Cell Biology of Archaea

Publications

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.
Redrejo-Rodríguez, Modesto, Carlos D. Ordóñez, Mónica Berjón-Otero, Juan Moreno-González, Cristian Aparicio-Maldonado, Patrick Forterre, Margarita Salas, and Mart Krupovic. 2017. “Primer-Independent DNA Synthesis by a Family B DNA Polymerase from Self-Replicating Mobile Genetic Elements.” Cell Reports 21 (6): 1574–87. https://doi.org/10.1016/j.celrep.2017.10.039.
Forterre, Patrick, Violette Da Cunha, and Ryan Catchpole. 2017. “Plasmid Vesicles Mimicking Virions.” Nature Microbiology 2 (10): 1340–41. https://doi.org/10.1038/s41564-017-0032-3.
Braun, Daniela A., Jia Rao, Geraldine Mollet, David Schapiro, Marie-Claire Daugeron, Weizhen Tan, Olivier Gribouval, et al. 2017. “Mutations in KEOPS-Complex Genes Cause Nephrotic Syndrome with Primary Microcephaly.” Nature Genetics 49 (10): 1529–38. https://doi.org/10.1038/ng.3933.
Forterre, Patrick. 2017. “Viruses in the 21st Century: From the Curiosity-Driven Discovery of Giant Viruses to New Concepts and Definition of Life.” Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America 65 (suppl_1): S74–79. https://doi.org/10.1093/cid/cix349.
Forterre, Patrick, and Didier Raoult. 2017. “The Transformation of a Bacterium into a Nucleated Virocell Reminds the Viral Eukaryogenesis Hypothesis.” Virologie (Montrouge, France) 21 (4): 28–30. https://doi.org/10.1684/vir.2017.0700.
Cossu, Matteo, Catherine Badel, Ryan Catchpole, Danièle Gadelle, Evelyne Marguet, Valérie Barbe, Patrick Forterre, and Jacques Oberto. 2017. “Flipping Chromosomes in Deep-Sea Archaea.” PLoS Genetics 13 (6): e1006847. https://doi.org/10.1371/journal.pgen.1006847.
Da Cunha, Violette, Morgan Gaia, Daniele Gadelle, Arshan Nasir, and Patrick Forterre. 2017. “Lokiarchaea Are Close Relatives of Euryarchaeota, Not Bridging the Gap between Prokaryotes and Eukaryotes.” PLoS Genetics 13 (6): e1006810. https://doi.org/10.1371/journal.pgen.1006810.
Dautin, Nathalie, Célia de Sousa-d’Auria, Florence Constantinesco-Becker, Cécile Labarre, Jacques Oberto, Ines Li de la Sierra-Gallay, Christiane Dietrich, Hanane Issa, Christine Houssin, and Nicolas Bayan. 2017. “Mycoloyltransferases: A Large and Major Family of Enzymes Shaping the Cell Envelope of Corynebacteriales.” Biochimica et Biophysica Acta (BBA) - General Subjects 1861 (1 Pt B): 3581–92. https://doi.org/10.1016/j.bbagen.2016.06.020.
Béguin, Pierre, Nicole Charpin, Eugene V. Koonin, Patrick Forterre, and Mart Krupovic. 2016. “Casposon Integration Shows Strong Target Site Preference and Recapitulates Protospacer Integration by CRISPR-Cas Systems.” Nucleic Acids Research 44 (21): 10367–76. https://doi.org/10.1093/nar/gkw821.
Forterre, Patrick. 2016. “To Be or Not to Be Alive: How Recent Discoveries Challenge the Traditional Definitions of Viruses and Life.” Studies in History and Philosophy of Biological and Biomedical Sciences 59 (October): 100–108. https://doi.org/10.1016/j.shpsc.2016.02.013.
Richarme, Gilbert, Evelyne Marguet, Patrick Forterre, Sonoko Ishino, and Yoshizumi Ishino. 2016. “DJ-1 Family Maillard Deglycases Prevent Acrylamide Formation.” Biochemical and Biophysical Research Communications 478 (3): 1111–16. https://doi.org/10.1016/j.bbrc.2016.08.077.
Quemin, Emmanuelle R. J., Petr Chlanda, Martin Sachse, Patrick Forterre, David Prangishvili, and Mart Krupovic. 2016. “Eukaryotic-Like Virus Budding in Archaea.” MBio 7 (5). https://doi.org/10.1128/mBio.01439-16.
Forterre, Patrick, and Morgan Gaïa. 2016. “Giant Viruses and the Origin of Modern Eukaryotes.” Current Opinion in Microbiology 31 (June): 44–49. https://doi.org/10.1016/j.mib.2016.02.001.
Dahmane, Narimane, Danièle Gadelle, Stéphane Delmas, Alexis Criscuolo, Stephan Eberhard, Nicole Desnoues, Sylvie Collin, et al. 2016. “TopIb, a Phylogenetic Hallmark Gene of Thaumarchaeota Encodes a Functional Eukaryote-like Topoisomerase IB.” Nucleic Acids Research 44 (6): 2795–2805. https://doi.org/10.1093/nar/gkw097.
Roux, Simon, Francois Enault, Viviane Ravet, Jonathan Colombet, Yvan Bettarel, Jean-Christophe Auguet, Thierry Bouvier, et al. 2016. “Analysis of Metagenomic Data Reveals Common Features of Halophilic Viral Communities across Continents.” Environmental Microbiology 18 (3): 889–903. https://doi.org/10.1111/1462-2920.13084.
Krupovic, Mart, Sergey Shmakov, Kira S. Makarova, Patrick Forterre, and Eugene V. Koonin. 2016. “Recent Mobility of Casposons, Self-Synthesizing Transposons at the Origin of the CRISPR-Cas Immunity.” Genome Biology and Evolution 8 (2): 375–86. https://doi.org/10.1093/gbe/evw006.
Mora, Liliana, Karine Moncoq, Patrick England, Jacques Oberto, and Miklos de Zamaroczy. 2015. “The Stable Interaction Between Signal Peptidase LepB of Escherichia Coli and Nuclease Bacteriocins Promotes Toxin Entry into the Cytoplasm.” The Journal of Biological Chemistry 290 (52): 30783–96. https://doi.org/10.1074/jbc.M115.691907.
Lossouarn, Julien, Samuel Dupont, Aurore Gorlas, Coraline Mercier, Nadege Bienvenu, Evelyne Marguet, Patrick Forterre, and Claire Geslin. 2015. “An Abyssal Mobilome: Viruses, Plasmids and Vesicles from Deep-Sea Hydrothermal Vents.” Research in Microbiology 166 (10): 742–52. https://doi.org/10.1016/j.resmic.2015.04.001.
Cossu, Matteo, Violette Da Cunha, Claire Toffano-Nioche, Patrick Forterre, and Jacques Oberto. 2015. “Comparative Genomics Reveals Conserved Positioning of Essential Genomic Clusters in Highly Rearranged Thermococcales Chromosomes.” Biochimie 118 (November): 313–21. https://doi.org/10.1016/j.biochi.2015.07.008.
Quemin, Emmanuelle R. J., Maija K. Pietilä, Hanna M. Oksanen, Patrick Forterre, W. Irene C. Rijpstra, Stefan Schouten, Dennis H. Bamford, David Prangishvili, and Mart Krupovic. 2015. “Sulfolobus Spindle-Shaped Virus 1 Contains Glycosylated Capsid Proteins, a Cellular Chromatin Protein, and Host-Derived Lipids.” Journal of Virology 89 (22): 11681–91. https://doi.org/10.1128/JVI.02270-15.
Prangishvili, David, Simonetta Gribaldo, Bruno Franzetti, and Patrick Forterre. 2015. “Special Section on Molecular Biology of Archaea.” Biochimie 118 (November): 253. https://doi.org/10.1016/j.biochi.2015.09.020.
Krupovic, Mart, and Patrick Forterre. 2015. “Single-Stranded DNA Viruses Employ a Variety of Mechanisms for Integration into Host Genomes.” Annals of the New York Academy of Sciences 1341 (April): 41–53. https://doi.org/10.1111/nyas.12675.
Soler, Nicolas, Mart Krupovic, Evelyne Marguet, and Patrick Forterre. 2015. “Membrane Vesicles in Natural Environments: A Major Challenge in Viral Ecology.” The ISME Journal 9 (4): 793–96. https://doi.org/10.1038/ismej.2014.184.
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