1
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Kozlov EN, Tokmatcheva EV, Khrustaleva AM, Grebenshchikov ES, Deev RV, Gilmutdinov RA, Lebedeva LA, Zhukova M, Savvateeva-Popova EV, Schedl P, Shidlovskii YV. Long-Term Memory Formation in Drosophila Depends on the 3'UTR of CPEB Gene orb2. Cells 2023; 12:cells12020318. [PMID: 36672258 PMCID: PMC9856895 DOI: 10.3390/cells12020318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/30/2022] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Activation of local translation in neurites in response to stimulation is an important step in the formation of long-term memory (LTM). CPEB proteins are a family of translation factors involved in LTM formation. The Drosophila CPEB protein Orb2 plays an important role in the development and function of the nervous system. Mutations of the coding region of the orb2 gene have previously been shown to impair LTM formation. We found that a deletion of the 3'UTR of the orb2 gene similarly results in loss of LTM in Drosophila. As a result of the deletion, the content of the Orb2 protein remained the same in the neuron soma, but significantly decreased in synapses. Using RNA immunoprecipitation followed by high-throughput sequencing, we detected more than 6000 potential Orb2 mRNA targets expressed in the Drosophila brain. Importantly, deletion of the 3'UTR of orb2 mRNA also affected the localization of the Csp, Pyd, and Eya proteins, which are encoded by putative mRNA targets of Orb2. Therefore, the 3'UTR of the orb2 mRNA is important for the proper localization of Orb2 and other proteins in synapses of neurons and the brain as a whole, providing a molecular basis for LTM formation.
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Affiliation(s)
- Eugene N. Kozlov
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Elena V. Tokmatcheva
- Institute of Physiology, Russian Academy of Sciences, 188680 St. Petersburg, Russia
| | - Anastasia M. Khrustaleva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Eugene S. Grebenshchikov
- Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
| | - Roman V. Deev
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Rudolf A. Gilmutdinov
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Lyubov A. Lebedeva
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Mariya Zhukova
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | | | - Paul Schedl
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
- Department of Molecular Biology, Princeton University, Princeton University, Princeton, NJ 08544-1014, USA
| | - Yulii V. Shidlovskii
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
- Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
- Correspondence:
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2
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Kachaev ZM, Ivashchenko SD, Kozlov EN, Lebedeva LA, Shidlovskii YV. Localization and Functional Roles of Components of the Translation Apparatus in the Eukaryotic Cell Nucleus. Cells 2021; 10:3239. [PMID: 34831461 PMCID: PMC8623629 DOI: 10.3390/cells10113239] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/15/2022] Open
Abstract
Components of the translation apparatus, including ribosomal proteins, have been found in cell nuclei in various organisms. Components of the translation apparatus are involved in various nuclear processes, particularly those associated with genome integrity control and the nuclear stages of gene expression, such as transcription, mRNA processing, and mRNA export. Components of the translation apparatus control intranuclear trafficking; the nuclear import and export of RNA and proteins; and regulate the activity, stability, and functional recruitment of nuclear proteins. The nuclear translocation of these components is often involved in the cell response to stimulation and stress, in addition to playing critical roles in oncogenesis and viral infection. Many components of the translation apparatus are moonlighting proteins, involved in integral cell stress response and coupling of gene expression subprocesses. Thus, this phenomenon represents a significant interest for both basic and applied molecular biology. Here, we provide an overview of the current data regarding the molecular functions of translation factors and ribosomal proteins in the cell nucleus.
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Affiliation(s)
- Zaur M. Kachaev
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Sergey D. Ivashchenko
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Eugene N. Kozlov
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Lyubov A. Lebedeva
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Yulii V. Shidlovskii
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia
- Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
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3
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Shidlovskii YV, Bylino OV, Shaposhnikov AV, Kachaev ZM, Lebedeva LA, Kolesnik VV, Amendola D, De Simone G, Formicola N, Schedl P, Digilio FA, Giordano E. Subunits of the PBAP Chromatin Remodeler Are Capable of Mediating Enhancer-Driven Transcription in Drosophila. Int J Mol Sci 2021; 22:ijms22062856. [PMID: 33799739 PMCID: PMC7999800 DOI: 10.3390/ijms22062856] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/03/2021] [Accepted: 03/08/2021] [Indexed: 12/11/2022] Open
Abstract
The chromatin remodeler SWI/SNF is an important participant in gene activation, functioning predominantly by opening the chromatin structure on promoters and enhancers. Here, we describe its novel mode of action in which SWI/SNF factors mediate the targeted action of an enhancer. We studied the functions of two signature subunits of PBAP subfamily, BAP170 and SAYP, in Drosophila. These subunits were stably tethered to a transgene reporter carrying the hsp70 core promoter. The tethered subunits mediate transcription of the reporter in a pattern that is generated by enhancers close to the insertion site in multiple loci throughout the genome. Both tethered SAYP and BAP170 recruit the whole PBAP complex to the reporter promoter. However, we found that BAP170-dependent transcription is more resistant to the depletion of other PBAP subunits, suggesting that BAP170 may play a more critical role in establishing enhancer-dependent transcription.
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Affiliation(s)
- Yulii V. Shidlovskii
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (O.V.B.); (A.V.S.); (Z.M.K.); (L.A.L.); (V.V.K.); (P.S.)
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia
- Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
- Correspondence: (Y.V.S.); (F.A.D.); (E.G.)
| | - Oleg V. Bylino
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (O.V.B.); (A.V.S.); (Z.M.K.); (L.A.L.); (V.V.K.); (P.S.)
| | - Alexander V. Shaposhnikov
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (O.V.B.); (A.V.S.); (Z.M.K.); (L.A.L.); (V.V.K.); (P.S.)
| | - Zaur M. Kachaev
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (O.V.B.); (A.V.S.); (Z.M.K.); (L.A.L.); (V.V.K.); (P.S.)
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Lyubov A. Lebedeva
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (O.V.B.); (A.V.S.); (Z.M.K.); (L.A.L.); (V.V.K.); (P.S.)
| | - Valeria V. Kolesnik
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (O.V.B.); (A.V.S.); (Z.M.K.); (L.A.L.); (V.V.K.); (P.S.)
| | - Diego Amendola
- Department of Biology, Università di Napoli Federico II, 80138 Naples, Italy; (D.A.); (G.D.S.)
| | - Giovanna De Simone
- Department of Biology, Università di Napoli Federico II, 80138 Naples, Italy; (D.A.); (G.D.S.)
- Department of Sciences, Roma Tre University, 00154 Rome, Italy
| | - Nadia Formicola
- Institute of Research on Terrestrial Ecosystems (IRET) National Research Council (CNR), 05010 Porano, Italy;
- Institut de Biologie Valrose iBV UMR CNRS 7277, Université Côte d’Azur, 06108 Nice, France
| | - Paul Schedl
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (O.V.B.); (A.V.S.); (Z.M.K.); (L.A.L.); (V.V.K.); (P.S.)
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014, USA
| | - Filomena Anna Digilio
- Institute of Research on Terrestrial Ecosystems (IRET) National Research Council (CNR), 05010 Porano, Italy;
- Correspondence: (Y.V.S.); (F.A.D.); (E.G.)
| | - Ennio Giordano
- Department of Biology, Università di Napoli Federico II, 80138 Naples, Italy; (D.A.); (G.D.S.)
- Correspondence: (Y.V.S.); (F.A.D.); (E.G.)
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Kachaev ZM, Lebedeva LA, Shaposhnikov AV, Moresco JJ, Yates JR, Schedl P, Shidlovskii YV. Paip2 cooperates with Cbp80 at an active promoter and participates in RNA Polymerase II phosphorylation in Drosophila. FEBS Lett 2019; 593:1102-1112. [PMID: 31001806 DOI: 10.1002/1873-3468.13391] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/28/2019] [Accepted: 04/09/2019] [Indexed: 01/01/2023]
Abstract
The Paip2 protein is a factor regulating mRNA translation and stability in the cytoplasm. It has also been found in the nuclei of several cell types in Drosophila. Here, we aim to elucidate the functions of Paip2 in the cell nucleus. We find that nuclear Paip2 is a component of an ~300-kDa protein complex. Paip2 interacts with mRNA capping factor and factors of RNA polymerase II (Pol II) transcription initiation and early elongation. Paip2 functionally cooperates with the Cbp80 subunit of the cap-binding complex, with both proteins ensuring proper Pol II C-terminal domain (CTD) Ser5 phosphorylation at the promoter. Thus, Paip2 is a novel player at the stage of mRNA capping and early Pol II elongation.
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Affiliation(s)
- Zaur M Kachaev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Lyubov A Lebedeva
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - James J Moresco
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Paul Schedl
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.,Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Yulii V Shidlovskii
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.,I.M. Sechenov First Moscow State Medical University, Russia
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5
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Abstract
In most animal species, newly formed primordial germ cells (PGCs) acquire the special characteristics that distinguish them from the surrounding somatic cells. Proper fate specification of the PGCs is coupled with transcriptional quiescence, whether they are segregated by determinative or inductive mechanisms. Inappropriate differentiation of PGCs into somatic cells is thought to be prevented due to repression of RNA polymerase (Pol) II-dependent transcription. In the case of a determinative mode of PGC formation (Drosophila, Caenorhabditis elegans, etc.), there is a broad downregulation of Pol II activity. By contrast, PGCs display only gene-specific repression in organisms that rely on inductive signaling-based mechanism (e.g., mice). In addition to the global block of Pol II activity in PGCs, gene expression can be suppressed in other ways, such as chromatin remodeling and Piwi-mediated RNAi. Here, we discuss the mechanisms responsible for the transcriptionally silent state of PGCs in common experimental animals, such as Drosophila, C. elegans, Danio rerio, Xenopus, and mouse. While a PGC-specific downregulation of transcription is a common feature among these organisms, the diverse nature of underlying mechanisms suggests that this functional trait likely evolved independently on several instances. We discuss the possible biological relevance of these silencing mechanisms vis-a-vis fate determination of PGCs.
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Affiliation(s)
- Lyubov A Lebedeva
- a Institute of Gene Biology , Russian Academy of Sciences , Moscow , Russia
| | - Konstantin V Yakovlev
- a Institute of Gene Biology , Russian Academy of Sciences , Moscow , Russia.,b Laboratory of Cytotechnology, National Scientific Center of Marine Biology, Far Eastern Branch , Russian Academy of Sciences , Vladivostok , Russia
| | - Eugene N Kozlov
- a Institute of Gene Biology , Russian Academy of Sciences , Moscow , Russia
| | - Paul Schedl
- a Institute of Gene Biology , Russian Academy of Sciences , Moscow , Russia.,c Department of Molecular Biology , Princeton University , Princeton , USA
| | - Girish Deshpande
- c Department of Molecular Biology , Princeton University , Princeton , USA
| | - Yulii V Shidlovskii
- a Institute of Gene Biology , Russian Academy of Sciences , Moscow , Russia.,d Department of Biology and General Genetics, I.M. Sechenov First Moscow State Medical University , Moscow , Russia
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6
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Kachaev ZM, Lebedeva LA, Kozlov EN, Toropygin IY, Schedl P, Shidlovskii YV. Paip2 is localized to active promoters and loaded onto nascent mRNA in Drosophila. Cell Cycle 2018; 17:1708-1720. [PMID: 29995569 DOI: 10.1080/15384101.2018.1496738] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Paip2 (Poly(A)-binding protein - interacting protein 2) is a conserved metazoan-specific protein that has been implicated in regulating the translation and stability of mRNAs. However, we have found that Paip2 is not restricted to the cytoplasm but is also found in the nucleus in Drosophila embryos, salivary glands, testes, and tissue culture cells. Nuclear Paip2 is associated with chromatin, and in chromatin immunoprecipitation experiments it maps to the promoter regions of active genes. However, this chromatin association is indirect, as it is RNA-dependent. Thus, Paip2 is one more item in the growing list of translation factors that are recruited to mRNAs co-transcriptionally.
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Affiliation(s)
- Zaur M Kachaev
- a Laboratory of Gene Expression Regulation in Development , Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia
| | - Lyubov A Lebedeva
- a Laboratory of Gene Expression Regulation in Development , Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia
| | - Eugene N Kozlov
- a Laboratory of Gene Expression Regulation in Development , Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia
| | - Ilya Y Toropygin
- d Center of Common Use "Human Proteome" , V.I. Orekhovich Research Institute of Biomedical Chemistry , Moscow , Russia
| | - Paul Schedl
- a Laboratory of Gene Expression Regulation in Development , Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia.,b Department of Molecular Biology , Princeton University , Princeton , NJ , USA
| | - Yulii V Shidlovskii
- a Laboratory of Gene Expression Regulation in Development , Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia.,c Department of Biology and General Genetics , I.M. Sechenov First Moscow State Medical University , Moscow , Russia
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Putlyaev EV, Ibragimov AN, Lebedeva LA, Georgiev PG, Shidlovskii YV. Structure and Functions of the Mediator Complex. Biochemistry (Mosc) 2018; 83:423-436. [PMID: 29626929 DOI: 10.1134/s0006297918040132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mediator is a key factor in the regulation of expression of RNA polymerase II-transcribed genes. Recent studies have shown that Mediator acts as a coordinator of transcription activation and participates in maintaining chromatin architecture in the cell nucleus. In this review, we present current concepts on the structure and functions of Mediator.
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Affiliation(s)
- E V Putlyaev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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8
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Zaitseva EV, Olneva TA, Kuleshov KV, Kondratyeva LM, Shikhina TM, Milikhina AV, Kalashnikova NA, Sidorova VF, Tchernyshova OA, Vasilyeva NI, Yakunina OY, Varenikova VV, Mnojina EG, Ivanova SA, Kaspirova LS, Fomina NS, Schaieva EI, Malokisher NS, Rud LA, Osipova SN, Tchernysheva OS, Prisiajnyuk EI, Lebedeva LA, Isaieva NV, Karavyanskaya TN, Tsarnenko OS, Podkolzin AT, Shipulin GA. [The results of monitoring of antigen types of rotaviruses of group A on the territory of the Russian Federation in 2011-2015.]. Klin Lab Diagn 2016; 61:445-448. [PMID: 31529927 DOI: 10.18821/0869-2084-2016-61-7-445-448] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 03/15/2016] [Indexed: 11/17/2022]
Abstract
The data of seasonal monitoring are presented concerning antigen types of rotaviruses group A circulating on the territory of the Russian Federation in the periods of seasonal uprising of morbidity in 2011-2015. Annually, the study included from 10 to 12 subjects of the Russian Federation with annual testing from 444 to 728 samples from children aged younger than 5 years with acute infection diarrhea. In the seasons of 2011-2012, 2012-2013, 2013-2014, 2014-2015 the most prevalent [P] G types of rotaviruses correspondingly made up to: G4[P]8 -50.2%-36.5%-43.8%-1.6%; G1[P]8 - 26.6%-14.3%-27.3%-22.5%; G3[P]8 - 4.4%-23.7%-4.2%-2.0%; G9[P]8 - 4.3%-5.3%-10.1%-7.1%; G2[P]4 - 7.7%-7.9%-9.0%-3.1%. The expressed territorial irregularity of prevalence of antigen types of retroviruses was observed.
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Affiliation(s)
- E V Zaitseva
- The central research institute of epidemiology of Rospotrebnadzor
| | - T A Olneva
- The central research institute of epidemiology of Rospotrebnadzor
| | - K V Kuleshov
- The central research institute of epidemiology of Rospotrebnadzor
| | - L M Kondratyeva
- The center of hygiene and epidemiology in the Tomskaia oblast
| | - T M Shikhina
- The center of hygiene and epidemiology in the Tomskaia oblast
| | - A V Milikhina
- The center of hygiene and epidemiology in the Republic of Dagestan
| | - N A Kalashnikova
- The center of hygiene and epidemiology in the Nijegorodskaia oblast
| | - V F Sidorova
- The center of hygiene and epidemiology in the Nijegorodskaia oblast
| | | | - N I Vasilyeva
- The center of hygiene and epidemiology in the Novosibirskaia oblast
| | - O Yu Yakunina
- The center of hygiene and epidemiology in the Novosibirskaia oblast
| | | | - E G Mnojina
- The center of hygiene and epidemiology in the Moskovskaia oblast
| | - S A Ivanova
- The center of hygiene and epidemiology in the Moskovskaia oblast
| | - L S Kaspirova
- The center of hygiene and epidemiology in the Moskovskaia oblast
| | - N S Fomina
- The center of hygiene and epidemiology in the Nenetskii avtonomnii okrug
| | - E I Schaieva
- The center of hygiene and epidemiology in the Kamchatskii kraii
| | - N S Malokisher
- The center of hygiene and epidemiology in the Kamchatskii kraii
| | - L A Rud
- The Petropavlovsk-Kamchatskii municipal children infection hospital
| | - S N Osipova
- The office of Rospotrebnadzor in the Sverdlovskaia oblast
| | - O S Tchernysheva
- The center of hygiene and epidemiology in the Sverdlovskaia oblast
| | - E I Prisiajnyuk
- The center of hygiene and epidemiology in the Khabarovskii kraii
| | - L A Lebedeva
- The center of hygiene and epidemiology in the Khabarovskii kraii
| | - N V Isaieva
- The center of hygiene and epidemiology in the Khabarovskii kraii
| | | | - O S Tsarnenko
- The A.K. Piotrovitch children kraievaia clinical hospital
| | - A T Podkolzin
- The central research institute of epidemiology of Rospotrebnadzor
| | - G A Shipulin
- The central research institute of epidemiology of Rospotrebnadzor
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9
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Ostrovskaya OV, Kholodok GN, Ivakhnishina NM, Morozova NV, Karavyanskaya TN, Golubeva EM, Reznik VI, Savosina LV, Lebedeva LA, Prisyazhnyuk EN, Kozlov VK. [Monitoring of influenza and other respiratory diseases causative agents in children, hospitalized with community-acquired pneumonia in 2012-2013 epidemic season]. Zh Mikrobiol Epidemiol Immunobiol 2015:59-65. [PMID: 26016346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
AIM Study the circulation of respiratory viruses in children with community-acquired pneumonia (CAP) during the period from October 2012 to May 2013. MATERIALS AND METHODS 136 children with CAP aged from 3 months to 16 years with ARI symptoms at the disease debut were studied. RNA/DNA of influenza A, B, parainfluenza (PI); adeno-, rhino-, RS-viruses, corona-, metapneumo- (MPV) and bocaviruses were detected in nasopharynx smears by PCR with hybridization-fluorescent detection in real time. Antibodies against influenza viruses A/H1N1/pdm09 California/07/09, epidemic reference strains of influenza viruses A/H1N1/Brisbane/59/07, A/ H3N2/Victoria/361/201 1, B/Wisconsin/1/10, against PI viruses type 1, 2, 3 were determined in paired sera by HAI. RESULTS In February-March 2013 the number of children protected by antibodies against influenza decreased, and circulation of influenza viruses A/H3N2 and A/H1N1/ pdm09 was detected. Rhinoviruses and PI viruses were determined throughout the epidemic season, bocavirus and adenoviruses--during the autumn-winter period, RS-virus and MPV--during winter-spring. Coronaviruses were not detected. The peak of virus detection was established in February when the threshold of influenza and ARI morbidity was exceeded. The main pathogens of children of the first 3 years of life are rhinoviruses, RS-virus, PI viruses and bocavirus. RS-virus infection at the debut of CAP in children younger than 3 years in 55.5% of cases is associated with the development of broncho-obstructive syndrome. Bocavirus infection in 50% of cases progresses with laryngo-tracheitis and bronchiolitis. CONCLUSION The fraction of viruses in etiologic structure ofARI in children varies depending on immune layer, season and age of children. Etiology of viral infection at the debut of CAP could only be proven using specialized laboratory studies.
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MESH Headings
- Adenoviruses, Human/genetics
- Adenoviruses, Human/isolation & purification
- Adolescent
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Child
- Child, Preschool
- Community-Acquired Infections
- Coronavirus/genetics
- Coronavirus/isolation & purification
- Disease Outbreaks
- Epidemiological Monitoring
- Female
- Hospitalization/statistics & numerical data
- Human bocavirus/genetics
- Human bocavirus/isolation & purification
- Humans
- Infant
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/isolation & purification
- Influenza, Human/epidemiology
- Influenza, Human/physiopathology
- Influenza, Human/virology
- Male
- Nasopharynx/virology
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/physiopathology
- Pneumonia, Viral/virology
- RNA, Viral/blood
- RNA, Viral/genetics
- Respiratory Tract Infections/epidemiology
- Respiratory Tract Infections/physiopathology
- Respiratory Tract Infections/virology
- Respirovirus/genetics
- Respirovirus/isolation & purification
- Rhinovirus/genetics
- Rhinovirus/isolation & purification
- Seasons
- Siberia/epidemiology
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10
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Lebedeva LA, Shaposhnikov AV, Panov VV, Shidlovskii YV. [Biological functions of Jak/Stat signaling pathway in Drosophila]. Genetika 2013; 49:1245-1250. [PMID: 25470924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The basic biological processes under the control of the Jak/Stat signaling pathway in Drosophila are reviewed. As shown, the fruit fly Drosophila melanogaster is a very convenient model organism for investigation of Jak/Stat functions in various aspects of ontogenesis.
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11
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Shaposhnikov AV, Komar'kov IF, Lebedeva LA, Shidlovskiĭ IV. [Molecular components of JAK/STAT signaling pathway and its connection with transcription machinery]. Mol Biol (Mosk) 2013; 47:388-97. [PMID: 23888769 DOI: 10.7868/s0026898413030130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
JAK/STAT is one of the conservative signaling pathways in higher eukaryotes which plays a critical role in different ontogenesis processes. This article gives a review of the pathway structure at the molecular level, mainly in a model organism Drosophila. There are data about relationship of the signaling pathway and transcription machinery of higher eukaryotes.
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Shaposhnikov AV, Kryndushkin AS, Nikolenko IV, Panov VV, Nabirochkina EN, Lebedeva LA, Shidlovskiĭ IV. [Activation of JAK/STAT signaling pathway in S2 Drosophila melanogaster cell culture]. Mol Biol (Mosk) 2013; 47:486-91. [PMID: 23888780 DOI: 10.7868/s0026898413030142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
JAK/STAT signaling pathway plays a critical role in different ontogenesis processes of higher eukaryotes. Fruit fly drosophila is a handy model system used to study this pathway since major components of the pathway are represented by unique factors. This article describes the usage of Drosophila melanogaster S2 cells in studies of the pathway's target genes activation. We showed that S2 cells contain plenty of STAT protein which migrates into nucleus under cells treatment with pervanadate. Then we demonstrated that under pervanadate action STAT protein along with other transcription factors is recruited onto regulatory sequences of target genes and activates their transcription.
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Kopytova DV, nikolenko IV, Lebedeva LA, Nabirochkina EN, Shidlovskiĭ IV, Georgieva SG, Krasnov AN. [Study of the Drosophila melanogaster trf2 gene and its protein product]. Genetika 2008; 44:163-169. [PMID: 18619033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The Drosophila melanogaster TRF2 protein regulates transcription of several genes. The trf2 gene structure was studied. The gene proved to code for two protein isoforms, a known 75-kDa isoform and a newly identified 175-kDa isoform. The new isoform combines the known isoform sequence with an extended N end containing a coiled-coil motif. The long TRF2 isoform was found to act as a component of a multiprotein complex, including ISWI ATPase as well.
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Lukashev AN, Reznik VI, Ivanova OE, Eremeeva TP, Karavianskaia TN, Pereskokova MA, Lebedeva LA, Lashkevich VA, Mikhaĭlov MI. [Molecular epidemiology of ECHO 6 virus, the causative agent of the 2006 outbreak of serous meningitis in Khabarovsk]. Vopr Virusol 2008; 53:16-21. [PMID: 18318129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A total of 3194 cases of enterovirus meningitis were notified in the Russian Federation in 2005, of them there were 1434 cases in the Khabarovsk Territory. Enteroviruses were isolated from 1020 out of the virologically studied 1362 patients from the Khabarovsk Territory. Viruses E6 and E30 were isolated in 80 and 14.7% of cases, respectively. E1, E3, E7, E33, Coxsackie virus B1, B4, B5, and A10 were sporadically detected. The E6 strains isolated in Komsomolsk-on-Amur were identical while E6 strains isolated in Khabarovsk belonged to two different genotypes and greatly differed from those isolated in Konsomolsk-on-Amur. The virus E30 strains isolated in Khabarovsk and Komsomolsk-on-Amur had a 1% difference in VP1 genome nucleotide sequence and belonged to E30 subtype that circulated in Russia and Kazakhstan in 2004-2005.
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Kurshakova MM, Nabirochkina EN, Lebedeva LA, Georgieva SG, Evgen'ev MB, Krasnov AN. Involvement of general transcriptional factors in the regulation of transcription of the hsp70 gene in vivo. Dokl Biol Sci 2007; 411:475-8. [PMID: 17425044 DOI: 10.1134/s0012496606060147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- M M Kurshakova
- Institute of Gene Biology, Russian Academy of Sciences, ul. Vavilova 34/5, Moscow, 119334 Russia
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Lebedeva LA, Nabirochkina EN, Evgen'ev MB, Georgieva SG, Krasnov AN. [Role of general transcription factors and the TFTC complex in transcription activation in vivo as revealed with a model of the hsp70 gene]. Genetika 2007; 43:32-7. [PMID: 17333936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
General transcription factors (GTFs) were tested for the presence on the promoter of the Drosophila melanogaster hsp70 gene in vivo. TBP, TBP-associated TAF proteins, TFIIB, TFIIF (RAP30), TFIIH (XPB), the TFTC complex (GCN5 and TRRAP), and a Mediator complex subunit (MEDI 3) were detected on the promoter before heat induction. Heat exposure significantly reduced the contents of TBP, TAF proteins, TFIIB, and TFIIF (RAP30), while these proteins were detected in ecdysone-inducible loci. It was assumed on the basis of these findings that a special mechanism induces transcription from the hsp70 promoter and that the apparent presence or absence of GTFs does not always reflect the transcriptional status of a gene.
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Lebedeva LA, Nabirochkina EN, Kurshakova MM, Robert F, Krasnov AN, Evgen'ev MB, Kadonaga JT, Georgieva SG, Tora L. Occupancy of the Drosophila hsp70 promoter by a subset of basal transcription factors diminishes upon transcriptional activation. Proc Natl Acad Sci U S A 2005; 102:18087-92. [PMID: 16330756 PMCID: PMC1306797 DOI: 10.1073/pnas.0509063102] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2005] [Indexed: 11/18/2022] Open
Abstract
The presence of general transcription factors and other coactivators at the Drosophila hsp70 gene promoter in vivo has been examined by polytene chromosome immunofluorescence and chromatin immunoprecipitation at endogenous heat-shock loci or at a hsp70 promoter-containing transgene. These studies indicate that the hsp70 promoter is already occupied by TATA-binding protein (TBP) and several TBP-associated factors (TAFs), TFIIB, TFIIF (RAP30), TFIIH (XPB), TBP-free/TAF-containg complex (GCN5 and TRRAP), and the Mediator complex subunit 13 before heat shock. After heat shock, there is a significant recruitment of the heat-shock transcription factor, RNA polymerase II, XPD, GCN5, TRRAP, or Mediator complex 13 to the hsp70 promoter. Surprisingly, upon heat shock, there is a marked diminution in the occupancy of TBP, six different TAFs, TFIIB, and TFIIF, whereas there is no change in the occupancy of these factors at ecdysone-induced loci under the same conditions. Hence, these findings reveal a distinct mechanism of transcriptional induction at the hsp70 promoters, and further indicate that the apparent promoter occupancy of the general transcriptional factors does not necessarily reflect the transcriptional state of a gene.
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Affiliation(s)
- Lyubov A Lebedeva
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de Recherche Scientifique, Unité Mixte de Recherche 7104, Université Louis Pasteur de Strasbourg, BP 10142, Illkirch, France
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Nikolenko IV, Shidlovskiĭ IV, Lebedeva LA, Krasnov AN, Georgieva SG, Nabirochkina EN. [Transcriptional coactivator SAYP can suppress transcription in heterochromatin]. Genetika 2005; 41:1033-7. [PMID: 16161622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The new transcriptional coactivator SAYP binds at many sites to transcriptionally active chromatin of polytene chromosomes, colocalizes with RNA polymerase II, and coactivates transcription. On the other hand, SAYP is present in heterochromatic regions of chromosome IV and in the chromocenter and suppresses transcription of transgenes located in heterochromatin. The conserved SAY domain of SAYP is involved in transcription activation, while its PHD domains are responsible for gene silencing in heterochromatin. Thus, SAYP plays a dual role in regulating transcription in euchromatic and heterochromatic regions.
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Lebedeva LA, Georgieva SG, Nabirochkina EN. Study of the Properties of Two Homologues of Yeast ADA2 in Drosophila melanogaster. DOKL BIOCHEM BIOPHYS 2004; 398:297-9. [PMID: 15584512 DOI: 10.1023/b:dobi.0000046642.75100.c7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- L A Lebedeva
- Institute of Gene Biology, Russian Academy of Sciences, ul. Vavilova 34/5, Moscow, 117334, Russia
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Lebedeva LA, Tillib SV. [Trithorax protein, a global factor for maintenance of tissue specific gene activation in Drosophila melanogaster, is associated with the nuclear matrix]. Genetika 2003; 39:250-258. [PMID: 12669422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Immunlfluorescence staining and Western blotting of proteins from the nuclear extract fractions showed for the first time that protein TRITHORAX, one of the most important proteins maintaining the tissue-specific transcriptionally active state of many Drosophila melanogaster genes, is associated with the nuclear matrix. TRITHORAX displayed similar staining at different stages of nuclear extraction and on the polytene chromosomes of the intact nuclei, as well as after partial or complete disruption of the nuclear envelope and chromosome release. This suggests that TRITHORAX bound to certain regulatory chromosome regions interacts with the adjacent elements of the nuclear scaffold, i.e., links the regions of actively transcribed genes with the nuclear matrix.
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Affiliation(s)
- L A Lebedeva
- Institute of Gene Biology, Russian Academy of Sciences, ul. Vavilova 34/5, Moscow, 119334 Russia
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Udina IG, Turkova SO, Kostiuchenko MV, Lebedeva LA, Sulimova GE. [Polymorphism of cattle prolactin gene: microsatellites, PSR-RFLP]. Genetika 2001; 37:511-516. [PMID: 11421124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In the samples of Russian Ayrshire and Gorbatov Red cattle breeds, distribution of frequencies of prolactin (PRL) gene alleles generated due to the presence of polymorphic RsaI site in exon 3 were studied. In the breeds, the frequencies of the B allele of the PRL gene (with RsaI(+) site) detected by the PCR-RFLP method were 14.1 and 8.6%, respectively. In Black Pied, Ayrshire and Gorbatov Red cattle breeds, variation of the microsatellite dinucleotide repeat in the regulatory region of the gene PRL was also studied. Gorbatov Red breed was monomorphic at the microsatellite locus with the only allele 164 bp in length. Two alleles (164 bp and 162 bp) were detected in the other breeds studied. The frequencies of 164-bp allele of the microsatellite locus were 93.7 and 90.0% in Black Pied and Ayrshire breeds, respectively. In Gorbatov Red breed of dairy type with good beef qualities and low milk-fat yield, lower level of heterozygosity for PRL gene was demonstrated compared to Ayrshire and Black Pied breeds with high milk-fat yield. In three cattle breeds, higher mean estimate of polymorphism information content of PCR-RFLP in exon 3 (PIC = 0.21) was revealed compared with the same estimate (PIC = 0.09) for the microsatellite locus variability in the regulatory region of the PRL gene. Characteristics of allele B distribution of the PRL gene in the representatives of the Bovidae family are considered.
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Affiliation(s)
- I G Udina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991.
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Kazeev KN, Antonov AV, Lebedeva LA, Glod OS. [A case of chromaffinoma associated with thymoma and myasthenia]. Probl Endokrinol (Mosk) 1991; 37:33-4. [PMID: 1780285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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