DepoCatalog: Mapping the Diversity of 105 Recombinant Klebsiella Phage Depolymerases Across Sequence, Structure, and Substrate Specificity

Otwinowska, A.; Olejniczak, S.; Latka, A.; Pozniak, M.; Majkowska-Skrobek, G.; Maciejewska, B.; Koszucki, J.; Panicker, V.; Jablonska, S.; Hulsens, M.; Bugert, J. J.; Tournebize, R.; Brouns, S. J. J.; Squeglia, F.; Berisio, R.; Briers, Y.; Mostowy, R.; Drulis-Kawa, Z.

doi:10.1101/2025.09.09.675204

bioRxiv · 10.1101/2025.09.09.675204

DepoCatalog: Mapping the Diversity of 105 Recombinant Klebsiella Phage Depolymerases Across Sequence, Structure, and Substrate Specificity

Otwinowska, A.·Olejniczak, S.·Latka, A.·Pozniak, M.·Majkowska-Skrobek, G.·Maciejewska, B.·Koszucki, J.·Panicker, V.·Jablonska, S.·Hulsens, M.·Bugert, J. J.·Tournebize, R.·Brouns, S. J. J.·Squeglia, F.·Berisio, R.·Briers, Y.·Mostowy, R.·Drulis-Kawa, Z.

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Abstract

A validated catalog of 105 recombinant depolymerases from Klebsiella phages covers 58 KL-types. 46 novel enzymes from prophages, jumbo phages, and common phages are linked to any known enzymatic activity against 14 classical serotypes and 12 genome-defined KL-types. Using activity-based profiling, structure prediction, and domain dissection, we developed a function-guided classification and a five-class structural catalog. This framework reveals highly specific enzymes active against up to three capsule types. K47 CPS was degraded by three diverse protein groups. Structurally similar depolymerases degrading particular CPS were found in distinct phage taxa, with highly conserved enzymes in Drulisvirus specific to K1-, K2-types. The exclusive depolymerases were found in siphoviruses targeting K2 and K62 serotypes. A case study of five structurally similar enzymes degrading KL22/KL37/KL111 and KL25/KL119 capsules suggested specificity switching via amino acid changes or C-domain modification. Klebsiella phage depolymerases catalog sheds light on their diversity, evolution, and potential application.

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Otwinowska, A., Olejniczak, S., Latka, A., Pozniak, M., Majkowska-Skrobek, G., Maciejewska, B., Koszucki, J., Panicker, V., Jablonska, S., Hulsens, M., Bugert, J. J., Tournebize, R., Brouns, S. J. J., Squeglia, F., Berisio, R., Briers, Y., Mostowy, R., Drulis-Kawa, Z.. 2025-09-09. DepoCatalog: Mapping the Diversity of 105 Recombinant Klebsiella Phage Depolymerases Across Sequence, Structure, and Substrate Specificity. https://doi.org/10.1101/2025.09.09.675204

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