Replacement of the Genomic Scaffold Improves the Replication Efficiency of Synthetic Klebsiella Phages

In this study, the impact of the genomic scaffold on the properties of bacteriophages was investigated by swapping the genomic scaffolds surrounding the tailspike genes between two Przondovirus phages, KP192 and KP195, which infect Klebsiella pneumoniae with different capsular types. A yeast-based t...

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Vydané v:	International journal of molecular sciences Ročník 26; číslo 14; s. 6824
Hlavní autori:	Baykov, Ivan K., Kurchenko, Olga M., Mikhaylova, Ekaterina E., Miroshnikova, Anna V., Morozova, Vera V., Khlebnikova, Marianna I., Tikunov, Artem Yu, Kozlova, Yuliya N., Tikunova, Nina V.
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	Switzerland MDPI AG 16.07.2025 MDPI
Predmet:	Amino acids Bacterial pneumonia Bacteriophages - genetics Bacteriophages - physiology Biology Cloning Efficiency Genes Genome, Viral Genomes Genomics Klebsiella pneumoniae - genetics Klebsiella pneumoniae - virology Phages Pneumonia Proteins Viral Tail Proteins - genetics Virus Replication - genetics United States Massachusetts Russia Klebsiella synthetic biology receptor-binding protein transformation-associated recombination cloning tailspike depolymerase bacteriophage genome assembly
ISSN:	1422-0067, 1661-6596, 1422-0067
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Abstract	In this study, the impact of the genomic scaffold on the properties of bacteriophages was investigated by swapping the genomic scaffolds surrounding the tailspike genes between two Przondovirus phages, KP192 and KP195, which infect Klebsiella pneumoniae with different capsular types. A yeast-based transformation-associated recombination cloning technique and subsequent “rebooting” of synthetic phage genomes in bacteria were used to construct the phages. Using Klebsiella strains with K2, K64, and KL111 capsular types, it was shown that the capsular specificity of the synthetic phages is fully consistent with that of the tailspike proteins (tsp). However, the efficiency of plating and the lytic efficiency of these phages strongly depended on the genomic scaffold used and the Klebsiella strain used. Synthetic phages with swapped genomic scaffolds demonstrated superior reproduction efficiency using a number of strains compared to wild-type phages, indicating that some elements of the swapped genomic scaffold enhance phage replication efficiency, presumably by blocking some of the host anti-phage defense systems. Our findings demonstrate that even in the case of closely related phages, the selection of the genomic scaffold used for tsp gene transplantation can have a profound impact on the efficiency of phage propagation on target bacterial strains.
AbstractList	In this study, the impact of the genomic scaffold on the properties of bacteriophages was investigated by swapping the genomic scaffolds surrounding the tailspike genes between two Przondovirus phages, KP192 and KP195, which infect Klebsiella pneumoniae with different capsular types. A yeast-based transformation-associated recombination cloning technique and subsequent "rebooting" of synthetic phage genomes in bacteria were used to construct the phages. Using Klebsiella strains with K2, K64, and KL111 capsular types, it was shown that the capsular specificity of the synthetic phages is fully consistent with that of the tailspike proteins (tsp). However, the efficiency of plating and the lytic efficiency of these phages strongly depended on the genomic scaffold used and the Klebsiella strain used. Synthetic phages with swapped genomic scaffolds demonstrated superior reproduction efficiency using a number of strains compared to wild-type phages, indicating that some elements of the swapped genomic scaffold enhance phage replication efficiency, presumably by blocking some of the host anti-phage defense systems. Our findings demonstrate that even in the case of closely related phages, the selection of the genomic scaffold used for tsp gene transplantation can have a profound impact on the efficiency of phage propagation on target bacterial strains.In this study, the impact of the genomic scaffold on the properties of bacteriophages was investigated by swapping the genomic scaffolds surrounding the tailspike genes between two Przondovirus phages, KP192 and KP195, which infect Klebsiella pneumoniae with different capsular types. A yeast-based transformation-associated recombination cloning technique and subsequent "rebooting" of synthetic phage genomes in bacteria were used to construct the phages. Using Klebsiella strains with K2, K64, and KL111 capsular types, it was shown that the capsular specificity of the synthetic phages is fully consistent with that of the tailspike proteins (tsp). However, the efficiency of plating and the lytic efficiency of these phages strongly depended on the genomic scaffold used and the Klebsiella strain used. Synthetic phages with swapped genomic scaffolds demonstrated superior reproduction efficiency using a number of strains compared to wild-type phages, indicating that some elements of the swapped genomic scaffold enhance phage replication efficiency, presumably by blocking some of the host anti-phage defense systems. Our findings demonstrate that even in the case of closely related phages, the selection of the genomic scaffold used for tsp gene transplantation can have a profound impact on the efficiency of phage propagation on target bacterial strains. In this study, the impact of the genomic scaffold on the properties of bacteriophages was investigated by swapping the genomic scaffolds surrounding the tailspike genes between two Przondovirus phages, KP192 and KP195, which infect Klebsiella pneumoniae with different capsular types. A yeast-based transformation-associated recombination cloning technique and subsequent “rebooting” of synthetic phage genomes in bacteria were used to construct the phages. Using Klebsiella strains with K2, K64, and KL111 capsular types, it was shown that the capsular specificity of the synthetic phages is fully consistent with that of the tailspike proteins (tsp). However, the efficiency of plating and the lytic efficiency of these phages strongly depended on the genomic scaffold used and the Klebsiella strain used. Synthetic phages with swapped genomic scaffolds demonstrated superior reproduction efficiency using a number of strains compared to wild-type phages, indicating that some elements of the swapped genomic scaffold enhance phage replication efficiency, presumably by blocking some of the host anti-phage defense systems. Our findings demonstrate that even in the case of closely related phages, the selection of the genomic scaffold used for tsp gene transplantation can have a profound impact on the efficiency of phage propagation on target bacterial strains. In this study, the impact of the genomic scaffold on the properties of bacteriophages was investigated by swapping the genomic scaffolds surrounding the tailspike genes between two phages, KP192 and KP195, which infect with different capsular types. A yeast-based transformation-associated recombination cloning technique and subsequent "rebooting" of synthetic phage genomes in bacteria were used to construct the phages. Using strains with K2, K64, and KL111 capsular types, it was shown that the capsular specificity of the synthetic phages is fully consistent with that of the tailspike proteins ( ). However, the efficiency of plating and the lytic efficiency of these phages strongly depended on the genomic scaffold used and the strain used. Synthetic phages with swapped genomic scaffolds demonstrated superior reproduction efficiency using a number of strains compared to wild-type phages, indicating that some elements of the swapped genomic scaffold enhance phage replication efficiency, presumably by blocking some of the host anti-phage defense systems. Our findings demonstrate that even in the case of closely related phages, the selection of the genomic scaffold used for gene transplantation can have a profound impact on the efficiency of phage propagation on target bacterial strains.
Audience	Academic
Author	Tikunova, Nina V. Mikhaylova, Ekaterina E. Khlebnikova, Marianna I. Miroshnikova, Anna V. Kurchenko, Olga M. Kozlova, Yuliya N. Baykov, Ivan K. Morozova, Vera V. Tikunov, Artem Yu
AuthorAffiliation	1 Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia morozova@niboch.nsc.ru (V.V.M.) 2 Shared Research Facility “Siberian Circular Photon Source” (SRF “SKIF”), Boreskov Institute of Catalysis of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia 3 Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
AuthorAffiliation_xml	– name: 1 Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia morozova@niboch.nsc.ru (V.V.M.) – name: 2 Shared Research Facility “Siberian Circular Photon Source” (SRF “SKIF”), Boreskov Institute of Catalysis of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia – name: 3 Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
Author_xml	– sequence: 1 givenname: Ivan K. orcidid: 0000-0003-4839-5673 surname: Baykov fullname: Baykov, Ivan K. – sequence: 2 givenname: Olga M. surname: Kurchenko fullname: Kurchenko, Olga M. – sequence: 3 givenname: Ekaterina E. surname: Mikhaylova fullname: Mikhaylova, Ekaterina E. – sequence: 4 givenname: Anna V. surname: Miroshnikova fullname: Miroshnikova, Anna V. – sequence: 5 givenname: Vera V. surname: Morozova fullname: Morozova, Vera V. – sequence: 6 givenname: Marianna I. surname: Khlebnikova fullname: Khlebnikova, Marianna I. – sequence: 7 givenname: Artem Yu orcidid: 0000-0001-5613-5447 surname: Tikunov fullname: Tikunov, Artem Yu – sequence: 8 givenname: Yuliya N. surname: Kozlova fullname: Kozlova, Yuliya N. – sequence: 9 givenname: Nina V. surname: Tikunova fullname: Tikunova, Nina V.
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Snippet	In this study, the impact of the genomic scaffold on the properties of bacteriophages was investigated by swapping the genomic scaffolds surrounding the...
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SubjectTerms	Amino acids Bacterial pneumonia Bacteriophages - genetics Bacteriophages - physiology Biology Cloning Efficiency Genes Genome, Viral Genomes Genomics Klebsiella pneumoniae - genetics Klebsiella pneumoniae - virology Phages Pneumonia Proteins Viral Tail Proteins - genetics Virus Replication - genetics
Title	Replacement of the Genomic Scaffold Improves the Replication Efficiency of Synthetic Klebsiella Phages
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