Transcriptional profiling of Mycobacterium smegmatis exposed to subinhibitory concentrations of G4-stabilizing ligands

Zaychikova MV, Bespiatykh DA, Malakhova MV, Bodoev IN, Vedekhina TS, Veselovsky VA, Klimina KM, Varizhuk AM, Shitikov EA
About authors

Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia

Correspondence should be addressed: Egor A. Shitikov
Malaya Pirogovskaya, 1a, Moscow, 119435, Russia; ur.liam@vokitihse

About paper

Funding: the study was funded by the Russian Science Foundation, project number 19-75-10109

Author contribution: Zaychikova MV — literature analysis, data analysis and interpretation, manuscript drafting; Bespiatykh DA — literature analysis, data analysis, manuscript drafting; Malakhova MV — research planning and implementation; Bodoev IN — literature analysis, data analysis, manuscript drafting; Vedekhina TS — research implementation, data interpretation; Veselovsky VA — research implementation, data analysis; Klimina KM — research implementation, data analysis and interpretation; Varizhuk AM — research planning and implementation, data interpretation; Shitikov EA — research planning, literature analysis, data analysis, manuscript drafting.

Received: 2022-04-08 Accepted: 2022-04-30 Published online: 2022-05-15

The spread of Mycobacterium tuberculosis drug resistance accentuates the demand for anti-tuberculosis drugs with a fundamentally new mechanism of action without conferring cross-resistance. G-quadruplexes (G4, non-canonical DNA structures) are plausible new drug targets. Although G4-stabilizing ligands have been shown to inhibit mycobacterial growth, the exact mechanism of their action is uncertain. The aim of this study was to assess a possible correlation between putative G4 elements in a model mycobacterial strain M. smegmatis MC2155 and transcriptomic changes under the action of subinhibitory concentrations of G4 ligands BRACO-19 and TMPyP4. We also planned to compare the results with corresponding data previously obtained by us using higher, inhibitory concentrations of these ligands. For BRACO-19, we identified 589 (316↑; 273↓) and 865 (555↑; 310↓) differentially expressed genes at 5 µМ and 10 µМ, respectively. For TMPyP4, we observed the opposite trend, the number of differentially expressed genes decreased at higher concentration of the ligand: 754 (337↑; 417↓) and 702 (359↑; 343↓) for 2 µМ and 4 µМ, respectively. Statistical analysis revealed no correlation between ligand-induced transcriptomic changes and genomic localization of the putative quadruplex-forming sequences. At the same time, the data indicate certain functional specificity of the ligand-mediated transcriptomic effects, with TMPyP4 significantly affecting expression levels of transcription factors and arginine biosynthesis genes and BRACO-19 significantly affecting expression levels of iron metabolism and replication and reparation system genes.

Keywords: Mycobacterium tuberculosis, Mycobacterium smegmatis, G-quadruplexes, transcriptomic analysis, BRACO-19, TMPyP4, antimicrobial therapy