DepoCatalog: mapping diversity of 129 recombinantly produced Klebsiella phage depolymerases
12 affiliations
- 1Department of Pathogen Biology and Immunology, University of Wroclaw, Wroclaw, Poland
- 2Department of Biotechnology, Ghent University, Ghent, Belgium
- 3Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
- 4Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- 5Bundeswehr Institute of Microbiology, Munich, Germany
- 6Department of Biosystems, KU Leuven, Leuven, Belgium
- 7Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses, CIMI, Paris, France
- 8UTechS Photonic BioImaging Direction de la Technologie, Centre de Recherche et de Ressources Technologiques, Institut Pasteur, Paris, France
- 9Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands
- 10Institute of Biostructures and Bioimaging, CNR, Naples, Italy
- 11Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
- 12Department of Pathogen Biology and Immunology, University of Wroclaw, Wroclaw, Poland. [email protected]
Abstract
Our understanding of how depolymerase sequence and structure determine substrate specificity is fragmentary due to the limited number of experimentally characterized enzymes. Here we show DepoCatalog - an experimentally validated collection of 129 recombinantly prepared Klebsiella phage depolymerases (90 enzymes produced in this study and 39 homologs from the literature), with specificity spanning 75 KL-types. Enzymes originated from podo-, sipho-, myo-, jumbo phages, and prophages. Using activity profiling, structural modeling, and domain dissection, we propose a five‑class framework that captures the architectural and functional diversity of these enzymes. DepoCatalog uncovers cross-reactivity and taxa‑specific enzymes. Structural comparisons indicate that specificity switching or extension is associated with modifications to the C‑terminal domain. We further hypothesize that podoviruses encoding up to two RBPs show greater receptor adaptability than jumbo phages with multiple specialized RBPs. Finally, we develop a publicly accessible, DepoCat dataset ( https://depocat.uwr.edu.pl ) for specificity, structural classification and comparison of newly identified depolymerases.
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BibTeX
@article{otwinowska2026depocatalog,
title = {{DepoCatalog: mapping diversity of 129 recombinantly produced Klebsiella phage depolymerases}},
author = {Aleksandra Otwinowska and Sebastian Olejniczak and Agnieszka Łątka and Maria Pozniak and Grażyna Majkowska-Skrobek and Barbara Maciejewska and Janusz Koszucki and Vyshakh R. Panicker and Sara Jablonska and Mathilde Hulsens and Jana Stender and Maha Niazi and S. K. Green and Joachim J. Bugert and Régis Tournebize and Stan J. J. Brouns and Flavia Squeglia and Rita Berisio and Jens A. Hammerl and Rob Lavigne and Yves Briers and Rafal J. Mostowy and Zuzanna Drulis‐Kawa},
journal = {Nature Communications},
year = {2026},
month = may,
doi = {10.1038/s41467-026-73570-7},
url = {https://doi.org/10.1038/s41467-026-73570-7},
note = {CC BY},
}
RIS
TY - JOUR
TI - DepoCatalog: mapping diversity of 129 recombinantly produced Klebsiella phage depolymerases
AU - Aleksandra Otwinowska
AU - Sebastian Olejniczak
AU - Agnieszka Łątka
AU - Maria Pozniak
AU - Grażyna Majkowska-Skrobek
AU - Barbara Maciejewska
AU - Janusz Koszucki
AU - Vyshakh R. Panicker
AU - Sara Jablonska
AU - Mathilde Hulsens
AU - Jana Stender
AU - Maha Niazi
AU - S. K. Green
AU - Joachim J. Bugert
AU - Régis Tournebize
AU - Stan J. J. Brouns
AU - Flavia Squeglia
AU - Rita Berisio
AU - Jens A. Hammerl
AU - Rob Lavigne
AU - Yves Briers
AU - Rafal J. Mostowy
AU - Zuzanna Drulis‐Kawa
PY - 2026
DA - 2026/05/22
JO - Nature Communications
DO - 10.1038/s41467-026-73570-7
UR - https://doi.org/10.1038/s41467-026-73570-7
AB - Our understanding of how depolymerase sequence and structure determine substrate specificity is fragmentary due to the limited number of experimentally characterized enzymes. Here we show DepoCatalog - an experimentally validated collection of 129 recombinantly prepared Klebsiella phage depolymerases (90 enzymes produced in this study and 39 homologs from the literature), with specificity spanning 75 KL-types. Enzymes originated from podo-, sipho-, myo-, jumbo phages, and prophages. Using activity profiling, structural modeling, and domain dissection, we propose a five‑class framework that captures the architectural and functional diversity of these enzymes. DepoCatalog uncovers cross-reactivity and taxa‑specific enzymes. Structural comparisons indicate that specificity switching or extension is associated with modifications to the C‑terminal domain. We further hypothesize that podoviruses encoding up to two RBPs show greater receptor adaptability than jumbo phages with multiple specialized RBPs. Finally, we develop a publicly accessible, DepoCat dataset ( https://depocat.uwr.edu.pl ) for specificity, structural classification and comparison of newly identified depolymerases.
SN - 2041-1723
ER -