Integrating a novel layer of synthetic biology tools in Pseudomonas, inspired by bacterial viruses

Project Information

BIONICbacteria

Grant agreement ID: 819800

DOI

10.3030/819800

Project closed

EC signature date 19 March 2019

Start date 1 September 2019

End date 31 August 2024

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 998 750,00

EU contribution

€ 1 998 750,00

Coordinated by

KATHOLIEKE UNIVERSITEIT LEUVEN
Belgium

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 (22)

Phage proteins target and co-opt host ribosomes immediately upon infection

Author(s): Milan Gerovac, Kotaro Chihara, Laura Wicke, Bettina Böttcher, Rob Lavigne, Jörg Vogel
Published in: Nature Microbiology, Issue 9(3), 2024, Page(s) 787-800, ISSN 2058-5276
Publisher: Nature Portfolio
DOI: 10.1038/s41564-024-01616-x

Refining the transcriptional landscapes for distinct clades of virulent phages infecting Pseudomonas aeruginosa

Author(s): Leena Putzeys, Laura Wicke, Maarten Boon, Vera van Noort, Jörg Vogel, Rob Lavigne
Published in: microLife, Issue 5, 2024, Page(s) uqae002, ISSN 2633-6693
Publisher: Oxford: Oxford University Press
DOI: 10.1093/femsml/uqae002

Impact of phage predation on <i>P. aeruginosa</i> adhered to human airway epithelium: major transcriptomic changes in metabolism and virulence-associated genes

Author(s): Ana C. Brandão; Leena Putzeys; Diana P. Pires; Marleen Voet; Jan Paeshuyse; Joana Azeredo; Rob Lavigne
Published in: RNA Biology, Issue Vol 20, Iss 1, 2023, Page(s) 235-247, ISSN 1555-8584
Publisher: Taylor & Francis
DOI: 10.1080/15476286.2023.2216065

Tail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail

Author(s): Anastasiia Chaban; Leonid Minakhin; Ekaterina Goldobina; Brain Bae; Yue Hao; Sergei Borukhov; Leena Putzeys; Maarten Boon; Florian Kabinger; Rob Lavigne; Kira S. Makarova; Eugene V. Koonin; Satish K. Nair; Shunsuke Tagami; Konstantin Severinov; Maria L. Sokolova
Published in: Nature Communications, Issue 15, 2024, Page(s) 317, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-44630-z

Exploring the transcriptional landscape of phage–host interactions using novel high-throughput approaches

Author(s): Leena Putzeys; Laura Wicke; Ana Brandão; Maarten Boon; Diana P Pires; Joana Azeredo; Jörg Vogel; Rob Lavigne; Milan Gerovac
Published in: Current Opinion in Microbiology, Issue 77, 2024, Page(s) 102419, ISSN 1369-5274
Publisher: Elsevier BV
DOI: 10.1016/j.mib.2023.102419

Sourcing Phage-Encoded Terminators Using ONT-cappable-seq for SynBio Applications in <i>Pseudomonas</i>

Author(s): Eveline-Marie Lammens; Leena Putzeys; Maarten Boon; Rob Lavigne
Published in: ACS Synthetic Biology, Issue 12(5), 2023, Page(s) 1415-1423, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.3c00101

SEVAtile: a standardised DNA assembly method optimised for Pseudomonas.

Author(s): Eveline-Marie Lammens; M. Boon; Dennis Grimon; Yves Briers; Rob Lavigne
Published in: Microbial biotechnology, 2021, ISSN 1751-7915
Publisher: Society for Applied Microbiology and John Wiley & Sons Ltd
DOI: 10.1111/1751-7915.13922

A SEVA-based, CRISPR-Cas3-assisted genome engineering approach for Pseudomonas with efficient vector curing

Author(s): Eveline-Marie Lammens, Daniel Christophe Volke, Kaat Schroven, Marleen Voet, Alison Kerremans, Rob Lavigne, Hanne Hendrix
Published in: Microbiology Spectrum, Issue 11(6), 2023, Page(s) e02707-23, ISSN 2165-0497
Publisher: Washington DC: ASM Press
DOI: 10.1128/spectrum.02707-23

Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria

Author(s): Eveline-Marie Lammens, Pablo Ivan Nikel, Rob Lavigne
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-19124-x

The phage-encoded PIT4 protein affects multiple two-component systems of Pseudomonas aeruginosa

Author(s): Kaat Schroven, Leena Putzeys, Alison Kerremans, Pieter-Jan Ceyssens, Marta Vallino, Jan Paeshuyse, Farhana Haque, Ahmed Yusuf, Matthias D Koch, Rob Lavigne
Published in: Microbiology Spectrum, Issue 12;11(6), 2023, Page(s) e0237223, ISSN 2165-0497
Publisher: Washington DC: ASM Press
DOI: 10.1128/spectrum.02372-23

Development of ONT-cappable-seq to unravel the transcriptional landscape of Pseudomonas phages

Author(s): Leena Putzeys; Maarten Boon; Eveline-Marie Lammens; Konstantin Kuznedelov; Konstantin Severinov; Rob Lavigne
Published in: Computational and Structural Biotechnology Journal, Issue 20010370, 2022, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2022.05.034

Transcriptomics-Driven Characterization of LUZ100, a T7-like Pseudomonas Phage with Temperate Features

Author(s): Leena Putzeys; Jorien Poppeliers; Maarten Boon; Cédric Lood; Marta Vallino; Rob Lavigne
Published in: mSystems, Issue Vol. 8 No. 2, 2023, Page(s) e01189-22, ISSN 2379-5077
Publisher: Washington DC: American Society for Microbiology
DOI: 10.1128/msystems.01189-22

SAPPHIRE: a neural network based classifier for σ70 promoter prediction in Pseudomonas

Author(s): Lucas Coppens, Rob Lavigne
Published in: BMC Bioinformatics, Issue 21/1, 2020, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-020-03730-z

‘Drc’, a structurally novel ssDNA-binding transcriptionregulator of N4-related bacterial viruses

Author(s): Maarten Boon, Elke De Zitter, Jeroen De Smet, Jeroen Wagemans, Marleen Voet, Lisa Friederike Pennemann, Thomas Schalk, Konstantin Kuznedelov, Konstantin Severinov, Luc Van Meervelt, Marc De Maeyer, Rob Lavigne
Published in: Nucleic Acids Research, Issue 48/1, 2020, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz1048

SAPPHIRE.CNN: Implementation of dRNA-seq-driven, species-specific promoter prediction using convolutional neural networks

Author(s): Lucas Coppens; Laura Wicke; Rob Lavigne
Published in: Computational and Structural Biotechnology Journal, Issue 20010370, 2022, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2022.09.006

The phage-encoded protein PIT2 impacts Pseudomonas aeruginosa quorum sensing by direct interaction with LasR

Author(s): Kaat Schroven, Leena Putzeys, Anne-Laure Swinnen, Hanne Hendrix, Jan Paeshuyse, Rob Lavigne
Published in: iScience, Issue 26(10), 2023, Page(s) 107745, ISSN 2589-0042
Publisher: Cell Press Elsevier Inc.
DOI: 10.1016/j.isci.2023.107745

Introducing differential RNA-seq mapping to track the early infection phase for Pseudomonas phage ɸKZ

Author(s): Laura Wicke, Falk Ponath, Lucas Coppens, Milan Gerovac, Rob Lavigne, Jörg Vogel
Published in: RNA Biology, 2020, ISSN 1547-6286
Publisher: Landes Bioscience
DOI: 10.1080/15476286.2020.1827785

A Grad-seq View of RNA and Protein Complexes in Pseudomonas aeruginosa under Standard and Bacteriophage Predation Conditions

Author(s): Milan Gerovac, Laura Wicke, Kotaro Chihara, Cornelius Schneider, Rob Lavigne, Jörg Vogel
Published in: mBio, Issue 12/1, 2021, ISSN 2150-7511
Publisher: American Society for Microbiology
DOI: 10.1128/mbio.03454-20

Bacteriophages as drivers of bacterial virulence and their potential for biotechnological exploitation

Author(s): Kaat Schroven, Abram Aertsen, Rob Lavigne
Published in: FEMS Microbiology Reviews, Issue 45/1, 2020, ISSN 1574-6976
Publisher: FEMS microbiology reviews
DOI: 10.1093/femsre/fuaa041

Assessing the Orthogonality of Phage-Encoded RNA Polymerases for Tailored Synthetic Biology Applications in Pseudomonas Species

Author(s): Eveline-Marie Lammens; Nathalie Feyaerts; Alison Kerremans; Maarten Boon; Rob Lavigne
Published in: International Journal of Molecular Sciences, Issue Volume 24; Issue 8, 2023, Page(s) 7175, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms24087175

Deconstructing the Phage–Bacterial Biofilm Interaction as a Basis to Establish New Antibiofilm Strategies

Author(s): Annegrete Visnapuu; Marie Van der Gucht; Jeroen Wagemans; Rob Lavigne
Published in: Viruses, 2022, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14051057

Differential transcription profiling of the phage LUZ19 infection process in different growth media

Author(s): Ana Brandão, Diana P. Pires, Lucas Coppens, Marleen Voet, Rob Lavigne, Joana Azeredo
Published in: RNA Biology, 2021, Page(s) 1-13, ISSN 1547-6286
Publisher: Landes Bioscience
DOI: 10.1080/15476286.2020.1870844

Book chapters (2)

Obtaining Detailed Phage Transcriptomes Using ONT-Cappable-Seq

Author(s): Leena Putzeys, Danish Intizar, Rob Lavigne, Maarten Boon
Published in: Methods in Molecular Biology, Phage Engineering and Analysis, Issue vol 2793, 2024, Page(s) 207-235
Publisher: Springer US
DOI: 10.1007/978-1-0716-3798-2_14

Targeted Genome Editing of Virulent Pseudomonas Phages Using CRISPR-Cas3

Author(s): Kaat Schroven, Marleen Voet, Rob Lavigne, Hanne Hendrix
Published in: Methods in Molecular Biology, Phage Engineering and Analysis, Issue Vol 2793, 2024, Page(s) 113-128
Publisher: Springer US
DOI: 10.1007/978-1-0716-3798-2_8