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Egger M, Bereiter R, Mair S, Micura R. Scaling Catalytic Contributions of Small Self-Cleaving Ribozymes. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202207590. [PMID: 38505292 PMCID: PMC10946891 DOI: 10.1002/ange.202207590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Indexed: 11/08/2022]
Abstract
Nucleolytic ribozymes utilize general acid-base catalysis to perform phosphodiester cleavage. In most ribozyme classes, a conserved active site guanosine is positioned to act as general base, thereby activating the 2'-OH group to attack the scissile phosphate (γ-catalysis). Here, we present an atomic mutagenesis study for the pistol ribozyme class. Strikingly, "general base knockout" by replacement of the guanine N1 atom by carbon results in only 2.7-fold decreased rate. Therefore, the common view that γ-catalysis critically depends on the N1 moiety becomes challenged. For pistol ribozymes we found that γ-catalysis is subordinate in overall catalysis, made up by two other catalytic factors (α and δ). Our approach allows scaling of the different catalytic contributions (α, β, γ, δ) with unprecedented precision and paves the way for a thorough mechanistic understanding of nucleolytic ribozymes with active site guanines.
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Affiliation(s)
- Michaela Egger
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Raphael Bereiter
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Stefan Mair
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
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2
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Egger M, Bereiter R, Mair S, Micura R. Scaling Catalytic Contributions of Small Self-Cleaving Ribozymes. Angew Chem Int Ed Engl 2022; 61:e202207590. [PMID: 35982640 PMCID: PMC9826390 DOI: 10.1002/anie.202207590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Indexed: 01/11/2023]
Abstract
Nucleolytic ribozymes utilize general acid-base catalysis to perform phosphodiester cleavage. In most ribozyme classes, a conserved active site guanosine is positioned to act as general base, thereby activating the 2'-OH group to attack the scissile phosphate (γ-catalysis). Here, we present an atomic mutagenesis study for the pistol ribozyme class. Strikingly, "general base knockout" by replacement of the guanine N1 atom by carbon results in only 2.7-fold decreased rate. Therefore, the common view that γ-catalysis critically depends on the N1 moiety becomes challenged. For pistol ribozymes we found that γ-catalysis is subordinate in overall catalysis, made up by two other catalytic factors (α and δ). Our approach allows scaling of the different catalytic contributions (α, β, γ, δ) with unprecedented precision and paves the way for a thorough mechanistic understanding of nucleolytic ribozymes with active site guanines.
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Affiliation(s)
- Michaela Egger
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Raphael Bereiter
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Stefan Mair
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
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Kim H, Kim M, Song H, Lee E. Indol‐2‐ylidene (IdY): Ambiphilic N‐Heterocyclic Carbene Derived from Indole**. Chemistry 2021; 27:3849-3854. [DOI: 10.1002/chem.202004879] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Hyunho Kim
- Department of Chemistry Pohang University of Science and Technology Pohang 790-784 Republic of Korea
| | - Minseop Kim
- Department of Chemistry Pohang University of Science and Technology Pohang 790-784 Republic of Korea
| | - Hayoung Song
- Department of Chemistry Pohang University of Science and Technology Pohang 790-784 Republic of Korea
| | - Eunsung Lee
- Department of Chemistry Pohang University of Science and Technology Pohang 790-784 Republic of Korea
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Teplova M, Falschlunger C, Krasheninina O, Egger M, Ren A, Patel DJ, Micura R. Crucial Roles of Two Hydrated Mg
2+
Ions in Reaction Catalysis of the Pistol Ribozyme. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201912522] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Marianna Teplova
- Structural Biology ProgramMemorial Sloan-Kettering Cancer Center New York New York 10065 USA
| | - Christoph Falschlunger
- Institute of Organic Chemistry and Center for Molecular BiosciencesLeopold-Franzens University Innrain 80–82 6020 Innsbruck Austria
| | - Olga Krasheninina
- Institute of Organic Chemistry and Center for Molecular BiosciencesLeopold-Franzens University Innrain 80–82 6020 Innsbruck Austria
| | - Michaela Egger
- Institute of Organic Chemistry and Center for Molecular BiosciencesLeopold-Franzens University Innrain 80–82 6020 Innsbruck Austria
| | - Aiming Ren
- Life Sciences InstituteZhejiang University Hangzhou Zhejiang 310058 China
| | - Dinshaw J. Patel
- Structural Biology ProgramMemorial Sloan-Kettering Cancer Center New York New York 10065 USA
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular BiosciencesLeopold-Franzens University Innrain 80–82 6020 Innsbruck Austria
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Teplova M, Falschlunger C, Krasheninina O, Egger M, Ren A, Patel DJ, Micura R. Crucial Roles of Two Hydrated Mg 2+ Ions in Reaction Catalysis of the Pistol Ribozyme. Angew Chem Int Ed Engl 2020; 59:2837-2843. [PMID: 31804735 PMCID: PMC7027511 DOI: 10.1002/anie.201912522] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Indexed: 12/19/2022]
Abstract
Pistol ribozymes constitute a new class of small self‐cleaving RNAs. Crystal structures have been solved, providing three‐dimensional snapshots along the reaction coordinate of pistol phosphodiester cleavage, corresponding to the pre‐catalytic state, a vanadate mimic of the transition state, and the product. The results led to the proposed underlying chemical mechanism. Importantly, a hydrated Mg2+ ion remains innersphere‐coordinated to N7 of G33 in all three states, and is consistent with its likely role as acid in general acid base catalysis (δ and β catalysis). Strikingly, the new structures shed light on a second hydrated Mg2+ ion that approaches the scissile phosphate from its binding site in the pre‐cleavage state to reach out for water‐mediated hydrogen bonding in the cyclophosphate product. The major role of the second Mg2+ ion appears to be the stabilization of product conformation. This study delivers a mechanistic understanding of ribozyme‐catalyzed backbone cleavage.
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Affiliation(s)
- Marianna Teplova
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA
| | - Christoph Falschlunger
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold-Franzens University, Innrain 80-82, 6020, Innsbruck, Austria
| | - Olga Krasheninina
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold-Franzens University, Innrain 80-82, 6020, Innsbruck, Austria
| | - Michaela Egger
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold-Franzens University, Innrain 80-82, 6020, Innsbruck, Austria
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold-Franzens University, Innrain 80-82, 6020, Innsbruck, Austria
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Neuner S, Falschlunger C, Fuchs E, Himmelstoss M, Ren A, Patel DJ, Micura R. Atom-Specific Mutagenesis Reveals Structural and Catalytic Roles for an Active-Site Adenosine and Hydrated Mg2+
in Pistol Ribozymes. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708679] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Sandro Neuner
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI); Leopold-Franzens University; Innrain 80-82 6020 Innsbruck Austria
| | - Christoph Falschlunger
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI); Leopold-Franzens University; Innrain 80-82 6020 Innsbruck Austria
| | - Elisabeth Fuchs
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI); Leopold-Franzens University; Innrain 80-82 6020 Innsbruck Austria
| | - Maximilian Himmelstoss
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI); Leopold-Franzens University; Innrain 80-82 6020 Innsbruck Austria
| | - Aiming Ren
- Life Science Institute; Zhejiang University; Hangzhou 310058 China
| | - Dinshaw J. Patel
- Structural Biology Program; Memorial Sloan-Kettering Cancer Center; New York NY 10065 USA
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI); Leopold-Franzens University; Innrain 80-82 6020 Innsbruck Austria
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Neuner S, Falschlunger C, Fuchs E, Himmelstoss M, Ren A, Patel DJ, Micura R. Atom-Specific Mutagenesis Reveals Structural and Catalytic Roles for an Active-Site Adenosine and Hydrated Mg 2+ in Pistol Ribozymes. Angew Chem Int Ed Engl 2017; 56:15954-15958. [PMID: 29098759 DOI: 10.1002/anie.201708679] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/14/2017] [Indexed: 12/15/2022]
Abstract
The pistol RNA motif represents a new class of self-cleaving ribozymes of yet unknown biological function. Our recent crystal structure of a pre-catalytic state of this RNA shows guanosine G40 and adenosine A32 close to the G53-U54 cleavage site. While the N1 of G40 is within 3.4 Å of the modeled G53 2'-OH group that attacks the scissile phosphate, thus suggesting a direct role in general acid-base catalysis, the function of A32 is less clear. We present evidence from atom-specific mutagenesis that neither the N1 nor N3 base positions of A32 are involved in catalysis. By contrast, the ribose 2'-OH of A32 seems crucial for the proper positioning of G40 through a H-bond network that involves G42 as a bridging unit between A32 and G40. We also found that disruption of the inner-sphere coordination of the active-site Mg2+ cation to N7 of G33 makes the ribozyme drastically slower. A mechanistic proposal is suggested, with A32 playing a structural role and hydrated Mg2+ playing a catalytic role in cleavage.
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Affiliation(s)
- Sandro Neuner
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University, Innrain 80-82, 6020, Innsbruck, Austria
| | - Christoph Falschlunger
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University, Innrain 80-82, 6020, Innsbruck, Austria
| | - Elisabeth Fuchs
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University, Innrain 80-82, 6020, Innsbruck, Austria
| | - Maximilian Himmelstoss
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University, Innrain 80-82, 6020, Innsbruck, Austria
| | - Aiming Ren
- Life Science Institute, Zhejiang University, Hangzhou, 310058, China
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University, Innrain 80-82, 6020, Innsbruck, Austria
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Gaines CS, York DM. Model for the Functional Active State of the TS Ribozyme from Molecular Simulation. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705608] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Colin S. Gaines
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research, and Department of Chemistry & Chemical Biology; Rutgers University; 174 Frelinghuysen Road Piscataway NJ 08854-8076 USA
| | - Darrin M. York
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research, and Department of Chemistry & Chemical Biology; Rutgers University; 174 Frelinghuysen Road Piscataway NJ 08854-8076 USA
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Gaines CS, York DM. Model for the Functional Active State of the TS Ribozyme from Molecular Simulation. Angew Chem Int Ed Engl 2017; 56:13392-13395. [PMID: 28763583 DOI: 10.1002/anie.201705608] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Indexed: 12/23/2022]
Abstract
Recently, a crystal structure has been reported of a new catalytic RNA, the TS ribozyme, that has been identified through comparative genomics and is believed to be a metalloribozyme having novel mechanistic features. Although this data provides invaluable structural information, analysis suggests a conformational change is required to arrive at a catalytically relevant state. We report results of molecular simulations that predict a spontaneous local rearrangement of the active site, leading to solution structures consistent with available functional data and providing competing mechanistic hypotheses that can be experimentally tested. The two competing hypotheses differ in the proposed identity of the catalytic general acid: either a water molecule coordinating a Mg2+ ion bound at the Watson-Crick edge of residue C7, or the N3 position of residue C7 itself.
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Affiliation(s)
- Colin S Gaines
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research, and Department of Chemistry & Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ, 08854-8076, USA
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research, and Department of Chemistry & Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ, 08854-8076, USA
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Kobori S, Yokobayashi Y. High-Throughput Mutational Analysis of a Twister Ribozyme. Angew Chem Int Ed Engl 2016; 55:10354-7. [PMID: 27461281 PMCID: PMC5113685 DOI: 10.1002/anie.201605470] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 07/04/2016] [Indexed: 01/17/2023]
Abstract
Recent discoveries of new classes of self‐cleaving ribozymes in diverse organisms have triggered renewed interest in the chemistry and biology of ribozymes. Functional analysis and engineering of ribozymes often involve performing biochemical assays on multiple ribozyme mutants. However, because each ribozyme mutant must be individually prepared and assayed, the number and variety of mutants that can be studied are severely limited. All of the single and double mutants of a twister ribozyme (a total of 10 296 mutants) were generated and assayed for their self‐cleaving activity by exploiting deep sequencing to count the numbers of cleaved and uncleaved sequences for every mutant. Interestingly, we found that the ribozyme is highly robust against mutations such that 71 % and 30 % of all single and double mutants, respectively, retain detectable activity under the assay conditions. It was also observed that the structural elements that comprise the ribozyme exhibit distinct sensitivity to mutations.
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Affiliation(s)
- Shungo Kobori
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904 0495, Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904 0495, Japan.
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Kobori S, Yokobayashi Y. High-Throughput Mutational Analysis of a Twister Ribozyme. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605470] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Shungo Kobori
- Nucleic Acid Chemistry and Engineering Unit; Okinawa Institute of Science and Technology Graduate University; Onna Okinawa 904 0495 Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit; Okinawa Institute of Science and Technology Graduate University; Onna Okinawa 904 0495 Japan
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