Cell Biology of Archaea

Laalami, Soumaya, Marina Cavaiuolo, Jacques Oberto, and Harald Putzer. 2024. “Membrane Localization of RNase Y Is Important for Global Gene Expression in Bacillus Subtilis.” International Journal of Molecular Sciences 25 (15): 8537. https://doi.org/10.3390/ijms25158537.

Mc Teer, Logan, Yann Moalic, Valérie Cueff-Gauchard, Ryan Catchpole, Gaëlle Hogrel, Yang Lu, Sébastien Laurent, et al. 2024. “Cooperation between Two Modes for DNA Replication Initiation in the Archaeon Thermococcus Barophilus.” MBio, February, e0320023. https://doi.org/10.1128/mbio.03200-23.

Hepp, Benjamin, Florence Lorieux, Augustin Degaugue, and Jacques Oberto. 2023. “VAPEX: An Interactive Web Server for the Deep Exploration of Natural Virus and Phage Genomes.” Bioinformatics (Oxford, England), August, btad528. https://doi.org/10.1093/bioinformatics/btad528.

Gaïa, Morgan, and Patrick Forterre. 2023. “From Mimivirus to Mirusvirus: The Quest for Hidden Giants.” Viruses 15 (8): 1758. https://doi.org/10.3390/v15081758.

Bénéfice, Maëlle, Aurore Gorlas, Baptiste Marthy, Violette Da Cunha, Patrick Forterre, Anne Sentenac, Patrick C. Chaumet, and Guillaume Baffou. 2023. “Dry Mass Photometry of Single Bacteria Using Quantitative Wavefront Microscopy.” Biophysical Journal, June, S0006-3495(23)00408-3. https://doi.org/10.1016/j.bpj.2023.06.020.

Catchpole, Ryan J., Valérie Barbe, Ghislaine Magdelenat, Evelyne Marguet, Michael Terns, Jacques Oberto, Patrick Forterre, and Violette Da Cunha. 2023. “A Self-Transmissible Plasmid from a Hyperthermophile That Facilitates Genetic Modification of Diverse Archaea.” Nature Microbiology, June. https://doi.org/10.1038/s41564-023-01387-x.

Gaïa, Morgan, Lingjie Meng, Eric Pelletier, Patrick Forterre, Chiara Vanni, Antonio Fernandez-Guerra, Olivier Jaillon, et al. 2023. “Mirusviruses Link Herpesviruses to Giant Viruses.” Nature, April. https://doi.org/10.1038/s41586-023-05962-4.

Daugeron, Marie-Claire, Sophia Missoury, Violette Da Cunha, Noureddine Lazar, Bruno Collinet, Herman van Tilbeurgh, and Tamara Basta. 2023. “A Paralog of Pcc1 Is the Fifth Core Subunit of the KEOPS TRNA-Modifying Complex in Archaea.” Nature Communications 14 (1): 526. https://doi.org/10.1038/s41467-023-36210-y.

Basta, Tamara, Estelle Crozat, and Ian Grainge. 2023. “Editorial: Chromosome Architecture and DNA Topology in Prokaryotes.” Frontiers in Microbiology 14:1355036. https://doi.org/10.3389/fmicb.2023.1355036.

Pichard-Kostuch, Adeline, Violette Da Cunha, Jacques Oberto, Ludovic Sauguet, and Tamara Basta. 2023. “The Universal Sua5/TsaC Family Evolved Different Mechanisms for the Synthesis of a Key TRNA Modification.” Frontiers in Microbiology 14:1204045. https://doi.org/10.3389/fmicb.2023.1204045.

Truong, Chloé, Sylvain Bernard, Pierre Le Pape, Guillaume Morin, Camille Baya, Pauline Merrot, Aurore Gorlas, and François Guyot. 2023. “Production of Carbon-Containing Pyrite Spherules Induced by Hyperthermophilic Thermococcales: A Biosignature?” Frontiers in Microbiology 14:1145781. https://doi.org/10.3389/fmicb.2023.1145781.

Forterre, Patrick, and Morgan Gaïa. 2022. “[Viruses and the evolution of modern eukaryotic cells].” Medecine Sciences: M/S 38 (12): 990–98. https://doi.org/10.1051/medsci/2022164.

Molinaro, Céline, Maëlle Bénéfice, Aurore Gorlas, Violette Da Cunha, Hadrien M. L. Robert, Ryan Catchpole, Laurent Gallais, Patrick Forterre, and Guillaume Baffou. 2022. “Life at High Temperature Observed in Vitro upon Laser Heating of Gold Nanoparticles.” Nature Communications 13 (1): 5342. https://doi.org/10.1038/s41467-022-33074-6.

Villain, Paul, Ryan Catchpole, Patrick Forterre, Jacques Oberto, Violette da Cunha, and Tamara Basta. 2022. “Expanded Dataset Reveals the Emergence and Evolution of DNA Gyrase in Archaea.” Molecular Biology and Evolution 39 (8): msac155. https://doi.org/10.1093/molbev/msac155.

Hogrel, Gaëlle, Laura Marino-Puertas, Sébastien Laurent, Ziad Ibrahim, Jacques Covès, Eric Girard, Frank Gabel, et al. 2022. “Characterization of a Small TRNA-Binding Protein That Interacts with the Archaeal Proteasome Complex.” Molecular Microbiology n/a (n/a). https://doi.org/10.1111/mmi.14948.

Yokoyama, Hideshi, Nanami Kamei, Keijiro Konishi, Kodai Hara, Yoshinobu Ishikawa, Ikuo Matsui, Patrick Forterre, and Hiroshi Hashimoto. 2022. “Structural Basis for Peptide Recognition by Archaeal Oligopeptide Permease A.” Proteins: Structure, Function, and Bioinformatics n/a (n/a). https://doi.org/10.1002/prot.26324.

Da Cunha, Violette, Morgan Gaia, Hiroyuki Ogata, Olivier Jaillon, Tom O Delmont, and Patrick Forterre. 2022. “Giant Viruses Encode Actin-Related Proteins.” Molecular Biology and Evolution, February, msac022. https://doi.org/10.1093/molbev/msac022.

Gorlas, A., T. Mariotte, L. Morey, C. Truong, S. Bernard, J.-M. Guigner, J. Oberto, et al. 2022. “Precipitation of Greigite and Pyrite Induced by Thermococcales: An Advantage to Live in Fe- and S-Rich Environments?” Environmental Microbiology 24 (2): 626–42. https://doi.org/10.1111/1462-2920.15915.

Takahashi, Diane T., Danièle Gadelle, Keli Agama, Evgeny Kiselev, Hongliang Zhang, Emilie Yab, Stephanie Petrella, Patrick Forterre, Yves Pommier, and Claudine Mayer. 2022. “Topoisomerase I (TOP1) Dynamics: Conformational Transition from Open to Closed States.” Nature Communications 13 (1): 59. https://doi.org/10.1038/s41467-021-27686-7.

Guglielmini, Julien, Morgan Gaia, Violette Da Cunha, Alexis Criscuolo, Mart Krupovic, and Patrick Forterre. 2022. “Viral Origin of Eukaryotic Type IIA DNA Topoisomerases.” Virus Evolution 8 (2): veac097. https://doi.org/10.1093/ve/veac097.

Forterre, Patrick. 2022. “Archaea: A Goldmine for Molecular Biologists and Evolutionists.” In Archaea: Methods and Protocols, edited by Sébastien Ferreira-Cerca, 1–21. Methods in Molecular Biology. New York, NY: Springer US. https://doi.org/10.1007/978-1-0716-2445-6_1.

Villain, Paul, Violette da Cunha, Etienne Villain, Patrick Forterre, Jacques Oberto, Ryan Catchpole, and Tamara Basta. 2021. “The Hyperthermophilic Archaeon Thermococcus Kodakarensis Is Resistant to Pervasive Negative Supercoiling Activity of DNA Gyrase.” Nucleic Acids Research, November, gkab869. https://doi.org/10.1093/nar/gkab869.

Molinaro, Céline, Violette Da Cunha, Aurore Gorlas, François Iv, Laurent Gallais, Ryan Catchpole, Patrick Forterre, and Guillaume Baffou. 2021. “Are Bacteria Claustrophobic? The Problem of Micrometric Spatial Confinement for the Culturing of Micro-Organisms.” RSC Advances 11 (21): 12500–506. https://doi.org/10.1039/D1RA00184A.

Hepp, Benjamin, Violette Da Cunha, Florence Lorieux, and Jacques Oberto. 2021. “BAGET 2.0: An Updated Web Tool for the Effortless Retrieval of Prokaryotic Gene Context and Sequence.” Bioinformatics (Oxford, England), February. https://doi.org/10.1093/bioinformatics/btab082.

Badel, Catherine, Violette Da Cunha, and Jacques Oberto. 2021. “Archaeal Tyrosine Recombinases.” FEMS Microbiology Reviews, no. fuab004 (February). https://doi.org/10.1093/femsre/fuab004.

Woo, Anthony C., Morgan Gaia, Julien Guglielmini, Violette Da Cunha, and Patrick Forterre. 2021. “Phylogeny of the Varidnaviria Morphogenesis Module: Congruence and Incongruence With the Tree of Life and Viral Taxonomy.” Frontiers in Microbiology 12:704052. https://doi.org/10.3389/fmicb.2021.704052.

Thiroux, Sarah, Samuel Dupont, Camilla L. Nesbø, Nadège Bienvenu, Mart Krupovic, Stéphane L’Haridon, Dominique Marie, Patrick Forterre, Anne Godfroy, and Claire Geslin. 2020. “The First Head-Tailed Virus, MFTV1, Produced by a Hyperthermophilic Methanogenic Deep-Sea Archaea.” Environmental Microbiology, October. https://doi.org/10.1111/1462-2920.15271.

Brázda, Václav, Yu Luo, Martin Bartas, Patrik Kaura, Otilia Porubiaková, Jiří Šťastný, Petr Pečinka, et al. 2020. “G-Quadruplexes in the Archaea Domain.” Biomolecules 10 (9): 1349. https://doi.org/10.3390/biom10091349.

Badel, Catherine, Violette Da Cunha, Patrick Forterre, and Jacques Oberto. 2020. “Pervasive Suicidal Integrases in Deep-Sea Archaea.” Molecular Biology and Evolution 37 (6): 1727–43. https://doi.org/10.1093/molbev/msaa041.

Takahashi, Tomio S., Hans-Peter Wollscheid, Jonathan Lowther, and Helle D. Ulrich. 2020. “Effects of Chain Length and Geometry on the Activation of DNA Damage Bypass by Polyubiquitylated PCNA.” Nucleic Acids Research 48 (6): 3042–52. https://doi.org/10.1093/nar/gkaa053.

Badel, Catherine, Violette Da Cunha, Ryan Catchpole, Patrick Forterre, and Jacques Oberto. 2020. “WASPS: Web-Assisted Symbolic Plasmid Synteny Server.” Bioinformatics 36 (5): 1629–31. https://doi.org/10.1093/bioinformatics/btz745.

Guglielmini, Julien, Anthony C. Woo, Mart Krupovic, Patrick Forterre, and Morgan Gaia. 2020. “Reply to Ku and Sun: Ancestors of Modern Giant and Large Eukaryotic DsDNA Viruses Infected Proto-Eukaryotes.” Proceedings of the National Academy of Sciences of the United States of America 117 (6): 2749–50. https://doi.org/10.1073/pnas.1920855117.

Soler, Nicolas, and Patrick Forterre. 2020. “Vesiduction: The Fourth Way of HGT.” Environmental Microbiology 22 (7): 2457–60. https://doi.org/https://doi.org/10.1111/1462-2920.15056.

Catchpole, Ryan, and Patrick Forterre. 2019. “The Evolution of Reverse Gyrase Suggests a Non-Hyperthermophilic Last Universal Common Ancestor.” Molecular Biology and Evolution 36 (12): 2737–47. https://doi.org/10.1093/molbev/msz180.

Badel, C., G. Erauso, A. Gomez, R. Catchpole, M. Gonnet, J. Oberto, P. Forterre, and V. Da Cunha. 2019. “The Global Distribution and Evolutionary History of the PT26-2 Archaeal Plasmid Family.” Environmental Microbiology 21 (12): 4685–4705. https://doi.org/10.1111/1462-2920.14800.

Guglielmini, Julien, Anthony C. Woo, Mart Krupovic, Patrick Forterre, and Morgan Gaia. 2019. “Diversification of Giant and Large Eukaryotic DsDNA Viruses Predated the Origin of Modern Eukaryotes.” Proceedings of the National Academy of Sciences 116 (39): 19585–92. https://doi.org/10.1073/pnas.1912006116.

Krupovic, Mart, Kira S. Makarova, Yuri I. Wolf, Sofia Medvedeva, David Prangishvili, Patrick Forterre, and Eugene V. Koonin. 2019. “Integrated Mobile Genetic Elements in Thaumarchaeota.” Environmental Microbiology 21 (6): 2056–78. https://doi.org/10.1111/1462-2920.14564.

Osman, Jorge R., Christophe Regeard, Catherine Badel, Gustavo Fernandes, and Michael S. DuBow. 2019. “Variation of Bacterial Biodiversity from Saline Soils and Estuary Sediments Present near the Mediterranean Sea Coast of Camargue (France).” Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology 112 (3): 351–65. https://doi.org/10.1007/s10482-018-1164-z.

Gorlas, A., R. Catchpole, E. Marguet, and P. Forterre. 2019. “Increase of Positive Supercoiling in a Hyperthermophilic Archaeon after UV Irradiation.” Extremophiles 23 (1): 141–49. https://doi.org/10.1007/s00792-018-1068-x.

Gill, Sukhvinder, Ryan Catchpole, and Patrick Forterre. 2019. “Extracellular Membrane Vesicles (EVs) in the Three Domains of Life and Beyond.” FEMS Microbiology Reviews 43 (3): 273–303. https://doi.org/10.1093/femsre/fuy042.

Béguin, Pierre, Yankel Chekli, Guennadi Sezonov, Patrick Forterre, and Mart Krupovic. 2019. “Sequence Motifs Recognized by the Casposon Integrase of Aciduliprofundum Boonei.” Nucleic Acids Research 47 (12): 6386–95. https://doi.org/10.1093/nar/gkz447.

Fujikane, Ryosuke, Isabelle Behm-Ansmant, Anne-Sophie Tillault, Christine Loegler, Valérie Igel-Bourguignon, Evelyne Marguet, Patrick Forterre, Christiane Branlant, Yuri Motorin, and Bruno Charpentier. 2018. “Contribution of Protein Gar1 to the RNA-Guided and RNA-Independent RRNA:Ψ-Synthase Activities of the Archaeal Cbf5 Protein.” Scientific Reports 8 (1): 13815. https://doi.org/10.1038/s41598-018-32164-0.

Gorlas, Aurore, Pierre Jacquemot, Jean-Michel Guigner, Sukhvinder Gill, Patrick Forterre, and Francois Guyot. 2018. “Greigite Nanocrystals Produced by Hyperthermophilic Archaea of Thermococcales Order.” Plos One 13 (8): e0201549. https://doi.org/10.1371/journal.pone.0201549.

Meyer, Laura, Geneviève Coste, Suzanne Sommer, Jacques Oberto, Fabrice Confalonieri, Pascale Servant, and Cécile Pasternak. 2018. “DdrI, a CAMP Receptor Protein Family Member, Acts as a Major Regulator for Adaptation of Deinococcus Radiodurans to Various Stresses.” Journal of Bacteriology 200 (13): e00129-18. https://doi.org/10.1128/JB.00129-18.

Pichard-Kostuch, Adeline, Wenhua Zhang, Dominique Liger, Marie-Claire Daugeron, Juliette Létoquart, Ines Li de la Sierra-Gallay, Patrick Forterre, Bruno Collinet, Herman van Tilbeurgh, and Tamara Basta. 2018. “Structure-Function Analysis of Sua5 Protein Reveals Novel Functional Motifs Required for the Biosynthesis of the Universal T6A TRNA Modification.” RNA (New York, N.Y.) 24 (7): 926–38. https://doi.org/10.1261/rna.066092.118.

Catchpole, Ryan, Aurore Gorlas, Jacques Oberto, and Patrick Forterre. 2018. “A Series of New E. Coli-Thermococcus Shuttle Vectors Compatible with Previously Existing Vectors.” Extremophiles: Life Under Extreme Conditions 22 (4): 591–98. https://doi.org/10.1007/s00792-018-1019-6.

Ishino, Yoshizumi, Mart Krupovic, and Patrick Forterre. 2018. “History of CRISPR-Cas from Encounter with a Mysterious Repeated Sequence to Genome Editing Technology.” Journal of Bacteriology 200 (7): e00580-17. https://doi.org/10.1128/JB.00580-17.

Da Cunha, Violette, Morgan Gaia, Arshan Nasir, and Patrick Forterre. 2018. “Asgard Archaea Do Not Close the Debate about the Universal Tree of Life Topology.” Edited by Antonis Rokas. PLOS Genetics 14 (3): e1007215. https://doi.org/10.1371/journal.pgen.1007215.

Kazlauskas, Darius, Guennadi Sezonov, Nicole Charpin, Česlovas Venclovas, Patrick Forterre, and Mart Krupovic. 2018. “Novel Families of Archaeo-Eukaryotic Primases Associated with Mobile Genetic Elements of Bacteria and Archaea.” Journal of Molecular Biology 430 (5): 737–50. https://doi.org/10.1016/j.jmb.2017.11.014.

Prangishvili, David, Dennis H. Bamford, Patrick Forterre, Jaime Iranzo, Eugene V. Koonin, and Mart Krupovic. 2017. “The Enigmatic Archaeal Virosphere.” Nature Reviews. Microbiology 15 (12): 724–39. https://doi.org/10.1038/nrmicro.2017.125.