Adaptive immunity in prokaryotes: how Bacteria do not forgive and do not forget their enemies

Publikacje

Evolution of BACON Domain Tandem Repeats in crAssphage and Novel Gut Bacteriophage Lineages

Autorzy: Patrick A. de Jonge, F. A. Bastiaan von Meijenfeldt, Laura E. van Rooijen, Stan J. J. Brouns, Bas E. Dutilh
Opublikowane w: Viruses, Numer 11/12, 2019, Strona(/y) 1085, ISSN 1999-4915
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v11121085

An educational guide for nanopore sequencing in the classroom

Autorzy: Alex N. Salazar, Franklin L. Nobrega, Christine Anyansi, Cristian Aparicio-Maldonado, Ana Rita Costa, Anna C. Haagsma, Anwar Hiralal, Ahmed Mahfouz, Rebecca E. McKenzie, Teunke van Rossum, Stan J. J. Brouns, Thomas Abeel
Opublikowane w: PLOS Computational Biology, Numer 16/1, 2020, Strona(/y) e1007314, ISSN 1553-7358
Wydawca: PLOS Computational Biology
DOI: 10.1371/journal.pcbi.1007314

Direct Visualization of Native CRISPR Target Search in Live Bacteria Reveals Cascade DNA Surveillance Mechanism

Autorzy: Jochem N.A. Vink, Koen J.A. Martens, Marnix Vlot, Rebecca E. McKenzie, Cristóbal Almendros, Boris Estrada Bonilla, Daan J.W. Brocken, Johannes Hohlbein, Stan J.J. Brouns
Opublikowane w: Molecular Cell, Numer 77/1, 2020, Strona(/y) 39-50.e10, ISSN 1097-2765
Wydawca: Cell Press
DOI: 10.1016/j.molcel.2019.10.021

Adsorption Sequencing as a Rapid Method to Link Environmental Bacteriophages to Hosts

Autorzy: Patrick A. de Jonge, F.A. Bastiaan von Meijenfeldt, Ana Rita Costa, Franklin L. Nobrega, Stan J.J. Brouns, Bas E. Dutilh
Opublikowane w: iScience, Numer 23/9, 2020, Strona(/y) 101439, ISSN 2589-0042
Wydawca: Elsevier
DOI: 10.1016/j.isci.2020.101439

Harnessing type I CRISPR–Cas systems for genome engineering in human cells

Autorzy: Peter Cameron, Mary M. Coons, Sanne E. Klompe, Alexandra M. Lied, Stephen C. Smith, Bastien Vidal, Paul D. Donohoue, Tomer Rotstein, Bryan W. Kohrs, David B. Nyer, Rachel Kennedy, Lynda M. Banh, Carolyn Williams, Mckenzi S. Toh, Matthew J. Irby, Leslie S. Edwards, Chun-Han Lin, Arthur L. G. Owen, Tim Künne, John van der Oost, Stan J. J. Brouns, Euan M. Slorach, Chris K. Fuller, Scott Gradia, Stev
Opublikowane w: Nature Biotechnology, Numer 37/12, 2019, Strona(/y) 1471-1477, ISSN 1087-0156
Wydawca: Nature Publishing Group
DOI: 10.1038/s41587-019-0310-0

Conserved motifs in the CRISPR leader sequence control spacer acquisition levels in Type I-D CRISPR-Cas systems

Autorzy: Sebastian N Kieper, Cristóbal Almendros, Stan J J Brouns
Opublikowane w: FEMS Microbiology Letters, Numer 366/11, 2019, ISSN 1574-6968
Wydawca: Oxford University Press
DOI: 10.1093/femsle/fnz129

Systematic analysis of Type I‐E Escherichia coli CRISPR‐Cas PAM sequences ability to promote interference and primed adaptation

Autorzy: Olga Musharova, Vasily Sitnik, Marnix Vlot, Ekaterina Savitskaya, Kirill A. Datsenko, Andrey Krivoy, Ivan Fedorov, Ekaterina Semenova, Stan J. J. Brouns, Konstantin Severinov
Opublikowane w: Molecular Microbiology, Numer 111/6, 2019, Strona(/y) 1558-1570, ISSN 0950-382X
Wydawca: Blackwell Publishing Inc.
DOI: 10.1111/mmi.14237

Molecular and Evolutionary Determinants of Bacteriophage Host Range

Autorzy: Patrick A. de Jonge, Franklin L. Nobrega, Stan J.J. Brouns, Bas E. Dutilh
Opublikowane w: Trends in Microbiology, Numer 27/1, 2019, Strona(/y) 51-63, ISSN 0966-842X
Wydawca: Elsevier BV
DOI: 10.1016/j.tim.2018.08.006

Complete Genome Sequences of Two T4-Like Escherichia coli Bacteriophages

Autorzy: Ana Rita Costa, Stan J. J. Brouns, Franklin L. Nobrega
Opublikowane w: Genome Announcements, Numer 6/26, 2018, ISSN 2169-8287
Wydawca: American Society for Microbiology Journals
DOI: 10.1128/genomea.00586-18

Bacteriophage DNA glucosylation impairs target DNA binding by type I and II but not by type V CRISPR–Cas effector complexes

Autorzy: Marnix Vlot, Joep Houkes, Silke J A Lochs, Daan C Swarts, Peiyuan Zheng, Tim Kunne, Prarthana Mohanraju, Carolin Anders, Martin Jinek, John van der Oost, Mark J Dickman, Stan J J Brouns
Opublikowane w: Nucleic Acids Research, Numer 46/2, 2017, Strona(/y) 873-885, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkx1264

Cas4 Facilitates PAM-Compatible Spacer Selection during CRISPR Adaptation

Autorzy: Sebastian N. Kieper, Cristóbal Almendros, Juliane Behler, Rebecca E. McKenzie, Franklin L. Nobrega, Anna C. Haagsma, Jochem N.A. Vink, Wolfgang R. Hess, Stan J.J. Brouns
Opublikowane w: Cell Reports, Numer 22/13, 2018, Strona(/y) 3377-3384, ISSN 2211-1247
Wydawca: Cell Press
DOI: 10.1016/j.celrep.2018.02.103

Complete Genome Sequence of the Escherichia coli Phage Ayreon

Autorzy: Marnix Vlot, Franklin L. Nobrega, Che F. A. Wong, Yue Liu, Stan J. J. Brouns
Opublikowane w: Genome Announcements, Numer 6/2, 2018, ISSN 2169-8287
Wydawca: American Society for Microbiology Journals
DOI: 10.1128/genomea.01354-17

Repetitive DNA Reeling by the Cascade-Cas3 Complex in Nucleotide Unwinding Steps

Autorzy: Luuk Loeff, Stan J.J. Brouns, Chirlmin Joo
Opublikowane w: Molecular Cell, Numer 70/3, 2018, Strona(/y) 385-394.e3, ISSN 1097-2765
Wydawca: Cell Press
DOI: 10.1016/j.molcel.2018.03.031

Role of nucleotide identity in effective CRISPR target escape mutations

Autorzy: Tim Künne, Yifan Zhu, Fausia da Silva, Nico Konstantinides, Rebecca E McKenzie, Ryan N Jackson, Stan JJ Brouns
Opublikowane w: Nucleic Acids Research, Numer 46/19, 2018, Strona(/y) 10395-10404, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gky687

CRISPR-Cas: Adapting to change

Autorzy: Simon A. Jackson, Rebecca E. McKenzie, Robert D. Fagerlund, Sebastian N. Kieper, Peter C. Fineran, Stan J. J. Brouns
Opublikowane w: Science, Numer 356/6333, 2017, Strona(/y) eaal5056, ISSN 0036-8075
Wydawca: American Association for the Advancement of Science
DOI: 10.1126/science.aal5056

Targeting mechanisms of tailed bacteriophages

Autorzy: Franklin L. Nobrega, Marnix Vlot, Patrick A. de Jonge, Lisa L. Dreesens, Hubertus J. E. Beaumont, Rob Lavigne, Bas E. Dutilh, Stan J. J. Brouns
Opublikowane w: Nature Reviews Microbiology, Numer 16, 2018, Strona(/y) 760 - 773, ISSN 1740-1526
Wydawca: Nature Publishing Group
DOI: 10.1038/s41579-018-0070-8

Cas3-Derived Target DNA Degradation Fragments Fuel Primed CRISPR Adaptation

Autorzy: Tim Künne, Sebastian N. Kieper, Jasper W. Bannenberg, Anne I.M. Vogel, Willem R. Miellet, Misha Klein, Martin Depken, Maria Suarez-Diez, Stan J.J. Brouns
Opublikowane w: Molecular Cell, Numer 63/5, 2016, Strona(/y) 852-864, ISSN 1097-2765
Wydawca: Cell Press
DOI: 10.1016/j.molcel.2016.07.011

An updated evolutionary classification of CRISPR–Cas systems

Autorzy: Kira S. Makarova, Yuri I. Wolf, Omer S. Alkhnbashi, Fabrizio Costa, Shiraz A. Shah, Sita J. Saunders, Rodolphe Barrangou, Stan J. J. Brouns, Emmanuelle Charpentier, Daniel H. Haft, Philippe Horvath, Sylvain Moineau, Francisco J. M. Mojica, Rebecca M. Terns, Michael P. Terns, Malcolm F. White, Alexander F. Yakunin, Roger A. Garrett, John van der Oost, Rolf Backofen, Eugene V. Koonin
Opublikowane w: Nature Reviews Microbiology, Numer 13/11, 2015, Strona(/y) 722-736, ISSN 1740-1526
Wydawca: Nature Publishing Group
DOI: 10.1038/nrmicro3569

CRISPR interference and priming varies with individual spacer sequences

Autorzy: Chaoyou Xue, Arun S. Seetharam, Olga Musharova, Konstantin Severinov, Stan J. J. Brouns, Andrew J. Severin, Dipali G. Sashital
Opublikowane w: Nucleic Acids Research, Numer 43/22, 2015, Strona(/y) 10831-10847, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkv1259

Using CAPTURE to detect spacer acquisition in native CRISPR arrays

Autorzy: Rebecca E. McKenzie, Cristóbal Almendros, Jochem N. A. Vink, Stan J. J. Brouns
Opublikowane w: Nature Protocols, Numer 14/3, 2019, Strona(/y) 976-990, ISSN 1754-2189
Wydawca: Nature Publishing Group
DOI: 10.1038/s41596-018-0123-5

Cas4–Cas1 fusions drive efficient PAM selection and control CRISPR adaptation

Autorzy: Cristóbal Almendros, Franklin L Nobrega, Rebecca E McKenzie, Stan J J Brouns
Opublikowane w: Nucleic Acids Research, Numer 47/10, 2019, Strona(/y) 5223-5230, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkz217

CRISPR sabotage

Autorzy: John van der Oost, Stan J. J. Brouns
Opublikowane w: Genome Biology, Numer 16/1, 2015, Strona(/y) 1-3, ISSN 1474-760X
Wydawca: BioMed Central
DOI: 10.1186/s13059-015-0820-0

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