Group of Microbial Genoms Editing

Anna V. Goncharenko
Head of the Group
Ph.D. (Biology)
INBI, build.3, room. 10
Telefone+7 (495) 660-34-30 ext. 117
E-Mail pylaevanna@gmail.com

Key words:
genome editing, CRISPR / Cas systems, homologous recombination, NHEJ DNA repair, mycobacteria, latent tuberculosis, persistence, toxin-antitoxin loci, BCG, live recombinant vaccines.

Research areas:

  • Applying CRISPR / Cas for editing mycobacterial genomes
  • CRISPR / Cas interference
  • Mycobacterium toxin-anti-toxin systems as regulators of persistence and transition of mycobacteria to the state of metabolic dormancy
  • Creation of recombinant BCG strains with improved protective properties

Basic research methods:
Molecular cloning, generation of gene knockouts by allelic exchange, CRISPR editing of bacterial genomes, creation of strains overexpressing target genes, and constructs for the heterologous expression of recombinant proteins, site-directed mutagenesis, Northern and Western blotting, Primer extension analysis, quantitative real-time PCR, microbiological methods for the study of recombinant bacterial strains.

Origins:
The group was created in March 2019 during the reorganization of the laboratory of Biochemistry of Stresses in Microorganisms. Now it is the part of the Department of Medical Microbiology in Research Center of Biotechnology RAS.

 

Relevant publications related to the group research directions:

  1. Mikhail Zamakhaev, Julia Bespyatykh, Anna Goncharenko, Mikhail Shumkov. The Benefits of Toxicity: M. smegmatis VapBC TA Module Is Induced by Tetracycline Exposure and Promotes Survival. Microorganisms. 2023; 11(12): 2863. DOI: 10.3390/microorganisms11122863
  2. Shchulkin AV, Erokhina PD, Goncharenko AV et al. Ethylmethylhydroxypyridine Succinate Is an Inhibitor but Not a Substrate of ABCB1 and SLCO1B1. Pharmaceuticals. 2023; 16(11): 1529. DOI: 10.3390/ph16111529
  3. Jamgochian HH, Zamakhaev MV, Sluchanko NN, Goncharenko AV, Shumkov MS. Development of Heterologous Expression System and Optimization of the Method of Cholera Toxin β-Subunit Production in E. coli. Biochemistry (Mosc). 2023 Sep;88(9):1304-1317. doi: 10.1134/S0006297923090109
  4. Nadolinskaia N.I., Kotliarova M.S., Goncharenko A.V. Fighting Tuberculosis: In Search of a BCG Replacement. Microorganisms. 2023; 11(1): 51. DOI: 10.3390/microorganisms11010051
  5. Artemiy O. Kurishev, Dmitry S. Karpov, Nonna I. Nadolinskaia, Anna V. Goncharenko et al. CRISPR/Cas-based approaches to study schizophrenia and other neurodevelopmental disorders. International Journal of Molecular Sciences. 2023; 24(1): 241. DOI: 10.3390/ijms24010241
  6. Mikhail Zamakhaev, Artem Grigorov, Julia Bespyatykh, Anna Goncharenko, Mikhail Shumkov. VapC toxin switches M. smegmatis cells into dormancy through 23S rRNA cleavage. Archives of Microbiology. 2023; Vol.205: 28. DOI: 10.1007/s00203-022-03363-1
  7. Nadolinskaia NI, Zamakhaev MV, Shumkov MS, Armianinova DK, Karpov DS, Goncharenko AV. CRISPR Interference of Adenylate Cyclases from Mycobacterium tuberculosis. Appl Biochem Microbiol. 2021;57(4):421-425. doi: 10.1134/S0003683821040128
  8. Karpov D. S., Goncharenko A. V., Usachev E. V., Vasina D. V., Divisenko E. V., Chalenko Y. M., Pochtovyi A. A., Ovchinnikov R. S., Makarov V. V., Yudin S. M., Tkachuk A. P., Gushchin V. A. A Strategy for the Rapid Development of a Safe Vibrio cholerae Candidate Vaccine Strain // International journal of molecular sciences. 2021; 22(21): 11657. DOI: 10.3390/ijms222111657
  9. Karpov DS, Domashin AI, Kotlov MI, Osipova PG, Kiseleva SV, Seregina TA, Goncharenko AV, Mironov AS, Karpov VL, Poddubko SV. [Biotechnological Potential of the Bacillus subtilis 20 Strain]. Mol Biol (Mosk). 2020 Jan-Feb;54(1):137-145. Russian. doi: 10.31857/S0026898420010085
  10. Nadolinskaia, N.I., Karpov, D.S. & Goncharenko, A.V. Vaccines Against Tuberculosis: Problems and Prospects (Review). Appl Biochem Microbiol 56, 497–504 (2020). https://doi.org/10.1134/S0003683820050129
  11. Elena A. Oleinik, Anna V. Goncharenko. The Relationship between Mutations in Gene-Specific Domains of Salivary Fibronectin (cFn) and Dynamin-2 (Dynm-2) and the Development of Porphyromonas gingivalis-Initiated Periodontitis. Journal of Molecular Pathology. 2022; 3(3): 182-189. DOI: 10.3390/jmp3030015
  12. Zamakhaev M., Tsyganov I., Nesterova L., Akhova A., Grigorov A., Bespyatykh J., Azhikina T., Tkachenko A., Shumkov M. Mycolicibacterium smegmatis possesses operational agmatinase but contains no detectable polyamines // International Journal of Mycobacteriology. 2020; 9(2): 138-143. DOI: 10.4103/ijmy.ijmy_48_20
  13. Shleeva, M.O., Kondratieva, T.K., Goncharenko, A.V. et al. cAMP-Dependent Transcription Factor in Mycobacterium tuberculosis Coded by the Rv3676 Gene as a Possible Target for the Development of Antituberculosis Drugs. Appl Biochem Microbiol 55, 380–385 (2019). https://doi.org/10.1134/S0003683819030128
  14. Margarita Shleeva, Tatyana Kondratieva, Galina Demina, Elvira Rubakova, Anna Goncharenko, Alexander Apt, Arseny Kaprelyants. Overexpression of Adenylyl Cyclase Encoded by the Mycobacterium tuberculosis Rv2212 Gene Confers Improved Fitness, Accelerated Recovery from Dormancy and Enhanced Virulence in Mice, FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY, 2017, v 7
  15. Alexander G. Tkachenko, Natalya M. Kashevarova, Elena A. Tyuleneva, Mikhail S. Shumkov; Stationary-phase genes upregulated by polyamines are responsible for the formation of Escherichia coli persister cells tolerant to netilmicin. // FEMS Microbiol Lett, 2017
  16. Toxin-antitoxin vapBC locus participates in formation of the dormant state in Mycobacterium smegmatis. Demidenok OI, Kaprelyants AS, Goncharenko AV. FEMS Microbiol Lett. 2014 Jan 13
  17. Cyclic amp-dependent resuscitation of dormant mycobacteria by exogenous free Fatty acids. Shleeva M, Goncharenko A, Kudykina Y, Young D, Young M, Kaprelyants A. PLoS One. 2013 Dec 23;8(12)
  18. Anuchin AM, Goncharenko AV, Demina GR, Mulyukin AL, Ostrovsky DN, Kaprelyants AS. The role of histone-like protein, Hlp, in Mycobacterium smegmatis dormancy. FEMS Microbiol Lett. 2010 Jul;308(2):101-7
  19. Koltunov V, Greenblatt CL, Goncharenko AV, Demina GR, Klein BY, Young M, Kaprelyants AS. Structural changes and cellular localization of resuscitation-promoting factor in environmental isolates of Micrococcus luteus. Microb Ecol. 2010 Feb;59(2):296-310