Citation: Limanskaya O., Balak O., Biloivan O., Limanskii A. (2026) 3D structure of 5'-UTR fragment of MycobacteriumBovis Rpsl gene associated with streptomycin resistance. VeterinaryBiotechnology, 48, 121-133. https://doi.org/10.31073/vet_biotech48-08
LIMANSKAYA O., 1, Doc. Sci. (biol.)., This email address is being protected from spambots. You need JavaScript enabled to view it., https://orcid.org/0000-0002-6022-0342
BALAK O.2, Cand. Sc. (Medicine), This email address is being protected from spambots. You need JavaScript enabled to view it., https://orcid.org/0009-0000-8745-8089
BILOIVAN O.1, Cand. Sci. (Vet. Med.), This email address is being protected from spambots. You need JavaScript enabled to view it., https://orcid.org/0000-0002-9973-4551
LIMANSKII A.3, Doc. Sci. (Vet. Med.)., This email address is being protected from spambots. You need JavaScript enabled to view it., https://orcid.org/0009-0007-9922-4619
1 The National Scientific Center “Institute of Experimental and Clinical Veterinary Medicine”
2Kharkiv National Medical University
3Institute of Physiological Active Compounds
3D STRUCTURE OF 5'-UTR FRAGMENT OF MYCOBACTERIUMBOVIS RPSL GENE ASSOCIATED WITH STREPTOMYCIN RESISTANCE
Introduction. For Mycobacterium tuberculosis complex (MBTC), 8 genes have been identified, mutations in which are linked to streptomycin resistance and belong to 1, 3 and 5 confidence group. RpsL gene encoding S12 ribosomal protein is one of the genes associated with streptomycin resistance.
The goal of the work was the determination of the differences in the spatial organization of the rpsL gene fragments (c.-165T>C) linking to streptomycin resistance.
Materialsandmethods. Fragment with length of 21 nucleotides containing SNP was cut out from the 5'-UTR of rpsL gene of the M. bovis. The point mutation (c.-165T>C) is located inside this fragment (position 11) at position -165 to the start codon. 3D models of oligomers were generated by artificial intelligence AlphaFold 3. Mfold software was applied for confirmation of the secondary structure and determination of thermodynamic parameters of oligomers.
Results of research and discussion. From 3D models with atomic resolution, it was determined that oligomer with the mutation (c.-165T>C) is stabilized by two hydrogen bonds and stacking interaction. In contrast to the oligomer with the mutation, the oligomer without one is characterized by the absence of hydrogen bonds. Free energy ΔG of the secondary structure was calculated for both variants of the 5'-UTR fragment of the rpsL gene. Oligomer with the mutation forms a hairpin structure with a 4 nucleotide loop and a 3 bp hairpin stem, in which the nucleotide C11 is located, and the free energy ΔG of such a structure is -1.02 kcal/mol.
Conclusions and prospects for further research. The spatial organization in the region of the point mutation c.-165T>Clinking with to streptomycin resistance in the 21-nucleotide fragment of the 5'-UTR of the M. bovis rpsL gene has been determined.
By 3D modeling with atomic resolution, it was established that the structures in the mutation site with the wobble nucleotide of the 5'-UTR of the rpsL gene differ in the network of hydrogen bonds.
The use of AlphaFold 3 technology, which predicts the 3D structure of proteins and oligonucleotides with an accuracy comparable to experimental methods, looks very promising for determining three-dimensional structure with atomic resolution of SNPs sites linking to resistance/susceptibility to a number of antimycobacterial drugs.
Keywords: bioinformatics, AlphaFold 3, 3D model, mycobacteria tuberculosis, Mycobacteriumbovis, streptomycin, point mutation, drug resistance.
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