Laboratory of mechanisms of gene expression

Department of functioning of living systems

Head: Georgij Shpakovski, D.Sc
gvs@ibch.ru+7(495)330-65-83

eukaryotic transcription, regulation of gene expression, segmental duplications, evolution of Homo sapiens

The Laboratory of Mechanisms of Gene Expression was organized in May of 2007 on the basis of an independent research group under the same name existed since December 2001.

Since the very beginning the main focus of our research is studies of basic mechanisms of transcription in eukaryotes. The functional complementations in vivo of certain subunits of nuclear RNA polymerases I—III among evolutionary remote species (yeast, drosophila, man) has been first demonstrated (Gene, 1994, 147: 63–69; Mol. Cell. Biol., 1995, 15: 4702–4710) and functional relatedness of small subunits of RNA polymerases in Archaea and Eucarya was established (Russ. J. Bioorg. Chem., 1997, 23: 100–106;J. Biol. Chem., 1999, 274: 8421–8427).

The first comprehensive studies of exchangeability in vivo (in the cells of yeast Saccharomyces cerevisiae) of the subunits of nuclear RNA polymerases I, II, and III between evolutionary distant species (Schizosaccharomyces pombe and Homo sapiens) have been performed, whereby many of the components of the basal transcription apparatus of the fission yeasts were cloned and thoroughly characterized (J. Mol. Biol., 2000, 295: 1119—1127; Mol. Biol. (Mosk), 2002, 36: 3—26;Nucleic Acids Res., 2006, 34: 3615—3624). As a part of the the International Project on total sequencing of the Sch. pombe genome in three loci of its chromosome I the primary structure gaps were closed and the nucleotide sequence continuity was restored with clones pYUK71, pYUL23 and pYUG7 isolated in our laboratory (Nature, 2002, 415: 871—880; see also S. pombe genetic map). In the collaborative work with French scientists from ESBS (Strasbourg) was found that one of the subunits of human RNA polymerase II is encoded by a multigene family which expression give rise to at least three protein isoforms (BMC Mol. Biol., 2001, 2:14). Four independent genes encoding various variants of this hRPB11 subunit were revealed (Russ. J. Bioorg. Chem., 2004, 30: 561—565). Coevolution of Homo sapiens POLR2J and PMS2 genes, both located on chromosome 7 and encoding two essential components of such important molecular processes of the living cell as transcription and DNA mismatch repair, was shown: both these gene families undergone multiple rounds of duplication events started in the hominoid ancestor less than 20 million years ago (Dokl. Biochem. Biophys., 2006, 408: 175—179). Moreover, according to data obtained the evolution of these two gene families includes stages specific for humans (Russ. J. Genet., 2010, 46: 1112-1114; Biochemistry, 2011, 76: 976-980; Cell & Tissue Biology, 2013, 7: 314-319).

Mapping on the human chromosome 7 several genes that are important for primate evolution: four POLR2J paralogues (J1J4) and sixteen PMS2 paralogues (PMS2, ψ0, ψ1ψ14). Different stages (1, 2 and 3) of POLR2J amplification are shown; two of them are specific for Homo sapiens (marked with pink circles). Mya — million years ago.

 

NamePositionContacts
Georgij Shpakovski, D.Scdepart. dir.gvs@ibch.ru+7(495)330-65-83
Valerij Klykov, Ph.D.s. r. f.kseniae10@mail.ru
Elena Shematorova, Ph.D.s. r. f.elenashe@ibch.ru+7(495)330-65-83
Dmitry Shpakovskij. r. f.mati@mail.ru+7(495)330-65-83,
Ivan Slovokhotovj. r. f.ivan_slovohotov@mail.ru+7(495)330-65-83, +7(916)4887172

Former members:

Galina Proshkina, Ph.D.s. r. f.
Andrey Aralov, Ph.D.r. f.Baruh238@mail.ru
Sergej Proshkinj. r. f.

Selected publications

  1. Shematorova EK, Shpakovski DG, Chernysheva AD, Shpakovski GV (2018). Molecular mechanisms of the juvenile form of Batten disease: Important role of MAPK signaling pathways (ERK1/ERK2, JNK and p38) in pathogenesis of the malady. Biol Direct 13 (1),
  2. Tsvetkov VB, Zatsepin TS, Belyaev ES, Kostyukevich YI, Shpakovski GV, Podgorsky VV, Pozmogova GE, Varizhuk AM, Aralov AV (2018). i-Clamp phenoxazine for the fine tuning of DNA i-motif stability. Nucleic Acids Res 46 (6), 2751–2764
  3. Shpakovski GV, Spivak SG, Berdichevets IN, Babak OG, Kubrak SV, Kilchevsky AV, Aralov AV, Slovokhotov IY, Shpakovski DG, Baranova EN, Khaliluev MR, Shematorova EK (2017). A key enzyme of animal steroidogenesis can function in plants enhancing their immunity and accelerating the processes of growth and development. BMC Plant Biol 17 (0), 189
  4. Zlobin IE, Kartashov AV, Shpakovski GV (2017). Different roles of glutathione in copper and zinc chelation in Brassica napus roots. Plant Physiol Biochem 118 (0), 333–341
  5. Varizhuk AM, Zatsepin TS, Golovin AV, Belyaev ES, Kostyukevich YI, Dedkov VG, Shipulin GA, Shpakovski GV, Aralov AV (2017). Synthesis of oligonucleotides containing novel G-clamp analogue with C8-tethered group in phenoxazine ring: Implication to qPCR detection of the low-copy Kemerovo virus dsRNA. Bioorg Med Chem 25 (14), 3597–3605
  6. Shematorova K, Slovokhotov Yu, Khaliluev R, Berdichevets N, Baranova N, Babak G, Shpakovski DG, Spivak SG, Shpakovski GV (2014). Mitochondria as a Possible Place for Initial Stages of Steroid Biosynthesis in Plants. 10 (4), 85–97
  7. Shematorova EK, Shpakovski DG, Shpakovski GV (2013). Novel complexes of gene expression and their role in the appearance and evolution of the genus Homo. Cell tissue biol 7 (4), 314–319
  8. Aralov AV, Klykov VN, Chakhmakhcheva OG, Efimov VA (2011). Monomers containing 2′-O-alkoxymethyl groups as synthons for the oligonucleotide synthesis by the phosphotriester method. Russ. J. Bioorganic Chem. 37 (5), 586–592
  9. Proshkin SA, Shematorova EK, Souslova EA, Proshkina GM, Shpakovski GV (2011). A minor isoform of the human RNA polymerase II subunit hRPB11 (POLR2J) interacts with several components of the translation initiation factor eIF3. Biochemistry (Mosc) 76 (8), 976–980
  10. Shematorova EK, Shpakovski DG, Shpakovski GV (2010). PMS2 and POLR2J gene families as molecular markers of the higher primates evolution. Russ J Genet 46 (9), 1112–1114
  11. Spivak SG, Berdichevets IN, Litvinovskaya RP, Drach SV, Kartel NA, Shpakovski GV (2010). Some peculiarities of steroid metabolism in transgenic Nicotiana tabacum plants bearing the CYP11A1 cDNA of cytochrome P450SCCfrom the bovine adrenal cortex. Russ. J. Bioorganic Chem. 36 (2), 224–232
  12. Efimov VA, Aralov AV, Klykov VN, Chakhmakhcheva OG (2009). Synthesis of RNA by the rapid phosphotriester method using azido-based 2'-O-protecting groups. Nucleosides Nucleotides Nucleic Acids 28 (9), 846–865
  13. Spivak SG, Berdichevets IN, Yarmolinsky DG, Maneshina TV, Shpakovski GV, Kartel NA (2009). Construction and characteristics of transgenic tobacco Nicotiana tabacum L. plants expressing CYP11A1 cDNA encoding cytochrome P450scc. Russ J Genet 45 (9), 1067–1073
  14. Efimov VA, Aralov AV, Fedunin SV, Klykov VN, Chakhmakhcheva OG (2009). An azidomethyl protective group in the synthesis of oligoribonucleotides by the phosphotriester method. Russ. J. Bioorganic Chem. 35 (2), 250–253
  15. Efimov VA, Klykov VN, Chakhmakhcheva OG (2007). Synthesis and properties of pyrrolidine-based negatively charged dna mimics. Nucleosides Nucleotides Nucleic Acids 26 (1012), 1595–1599
  16. Sobennikova MV, Shematorova EK, Shpakovski GV (2007). C-terminal domain of subunit Rpb1 of nuclear RNA polymerase II and its role in the transcription cycle. Mol Biol 41 (3), 387–401
  17. Proshkina GM, Shematorova EK, Proshkin SA, Zaros C, Thuriaux P, Shpakovski GV (2006). Ancient origin, functional conservation and fast evolution of DNA-dependent RNA polymerase III. Nucleic Acids Res 34 (13), 3615–3624
  18. Shpakovski DG, Shematorova EK, Shpakovski GV (2006). Human PMS2 gene family: origin, molecular evolution, and biological implications. 408 (5), 175–179
  19. Shpakovskii DG, Shematorova EK, Shpakovskii GV (2006). Human PMS2 gene family: Origin, molecular evolution, and biological implications. Dokl Biochem Biophys 408 (1), 175–179
  20. Benga WJ, Grandemange S, Shpakovski GV, Shematorova EK, Kedinger C, Vigneron M (2005). Distinct regions of RPB11 are required for heterodimerization with RPB3 in human and yeast RNA polymerase II. Nucleic Acids Res 33 (11), 3582–3590
  21. Shpakovski DG, Shematorova EK, Shpakovski GV (2004). New genes on human chromosome 7: Bioinformation analysis of a cluster of genes from the POLR2J family. Russ. J. Bioorganic Chem. 30 (6), 561–565
  22. Wery M, Shematorova E, Van Driessche B, Vandenhaute J, Thuriaux P, Van Mullem V (2004). Members of the SAGA and Mediator complexes are partners of the transcription elongation factor TFIIS. EMBO J 23 (21), 4232–4242
  23. Proshkin SA, Shpakovski GV (2004). Heterologous overexpression and purification of four common subunits of nuclear RNA polymerases I, II and III of Schizosaccharomyces pombe. J Chromatogr B Analyt Technol Biomed Life Sci 800 (12), 121–126
  24. Efimov VA, Klykov VN, Chakhmakhcheva OG (2003). Phosphono peptide nucleic acids with a constrained hydroxyproline-based backbone. Nucleosides Nucleotides Nucleic Acids 22 (58), 593–599
  25. Shematorova EK, Shpakovski GV (2002). Structure and functions of eukaryotic nuclear DNA-dependent RNA polymerase I. Mol Biol 36 (1), 1–17
  26. Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S, Basham D, Bowman S, Brooks K, Brown D, Brown S, Chillingworth T, Churcher C, Collins M, Connor R, Cronin A, Davis P, Feltwell T, Fraser A, Gentles S, Goble A, Hamlin N, Harris D, Hidalgo J, Hodgson G, Holroyd S, Hornsby T, Howarth S, Huckle EJ, Hunt S, Jagels K, James K, Jones L, Jones M, Leather S, McDonald S, McLean J, Mooney P, Moule S, Mungall K, Murphy L, Niblett D, Odell C, Oliver K, ONeil S, Pearson D, Quail MA, Rabbinowitsch E, Rutherford K, Rutter S, Saunders D, Seeger K, Sharp S, Skelton J, Simmonds M, Squares R, Squares S, Stevens K, Taylor K, Taylor RG, Tivey A, Walsh S, Warren T, Whitehead S, Woodward J, Volckaert G, Aert R, Robben J, Grymonprez B, Weltjens I, Vanstreels E, Rieger M, Schäfer M, Müller-Auer S, Gabel C, Fuchs M, Fritzc C, Holzer E, Moestl D, Hilbert H, Borzym K, Langer I, Beck A, Lehrach H, Reinhardt R, Pohl TM, Eger P, Zimmermann W, Wedler H, Wambutt R, Purnelle B, Goffeau A, Cadieu E, Dréano S, Gloux S, Lelaure V (2002). The genome sequence of Schizosaccharomyces pombe. Nature 415 (6874), 871–880
  27. Shematorova EK, Shpakovskiǐ GV (2002). Structure and function of eukaryotic nuclear DNA-dependent RNA polymerase I. Mol Biol (Mosk) 36 (1), 3–26
  28. Shpakovski GV, Lebedenko EN (2001). Molecular evolution and structure of subunits of nuclear RNA polymerases of eukaryotes in context of the exon-intron organization of their genes. Bioorg Khim 25 (11), 828–837
  29. Grandemange S, Schaller S, Yamano S, Du Manoir S, Shpakovski GV, Mattei MG, Kedinger C, Vigneron M (2001). A human RNA polymerase II subunit is encoded by a recently generated multigene family. BMC Mol Biol 2 (0),
  30. Shpakovski GV, Baranova GM (2000). Chromosomal localization of the rpb9+and tfa1+genes encoding components of the mRNA synthesis machinery of Schizosaccharomyces pombe. Russ. J. Bioorganic Chem. 26 (8), 559–565
  31. Shpakovski GV, Gadal O, Labarre-Mariotte S, Lebedenko EN, Miklos I, Sakurai H, Proshkin SA, Van Mullem V, Ishihama A, Thuriaux P (2000). Functional conservation of RNA polymerase II in fission and budding yeasts. J Mol Biol 295 (5), 1119–1127
  32. Shpakovski GV (2000). The unlimited complexity of biological systems and astonishing diversity of living organisms will remain the driving force of the physicochemical biology in the first third of the XXI century. Russ. J. Bioorganic Chem. 26 (10), 708–709
  33. Shpakovski GV, Baranova GM (1999). RNA polymerase II of Schizosaccharomyces pombe contains twelve different subunits: Identification and characterization of subunit Rpb4. Russ. J. Bioorganic Chem. 25 (12), 834–838
  34. Schaller S, Grandemange S, Shpakovski GV, Golemis EA, Kedinger C, Vigneron M (1999). Interactions between the full complement of human RNA polymerase II subunits. FEBS Lett 461 (3), 253–257
  35. Shpakovski GV, Lebedenko EN (1999). Molecular evolution and structure of subunits of nuclear RNA polymerases of eukaryotes in the context of the exon-intron organization of their genes. Russ. J. Bioorganic Chem. 25 (11), 732–741
  36. Shpakovski GV, Shematorova EK (1999). Rpc19 and Rpc40, two α-like subunits shared by nuclear RNA polymerases I and III, are interchangeable between the fission and budding yeasts. Curr Genet 36 (4), 208–214
  37. Shpakovski GV, Shematorova EK (1999). Characterization of the rpa43+cDNA of Schizosaccharomyces pombe: Structural similarity of subunit Rpa43 of RNA polymerase I and subunit Rpc25 of RNA polymerase III. Russ. J. Bioorganic Chem. 25 (10), 700–704
  38. Shpakovski GV, Baranova GM, Wood V, Gwilliam RG, Shematorova EK, Korolchuk OL, Lebedenko EN (1999). Molecular cloning of some components of the translation apparatus of fission yeast Schizosaccharomyces pombe and a unified list of genes of its cytoplasmic ribosomal proteins. Russ. J. Bioorganic Chem. 25 (6), 397–409
  39. Shpakovski GV, Lebedenko EN (1998). Molecular identification and characterization of hRPC11, the smallest subunit specific for human RNA polymerase III. Russ. J. Bioorganic Chem. 24 (11), 778–781
  40. Shpakovski GV, Lebedenko EN (1998). Exon-intron structure of the fet5+ gene of schizosaccharomyces pombe and the physical mapping of the encompassing regions of the genome. Russ. J. Bioorganic Chem. 24 (1), 35–39
  41. Shpakovski GV, Shematorova EK (1998). Molecular cloning and characterization of the rpc19+ and rpc40+ genes of Schizosaccharomyces pombe encoding subunits shared by nuclear RNA polymerases I and III. Russ. J. Bioorganic Chem. 24 (12), 828–832
  42. Shpakovski GV, Proshkin SA, Kayushin AL, Korosteleva MD, Lebedenko EN (1998). Structural and functional characterization of the rpb8+gene of schizosaccharomyces pombe encoding a subunit of RNA polymerases I-III only specific for eukaryotes. Russ. J. Bioorganic Chem. 24 (2), 105–111
  43. Shpakovski GV, Proshkin SA, Lebedenko EN (1998). Exon-intron organization of Schizosaccharomyces pombe genes rpb10+and rpc10+encoding minisubunits of nuclear RNA polymerases I-III. Mol Biol 32 (2), 249–254
  44. Shpakovski GV, Lebedenko EN (1997). Molecular cloning of the rpb5+, rpb7+, and rpb11+genes of the fission yeast Schizosaccharomyces pombe: Completing the primary structure of all indispensable subunits of its RNA polymerase II. Russ. J. Bioorganic Chem. 23 (12), 874–877
  45. Shpakovski GV, Lebedenko EN (1997). Molecular cloning and characterization of cDNA of the rpb10+gene encoding the smallest subunit of nuclear RNA polymerases of Schizosaccharomyces pombe. Russ. J. Bioorganic Chem. 23 (5), 412–418
  46. Shpakovski GV, Lebedenko EN (1997). The First Member of a Novel Family of Protein Factors of Eukaryotic Transcription Discovered by the Heterospecific Complementation. Bioorg Khim 23 (3), 237
  47. Shpakovski GV, Lebedenko EN, Thuriaux P (1997). Cloning of an RNA polymerase subunit cDNA of the fission yeast Schizosaccharomyces pombe by heterospecific complementation in Saccharomyces cerevisiae. Russ. J. Bioorganic Chem. 23 (2), 100–106
  48. Shpakovski GV, Lebedenko EN (1996). Three structural motifs of the Rbp10 minisubunit of nuclear RNA polymerases are strictly conserved between eukaryotes. Russ. J. Bioorganic Chem. 22 (12), 821–823
  49. Shpakovski GV, Acker J, Wintzerith M, Lacroix JF, Thuriaux P, Vigneron M (1995). Four subunits that are shared by the three classes of RNA polymerase are functionally interchangeable between Homo sapiens and Saccharomyces cerevisiae. Mol Cell Biol 15 (9), 4702–4710
  50. Shpakovski GV, Karakashly MP, Berlin YA (1989). λplac10 Transducing bacteriophage: DNA primary structure of the region of the abnormal excision. FEBS Lett 258 (1), 171–174
  51. Shpakovski GV, Akhrem AA, Berlin YA (1988). Structural bases of a long-stretched deletion: Completing the λplac5 DNA primary structure. Nucleic Acids Res 16 (21), 10199–10212
  52. Shpakovski GV, Berlin YA (1984). Site-specificity of abnormal excision: The mechanism of formation of a specialized transducing bacteriophage 5§. Nucleic Acids Res 12 (17), 6779–6795

Georgij Shpakovski

  • Russia, Moscow, Ul. Miklukho-Maklaya 16/10 — On the map
  • IBCh RAS, build. 52, office. 364
  • Phone: +7(495)330-65-83
  • E-mail: gvs@ibch.ru

Progesterone as a very ancient bioregulator of plant cells (2017-11-29)

The compatibility in vivo of even the most specific components of biosynthesis systems of steroid hormones in Plantae and Animalia was demonstrated for the first time. By increasing the level of the endogenic progesterone in the specially engineered CYP11A1 transgenic tobacco and tomato plants, we were able to accelerate the processes of growth and development and enhance the plants’ resistance to biotic and abiotic stresses. The formation of the above-noted successful (desirable) phenotypes of transgenic Solanaceae plants expressing mammalian cytochrome P450scc (CYP11A1) cDNA implies that progesterone can be considered as a very ancient bioregulator of plant cells and the first real hormone common to plants and animals. The results indicate a definite similarity of the steroid compounds biosynthesis and steroid regulatory systems of plants and animals and can be used in new biotechnologies for agriculture and pharmacology.

Novel nucleotide modifications for stabilization of the canonical and non-canonical secondary structures of nucleic acids (2017-11-29)

New phenoxazine-based nucleotide modifications for the stabilizing of canonical (G8AE-clamp) and non-canonical (i-Clamp) secondary structures of nucleic acids were developed. G8AE-clamp modification was shown to considerably stabilize nucleic acid duplexes and primers containing G8AE-clamp demonstrated superior sensitivity in qPCR detection of dsRNA of Kemerovo virus in natural isolates as compared with common oligonucleotides. To date i-clamp modification reveals the highest i-motif-stabilizing effect within the broad acidic pH range and could be used for tuning iM-based nanodevices such as pH sensors, molecular motor, hydrogels, delivery systems, etc.