EVOLUTIONARY SIGNIFICANCE OF NON-SYNONYMOUS SUBSTITUTIONS FOR MYCOBACTERIUM TUBERCULOSIS OF URAL GENOTYPE

DOI: https://doi.org/None

V.V. Sin’kov (1,2), O.B. Ogarkov (1,3), I.V. Mokrousov (4), S.N. Zhdanova (1,5) 1 -Scientific Centre for Family Health and Human Reproduction Problems, Timiryazeva str., 16, Irkutsk, 664003, Russian Federation; 2 -Irkutsk Regional Clinical Consulting-diagnostic center, Baykalskayastr, 109, Irkutsk, 664047, Russian Federation; 3 -Irkutsk State Medical Academy of Continuing Education, Yubileynymikroraion str., 100k4, Irkutsk, 664049, Russian Federation; 4 -Saint Petersburg Pasteur Institute, Mira str., 14, Saint Petersburg, 197101, Russian Federation; 5 -Irkutsk State University, Karla Marksa str, 1, Irkutsk, 664003, Russian Federation

Introduction. Russian population of Mycobacterium tuberculosis includes both highly virulent and less virulent strains; the Ural genotype makes an example of the latters. The aim of study was investigation of the most significant synonymous and non-synonymous nucleotide substitutions in 110 genomes of M. tuberculosis, Ural genotype, available in GenBank and obtained through GMTV database. Methods. The VCF files were proceeded with our own scripts written in Ruby and Bash programming language for single nucleotide polymorphism (SNP) annotation (ene name, function, COG, PFAM and KEGG groups, type of change). A comparative phylogenetic analysis of the polymorphic characters was performed with MEGA software.Results. A total of 5183 synonymous and non-synonymous SNP were found, but only 8 unique nonsynonymous SNPs, specific of the Ural genotype were identified. These substitutions were in the following genes: Rv1901; Rv1966; Rv1967; Rv2345; Rv2485c; Rv2933 and Rv3498c. Both synonymous and non-synonymous substitutions were used for phylogenetic reconstruction of the evolution of the Ural genotype. Phylogenetic tree of genotype Ural strains was subdivided into two clusters with the level of bootstrap support of more than 95%: (i) a small and heterogeneous «ancient» group (Ural-a [a=ancient]) and (ii) a large and homogeneous «young/modern» (Ural-m [m=modern]) group. Ural-m strains appear to be more successful epidemic strains since they form the most phylogenetically compact group. Furthermore, Ural-m strains are carriers of multidrug resistance (MDR) mutations significantly more frequently than Ural-a strains (χ2=5,9; p=0,01). The analysis of 8 amino acid substitutions unique to the Ural genotype suggests that the most of mutations occurred in their progenitor genome, were important for lipid metabolism. Probably those events could ultimately lead to a decrease of virulence of the Ural genotype. Conclusion. Separate analysis of mutations that are unique to the Ural-a and Ural-m groups, suggests that natural selection occurred in Ural-m group in direction of increasing the resistance to antibiotics due to mutations in regulatory genes. Also in both groups, specific mutations in the regulatory genes could lead to the restoration of virulence as compared to a hypothetical founder.
Keywords: 
Mycobacterium. tuberculosis, Ural genotype, SNP, virulence, persisters
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