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Czernecki D, Nourisson A, Legrand P, Delarue M. Reclassification of family A DNA polymerases reveals novel functional subfamilies and distinctive structural features. Nucleic Acids Res 2023; 51:4488-4507. [PMID: 37070157 PMCID: PMC10201439 DOI: 10.1093/nar/gkad242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 03/07/2023] [Accepted: 03/24/2023] [Indexed: 04/19/2023] Open
Abstract
Family A DNA polymerases (PolAs) form an important and well-studied class of extant polymerases participating in DNA replication and repair. Nonetheless, despite the characterization of multiple subfamilies in independent, dedicated works, their comprehensive classification thus far is missing. We therefore re-examine all presently available PolA sequences, converting their pairwise similarities into positions in Euclidean space, separating them into 19 major clusters. While 11 of them correspond to known subfamilies, eight had not been characterized before. For every group, we compile their general characteristics, examine their phylogenetic relationships and perform conservation analysis in the essential sequence motifs. While most subfamilies are linked to a particular domain of life (including phages), one subfamily appears in Bacteria, Archaea and Eukaryota. We also show that two new bacterial subfamilies contain functional enzymes. We use AlphaFold2 to generate high-confidence prediction models for all clusters lacking an experimentally determined structure. We identify new, conserved features involving structural alterations, ordered insertions and an apparent structural incorporation of a uracil-DNA glycosylase (UDG) domain. Finally, genetic and structural analyses of a subset of T7-like phages indicate a splitting of the 3'-5' exo and pol domains into two separate genes, observed in PolAs for the first time.
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Affiliation(s)
- Dariusz Czernecki
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unit of Architecture and Dynamics of Biological Macromolecules, 75015 Paris, France
- Sorbonne Université, Collège Doctoral, ED 515, 75005 Paris, France
| | - Antonin Nourisson
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unit of Architecture and Dynamics of Biological Macromolecules, 75015 Paris, France
- Sorbonne Université, Collège Doctoral, ED 515, 75005 Paris, France
| | - Pierre Legrand
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unit of Architecture and Dynamics of Biological Macromolecules, 75015 Paris, France
- Synchrotron SOLEIL, L’Orme des Merisiers, 91190 Saint-Aubin, France
| | - Marc Delarue
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unit of Architecture and Dynamics of Biological Macromolecules, 75015 Paris, France
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Boon M, Holtappels D, Lood C, van Noort V, Lavigne R. Host Range Expansion of Pseudomonas Virus LUZ7 Is Driven by a Conserved Tail Fiber Mutation. PHAGE (NEW ROCHELLE, N.Y.) 2020; 1:87-90. [PMID: 36147895 PMCID: PMC9041470 DOI: 10.1089/phage.2020.0006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Background: When subjected to phage infection, bacteria can rapidly become resistant by changes in the phage receptors at the bacterial surface. Phages thus require adaptive mechanisms to circumvent this type of resistance. Methods: LUZ7 phage with an altered host range were isolated and analysed for mutations and their effect. Results: We find that Pseudomonas virus LUZ7 has an unusually high number of mutants (0.01-0.1% of the population) that drive host range expansion. Interestingly, all tested mutants have a single D737Y mutation in the tail fiber. This mutation allows the phage to adsorb to P. aeruginosa strains that are not natively recognized by the wild-type phage. Conclusion: The high number and specificity of mutants suggests the presence of an uncharacterized mechanism that drives these mutations. This mechanism enables the phage to better evade host resistance at the surface level and expand its host range in general, a feature that could be valuable in phage therapeutic settings or for phage engineering.
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Affiliation(s)
- Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Dominique Holtappels
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Cédric Lood
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Vera van Noort
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
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Botka T, Pantůček R, Mašlaňová I, Benešík M, Petráš P, Růžičková V, Havlíčková P, Varga M, Žemličková H, Koláčková I, Florianová M, Jakubů V, Karpíšková R, Doškař J. Lytic and genomic properties of spontaneous host-range Kayvirus mutants prove their suitability for upgrading phage therapeutics against staphylococci. Sci Rep 2019; 9:5475. [PMID: 30940900 PMCID: PMC6445280 DOI: 10.1038/s41598-019-41868-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 03/17/2019] [Indexed: 12/20/2022] Open
Abstract
Lytic bacteriophages are valuable therapeutic agents against bacterial infections. There is continual effort to obtain new phages to increase the effectivity of phage preparations against emerging phage-resistant strains. Here we described the genomic diversity of spontaneous host-range mutants of kayvirus 812. Five mutant phages were isolated as rare plaques on phage-resistant Staphylococcus aureus strains. The host range of phage 812-derived mutants was 42% higher than the wild type, determined on a set of 186 methicillin-resistant S. aureus strains representing the globally circulating human and livestock-associated clones. Comparative genomics revealed that single-nucleotide polymorphisms from the parental phage 812 population were fixed in next-step mutants, mostly in genes for tail and baseplate components, and the acquired point mutations led to diverse receptor binding proteins in the phage mutants. Numerous genome changes associated with rearrangements between direct repeat motifs or intron loss were found. Alterations occurred in host-takeover and terminal genomic regions or the endolysin gene of mutants that exhibited the highest lytic activity, which implied various mechanisms of overcoming bacterial resistance. The genomic data revealed that Kayvirus spontaneous mutants are free from undesirable genes and their lytic properties proved their suitability for rapidly updating phage therapeutics.
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Affiliation(s)
- Tibor Botka
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
| | - Roman Pantůček
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic.
| | - Ivana Mašlaňová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
| | - Martin Benešík
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
| | - Petr Petráš
- National Institute of Public Health, Praha, 100 42, Czech Republic
| | - Vladislava Růžičková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
| | - Pavla Havlíčková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
| | - Marian Varga
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
| | - Helena Žemličková
- National Institute of Public Health, Praha, 100 42, Czech Republic.,Department of Clinical Microbiology, University Hospital and Faculty of Medicine in Hradec Králové, Charles University, Hradec Králové, 500 05, Czech Republic
| | | | | | - Vladislav Jakubů
- National Institute of Public Health, Praha, 100 42, Czech Republic
| | | | - Jiří Doškař
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
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