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  1. Article ; Online: Mechanisms and biomedical implications of -1 programmed ribosome frameshifting on viral and bacterial mRNAs.

    Korniy, Natalia / Samatova, Ekaterina / Anokhina, Maria M / Peske, Frank / Rodnina, Marina V

    FEBS letters

    2019  Volume 593, Issue 13, Page(s) 1468–1482

    Abstract: Some proteins are expressed as a result of a ribosome frameshifting event that is facilitated by a slippery site and downstream secondary structure elements in the mRNA. This review summarizes recent progress in understanding mechanisms of -1 ... ...

    Abstract Some proteins are expressed as a result of a ribosome frameshifting event that is facilitated by a slippery site and downstream secondary structure elements in the mRNA. This review summarizes recent progress in understanding mechanisms of -1 frameshifting in several viral genes, including IBV 1a/1b, HIV-1 gag-pol, and SFV 6K, and in Escherichia coli dnaX. The exact frameshifting route depends on the availability of aminoacyl-tRNAs: the ribosome normally slips into the -1-frame during tRNA translocation, but can also frameshift during decoding at condition when aminoacyl-tRNA is in limited supply. Different frameshifting routes and additional slippery sites allow viruses to maintain a constant production of their key proteins. The emerging idea that tRNA pools are important for frameshifting provides new direction for developing antiviral therapies.
    MeSH term(s) Frameshifting, Ribosomal ; RNA, Bacterial/genetics ; RNA, Messenger/genetics ; RNA, Viral/genetics
    Chemical Substances RNA, Bacterial ; RNA, Messenger ; RNA, Viral
    Keywords covid19
    Language English
    Publishing date 2019-06-20
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 212746-5
    ISSN 1873-3468 ; 0014-5793
    ISSN (online) 1873-3468
    ISSN 0014-5793
    DOI 10.1002/1873-3468.13478
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Vesicular Release and Uptake of Circular LSD1-RNAs from Non-Cancer and Cancer Lung Cells.

    Galang, Joelle Noriko / Shen, Yefeng / Koitzsch, Ulrike / Yu, Xiaojie / Eischeid-Scholz, Hannah / Bachurski, Daniel / Rau, Tilman T / Neppl, Christina / Herling, Marco / Bulimaga, Bianca / Vasyutina, Elena / Schweiger, Michal R / Büttner, Reinhard / Odenthal, Margarete / Anokhina, Maria M

    International journal of molecular sciences

    2023  Volume 24, Issue 18

    Abstract: Lysine-specific demethylase 1 (LSD1) is highly expressed in many cancer types and strongly associated with cancer progression and metastasis. Circular RNAs (circRNAs) are produced by back-splicing and influence the interactive RNA network by microRNA and ...

    Abstract Lysine-specific demethylase 1 (LSD1) is highly expressed in many cancer types and strongly associated with cancer progression and metastasis. Circular RNAs (circRNAs) are produced by back-splicing and influence the interactive RNA network by microRNA and protein sponging. In the present study, we aimedto identify circRNAs that derive from the LSD1-encoding
    Language English
    Publishing date 2023-09-12
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms241813981
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  3. Article ; Online: Identification of a small molecule inhibitor that stalls splicing at an early step of spliceosome activation.

    Sidarovich, Anzhalika / Will, Cindy L / Anokhina, Maria M / Ceballos, Javier / Sievers, Sonja / Agafonov, Dmitry E / Samatov, Timur / Bao, Penghui / Kastner, Berthold / Urlaub, Henning / Waldmann, Herbert / Lührmann, Reinhard

    eLife

    2017  Volume 6

    Abstract: Small molecule inhibitors of pre-mRNA splicing are important tools for identifying new spliceosome assembly intermediates, allowing a finer dissection of spliceosome dynamics and function. Here, we identified a small molecule that inhibits human pre-mRNA ...

    Abstract Small molecule inhibitors of pre-mRNA splicing are important tools for identifying new spliceosome assembly intermediates, allowing a finer dissection of spliceosome dynamics and function. Here, we identified a small molecule that inhibits human pre-mRNA splicing at an intermediate stage during conversion of pre-catalytic spliceosomal B complexes into activated B
    Language English
    Publishing date 2017-03-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.23533
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  4. Article ; Online: A spliceosome intermediate with loosely associated tri-snRNP accumulates in the absence of Prp28 ATPase activity.

    Boesler, Carsten / Rigo, Norbert / Anokhina, Maria M / Tauchert, Marcel J / Agafonov, Dmitry E / Kastner, Berthold / Urlaub, Henning / Ficner, Ralf / Will, Cindy L / Lührmann, Reinhard

    Nature communications

    2016  Volume 7, Page(s) 11997

    Abstract: The precise role of the spliceosomal DEAD-box protein Prp28 in higher eukaryotes remains unclear. We show that stable tri-snRNP association during pre-catalytic spliceosomal B complex formation is blocked by a dominant-negative hPrp28 mutant lacking ... ...

    Abstract The precise role of the spliceosomal DEAD-box protein Prp28 in higher eukaryotes remains unclear. We show that stable tri-snRNP association during pre-catalytic spliceosomal B complex formation is blocked by a dominant-negative hPrp28 mutant lacking ATPase activity. Complexes formed in the presence of ATPase-deficient hPrp28 represent a novel assembly intermediate, the pre-B complex, that contains U1, U2 and loosely associated tri-snRNP and is stalled before disruption of the U1/5'ss base pairing interaction, consistent with a role for hPrp28 in the latter. Pre-B and B complexes differ structurally, indicating that stable tri-snRNP integration is accompanied by substantial rearrangements in the spliceosome. Disruption of the U1/5'ss interaction alone is not sufficient to bypass the block by ATPase-deficient hPrp28, suggesting hPrp28 has an additional function at this stage of splicing. Our data provide new insights into the function of Prp28 in higher eukaryotes, and the requirements for stable tri-snRNP binding during B complex formation.
    MeSH term(s) Biocatalysis ; Cross-Linking Reagents/metabolism ; DEAD-box RNA Helicases/metabolism ; Electrophoresis, Gel, Two-Dimensional ; Humans ; Models, Biological ; Mutation/genetics ; RNA/metabolism ; Ribonucleoproteins, Small Nuclear/metabolism ; Saccharomyces cerevisiae/metabolism ; Spliceosomes/metabolism ; Spliceosomes/ultrastructure
    Chemical Substances Cross-Linking Reagents ; Ribonucleoproteins, Small Nuclear ; RNA (63231-63-0) ; DDX23 protein, human (EC 2.7.7.-) ; DEAD-box RNA Helicases (EC 3.6.4.13)
    Language English
    Publishing date 2016-07-05
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2041-1723
    ISSN (online) 2041-1723
    DOI 10.1038/ncomms11997
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  5. Article ; Online: Mapping of the second tetracycline binding site on the ribosomal small subunit of E.coli.

    Anokhina, Maria M / Barta, Andrea / Nierhaus, Knud H / Spiridonova, Vera A / Kopylov, Alexei M

    Nucleic acids research

    2004  Volume 32, Issue 8, Page(s) 2594–2597

    Abstract: Tetracycline blocks stable binding of aminoacyl-tRNA to the bacterial ribosomal A-site. Various tetracycline binding sites have been identified in crystals of the 30S ribosomal small subunit of Thermus thermophilus. Here we describe a direct photo- ... ...

    Abstract Tetracycline blocks stable binding of aminoacyl-tRNA to the bacterial ribosomal A-site. Various tetracycline binding sites have been identified in crystals of the 30S ribosomal small subunit of Thermus thermophilus. Here we describe a direct photo- affinity modification of the ribosomal small subunits of Escherichia coli with 7-[3H]-tetracycline. To select for specific interactions, an excess of the 30S subunits over tetracycline has been used. Primer extension analysis of the 16S rRNA revealed two sites of the modifications: C936 and C948. Considering available data on tetracycline interactions with the prokaryotic 30S subunits, including the presented data (E.coli), X-ray data (T.thermophilus) and genetic data (Helicobacter pylori, E.coli), a second high affinity tetracycline binding site is proposed within the 3'-major domain of the 16S rRNA, in addition to the A-site related tetracycline binding site.
    MeSH term(s) Anti-Bacterial Agents/chemistry ; Anti-Bacterial Agents/metabolism ; Binding Sites ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Models, Molecular ; Protein Synthesis Inhibitors/chemistry ; Protein Synthesis Inhibitors/metabolism ; RNA, Ribosomal, 16S/chemistry ; RNA, Ribosomal, 16S/metabolism ; Ribosomes/chemistry ; Ribosomes/metabolism ; Tetracycline/chemistry ; Tetracycline/metabolism
    Chemical Substances Anti-Bacterial Agents ; Protein Synthesis Inhibitors ; RNA, Ribosomal, 16S ; Tetracycline (F8VB5M810T)
    Language English
    Publishing date 2004-05-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkh583
    Database MEDical Literature Analysis and Retrieval System OnLINE

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