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28S Ribosomal RNA

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Wang-yi Liu – One of the best experts on this subject based on the ideXlab platform.

  • In vitro interaction of eukaryotic elongation factor 2 with synthetic oligoribonucleotide that mimics GTPase domain of rat 28S Ribosomal RNA.
    The International Journal of Biochemistry & Cell Biology, 2002
    Co-Authors: Shuang Tang, Wang-yi Liu

    Abstract:

    Eukaryotic elongation factor 2 (eEF2) catalyzed the translocation of peptidyl-tRNA from the Ribosomal A site to the P site. In this paper, the interaction between eEF2 and GTD RNA, a synthetic oligoribonucleotide that mimicked the GTPase domain of rat 28S Ribosomal RNA, was studied in vitro. The purified eEF2 could bind to GTD RNA, forming a stable complex. Transfer RNA competed with GTD RNA in binding to eEF2, whereas poly(A), poly(U) and poly(I, C) did not interfere with the interaction between eEF2 and GTD RNA, demonstrating that the tertiary structure of RNA might be necessary for the recognition of and binding to eEF2. The complex formation of eEF2 with GTD RNA was inhibited by SRD RNA, a synthetic oligoribonucleotide mimic of Sarcin/Ricin domain RNA of rat 28S RNA. Similarly, GTD RNA inhibited the interaction between eEF2 and SRD RNA. This fact implies that these small oligoribonucleotides probably share similar recognition or binding identity elements in their tertiary structures. In addition, the binding of eEF2 to GTD RNA could be obviously weakened by the ADP-ribosylation of eEF2 with diphtheria toxin. These results indicate that eEF2 behaves differently from prokaryotic EF-G in binding to Ribosomal RNA.

  • Eukaryotic elongation factor 2 can bind to the synthetic oligoribonucleotide that mimics sarcin/ricin domain of rat 28S Ribosomal RNA
    Molecular and Cellular Biochemistry, 2001
    Co-Authors: Shuang Tang, Wang-yi Liu, Kang-cheng Ruan

    Abstract:

    Eukaryotic elongation factor 2 (eEF2) catalyzes the translocation of peptidyl-tRNA from the A site to P site by binding to the ribosome. In this work, the complex formation of rat liver eEF2 with a synthetic oligoribonucleotide (SRD RNA) that mimics sarcin/ricin domain of rat 28S Ribosomal RNA is invested in vitro. Purified eEF2 can specifically bind SRD RNA to form a stable complex. tRNA competes with SRD RNA in binding to eEF2 in a less extent. Pretreatment of eEF2 with GDP or ADP-ribosylation of eEF2 by diphtheria toxin can obviously reduce the ability of eEF2 to form the complex with the synthetic oligoribonucleotide. These results indicate that eEF2 is likely to bind directly to the sarcin/ricin domain of 28S Ribosomal RNA in the process of protein synthesis.

  • eukaryotic elongation factor 2 can bind to the synthetic oligoribonucleotide that mimics sarcin ricin domain of rat 28S Ribosomal RNA
    Molecular and Cellular Biochemistry, 2001
    Co-Authors: Shuang Tang, Wang-yi Liu, Kang-cheng Ruan

    Abstract:

    Eukaryotic elongation factor 2 (eEF2) catalyzes the translocation of peptidyl-tRNA from the A site to P site by binding to the ribosome. In this work, the complex formation of rat liver eEF2 with a synthetic oligoribonucleotide (SRD RNA) that mimics sarcin/ricin domain of rat 28S Ribosomal RNA is invested in vitro. Purified eEF2 can specifically bind SRD RNA to form a stable complex. tRNA competes with SRD RNA in binding to eEF2 in a less extent. Pretreatment of eEF2 with GDP or ADP-ribosylation of eEF2 by diphtheria toxin can obviously reduce the ability of eEF2 to form the complex with the synthetic oligoribonucleotide. These results indicate that eEF2 is likely to bind directly to the sarcin/ricin domain of 28S Ribosomal RNA in the process of protein synthesis.

I.g. Wool – One of the best experts on this subject based on the ideXlab platform.

  • The conformation of the sarcin/ricin loop from 28S Ribosomal RNA
    Proceedings of the National Academy of Sciences, 1993
    Co-Authors: Alexander A. Szewczak, Peter B. Moore, Y L Chang, I.g. Wool

    Abstract:

    Abstract
    The sarcin/ricin loop is a highly conserved sequence found in the RNA of all large Ribosomal subunits. The cytotoxins alpha-sarcin and ricin both inactivate ribosomes by cleaving a single bond in that loop. Once it has been attacked, ribosomes no longer interact with elongation factors properly, and translation stops. We have determined the conformation of the sarcin/ricin loop by multinuclear NMR spectroscopy using E73, a 29-nucleotide RNA that has the sarcin/ricin loop sequence and that is sensitive to both toxins in vitro. The sarcin/ricin loop has a compact structure that contains several purine.purine base pairs, a GAGA tetraloop, and a bulged guanosine adjacent to a reverse Hoogsteen A.U pair. It is stabilized by an unusual set of cross-strand base-stacking interactions and imino proton to phosphate oxygen hydrogen bonds. In addition to having interesting structural features, this model explains many of the biochemical observations made about the loop’s structure and its reactivity with cytotoxins, and it sheds light on the loop’s interactions with elongation factors.

  • the conformation of the sarcin ricin loop from 28S Ribosomal RNA
    Proceedings of the National Academy of Sciences of the United States of America, 1993
    Co-Authors: Alexander A. Szewczak, Peter B. Moore, Y L Chang, I.g. Wool

    Abstract:

    Abstract
    The sarcin/ricin loop is a highly conserved sequence found in the RNA of all large Ribosomal subunits. The cytotoxins alpha-sarcin and ricin both inactivate ribosomes by cleaving a single bond in that loop. Once it has been attacked, ribosomes no longer interact with elongation factors properly, and translation stops. We have determined the conformation of the sarcin/ricin loop by multinuclear NMR spectroscopy using E73, a 29-nucleotide RNA that has the sarcin/ricin loop sequence and that is sensitive to both toxins in vitro. The sarcin/ricin loop has a compact structure that contains several purine.purine base pairs, a GAGA tetraloop, and a bulged guanosine adjacent to a reverse Hoogsteen A.U pair. It is stabilized by an unusual set of cross-strand base-stacking interactions and imino proton to phosphate oxygen hydrogen bonds. In addition to having interesting structural features, this model explains many of the biochemical observations made about the loop’s structure and its reactivity with cytotoxins, and it sheds light on the loop’s interactions with elongation factors.

Kang-cheng Ruan – One of the best experts on this subject based on the ideXlab platform.

  • Eukaryotic elongation factor 2 can bind to the synthetic oligoribonucleotide that mimics sarcin/ricin domain of rat 28S Ribosomal RNA
    Molecular and Cellular Biochemistry, 2001
    Co-Authors: Shuang Tang, Wang-yi Liu, Kang-cheng Ruan

    Abstract:

    Eukaryotic elongation factor 2 (eEF2) catalyzes the translocation of peptidyl-tRNA from the A site to P site by binding to the ribosome. In this work, the complex formation of rat liver eEF2 with a synthetic oligoribonucleotide (SRD RNA) that mimics sarcin/ricin domain of rat 28S Ribosomal RNA is invested in vitro. Purified eEF2 can specifically bind SRD RNA to form a stable complex. tRNA competes with SRD RNA in binding to eEF2 in a less extent. Pretreatment of eEF2 with GDP or ADP-ribosylation of eEF2 by diphtheria toxin can obviously reduce the ability of eEF2 to form the complex with the synthetic oligoribonucleotide. These results indicate that eEF2 is likely to bind directly to the sarcin/ricin domain of 28S Ribosomal RNA in the process of protein synthesis.

  • eukaryotic elongation factor 2 can bind to the synthetic oligoribonucleotide that mimics sarcin ricin domain of rat 28S Ribosomal RNA
    Molecular and Cellular Biochemistry, 2001
    Co-Authors: Shuang Tang, Wang-yi Liu, Kang-cheng Ruan

    Abstract:

    Eukaryotic elongation factor 2 (eEF2) catalyzes the translocation of peptidyl-tRNA from the A site to P site by binding to the ribosome. In this work, the complex formation of rat liver eEF2 with a synthetic oligoribonucleotide (SRD RNA) that mimics sarcin/ricin domain of rat 28S Ribosomal RNA is invested in vitro. Purified eEF2 can specifically bind SRD RNA to form a stable complex. tRNA competes with SRD RNA in binding to eEF2 in a less extent. Pretreatment of eEF2 with GDP or ADP-ribosylation of eEF2 by diphtheria toxin can obviously reduce the ability of eEF2 to form the complex with the synthetic oligoribonucleotide. These results indicate that eEF2 is likely to bind directly to the sarcin/ricin domain of 28S Ribosomal RNA in the process of protein synthesis.

  • Non-specific deadenylation and deguanylation of naked RNA catalyzed by ricin under acidic condition.
    Biochimica et Biophysica Acta (BBA) – Gene Structure and Expression, 2001
    Co-Authors: Shuang Tang, Wang-yi Liu, Liang Xie, Fa-jian Hou, Kang-cheng Ruan

    Abstract:

    Ricin A-chain catalyzes the hydrolysis of the N-glycosidic bond of a conserved adenosine residue at position 4324 in the sarcin/ricin domain of 28S RNA of rat ribosome. The GAGA tetraloop closed by C-G pairs is required for recognition of the cleavage site on 28S Ribosomal RNA by ricin A-chain. In this study, ricin A-chain (reduced ricin) exhibits specific depurination on a synthetic oligoribonucleotide (named SRD RNA) mimic of the sarcin/ricin domain of rat 28S Ribosomal RNA under neutral and weak acidic conditions. Furthermore, the activity of intact ricin is also similar to that of ricin A-chain. However, under more acidic conditions, both enzymes lose their site specificity. The alteration in specificity of depurination is not dependent on the GAGA tetraloop of SRD RNA. A higher concentration of KCI inhibits the non-specific N-glycosidase activity much more than the specific activity of ricin A-chain. In addition, characterization of depurination sites by RNA sequencing reveals that under acidic conditions ricin A-chain can release not only adenines, but also guanines from SRD RNA or 5S Ribosomal RNA. This is the first report of the non-specific deadenylation and deguanylation activity of ricin A-chain to the naked RNA under acidic conditions. (C) 2001 Elsevier Science B.V. All rights reserved.