Biopolym. Cell. 2026; 42(Special Issue):36.
Computational biology, bioinformatics, and AI-driven research
Putative G-quadruplexes in genes encoding hydrogen sulfide biosynthesis enzymes of Mycobacterium bovis
1Limanskaya O. Yu., 2Balak O. K., 1Biloivan O. V., 3Limanskii A. P.
  1. NSC “Institute of Experimental and Clinical Veterinary Medicine�
    83, Hryhoriia Skovorody Str., Kharkiv, Ukraine, 61023
  2. Kharkiv National Medical University
    4, Nauky Ave., Kharkiv, Ukraine, 61022
  3. LLC “Institute of Physiological Active Compounds�
    58, Nauky Ave., Kharkiv, Ukraine, 61072

Abstract

Background. Bacteria synthesize H2S by enzymes of defense system orthologous to mammalian cystathionine-γ-lyase (CSE), cystathionine-β-synthase (CBS) or 3-mercaptopyruvate sulfurtransferase (3MST). Genetic disruption of H2S biogenesis increases bacterial sensitivity to drugs, and enzymes of defense system may be targets for H2S biosynthesis inhibition. The aim of the present study was the determining putative G-quadruplexes (G4s) formed by two G-tetrades in promoters and genes of M. bovis defense system encoding enzymes of H2S biosynthesis. Methods. QGRS Mapper software was used for search of G4s motifs and determination of their G-scores in DNA sense and antisense strands of M. bovis AF2122/97 reference strain [1]. 3D models G4s were predicted with AlphaFold 3 AI (AF3) [2]. Results. A search of G4s in promoters and genes encoding H2S biosynthesis enzymes of the reference strain M. bovis AF2122/97 with subsequent their estimation and confirmation by 3D modeling was performed. Promoter regions and genes (i) cbs encoding CBS, (ii) cds1 (Rv3684) encoding cysteine desulfhydrase, (iii) metB (Rv1079) encoding cystathionine gamma- synthase, (iv) sseA encoding 3MST were analyzed for the G4s presence. In the cbs gene, four G4s with length of 11—14 nucleotides (nt) were found and characterized by a G-score from 19 to 21. Their 3D models were confirmed by AF3 with a parameter indicating the quality of the prediction: from 70> pLDDT>50 to pLDDT>90. In the cds1 (Rv3684) gene, two G4s with length of 17 nt (G-score = 18, 90>pLDDT>70) and 11 nt (G-score = 21, pLDDT>90) were found. In the promoter of the metB gene (Rv1079), G4 with length of 14 nt was found (G-score = 19, 90>pLDDT> 70 — pLDDT>90). In the promoter of the sseA gene, two G4s (15 nt, G-score = 20, pLDDT>90) were identified. Conclusions. Putative G-quadruplexes of two tetrads were identified in the genes and promoters of genes encoding enzymes of the M. bovis defense system of hydrogen sulfide synthesis. Their structures were confirmed by AF3 with high reliability (pLDDT>90). Determined G4s in the gene promoter regions may be targets for the H2S synthesis inhibition. Grants. 35.00.03.02 from NAAS of Ukraine.
Keywords: G-quadruplex, hydrogen sulfide, Mycobacterium bovis, AlphaFold 3