New classes of self-cleaving ribozymes revealed by comparative genomics analysis
Identifieur interne : 000677 ( Pmc/Curation ); précédent : 000676; suivant : 000678New classes of self-cleaving ribozymes revealed by comparative genomics analysis
Auteurs : Zasha Weinberg [États-Unis] ; Peter B. Kim [États-Unis] ; Tony H. Chen [États-Unis] ; Sanshu Li [États-Unis] ; Kimberly A. Harris [États-Unis] ; Christina E. Lünse [États-Unis] ; Ronald R. Breaker [États-Unis]Source :
- Nature chemical biology [ 1552-4450 ] ; 2015.
Abstract
Enzymes made of RNA catalyze reactions that are essential for protein synthesis and RNA processing. However, such natural ribozymes are exceedingly rare, as evident by the fact that the discovery rate for new classes has dropped to one per decade from about one per year during the 1980s. Indeed, only 11 distinct ribozyme classes have been experimentally validated to date. Recently, we recognized that self-cleaving ribozymes frequently associate with certain types of genes from bacteria. Herein this synteny was exploited to identify divergent architectures for two previously known ribozyme classes and to discover additional noncoding RNA motifs that are self-cleaving RNA candidates. Three new self-cleaving classes, named twister sister, pistol and hatchet, have been identified from this collection, suggesting that even more ribozymes remain hidden in modern cells.
Url:
DOI: 10.1038/nchembio.1846
PubMed: 26167874
PubMed Central: 4509812
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Lünse</name><affiliation wicri:level="1"><nlm:aff id="A2">Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520-8103, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520-8103</wicri:regionArea></affiliation></author><author><name sortKey="Breaker, Ronald R" sort="Breaker, Ronald R" uniqKey="Breaker R" first="Ronald R." last="Breaker">Ronald R. Breaker</name><affiliation wicri:level="1"><nlm:aff id="A1">Howard Hughes Medical Institute, Yale University, Box 208103, New Haven, CT 06520-8103, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Howard Hughes Medical Institute, Yale University, Box 208103, New Haven, CT 06520-8103</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="A2">Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520-8103, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520-8103</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="A3">Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103</wicri:regionArea></affiliation></author></analytic><series><title level="j">Nature chemical biology</title><idno type="ISSN">1552-4450</idno><idno type="eISSN">1552-4469</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P1">Enzymes made of RNA catalyze reactions that are essential for protein synthesis and RNA processing. However, such natural ribozymes are exceedingly rare, as evident by the fact that the discovery rate for new classes has dropped to one per decade from about one per year during the 1980s. Indeed, only 11 distinct ribozyme classes have been experimentally validated to date. Recently, we recognized that self-cleaving ribozymes frequently associate with certain types of genes from bacteria. Herein this synteny was exploited to identify divergent architectures for two previously known ribozyme classes and to discover additional noncoding RNA motifs that are self-cleaving RNA candidates. Three new self-cleaving classes, named twister sister, pistol and hatchet, have been identified from this collection, suggesting that even more ribozymes remain hidden in modern cells.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Benner, Sa" uniqKey="Benner S">SA Benner</name></author><author><name sortKey="Ellington, Ad" uniqKey="Ellington A">AD Ellington</name></author><author><name sortKey="Tauer, A" uniqKey="Tauer A">A Tauer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nissen, P" uniqKey="Nissen P">P Nissen</name></author><author><name sortKey="Hansen, J" uniqKey="Hansen J">J Hansen</name></author><author><name sortKey="Ban, N" uniqKey="Ban N">N Ban</name></author><author><name sortKey="Moore, Pb" uniqKey="Moore P">PB Moore</name></author><author><name sortKey="Steitz, Ta" uniqKey="Steitz T">TA Steitz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lambowitz, Am" uniqKey="Lambowitz A">AM Lambowitz</name></author><author><name sortKey="Caprara, Mg" uniqKey="Caprara M">MG Caprara</name></author><author><name sortKey="Zimmerly, S" uniqKey="Zimmerly S">S Zimmerly</name></author><author><name sortKey="Perlman, Ps" uniqKey="Perlman P">PS Perlman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ellis, Jc" uniqKey="Ellis J">JC Ellis</name></author><author><name sortKey="Brown, Jw" uniqKey="Brown J">JW Brown</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ferre D Mare, Ar" uniqKey="Ferre D Mare A">AR Ferre-D’Amare</name></author><author><name sortKey="Scott, Wg" uniqKey="Scott W">WG Scott</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Perreault, J" uniqKey="Perreault J">J Perreault</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Webb, Cht" uniqKey="Webb C">CHT Webb</name></author><author><name sortKey="Luptak, A" uniqKey="Luptak A">A Lupták</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Roth, A" uniqKey="Roth A">A Roth</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hutchins, Cj" uniqKey="Hutchins C">CJ Hutchins</name></author><author><name sortKey="Rathjen, Pd" uniqKey="Rathjen P">PD Rathjen</name></author><author><name sortKey="Forster, Ac" uniqKey="Forster A">AC Forster</name></author><author><name sortKey="Symons, Rh" uniqKey="Symons R">RH Symons</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Saville, Bj" uniqKey="Saville B">BJ Saville</name></author><author><name sortKey="Collins, Ra" uniqKey="Collins R">RA Collins</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Winkler, Wc" uniqKey="Winkler W">WC Winkler</name></author><author><name sortKey="Nahvi, A" uniqKey="Nahvi A">A Nahvi</name></author><author><name sortKey="Roth, A" uniqKey="Roth A">A Roth</name></author><author><name sortKey="Collins, Ja" uniqKey="Collins J">JA Collins</name></author><author><name sortKey="Breaker, Rr" uniqKey="Breaker R">RR Breaker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Salehi Ashtiani, K" uniqKey="Salehi Ashtiani K">K Salehi-Ashtiani</name></author><author><name sortKey="Luptak, A" uniqKey="Luptak A">A Lupták</name></author><author><name sortKey="Litovchick, A" uniqKey="Litovchick A">A Litovchick</name></author><author><name sortKey="Szostak, Jw" uniqKey="Szostak J">JW Szostak</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Marchler Bauer, A" uniqKey="Marchler Bauer A">A Marchler-Bauer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Johnson, Ls" uniqKey="Johnson L">LS Johnson</name></author><author><name sortKey="Eddy, Sr" uniqKey="Eddy S">SR Eddy</name></author><author><name sortKey="Portugaly, E" uniqKey="Portugaly E">E Portugaly</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yao, Z" uniqKey="Yao Z">Z Yao</name></author><author><name sortKey="Weinberg, Z" uniqKey="Weinberg Z">Z Weinberg</name></author><author><name sortKey="Ruzzo, Wl" uniqKey="Ruzzo W">WL Ruzzo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Weinberg, Z" uniqKey="Weinberg Z">Z Weinberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pace, Nr" uniqKey="Pace N">NR Pace</name></author><author><name sortKey="Thomas, Bc" uniqKey="Thomas B">BC Thomas</name></author><author><name sortKey="Crw" uniqKey="Crw">CRW</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Michel, F" uniqKey="Michel F">F Michel</name></author><author><name sortKey="Westhof, E" uniqKey="Westhof E">E Westhof</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Weinberg, Z" uniqKey="Weinberg Z">Z Weinberg</name></author><author><name sortKey="Perreault, J" uniqKey="Perreault J">J Perreault</name></author><author><name sortKey="Meyer, Mm" uniqKey="Meyer M">MM Meyer</name></author><author><name sortKey="Breaker, Rr" uniqKey="Breaker R">RR Breaker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Westhof, E" uniqKey="Westhof E">E Westhof</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sanchez Luque, Fj" uniqKey="Sanchez Luque F">FJ Sanchez-Luque</name></author><author><name sortKey="Lopez, Mc" uniqKey="Lopez M">MC Lopez</name></author><author><name sortKey="Macias, F" uniqKey="Macias F">F Macias</name></author><author><name sortKey="Alonso, C" uniqKey="Alonso C">C Alonso</name></author><author><name sortKey="Thomas, Mc" uniqKey="Thomas M">MC Thomas</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Breaker, Rr" uniqKey="Breaker R">RR Breaker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, Y" uniqKey="Liu Y">Y Liu</name></author><author><name sortKey="Wilson, Tj" uniqKey="Wilson T">TJ Wilson</name></author><author><name sortKey="Mcphee, Sa" uniqKey="Mcphee S">SA McPhee</name></author><author><name sortKey="Lilley, Dmj" uniqKey="Lilley D">DMJ Lilley</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Eiler, D" uniqKey="Eiler D">D Eiler</name></author><author><name sortKey="Wang, J" uniqKey="Wang J">J Wang</name></author><author><name sortKey="Steitz, Ta" uniqKey="Steitz T">TA Steitz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ren, A" uniqKey="Ren A">A Ren</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tang, J" uniqKey="Tang J">J Tang</name></author><author><name sortKey="Breaker, Rr" uniqKey="Breaker R">RR Breaker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Salehi Ashtiani, K" uniqKey="Salehi Ashtiani K">K Salehi-Ashtiani</name></author><author><name sortKey="Szostak, Jw" uniqKey="Szostak J">JW Szostak</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pruitt, Kd" uniqKey="Pruitt K">KD Pruitt</name></author><author><name sortKey="Tatusova, T" uniqKey="Tatusova T">T Tatusova</name></author><author><name sortKey="Maglott, Dr" uniqKey="Maglott D">DR Maglott</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Markowitz, Vm" uniqKey="Markowitz V">VM Markowitz</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Meyer, F" uniqKey="Meyer F">F Meyer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sun, S" uniqKey="Sun S">S Sun</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Benson, Da" uniqKey="Benson D">DA Benson</name></author><author><name sortKey="Karsch Mizrachi, I" uniqKey="Karsch Mizrachi I">I Karsch-Mizrachi</name></author><author><name sortKey="Lipman, Dj" uniqKey="Lipman D">DJ Lipman</name></author><author><name sortKey="Ostell, J" uniqKey="Ostell J">J Ostell</name></author><author><name sortKey="Wheeler, Dl" uniqKey="Wheeler D">DL Wheeler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Noguchi, H" uniqKey="Noguchi H">H Noguchi</name></author><author><name sortKey="Park, J" uniqKey="Park J">J Park</name></author><author><name sortKey="Takagi, T" uniqKey="Takagi T">T Takagi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhu, W" uniqKey="Zhu W">W Zhu</name></author><author><name sortKey="Lomsadze, A" uniqKey="Lomsadze A">A Lomsadze</name></author><author><name sortKey="Borodovsky, M" uniqKey="Borodovsky M">M Borodovsky</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Baker, Jl" uniqKey="Baker J">JL Baker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nawrocki, Ep" uniqKey="Nawrocki E">EP Nawrocki</name></author><author><name sortKey="Eddy, Sr" uniqKey="Eddy S">SR Eddy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Burge, Sw" uniqKey="Burge S">SW Burge</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lowe, Tm" uniqKey="Lowe T">TM Lowe</name></author><author><name sortKey="Eddy, Sr" uniqKey="Eddy S">SR Eddy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bland, C" uniqKey="Bland C">C Bland</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huang, Y" uniqKey="Huang Y">Y Huang</name></author><author><name sortKey="Gilna, P" uniqKey="Gilna P">P Gilna</name></author><author><name sortKey="Li, W" uniqKey="Li W">W Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gardner, Pp" uniqKey="Gardner P">PP Gardner</name></author><author><name sortKey="Barquist, L" uniqKey="Barquist L">L Barquist</name></author><author><name sortKey="Bateman, A" uniqKey="Bateman A">A Bateman</name></author><author><name sortKey="Nawrocki, Ep" uniqKey="Nawrocki E">EP Nawrocki</name></author><author><name sortKey="Weinberg, Z" uniqKey="Weinberg Z">Z Weinberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Weinberg, Z" uniqKey="Weinberg Z">Z Weinberg</name></author><author><name sortKey="Breaker, Rr" uniqKey="Breaker R">RR Breaker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ruminski, Dj" uniqKey="Ruminski D">DJ Ruminski</name></author><author><name sortKey="Webb, Ch" uniqKey="Webb C">CH Webb</name></author><author><name sortKey="Riccitelli, Nj" uniqKey="Riccitelli N">NJ Riccitelli</name></author><author><name sortKey="Luptak, A" uniqKey="Luptak A">A Luptak</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Qin, J" uniqKey="Qin J">J Qin</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
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<front><journal-meta><journal-id journal-id-type="nlm-journal-id">101231976</journal-id><journal-id journal-id-type="pubmed-jr-id">32624</journal-id><journal-id journal-id-type="nlm-ta">Nat Chem Biol</journal-id><journal-id journal-id-type="iso-abbrev">Nat. Chem. Biol.</journal-id><journal-title-group><journal-title>Nature chemical biology</journal-title></journal-title-group><issn pub-type="ppub">1552-4450</issn><issn pub-type="epub">1552-4469</issn></journal-meta><article-meta><article-id pub-id-type="pmid">26167874</article-id><article-id pub-id-type="pmc">4509812</article-id><article-id pub-id-type="doi">10.1038/nchembio.1846</article-id><article-id pub-id-type="manuscript">NIHMS690662</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>New classes of self-cleaving ribozymes revealed by comparative genomics analysis</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Weinberg</surname><given-names>Zasha</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref rid="FN2" ref-type="author-notes">*</xref></contrib><contrib contrib-type="author"><name><surname>Kim</surname><given-names>Peter B.</given-names></name><xref ref-type="aff" rid="A2">2</xref><xref rid="FN2" ref-type="author-notes">*</xref></contrib><contrib contrib-type="author"><name><surname>Chen</surname><given-names>Tony H.</given-names></name><xref ref-type="aff" rid="A3">3</xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Sanshu</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>Harris</surname><given-names>Kimberly A.</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>Lünse</surname><given-names>Christina E.</given-names></name><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>Breaker</surname><given-names>Ronald R.</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="aff" rid="A2">2</xref><xref ref-type="aff" rid="A3">3</xref></contrib></contrib-group><aff id="A1"><label>1</label>Howard Hughes Medical Institute, Yale University, Box 208103, New Haven, CT 06520-8103, USA</aff><aff id="A2"><label>2</label>Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520-8103, USA</aff><aff id="A3"><label>3</label>Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103, USA</aff><author-notes><corresp id="FN1">Correspondence should be addressed to R.R.B. (<email>ronald.breaker@yale.edu</email>)</corresp><fn id="FN2" fn-type="equal"><label>*</label><p>These authors contributed equally to this work.</p></fn></author-notes><pub-date pub-type="nihms-submitted"><day>23</day><month>5</month><year>2015</year></pub-date><pub-date pub-type="epub"><day>13</day><month>7</month><year>2015</year></pub-date><pub-date pub-type="ppub"><month>8</month><year>2015</year></pub-date><pub-date pub-type="pmc-release"><day>01</day><month>2</month><year>2016</year></pub-date><volume>11</volume><issue>8</issue><fpage>606</fpage><lpage>610</lpage><pmc-comment>elocation-id from pubmed: 10.1038/nchembio.1846</pmc-comment>
<permissions><license xlink:href="http://www.nature.com/authors/editorial_policies/license.html#terms"><license-p>Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:<ext-link ext-link-type="uri" xlink:href="http://www.nature.com/authors/editorial_policies/license.html#terms">http://www.nature.com/authors/editorial_policies/license.html#terms</ext-link></license-p></license></permissions><abstract><p id="P1">Enzymes made of RNA catalyze reactions that are essential for protein synthesis and RNA processing. However, such natural ribozymes are exceedingly rare, as evident by the fact that the discovery rate for new classes has dropped to one per decade from about one per year during the 1980s. Indeed, only 11 distinct ribozyme classes have been experimentally validated to date. Recently, we recognized that self-cleaving ribozymes frequently associate with certain types of genes from bacteria. Herein this synteny was exploited to identify divergent architectures for two previously known ribozyme classes and to discover additional noncoding RNA motifs that are self-cleaving RNA candidates. Three new self-cleaving classes, named twister sister, pistol and hatchet, have been identified from this collection, suggesting that even more ribozymes remain hidden in modern cells.</p></abstract></article-meta></front><floats-group><fig id="F1" orientation="portrait" position="float"><label>Figure 1</label><caption><title>Self-cleaving ribozyme candidates</title><p><bold>(a)</bold> Consensus sequence and secondary structure model for distinct variants of hammerhead ribozymes. R and Y represent purine and pyrimidine nucleotides, respectively. The site of ribozyme-mediated RNA cleavage (Clv) is identified by arrowhead. <bold>(b)</bold> Consensus sequence and secondary structure model for distinct variants of newly found variants of HDV ribozymes. <bold>(c)</bold> Consensus models for twister and twister sister ribozymes. Noncanonical base pairs and other additional structural interactions for twister ribozymes recently revealed by biophysical studies are not included.</p></caption><graphic xlink:href="nihms690662f1"></graphic></fig><fig id="F2" orientation="portrait" position="float"><label>Figure 2</label><caption><title>Activity of a bimolecular twister sister ribozyme</title><p><bold>(a)</bold> Sequence and secondary structure model of a bimolecular construct derived from TS-1 (<xref rid="SD1" ref-type="supplementary-material">Supplementary Fig. 1</xref>). Highly conserved nucleotides are depicted in red and Clv designates the cleavage site. Lowercase letters identify non-native guanosine residues that were added to facilitate <italic>in vitro</italic> transcription. <bold>(b)</bold> PAGE separation of bimolecular TS-1 ribozyme assay products demonstrating the requirement for the enzyme strand and for divalent metal ions. S designates the 5′ <sup>32</sup>P-labeled 23-nucleotide RNA substrate and 5′ Clv identifies the cleavage product. Reactions were conducted as described (see <bold>Online Methods</bold>) with variations noted. <bold>(c)</bold> PAGE separation of ribozyme cleavage products. S designates the 5′ <sup>32</sup>P-labeled 23-nucleotide RNA substrate, and C13 identifies the 5′ <sup>32</sup>P-labeled fragment band produced by incubation with excess unlabeled ribozyme for 30 min (Rxn lane). NR, T1 and <sup>−</sup>OH lanes designate no reaction, RNase T1 partial digestion (cleaves after G nucleotides), or partial alkaline digestion (cleaves all internucleotides), respectively. <bold>(d)</bold> Mass spectrum analysis of bimolecular TS-1 cleavage reaction products were examined by mass spectrometry (see <bold>Online Methods</bold>). The second largest peak near the 5′ Clv annotation is the spontaneously formed opened version (observed mass, 4304.576) of the initial 2′,3′-cyclic phosphate product. Intensity is abbreviated int. <bold>(e)</bold> The dependence of twister sister rate constants on pH. <bold>(f)</bold> The dependence of Mg<sup>2+</sup> concentration on twister sister rate constants. A version of this figure containing full-length gel images is shown in <xref rid="SD1" ref-type="supplementary-material">Supplementary Figure 11</xref>.</p></caption><graphic xlink:href="nihms690662f2"></graphic></fig><fig id="F3" orientation="portrait" position="float"><label>Figure 3</label><caption><title>Structure and activity of pistol self-cleaving ribozymes</title><p><bold>(a)</bold> Consensus sequence and secondary structure model for pistol self-cleaving ribozymes based on 449 unique examples. Annotations are as described in <xref rid="F1" ref-type="fig">Fig 1a</xref>. (b) A bimolecular pistol ribozyme construct based on a representative from the bacterium <italic>Aliistipes putredinis</italic>. Annotations are as described in the legend for <xref rid="F2" ref-type="fig">Fig. 2a</xref>. (c) Pistol ribozyme activity and cleavage site mapping of the <italic>A. putredinis</italic> bimolecular construct wherein the substrate RNA (S) was 5′-labeled with <sup>32</sup>P. Other annotations are as described in the legend to <xref rid="F2" ref-type="fig">Fig. 2c</xref>. Trace amount of substrate was incubated with excess WT or M10 enzyme strand either with (+) or without (−) 20 mM MgCl<sub>2</sub>. RNA cleavage products were separated by denaturing 20% PAGE. A version of this figure containing full-length gel images is shown in <xref rid="SD1" ref-type="supplementary-material">Supplementary Figure 12</xref>.</p></caption><graphic xlink:href="nihms690662f3"></graphic></fig><fig id="F4" orientation="portrait" position="float"><label>Figure 4</label><caption><title>Structure and activity of hatchet self-cleaving ribozymes</title><p><bold>(a)</bold> Consensus sequence and secondary structure model for hatchet self-cleaving ribozymes based on 159 unique examples. <bold>(b)</bold> A bimolecular hatchet ribozyme construct based on a representative from a metagenomic DNA sample. <bold>(c)</bold> Hatchet ribozyme activity and cleavage site mapping of the bimolecular hatchet ribozyme construct. A version of this figure containing full-length gel images is shown in <xref rid="SD1" ref-type="supplementary-material">Supplementary Figure 13</xref>.</p></caption><graphic xlink:href="nihms690662f4"></graphic></fig></floats-group></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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