2022 / 03

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DOI: 10.24075/brsmu.2022.024

ORIGINAL RESEARCH

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
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  1. Global Tuberculosis Report 2021 [cited 2022 Apr 7]. Available from: https://www.who.int/teams/global-tuberculosis-programme/tbreports/global-tuberculosis-report-2021.
  2. Kadura S, King N, Nakhoul M, Zhu H, Theron G, Köser CU, et al. Systematic review of mutations associated with resistance to the new and repurposed Mycobacterium tuberculosis drugs bedaquiline, clofazimine, linezolid, delamanid and pretomanid. Journal of Antimicrobial Chemotherapy. 2020; 75 (8): 2031.
  3. Spiegel J, Adhikari S, Balasubramanian S. The structure and function of DNA G-quadruplexes. Trends Chem. 2020; 2 (2): 123–36.
  4. Masai H, Tanaka T. G-quadruplex DNA and RNA: Their roles in regulation of DNA replication and other biological functions. Biochemical and Biophysical Research Communications. 2020; 531 (1): 25–38.
  5. Bartas M, Cutová M, Brázda V, Kaura P, Št’Astný J, Kolomazník J, et al. The presence and localization of G-quadruplex forming sequences in the domain of bacteria. Molecules. 2019; 24 (9).
  6. Yadav P, Kim N, Kumari M, Verma S, Sharma TK, Yadav V, et al. G-quadruplex structures in bacteria: biological relevance and potential as an antimicrobial target. Journal of Bacteriology. 2021; 203 (13).
  7. Perrone R, Lavezzo E, Riello E, Manganelli R, Palù G, Toppo S, et al. Mapping and characterization of G-quadruplexes in Mycobacterium tuberculosis gene promoter regions. Sci Rep. 2017; 7 (1).
  8. Mishra SK, Shankar U, Jain N, Sikri K, Tyagi JS, Sharma TK, et al. Characterization of G-quadruplex motifs in espB, espK, and cyp51 genes of mycobacterium tuberculosis aspotential drug targets. Mol Ther Nucleic Acids. 2019; 16: 698–706.
  9. Shitikov E, Bespiatykh D, Malakhova M, Bespyatykh J, Bodoev I, Vedekhina T, et al. Genome-wide tanscriptional response of mycobacterium smegmatis MC 2 155 to G-quadruplex ligands BRACO-19 and TMPyP4. Front Microbiol. 2022; 13.
  10. Logsdon MM, Aldridge BB. Stable regulation of cell cycle events in mycobacteria: insights from Inherently heterogeneous bacterial populations. Front Microbiol. 2018; 9 (MAR).
  11. Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015; 12 (4): 357–60.
  12. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009; 25 (16): 2078–9.
  13. Okonechnikov K, Conesa A, García-Alcalde F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics. 2016; 32 (2): 292–4.
  14. Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016; 32 (19): 3047–8.
  15. Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014; 30 (7): 923–30.
  16. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010; 26 (1): 139–40.
  17. Smid M, Coebergh van den Braak RRJ, van de Werken HJG, van Riet J, van Galen A, de Weerd V, et al. Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons. BMC Bioinformatics. 2018; 19 (1).
  18. Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012; 16 (5): 284–7.
  19. W Yang, Y Gao. Translesion and repair DNA polymerases: diverse structure and mechanism. Annu Rev Biochem. 2018; 87: 239–61.
  20. Mdluli K, Ma Z. Mycobacterium tuberculosis DNA gyrase as a target for drug discovery. Infect Disord Drug Targets. 2007; 7 (2): 159–68.
  21. Yang M, Aamodt RM, Dalhus B, Balasingham S, Helle I, Andersen P, et al. The ada operon of Mycobacterium tuberculosis encodes two DNA methyltransferases for inducible repair of DNA alkylation damage. DNA Repair. 2011; 10 (6): 595–602.
  22. Namouchi A, Gómez-Muñoz M, Frye SA, Moen LV, Rognes T, Tønjum T, et al. The Mycobacterium tuberculosis transcriptional landscape under genotoxic stress. BMC Genomics. 2016; 17 (1): 1–13.
  23. Wu X, Maizels N. Substrate-specific inhibition of RecQ helicase. Nucleic Acids Research. 2001; 29 (8): 1765–71.
  24. Robinson J, Raguseo F, Nuccio SP, Liano D, di Antonio M. DNA G-quadruplex structures: more than simple roadblocks to transcription? Nucleic Acids Res. 2021; 49 (15): 8419–31.
  25. Cebrián R, Belmonte-Reche E, Pirota V, de Jong A, Morales JC, Freccero M, et al. G-quadruplex DNA as a target in pathogenic bacteria: efficacy of an extended naphthalene diimide ligand and Its mode of action. Journal of Medicinal Chemistry. 2021.
  26. Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, et al. RNA G-quadruplex structures mediate gene regulation in bacteria. mBio. 2020; 11 (1).