Genome editing of industrial microorganisms

Michael O. Agaphonov
Head of the Group
Ph.D. (Biology)
INBI, build. 2, room 304
Телефон +7 (495) 954-40-97 ext. 454

Directions of research

The major directions of research of the group involve the study of functioning of secretory organelles using the yeasts Ogataea polymorpha and O. parapolymorpha as model organisms. One of the projects involves study of the role of the secretory-pathway protein glycosylation in the regulation of cell physiology. Many biological processes depend on protein glycosylation in the secretory pathway, such as protein folding in the endoplasmic reticulum, maintenance of cell wall integrity, stability of a number of plasma membrane proteins, which are related to transport of different ions and nutrients, as well as those involved in sensing of the cell wall integrity or environmental conditions. In contrast to the attachment of glycoside chains to polypeptides in the endoplasmic reticulum, which has been extensively studied, the role of sugar moieties attached in the Golgi apparatus remains insufficiently studied. This is why the study of manifestations of Golgi glycosylation defects is one of the major research directions of the group.

Beside this, the group is involved development of different approaches for the creation of O. polymorpha and O. parapolymorpha strains producing recombinant proteins for industrial applications.


Selected publications

  1. Karginov AV, Alexandrov AI, Kushnirov VV, Agaphonov MO. Perturbations in the Heme and Siroheme Biosynthesis Pathways Causing Accumulation of Fluorescent Free Base Porphyrins and Auxotrophy in Ogataea Yeasts. J Fungi (Basel). 2021 7:884. doi: 10.3390/jof7100884.
  2. Dergalev AA, Urakov VN, Agaphonov MO, Alexandrov AI, Kushnirov VV. Dangerous Stops: Nonsense Mutations Can Dramatically Increase Frequency of Prion Conversion. Int J Mol Sci. 2021 22:1542. doi: 10.3390/ijms22041542.
  3. Bidiuk VA, Agaphonov MO, Alexandrov AI. Modulation of green to red photoconversion of GFP during fluorescent microscopy by carbon source and oxygen availability. Yeast. 2021 38:295-301. doi: 10.1002/yea.3543.
  4. Alexandrov AI, Grosfeld EV, Dergalev AA, Kushnirov VV, Chuprov-Netochin RN, Tyurin-Kuzmin PA, Kireev II, Ter-Avanesyan MD, Leonov SV, Agaphonov MO. Analysis of novel hyperosmotic shock response suggests ‘beads in liquid’ cytosol structure. Biol Open. 2019 8:bio044529. doi: 10.1242/bio.044529.
  5. Karginov AV, Fokina AV, Kang HA, Kalebina TS, Sabirzyanova TA, Ter-Avanesyan MD, Agaphonov MO. Dissection of differential vanadate sensitivity in two Ogataea species links protein glycosylation and phosphate transport regulation. Sci Rep. 2018, 8:16428. doi: 10.1038/s41598-018-34888-5.
  6. Agaphonov MO. Improvement of a yeast self-excising integrative vector by prevention of expression leakage of the intronated Cre recombinase gene during plasmid maintenance in Escherichia coli. FEMS Microbiol Lett. 2017 364(22).doi: 10.1093/femsle/fnx222.
  7. Karginov A, Agaphonov M. A simple enrichment procedure improves detection of membrane proteins by immunoblotting. Biotechniques. 2016, 61:260-261.
  8. Fokina AV, Chechenova MB, Karginov AV, Ter-Avanesyan MD, Agaphonov MO. Genetic Evidence for the Role of the Vacuole in Supplying Secretory Organelles with Ca2+ in Hansenula polymorpha. PLoS One. 2015, 10:e0145915. doi:10.1371/journal.pone.0145915.
  9. Moon HY, Cheon SA, Kim H, Agaphonov MO, Kwon O, Oh DB, Kim JY, Kang HA. Hansenula polymorpha Hac1p Is Critical to Protein N-Glycosylation Activity Modulation, as Revealed by Functional and Transcriptomic Analyses. Appl Environ Microbiol. 2015, 81:6982-93. doi: 10.1128/AEM.01440-15.
  10. Kim H, Thak EJ, Lee DJ, Agaphonov MO, Kang HA. Hansenula polymorpha Pmt4p Plays Critical Roles in O-Mannosylation of Surface Membrane Proteins and Participates in Heteromeric Complex Formation. PLoS One. 2015, 10:e0129914. doi: 10.1371/journal.pone.0129914.
  11. Agaphonov M, Alexandrov A. Self-excising integrative yeast plasmid vectors containing an intronated recombinase gene. FEMS Yeast Res. 2014, 14:1048-1054. doi: 10.1111/1567-1364.12197.
  12. Kim H, Moon HY, Lee DJ, Cheon SA, Yoo SJ, Park JN, Agaphonov MO, Oh DB, Kwon O, Kang HA. Functional and molecular characterization of novel Hansenula polymorpha genes, HpPMT5 and HpPMT6, encoding protein O-mannosyltransferases. Fungal Genet Biol. 2013, 58-59:10-24. doi: 10.1016/j.fgb.2013.08.003.
  13. Fokina AV, Sokolov SS, Kang HA, Kalebina TS, Ter-Avanesyan MD, Agaphonov MO. Inactivation of Pmc1 vacuolar Ca2+ ATPase causes G2 cell cycle delay in Hansenula polymorpha. Cell Cycle. 2012, 11:778-784. doi:10.4161/cc.11.4.19220.
  14. Agaphonov M, Romanova N, Choi ES, Ter-Avanesyan M. A novel kanamycin/G418 resistance marker for direct selection of transformants in Escherichia coli and different yeast species. Yeast. 2010, 27:189-195. doi: 10.1002/yea.1741.
  15. Agaphonov MO, Plotnikova TA, Fokina AV, Romanova NV, Packeiser AN, Kang HA, Ter-Avanesyan MD. Inactivation of the Hansenula polymorpha PMR1 gene affects cell viability and functioning of the secretory pathway. FEMS Yeast Res. 2007 7:1145-1152.
  16. Agaphonov MO, Sokolov SS, Romanova NV, Sohn JH, Kim SY, Kalebina TS, Choi ES, Ter-Avanesyan MD. Mutation of the protein-O-mannosyltransferase enhances secretion of the human urokinase-type plasminogen activator in Hansenula polymorpha. Yeast. 2005, 22:1037-1047.
  17. Agaphonov M, Romanova N, Sokolov S, Iline A, Kalebina T, Gellissen G, Ter-Avanesyan M. Defect of vacuolar protein sorting stimulates proteolytic processing of human urokinase-type plasminogen activator in the yeast Hansenula polymorpha. FEMS Yeast Res. 2005, 5:1029-1035.
  18. Chechenova MB, Romanova NV, Deev AV, Packeiser AN, Smirnov VN, Agaphonov MO, Ter-Avanesyan MD. C-terminal truncation of alpha-COP affects functioning of secretory organelles and calcium homeostasis in Hansenula polymorpha. Eukaryot Cell. 2004, 3:52-60.
  19. Agaphonov MO, Romanova NV, Trushkina PM, Smirnov VN, Ter-Avanesyan MD. Aggregation and retention of human urokinase type plasminogen activator in the yeast endoplasmic reticulum. BMC Mol Biol. 2002, 3:15.
  20. Kang, H.A., Sohn, J.H., Agaphonov, M.O., Choi, E.S., M.D., T.-A., and Rhee, S.K. 2002. Development of expression systems for the production of recombinant proteins in Hansenula polymorpha DL-1, pp. 124–146. In Gellissen, G. (ed.), Hansenula polymorpha-Biology and Applications. Wiley-VCH, Weinheim, Germany.
  21. Kim MW, Agaphonov MO, Kim JY, Rhee SK, Kang HA. Sequencing and functional analysis of the Hansenula polymorpha genomic fragment containing the YPT1 and PMI40 genes. Yeast. 2002, 19:863-871.
  22. Agaphonov MO, Packeiser AN, Chechenova MB, Choi ES, Ter-Avanesyan MD. Mutation of the homologue of GDP-mannose pyrophosphorylase alters cell wall structure, protein glycosylation and secretion in Hansenula polymorpha. Yeast. 2001, 18:391-402.
  23. Agaphonov MO, Trushkina PM, Sohn JH, Choi ES, Rhee SK, Ter-Avanesyan MD. Vectors for rapid selection of integrants with different plasmid copy numbers in the yeast Hansenula polymorpha DL1. Yeast. 1999, 15:541-551.
  24. Bogdanova AI, Kustikova OS, Agaphonov MO, Ter-Avanesyan MD. Sequences of Saccharomyces cerevisiae 2 microns DNA improving plasmid partitioning in Hansenula polymorpha. Yeast. 1998, 14:1-9.
  25. Sohn JH, Choi ES, Kim CH, Agaphonov MO, Ter-Avanesyan MD, Rhee JS, Rhee SK. A novel autonomously replicating sequence (ARS) for multiple integration in the yeast Hansenula polymorpha DL-1. J Bacteriol. 1996, 178:4420-4428.
  26. Agaphonov MO, Beburov MYu, Ter-Avanesyan MD, Smirnov VN. A disruption-replacement approach for the targeted integration of foreign genes in Hansenula polymorpha. Yeast. 1995, 11:1241-1247.
  27. Bogdanova AI, Agaphonov MO, Ter-Avanesyan MD. Plasmid reorganization during integrative transformation in Hansenula polymorpha. Yeast. 1995, 11:343-353.
  28. Agaphonov MO, Poznyakovski AI, Bogdanova AI, Ter-Avanesyan MD. Isolation and characterization of the LEU2 gene of Hansenula polymorpha. Yeast. 1994, 10:509-513.