Novel mechanisms of adaptive and innate bacteriophage immunity

Project Information

DEFEND

Grant agreement ID: 101003229

DOI

10.3030/101003229

EC signature date 4 February 2021

Start date 1 June 2021

End date 31 May 2026

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 000 000,00

EU contribution

€ 2 000 000,00

Coordinated by

TECHNISCHE UNIVERSITEIT DELFT
Netherlands

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (24)

KlebPhaCol: a community-driven resource for <i>Klebsiella</i> research identified a novel phage family

Author(s): Daniela Rothschild-Rodriguez, Kai S Lambon, Simran Krishnakant Kushwaha, Sofya K Garushyants, Moritz Ertelt, Agnieszka Latka, Ana Rita Costa, Anna Mantzouratou, Claire King, Dimitri Boeckaerts, Elizab
Published in: Nucleic Acids Research, Issue 53, 2025, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaf1122

Modulating CRISPR-Cas genome editing using guide-complementary DNA oligonucleotides

Author(s): Thomas Swartjes; Peng Shang; Dennis van den Berg; Tim A. Künne; Niels Geijsen; Stan J.J. Brouns; John van der Oost; Raymond H.J. Staals; Richard A. Notebaart
Published in: The CRISPR Journal, 2022, ISSN 2573-1599
Publisher: Mary Ann Liebert
DOI: 10.1101/2022.01.15.475214

Structural basis for broad anti-phage immunity by DISARM

Author(s): Jack P. K. Bravo; Cristian Aparicio-Maldonado; Franklin L. Nobrega; Stan J. J. Brouns; David W. Taylor
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/2021.12.26.474123

Phage tRNAs evade tRNA-targeting host defenses through anticodon loop mutations

Author(s): Daan F. van den Berg; Baltus A. van der Steen; Ana Rita Costa; Stan J. J. Brouns
Published in: eLife, 2023, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.21203/rs.3.rs-2166710/v1

Bacteriophage genomes encode both broad and specific counter-defense repertoires to overcome bacterial defense systems

Author(s): Ana Rita Costa, Daan F. van den Berg, Jelger Q. Esser, Halewijn van den Bossche, Nadiia Pozhydaieva, Konstantinos Kalogeropoulos, Stan J.J. Brouns
Published in: Cell Host &amp; Microbe, Issue 33, 2025, Page(s) 1161-1172.e5, ISSN 1931-3128
Publisher: Cell Press
DOI: 10.1016/j.chom.2025.06.010

Craspase is a CRISPR RNA-guided, RNA-activated protease

Author(s): Chunyi Hu; Sam P. B. van Beljouw; Ki Hyun Nam; Gabriel Schuler; Fran Ding; Yanru Cui; Alicia Rodríguez-Molina; Anna C. Haagsma; Menno Valk; Martin Pabst; Stan J. J. Brouns; Ailong Ke
Published in: Science, 2022, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.add5064

Single cell variability of CRISPR‐Cas interference and adaptation

Author(s): Rebecca E McKenzie, Emma M Keizer, Jochem N A Vink, Jasper van Lopik, Ferhat Büke, Vera Kalkman, Christian Fleck, Sander J Tans, Stan J J Brouns
Published in: Molecular Systems Biology, 2022, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.202110680

An OmpW-dependent T4-like phage infects Serratia sp. ATCC 39006

Author(s): Marina Mahler; Lucia M. Malone; Daan F. van den Berg; Leah M. Smith; Stan J. J. Brouns; Peter C. Fineran
Published in: Microbial Genomics, 2023, ISSN 2057-5858
Publisher: London Society for General Microbiology
DOI: 10.1099/mgen.0.000968

Short prokaryotic Argonaute systems trigger cell death upon detection of invading DNA

Author(s): Balwina Koopal; Ana Potocnik; Sumanth K. Mutte; Cristian Aparicio-Maldonado; Simon Lindhoud; Jacques J.M. Vervoort; Stan J.J. Brouns; Daan C. Swarts
Published in: Cell, 2022, ISSN 1097-4172
Publisher: Cell press
DOI: 10.1016/j.cell.2022.03.012

Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses

Author(s): Daan F. van den Berg, Ana Rita Costa, Jelger Q. Esser, Ilinka Stanciu, Jasper Q. Geissler, Adja Damba Zoumaro-Djayoon, Pieter-Jan Haas, Stan J.J. Brouns
Published in: Cell Host &amp; Microbe, Issue 32, 2025, Page(s) 1427-1443.e8, ISSN 1931-3128
Publisher: Cell Press
DOI: 10.1016/j.chom.2024.07.007

Mechanisms and clinical importance of bacteriophage resistance.

Author(s): Julia E Egido; Ana Rita Costa; Ana Rita Costa; Cristian Aparicio-Maldonado; Cristian Aparicio-Maldonado; Pieter-Jan A. Haas; Stan J. J. Brouns; Stan J. J. Brouns
Published in: FEMS Microbiology Reviews, 2022, ISSN 1574-6976
Publisher: Elsevier
DOI: 10.1093/femsre/fuab048

Phage arabinosyl-hydroxy-cytosine DNA modifications result in distinct evasion and sensitivity responses to phage defense systems

Author(s): Marina Mahler, Liang Cui, Leah M. Smith, Katharina G. Wandera, Oliver Dietrich, David Mayo-Muñoz, Seetharamsing Balamkundu, Megan En Lee, Hong Ye, Chuan-Fa Liu, Junzhou Wu, Juby Mathew, Jeremy Dubrul
Published in: Cell Host &amp; Microbe, Issue 33, 2025, Page(s) 1173-1190.e9, ISSN 1931-3128
Publisher: Cell Press
DOI: 10.1016/j.chom.2025.06.005

Reduced prevalence of phage defense systems in <i>Pseudomonas aeruginosa</i> strains from cystic fibrosis patients

Author(s): Daan F. van den Berg, Stan J. J. Brouns
Published in: mBio, Issue 16, 2025, ISSN 2150-7511
Publisher: American Society for Microbiology
DOI: 10.1128/mbio.03548-24

CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes

Author(s): Benjamin A Adler; Marena I Trinidad; Daniel Bellieny-Rabelo; Elaine Zhang; Hannah M Karp; Petr Skopintsev; Brittney W Thornton; Rachel F Weissman; Peter H Yoon; LinXing Chen; Tomas Hessler; Amy R Eggers; David Colognori; Ron Boger; Erin E Doherty; Connor A Tsuchida; Ryan V Tran; Laura Hofman; Honglue Shi; Kevin M Wasko; Zehan Zhou; Chenglong Xia; Muntathar J Al-Shimary; Jaymin R Patel; Vienna C J
Published in: Nucleic Acids Research, 2023, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkad890

Proteases in bacteriophage defense systems and their potential in bioengineering

Author(s): Konstantinos Kalogeropoulos, Sam P.B. van Beljouw, Dani Feldmann, Daan F. van den Berg, Stan J.J. Brouns
Published in: Trends in Biochemical Sciences, Issue 51, 2026, Page(s) 64-79, ISSN 0968-0004
Publisher: Elsevier BV
DOI: 10.1016/j.tibs.2025.10.006

Craspase Orthologs Cleave a Nonconserved Site in Target Protein Csx30

Author(s): Sam P. B. van Beljouw, Anna C. Haagsma, Konstantinos Kalogeropoulos, Martin Pabst, Stan J. J. Brouns
Published in: ACS Chemical Biology, Issue 19, 2024, Page(s) 1051-1055, ISSN 1554-8929
Publisher: American Chemical Society
DOI: 10.1021/acschembio.3c00788

The gRAMP CRISPR-Cas effector is an RNA endonuclease complexed with a caspase-like peptidase.

Author(s): Sam P. B. van Beljouw; Sam P. B. van Beljouw; Anna C. Haagsma; Anna C. Haagsma; Alicia Rodríguez-Molina; Alicia Rodríguez-Molina; Daan F. van den Berg; Daan F. van den Berg; Jochem N.A. Vink; Jochem N.A. Vink; Stan J. J. Brouns; Stan J. J. Brouns
Published in: Science, 2021, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abk2718

Adaptation by Type V-A and V-B CRISPR-Cas Systems Demonstrates Conserved Protospacer Selection Mechanisms Between Diverse CRISPR-Cas Types

Author(s): Wen Y. Wu; Simon A. Jackson; Cristóbal Almendros; Anna C. Haagsma; Suzan Yilmaz; Gerrit Gort; John van der Oost; Stan J.J. Brouns; Raymond H.J. Staals
Published in: The CRISPR Journal, 2022, ISSN 2573-1602
Publisher: Mary Ann Liebert
DOI: 10.1089/crispr.2021.0150

PAM-repeat associations and spacer selection preferences in single and co-occurring CRISPR-Cas systems.

Author(s): Jochem N.A. Vink; Jochem N.A. Vink; Jan H. L. Baijens; Jan H. L. Baijens; Stan J. J. Brouns; Stan J. J. Brouns
Published in: Genome Biology, 2021, ISSN 1474-760X
Publisher: London BioMed Central
DOI: 10.1186/s13059-021-02495-9

RNA-targeting CRISPR–Cas systems

Author(s): Sam P. B. van Beljouw, Jasper Sanders, Alicia Rodríguez-Molina, Stan J. J. Brouns
Published in: Nature Reviews Microbiology, Issue 21, 2022, Page(s) 21-34, ISSN 1740-1526
Publisher: Nature Publishing Group
DOI: 10.1038/s41579-022-00793-y

Monitoring phage-induced lysis of Gram-negatives in real time using a fluorescent DNA dye

Author(s): Julia E. Egido; Catherine Toner-Bartelds; Ana Rita Costa; Stan J. J. Brouns; Suzan H. M. Rooijakkers; Bart W. Bardoel; Pieter-Jan Haas
Published in: Scientific Reports, 2023, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-023-27734-w

Approaches for bacteriophage genome engineering

Author(s): Marina Mahler, Ana Rita Costa, Sam P.B. van Beljouw, Peter C. Fineran, Stan J.J. Brouns
Published in: Trends in Biotechnology, Issue 41, 2025, Page(s) 669-685, ISSN 0167-7799
Publisher: Elsevier BV
DOI: 10.1016/j.tibtech.2022.08.008

High-resolution reconstruction of a Jumbo-bacteriophage infecting capsulated bacteria using hyperbranched tail fibers

Author(s): Ruochen Ouyang; Ana Rita Costa; C. Keith Cassidy; Aleksandra Otwinowska; Vera C. J. Williams; Agnieszka Latka; Phill J. Stansfeld; Zuzanna Drulis-Kawa; Yves Briers; Daniël M. Pelt; Stan J. J. Brouns; Ariane Briegel
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-34972-5

Accumulation of defense systems in phage-resistant strains of Pseudomonas aeruginosa

Author(s): Costa AR, van den Berg DF, Esser JQ, Muralidharan A, van den Bossche H, Bonilla BE, van der Steen BA, Haagsma AC, Fluit AC, Nobrega FL, Haas PJ, Brouns SJJ
Published in: Science Advances, 2024, ISSN 2375-2548
Publisher: Washington, DC American Association for the Advancement of Science
DOI: 10.1126/sciadv.adj0341