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2022, № 97

UDC: 578.544
GSNTI: 34.27.21

Homologs of the majer antigene of bacteriophage RB30 from compost methagenome

The article is devoted to the search for homologues of the Highly antigenic Outer Capsid protein (Hoc-protein) of the bacteriophage RB30 in the metagenome of the compost microbiota in order to create fundamental foundations for constructing bacteriophages with high affinity for the substrates of this environment using genomic engineering methods. The Hoc-protein of bacteriophage RB30 has an additional immunoglobulin-like PKD domain, which provides additional, Ca2+-mediated binding of oligo- and polysaccharides from various biotopes. Bacteriophages created on the basis of the use of specific protein sequences found on the surface of their capsid, which have an increased affinity for the substrates of this environment, could serve for more effective control of enterobacterial contamination by bacteriophage treatment by analogy with phage therapy in humans or farm animals. Using the DELTA-BLAST software tool, 367 homologues were found in the GenBank database. Among these protein sequences, those previously characterized as carrying the PKD omene and having a statistical characteristic E-vaule less than 10-8 were selected. A phylogenetic analysis of the selected sequences was carried out, in which sequences of phage proteins close to the Hoc-protein of bacteriophage RB30 were used as controls. This analysis showed that only five of the sequences were co-located with Hoc RB30 and its closest homologue from the bacteriophage RB27 genome. Structural modeling was performed for the closest homologue from the compost metagenome And it was shown that the protein MNE16030.1. carries domains responsible for binding glycosides. In this way, using the methods of bioinformatics and using methods of molecular modeling of the protein structure, the selection of the most promising sequences suitable for obtaining an artificial surface of bacteriophages, which could be used to control the contamination of compost with enterobacteria by prophylactic bacteriophage treatment, was carried out.
Keywords: Bacteriophage T4, bacteriophage RB30, majer antigene of T4-pages, A2-milk, metagenome of the compost microbiota, UPGMA algoritm, phylogenetic analysis, protein structural modeling.
DOI: 10.21515/1999-1703-97-215-227

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Authors:

1. Zimin Andrei Antonovich, PhD in Biology, senior researcher, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS - a separate subdivision of the Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences".
2. Nikulina Aleksandra Nikolaevna, postgraduate student, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS - a separate subdivision of the Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences".
3. Nikulin Nikita Alekseevich, postgraduate student, CEOS, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS - a separate subdivision of the Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences".
4. Xia H., professor, School of Life Sciences, Taizhou University.
5. Lu Y., professor, School of Life Sciences, Shanghai Normal University.
6. Osepchuk Denis Vasilyevich, DSc in Agriculture, leading researcher, Federal State Budgetary Scientific Institution Krasnodar Research Centre for Animal Husbandry and Veterinary Medicine.
7. Koshchaev Andrey Georgievich, DSc in Biology, professor, academican RAS, Federal State Budgetary Educational Institution of Higher Education “I.T. Trubilin Kuban State Agrarian University”.