Department of molecular biology of microorganisms

ravin_2015_1 Nikolay V. Ravin
Professor, Dr.Sci. (Biology)
Head of Department
Head of Laboratory of Molecular Cloning
Deputy Dorector
INB, room 403
Телефон  +7 (499) 783-32-64
E-Mail  nravin@biengi.ac.ru
Марданов_3 Andrey V. Mardanov
Dr.Sci. (Biology), Professor
Head of Group of Microbial Genomics
INB, room 405
Телефон  +7 (499) 783-32-64
E-Mail  mardanov@biengi.ac.ru

Main research areas:

  • Studies of extremophilic and biotechnologically-important microorganisms using genomics and other “omics” techniques
  • Metagenomic analysis of microbial communities
  • Identification and characterization of new enzymes for biotechnology and biomedicine
  • Analysis of the structure and evolution of plant genomes
  • Development of recombinant vaccines using nanotechnological approaches
  • Expression of vaccine proteins in plants (“plants as biofactories”)

Main achievements:

  • The first experimentally confirmed model of replication of linear DNA with covalently closed telomeres in prokaryotes (on temperate bacteriophage N15 as a model system).
  • Complete nucleotide sequences of genome of more than 20 extremophilic microorganisms, including ten hyperthermophilic archaea, were determined. Genome data allowed characterizing the metabolic pathways of these microorganisms, their evolutionary relationships and ecological roles.
  • Several enzymes from extremophiles were functionally characterized (DNA ligases, proteases, carbohydrate-active enzymes, lipases transaminases etc)
  • Microbial communities of several hot springs of Kamchatka peninsula with different pH and temperatures were characterized by pyrosequencing of 16S rRNA genes.
  • Microbial communities associated with methane hydrate bearing sediments of the Lake Baikal were characterized by metagenomics approach. The data obtained are consistent with biological origin of hydrates.
  • Metagenomic analysis of deep subsurface aquifers of Western Siberia revealed a number of novel uncultured bacterial lineages.
  • The lab participated in successfully completed international potato genome sequencing project. We performed sequencing of BAC library of the chromosome XII.
  • Complete genome and transcriptome of thermotolerant methylotrophic yeasts Hansenula polymorpha DL1 was sequenced. The results facilitated development of new planforms for expression of recombinant proteins in these yeasts.
  • New approaches for high-level transient expression of recombinant proteins in plants using self-replicating viral vectors were developed.
  • A candidate recombinant influenza vaccine based on the M2e peptide exposed on the surface of virus-0like particles was developed. The vaccine successfully passed preclinical trials in Research institute of Influenza.

 

Selected publications:

  1. Ravin N.V., Ravin V.K. Use of a linear multicopy vector based on the mini-replicon of temperate coliphage N15 for cloning DNA with abnormal secondary structures. — Nucleic Acids Research, 1999, 27, 13
  2. Ravin N., Svarchevsky, A., Deho G. The antiimunity system of phage-plasmid N15: identification of the antirepressor gene and its control by a small processed RNA. — Molecular Microbiology, 1999, 34: 980-994
  3. Ravin V., Ravin N., Casjens S., Ford M., Hatfull G., & Hendrix R. Genomic sequence and analysis of the atypical bacteriophage N15. — J. Mol. Biol., 2000, 299, 53-73
  4. Ravin, N.V., Kuprianov, V.V., Gilcrease, E.B., & Casjens, S.R. Bidirectional replication from an internal ori site of the linear N15 plasmid prophage. — Nucleic Acids Research, 2003, 31, 6552-6560
  5. Mardanov A.V., Ravin N.V., Svetlitchnyi V.A., Beletsky A.V., Miroshnichenko M.L., Bonch-Osmolovskaya E.A., Skryabin K.G. Metabolic versatility and indigenous origin of the archaeon Thermococcus sibiricus, isolated from a Siberian oil reservoir, as revealed by genome analysis. — Appl. Environ. Microbiol., 2009, 75,  4580-4588
  6. Godiska R., Mead D., Dhodda V., Wu C., Hochstein R., Karsi A., Usdin K., Entezam A., Ravin N. Linear plasmid vector for cloning of repetitive or unstable sequences in Escherichia coli. — Nucleic Acids Res, 2010, 38(6), e88
  7. Potato Genome Sequencing Consortium, Xu X., Pan S., Cheng S., Zhang B., Mu D., Ni P., Zhang G., Yang S., Li R., Wang J., Orjeda G., Guzman F., Torres M., Lozano R., Ponce O., Martinez D., De la Cruz G., Chakrabarti S.K., Patil V.U., Skryabin K.G., Kuznetsov B.B., Ravin N.V., Kolganova T.V., Beletsky A.V., Mardanov A.V., Di Genova A., Bolser D.M., Martin D.M., Li G., Yang Y., Kuang H., Hu Q., Xiong X., Bishop G.J., Sagredo B., Mejía N., Zagorski W., Gromadka R., Gawor J., Szczesny P., Huang S., Zhang Z., Liang C., He J., Li Y., He Y., Xu J., Zhang Y., Xie B., Du Y., Qu D., Bonierbale M., Ghislain M., Herrera M.del R., Giuliano G., Pietrella M., Perrotta G., Facella P., O’Brien K., Feingold S.E., Barreiro L.E., Massa G.A., Diambra L., Whitty B.R., Vaillancourt B., Lin H., Massa A.N., Geoffroy M., Lundback S., Della Penna D., Buell C.R., Sharma S.K., Marshall D.F., Waugh R., Bryan G.J., Destefanis M., Nagy I., Milbourne D., Thomson S.J., Fiers M., Jacobs J.M., Nielsen K.L., Sønderkær M., Iovene M., Torres G.A., Jiang J., Veilleux R.E., Bachem C.W., de Boer J., Borm T., Kloosterman B., van Eck H., Datema E., Hekkert B.L., Goverse A., van Ham R.C., Visser R.G. Genome sequence and analysis of the tuber crop potato. — Nature, 2011, 475(7355), 189-195
  8. Kadnikov VV, Mardanov AV, Beletsky AV, Shubenkova OV, Pogodaeva TV, Zemskaya TI, Ravin NV, Skryabin KG. Microbial community structure in methane hydrate-bearing sediments of freshwater Lake Baikal. — FEMS Microbiol Ecol. 72012, 9, 348-358
  9. Podosokorskaya O.A., Kadnikov V.V., Gavrilov S.N., Mardanov A.V., Merkel A.Y., Karnachuk O.V., Ravin N.V., Bonch-Osmolovskaya E.A., Kublanov I.V. Characterization of Melioribacter roseus gen. nov., sp. nov., a novel facultatively anaerobic thermophilic cellulolytic bacterium from the class Ignavibacteria, and a proposal of a novel bacterial phylum Ignavibacteriae. — Environ. Microbiol., 2013, 15(6): 1759-1571
  10. Ravin NV, Eldarov MA, Kadnikov VV, Beletsky AV, Schneider J, Mardanova ES, Smekalova EM, Zvereva MI, Dontsova OA, Mardanov AV, Skryabin KG. Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1. — BMC Genomics, 2013, 14(1): 837
  11. Blokhina E.A., Kuprianov V.V., Tsybalova L.M., Kiselev O.I., Ravin N.V., Skryabin K.G. A molecular assembly system for presentation of antigens on the surface of HBc virus-like particles. — Virology, 2013, 435, 293-300
  12. Sorokin DY, Gumerov VM, Rakitin AL, Beletsky AV, Damsté JS, Muyzer G, Mardanov AV, Ravin NV. Genome analysis of Chitinivibrio alkaliphilus gen. nov., sp. nov., a novel extremely haloalkaliphilic anaerobic chitinolytic bacterium from the candidate phylum Termite Group 3. — Environ Microbiol., 2014, 16(6):1549-65
  13. Pezeshgi Modarres H, Dorokhov BD, Popov VO, Ravin NV, Skryabin KG, Dal Peraro M. Understanding and engineering thermostability in DNA ligase from Thermococcus sp. 1519. — Biochemistry, 2015, 54(19):3076-85
  14. Ravin NV, Blokhina EA, Kuprianov VV, Stepanova LA, Shaldjan AA, Kovaleva AA, Tsybalova LM, Skryabin KG. (2015) Development of a candidate influenza vaccine based on virus-like particles displaying influenza M2e peptide into the immunodominant loop region of hepatitis B core antigen: Insertion of multiple copies of M2e increases immunogenicity and protective efficiency. – Vaccine, 2015, 33(29):3392-3397
  15. Mardanova ES, Kotlyarov RY, Kuprianov VV, Stepanova LA, Tsybalova LM, Lomonosoff GP, Ravin NV. Rapid high-yield expression of a candidate influenza vaccine based on the ectodomain of M2 protein linked to flagellin in plants using viral vectors. — BMC Biotechnology, 2015, 15: 42
  16. Mardanov AV, Panova IA, Beletsky AV, Avakyan MR, Kadnikov VV, Antsiferov DV, Banks D, Frank YA, Pimenov NV, Ravin NV, Karnachuk OV. Genomic insights into a new acidophilic, copper-resistant Desulfosporosinus isolate from the oxidized tailings area of an abandoned gold mine. — FEMS Microbiol Ecol, 2015, 92(8): fiw111.
  17. Ravin N.V., Gruzdev E.V., Beletsky A.B., Mazur A.M., Prokhortchouk E.B., Filyushin M.A.,  Kochieva E.Z., Kadnikov V.V., Mardanov A.B., Skryabin K.G. The loss of photosynthetic pathways in the plastid and nuclear genomes of the non-photosynthetic mycoheterotrophic eudicot Monotropa hypopitys. — BMC Plant Biology, 2016, 16: 929.
  18. Mardanova E.S., Blokhina E.A., Tsybalova L.M., Peyret H., Lomonossoff G.P., Ravin N.V. Efficient transient expression of recombinant proteins in plants by the novel pEff vector based on the genome of Potato Virus X. — Front. Plant Sci. 2017, 8: 247
  19. Ravin NV, Rakitin AL, Ivanova AA, Beletsky AV, Kulichevskaya IS, Mardanov AV, Dedysh SN. Genome analysis of Fimbriiglobus ruber SP5T, a planctomycete with confirmed chitinolytic capability. — Appl Environ Microbiol., 2018, 84: e02645-17.
  20. Kadnikov VV, Mardanov AV, Ivasenko DA, Antsiferov DV, Beletsky AV, Karnachuk OV, Ravin NV. Lignite coal burning seam in the remote Altai Mountains harbors a hydrogen-driven thermophilic microbial community. — Sci Rep., 2018, 8(1): 6730.
  21. Eldarov MA, Beletsky AV, Tanashchuk TN, Kishkovskaya SA, Ravin NV and Mardanov AV Whole-genome analysis of three yeast strains used for production of sherry-like wines revealed genetic traits specific to flor yeasts. — Front. Microbiol., 2018, 9: 965.
  22. International Wheat Genome Sequencing Consortium, Appels R, Eversole K,….Ravin N, Ravin N, Skryabin K, Beletsky A, Kadnikov V, Mardanov A, Nesterov M, Rakitin A,….Uauy C. Shifting the limits in wheat research and breeding using a fully annotated reference genome. — Science, 361(6403): pii: eaar7191.
  23. Kadnikov VV, Mardanov AV, Beletsky AV, Banks D, Pimenov NV, Frank YA, Karnachuk OV, Ravin NV. A metagenomic window into the 2-km-deep terrestrial subsurface aquifer revealed multiple pathways of organic matter decomposition. — FEMS Microbiol Ecol, 2018, 94(10): fiy152.
  24. Kadnikov VV, Mardanov AV, Beletsky AV, Rakitin AL, Frank YA, Karnachuk OV, Ravin NV. Phylogeny and physiology of candidate phylum BRC1 inferred from the first complete metagenome-assembled genome obtained from deep subsurface aquifer. — Syst Appl Microbiol., 2019, 42(1): 67-76.
  25. Karnachuk OV, Frank YA, Lukina AP, Kadnikov VV, Beletsky AV, Mardanov AV, Ravin NV. Domestication of previously uncultivated Candidatus Desulforudis audaxviator from a deep aquifer in Siberia sheds light on its physiology and evolution. — ISME J, 2019, doi: 10.1038/s41396-019-0402-3.