Laboratory of mechanisms of gene expression

Scientific units

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

Selected publications

  1. Shpakovski D.G., Shematorova E.K., Shpakovski G.V. (2006). Human PMS2 gene family: origin, molecular evolution, and biological implications. Dokl. Biochem. Biophys. 408 (5), 175–179 ID:61
  2. Proshkina G.M., Shematorova E.K., Proshkin S.A., Zaros C., Thuriaux P., Shpakovski G.V. (2006). Ancient origin, functional conservation and fast evolution of DNA-dependent RNA polymerase III. Nucleic Acids Res. 34 (13), 3615–24 [+]

    RNA polymerase III contains seventeen subunits in yeasts (Saccharomyces cerevisiae and Schizosaccharomyces pombe) and in human cells. Twelve of them are akin to the core RNA polymerase I or II. The five other are RNA polymerase III-specific and form the functionally distinct groups Rpc31-Rpc34-Rpc82 and Rpc37-Rpc53. Currently sequenced eukaryotic genomes revealed significant homology to these seventeen subunits in Fungi, Animals, Plants and Amoebozoans. Except for subunit Rpc31, this also extended to the much more distantly related genomes of Alveolates and Excavates, indicating that the complex subunit organization of RNA polymerase III emerged at a very early stage of eukaryotic evolution. The Sch.pombe subunits were expressed in S.cerevisiae null mutants and tested for growth. Ten core subunits showed heterospecific complementation, but the two largest catalytic subunits (Rpc1 and Rpc2) and all five RNA polymerase III-specific subunits (Rpc82, Rpc53, Rpc37, Rpc34 and Rpc31) were non-functional. Three highly conserved RNA polymerase III-specific domains were found in the twelve-subunit core structure. They correspond to the Rpc17-Rpc25 dimer, involved in transcription initiation, to an N-terminal domain of the largest subunit Rpc1 important to anchor Rpc31, Rpc34 and Rpc82, and to a C-terminal domain of Rpc1 that presumably holds Rpc37, Rpc53 and their Rpc11 partner.

    ID:60
  3. Shpakovski D.G., Shematorova E.K., Shpakovski G.V. (2004). New genes on human chromosome 7: bioinformatic analysis of a gene cluster from the POLR2J family. Bioorg. Khim. 30 (6), 621–5 [+]

    Four independent genes encoding various variants of the hRPB11 subunit of Homo sapiens RNA polymerase II were revealed in human chromosome 7. Three genes (POLR2J1, POLR2J2, and POLR2J3) form a cluster of total length 214530 bp in the genetic locus 7q22.1 on the long arm of chromosome 7 (contig NT_007933). The fourth gene (POLR2J4, 31040 bp) was localized in the cytogenetic locus 7p13 of the short arm of chromosome 7 (contig NT_007819). An analysis enabled us to refine dissimilar experimental data on the mapping of the hRPB11 subunit gene on chromosome 7. In particular, the presence of three sites of its localization according to data on hybridization with fluorescent-labeled probes (the FISH method) was explained. It was established that, upon the expression of the four human POLR2J genes, at least 14 types of mature mRNAs encoding somewhat differing hRPB11 isoforms can be synthesized. Eleven of these mRNAs were revealed (as full-length copies or clearly identifiable fragments) in the available databases of expressed sequence tags and cDNAs. The most probable scheme of origination of the multiple genes of the POLR2J family, as a result of three consecutive segmented duplications increasing in size, was proposed and substantiated. On the basis of the scheme, some assumptions on the pathways of evolution of separate human genes and the mechanisms of generation of protein diversity in higher eukaryotes were made. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2004, vol. 30, no. 6; see also http://www.maik.ru.

    ID:59
  4. Wood V., Gwilliam R., Rajandream M.A., Lyne M., Lyne R., (> 100 authors here) , Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P., Cerrutti L. (2002). The genome sequence of Schizosaccharomyces pombe. Nature 415 (6874), 871–80 [+]

    We have sequenced and annotated the genome of fission yeast (Schizosaccharomyces pombe), which contains the smallest number of protein-coding genes yet recorded for a eukaryote: 4,824. The centromeres are between 35 and 110 kilobases (kb) and contain related repeats including a highly conserved 1.8-kb element. Regions upstream of genes are longer than in budding yeast (Saccharomyces cerevisiae), possibly reflecting more-extended control regions. Some 43% of the genes contain introns, of which there are 4,730. Fifty genes have significant similarity with human disease genes; half of these are cancer related. We identify highly conserved genes important for eukaryotic cell organization including those required for the cytoskeleton, compartmentation, cell-cycle control, proteolysis, protein phosphorylation and RNA splicing. These genes may have originated with the appearance of eukaryotic life. Few similarly conserved genes that are important for multicellular organization were identified, suggesting that the transition from prokaryotes to eukaryotes required more new genes than did the transition from unicellular to multicellular organization.

    ID:58
  5. Shpakovski G.V., Gadal O., Labarre-Mariotte S., Lebedenko E.N., Miklos I., Sakurai H., Proshkin S.A., Van Mullem V., Ishihama A., Thuriaux P. (2000). Functional conservation of RNA polymerase II in fission and budding yeasts. J. Mol. Biol. 295 (5), 1119–27 [+]

    The complementary DNAs of the 12 subunits of fission yeast (Schizosaccharomyces pombe) RNA polymerase II were expressed from strong promoters in Saccharomyces cerevisiae and tested for heterospecific complementation by monitoring their ability to replace in vivo the null mutants of the corresponding host genes. Rpb1 and Rpb2, the two largest subunits and Rpb8, a small subunit shared by all three polymerases, failed to support growth in S. cerevisiae. The remaining nine subunits were all proficient for heterospecific complementation and led in most cases to a wild-type level of growth. The two alpha-like subunits (Rpb3 and Rpb11), however, did not support growth at high (37 degrees C) or low (25 degrees C) temperatures. In the case of Rpb3, growth was restored by increasing the gene dosage of the host Rpb11 or Rpb10 subunits, confirming previous evidence of a close genetic interaction between these three subunits.

    ID:57

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.