permease and a Host Colonization-Related ABC Transporter for Maltodextrin Uptake. J. Bacteriol. 2017, 199 (9), e00878-16 https://doi.org/10.1128/JB.00878-16.

(37) Durand, S.; Braun, F.; Helfer, A.-C.; Romby, P.; Condon, C. SRNA-Mediated Activation of Gene Expression by Inhibition of 5’-3’ Exonucleolytic MRNA Degradation. Elife 2017, 6 https://doi.org/10.7554/eLife.23602.

(38) Laurin, Y.; Eyer, J.; Robert, C. H.; Prevost, C.; Sacquin-Mora, S. Mobility and Core-Protein Binding Patterns of Disordered C-Terminal Tails in β-Tubulin Isotypes. Biochemistry 2017, 56 (12), 1746–1756 https://doi.org/10.1021/acs.biochem.6b00988.

(39) Fogeron, T.; Retailleau, P.; Chamoreau, L.-M.; Fontecave, M.; Li, Y. The Unusual Ring Scission of a Quinoxaline-Pyran-Fused Dithiolene System Related to Molybdopterin. Dalton Trans. 2017, 46 (13), 4161–4164 https://doi.org/10.1039/C7DT00377C.

(40) Maes, A.; Gracia, C.; Innocenti, N.; Zhang, K.; Aurell, E.; Hajnsdorf, E. Landscape of RNA Polyadenylation in E. Coli. Nucleic Acids Res. 2017, 45 (5), 2746–2756 https://doi.org/10.1093/nar/gkw894.

(41) Roy, S.; Sharma, B.; Pécaut, J.; Simon, P.; Fontecave, M.; Tran, P. D.; Derat, E.; Artero, V. Molecular Cobalt Complexes with Pendant Amines for Selective Electrocatalytic Reduction of Carbon Dioxide to Formic Acid. J. Am. Chem. Soc. 2017, 139 (10), 3685–3696 https://doi.org/10.1021/jacs.6b11474.

(42) Jagodnik, J.; Brosse, A.; Le Lam, T. N.; Chiaruttini, C.; Guillier, M. Mechanistic Study of Base-Pairing Small Regulatory RNAs in Bacteria. Methods 2017, 117, 67–76 https://doi.org/10.1016/j.ymeth.2016.09.012.

(43) Hamouche, L.; Laalami, S.; Daerr, A.; Song, S.; Holland, I. B.; Séror, S. J.; Hamze, K.; Putzer, H. Bacillus Subtilis Swarmer Cells Lead the Swarm, Multiply, and Generate a Trail of Quiescent Descendants. MBio 2017, 8 (1) https://doi.org/10.1128/mBio.02102-16.

(44) Elgrishi, N.; Chambers, M. B.; Wang, X.; Fontecave, M. Molecular Polypyridine-Based Metal Complexes as Catalysts for the Reduction of CO2. Chem. Soc. Rev. 2017, 46 (3), 761–796 https://doi.org/10.1039/C5CS00391A.

(45) Katava, M.; Maccarini, M.; Villain, G.; Paciaroni, A.; Sztucki, M.; Ivanova, O.; Madern, D.; Sterpone, F. Thermal Activation of “allosteric-like” Large-Scale Motions in a Eukaryotic Lactate Dehydrogenase. Sci Rep 2017, 7, 41092 https://doi.org/10.1038/srep41092.

(46) Eugene, S.; Bourgeron, T.; Xu, Z. Effects of Initial Telomere Length Distribution on Senescence Onset and Heterogeneity. J. Theor. Biol. 2017, 413, 58–65 https://doi.org/10.1016/j.jtbi.2016.11.010.

(47) Wang, F.; Qi, Y.; Malnoë, A.; Choquet, Y.; Wollman, F.-A.; de Vitry, C. The High Light Response and Redox Control of Thylakoid FtsH Protease in Chlamydomonas Reinhardtii. Mol Plant 2017, 10 (1), 99–114 https://doi.org/10.1016/j.molp.2016.09.012.

(48) Bujaldon, S.; Kodama, N.; Rappaport, F.; Subramanyam, R.; de Vitry, C.; Takahashi, Y.; Wollman, F.-A. Functional Accumulation of Antenna Proteins in Chlorophyll B-Less Mutants of Chlamydomonas Reinhardtii. Mol Plant 2017, 10 (1), 115–130 https://doi.org/10.1016/j.molp.2016.10.001.

(49) Huan, T. N.; Simon, P.; Rousse, G.; Génois, I.; Artero, V.; Fontecave, M. Porous Dendritic Copper: An Electrocatalyst for Highly Selective CO2 Reduction to Formate in Water/Ionic Liquid Electrolyte. Chem Sci 2017, 8 (1), 742–747 https://doi.org/10.1039/c6sc03194c.

(50) Carranza, G.; Angius, F.; Ilioaia, O.; Solgadi, A.; Miroux, B.; Arechaga, I. Cardiolipin Plays an Essential Role in the Formation of Intracellular Membranes in Escherichia Coli. Biochim. Biophys. Acta 2017, 1859 (6), 1124–1132 https://doi.org/10.1016/j.bbamem.2017.03.006.

(51) Ngoc Huan, T.; Simon, P.; Rousse, G.; Génois, I.; Artero, V.; Fontecave, M. Porous Dendritic Copper: An Electrocatalyst for Highly Selective CO 2 Reduction to Formate in Water/Ionic Liquid Electrolyte. Chemical Science 2017, 8 (1), 742–747 https://doi.org/10.1039/C6SC03194C.

(52) Gold, V. A. M.; Brandt, T.; Cavellini, L.; Cohen, M. M.; Ieva, R.; Laan, M. van der. Analysis of Mitochondrial Membrane Protein Complexes by Electron Cryo-Tomography. In Mitochondria; Methods in Molecular Biology; Humana Press, New York, NY, 2017; pp 315–336.

(53) Gold, V. A. M.; Brandt, T.; Cavellini, L.; Cohen, M. M.; Ieva, R.; van der Laan, M. Analysis of Mitochondrial Membrane Protein Complexes by Electron Cryo-Tomography. Methods Mol. Biol. 2017, 1567, 315–336 https://doi.org/10.1007/978-1-4939-6824-4_19.

(54) Belgareh-Touze, N.; Cavellini, L.; Cohen, M. M. Ubiquitination of ERMES Components by the E3 Ligase Rsp5 Is Involved in Mitophagy. Autophagy 2017, 13 (1), 114–132 https://doi.org/10.1080/15548627.2016.1252889.

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