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Elder JJH, Papadopoulos R, Hayne CK, Stanley RE. The making and breaking of tRNAs by ribonucleases. Trends Genet 2024; 40:511-525. [PMID: 38641471 PMCID: PMC11152995 DOI: 10.1016/j.tig.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/21/2024]
Abstract
Ribonucleases (RNases) play important roles in supporting canonical and non-canonical roles of tRNAs by catalyzing the cleavage of the tRNA phosphodiester backbone. Here, we highlight how recent advances in cryo-electron microscopy (cryo-EM), protein structure prediction, reconstitution experiments, tRNA sequencing, and other studies have revealed new insight into the nucleases that process tRNA. This represents a very diverse group of nucleases that utilize distinct mechanisms to recognize and cleave tRNA during different stages of a tRNA's life cycle including biogenesis, fragmentation, surveillance, and decay. In this review, we provide a synthesis of the structure, mechanism, regulation, and modes of tRNA recognition by tRNA nucleases, along with open questions for future investigation.
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Affiliation(s)
- Jessica J H Elder
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Ry Papadopoulos
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA; Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Cassandra K Hayne
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
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2
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Ellaway JIJ, Anyango S, Nair S, Zaki HA, Nadzirin N, Powell HR, Gutmanas A, Varadi M, Velankar S. Identifying protein conformational states in the Protein Data Bank: Toward unlocking the potential of integrative dynamics studies. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:034701. [PMID: 38774441 PMCID: PMC11106648 DOI: 10.1063/4.0000251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/08/2024] [Indexed: 05/24/2024]
Abstract
Studying protein dynamics and conformational heterogeneity is crucial for understanding biomolecular systems and treating disease. Despite the deposition of over 215 000 macromolecular structures in the Protein Data Bank and the advent of AI-based structure prediction tools such as AlphaFold2, RoseTTAFold, and ESMFold, static representations are typically produced, which fail to fully capture macromolecular motion. Here, we discuss the importance of integrating experimental structures with computational clustering to explore the conformational landscapes that manifest protein function. We describe the method developed by the Protein Data Bank in Europe - Knowledge Base to identify distinct conformational states, demonstrate the resource's primary use cases, through examples, and discuss the need for further efforts to annotate protein conformations with functional information. Such initiatives will be crucial in unlocking the potential of protein dynamics data, expediting drug discovery research, and deepening our understanding of macromolecular mechanisms.
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Affiliation(s)
- Joseph I. J. Ellaway
- Protein Data Bank in Europe, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Stephen Anyango
- Protein Data Bank in Europe, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Sreenath Nair
- Protein Data Bank in Europe, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Hossam A. Zaki
- The Warren Alpert Medical School of Brown University, Providence, Rhode Island 02903, USA
| | - Nurul Nadzirin
- Protein Data Bank in Europe, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Harold R. Powell
- Imperial College London, Department of Life Sciences, London, United Kingdom
| | - Aleksandras Gutmanas
- WaveBreak Therapeutics Ltd., Clarendon House, Clarendon Road, Cambridge, United Kingdom
| | - Mihaly Varadi
- Protein Data Bank in Europe, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Sameer Velankar
- Protein Data Bank in Europe, European Bioinformatics Institute, Hinxton, United Kingdom
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3
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Krempl C, Lazzaretti D, Sprangers R. A structural biology view on the enzymes involved in eukaryotic mRNA turnover. Biol Chem 2023; 404:1101-1121. [PMID: 37709756 DOI: 10.1515/hsz-2023-0182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/24/2023] [Indexed: 09/16/2023]
Abstract
The cellular environment contains numerous ribonucleases that are dedicated to process mRNA transcripts that have been targeted for degradation. Here, we review the three dimensional structures of the ribonuclease complexes (Pan2-Pan3, Ccr4-Not, Xrn1, exosome) and the mRNA decapping enzymes (Dcp2, DcpS) that are involved in mRNA turnover. Structures of major parts of these proteins have been experimentally determined. These enzymes and factors do not act in isolation, but are embedded in interaction networks which regulate enzyme activity and ensure that the appropriate substrates are recruited. The structural details of the higher order complexes that form can, in part, be accurately deduced from known structural data of sub-complexes. Interestingly, many of the ribonuclease and decapping enzymes have been observed in structurally different conformations. Together with experimental data, this highlights that structural changes are often important for enzyme function. We conclude that the known structural data of mRNA decay factors provide important functional insights, but that static structural data needs to be complemented with information regarding protein motions to complete the picture of how transcripts are turned over. In addition, we highlight multiple aspects that influence mRNA turnover rates, but that have not been structurally characterized so far.
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Affiliation(s)
- Christina Krempl
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Daniela Lazzaretti
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Remco Sprangers
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
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4
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Schneider C, Bohnsack KE. Caught in the act-Visualizing ribonucleases during eukaryotic ribosome assembly. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1766. [PMID: 36254602 DOI: 10.1002/wrna.1766] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 07/20/2023]
Abstract
Ribosomes are essential macromolecular machines responsible for translating the genetic information encoded in mRNAs into proteins. Ribosomes are composed of ribosomal RNAs and proteins (rRNAs and RPs) and the rRNAs fulfill both catalytic and architectural functions. Excision of the mature eukaryotic rRNAs from their precursor transcript is achieved through a complex series of endoribonucleolytic cleavages and exoribonucleolytic processing steps that are precisely coordinated with other aspects of ribosome assembly. Many ribonucleases involved in pre-rRNA processing have been identified and pre-rRNA processing pathways are relatively well defined. However, momentous advances in cryo-electron microscopy have recently enabled structural snapshots of various pre-ribosomal particles from budding yeast (Saccharomyces cerevisiae) and human cells to be captured and, excitingly, these structures not only allow pre-rRNAs to be observed before and after cleavage events, but also enable ribonucleases to be visualized on their target RNAs. These structural views of pre-rRNA processing in action allow a new layer of understanding of rRNA maturation and how it is coordinated with other aspects of ribosome assembly. They illuminate mechanisms of target recognition by the diverse ribonucleases involved and reveal how the cleavage/processing activities of these enzymes are regulated. In this review, we discuss the new insights into pre-rRNA processing gained by structural analyses and the growing understanding of the mechanisms of ribonuclease regulation. This article is categorized under: Translation > Ribosome Biogenesis RNA Processing > rRNA Processing.
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Affiliation(s)
- Claudia Schneider
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
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5
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Overbeck JH, Vögele J, Nussbaumer F, Duchardt‐Ferner E, Kreutz C, Wöhnert J, Sprangers R. 19F NMR Untersuchung des Konformationsaustauschs mehrerer Zustände im synthetischen Neomycin-bindenden Riboschalter. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202218064. [PMID: 38516132 PMCID: PMC10953372 DOI: 10.1002/ange.202218064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Indexed: 03/29/2023]
Abstract
AbstractDer synthetische Neomycin‐bindende Riboschalter interagiert mit seinem Liganden Neomycin sowie mit den verwandten Antibiotika Ribostamycin und Paromomycin. Die Bindung dieser Aminoglykoside induziert sehr ähnliche Grundzustandsstrukturen in der RNA, allerdings kann nur Neomycin die Initiierung der Translation effizient unterdrücken. Der molekulare Ursprung dieser Unterschiede wurde auf Unterschiede in der Dynamik der Ligand‐Riboschalter‐Komplexe zurückgeführt. In diesem Artikel kombinieren wir fünf komplementäre fluorbasierte NMR‐Methoden, um die Dynamik der drei Riboschalter‐Komplexe im Sekunden‐ bis Mikrosekundenbereich genau zu quantifizieren. Unsere Daten offenbaren komplexe Austauschprozesse mit bis zu vier strukturell unterschiedlichen Zuständen. Wir interpretieren unsere Ergebnisse in einem Modell, das ein Zusammenspiel zwischen verschiedenen chemischen Gruppen in den Antibiotika und spezifischen Basen im Riboschalter zeigt. Allgemeiner unterstreichen unsere Daten das Potenzial von 19F NMR‐Methoden, komplexe Austauschprozesse mit mehreren angeregten Zuständen zu charakterisieren.
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Affiliation(s)
- Jan H. Overbeck
- Department of Biophysics IRegensburg Center for BiochemistryUniversity of RegensburgUniversitätsstrasse 3193051RegensburgDeutschland
| | - Jennifer Vögele
- Institute for Molecular BiosciencesGoethe-University FrankfurtMax-von-Laue-Str. 960438Frankfurt/M.Deutschland
| | - Felix Nussbaumer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnsbruckÖsterreich
| | - Elke Duchardt‐Ferner
- Institute for Molecular BiosciencesGoethe-University FrankfurtMax-von-Laue-Str. 960438Frankfurt/M.Deutschland
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnsbruckÖsterreich
| | - Jens Wöhnert
- Institute for Molecular BiosciencesGoethe-University FrankfurtMax-von-Laue-Str. 960438Frankfurt/M.Deutschland
| | - Remco Sprangers
- Department of Biophysics IRegensburg Center for BiochemistryUniversity of RegensburgUniversitätsstrasse 3193051RegensburgDeutschland
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6
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Overbeck JH, Vögele J, Nussbaumer F, Duchardt‐Ferner E, Kreutz C, Wöhnert J, Sprangers R. Multi-Site Conformational Exchange in the Synthetic Neomycin-Sensing Riboswitch Studied by 19 F NMR. Angew Chem Int Ed Engl 2023; 62:e202218064. [PMID: 36970768 PMCID: PMC10952710 DOI: 10.1002/anie.202218064] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/24/2023] [Accepted: 03/22/2023] [Indexed: 03/28/2023]
Abstract
The synthetic neomycin-sensing riboswitch interacts with its cognate ligand neomycin as well as with the related antibiotics ribostamycin and paromomycin. Binding of these aminoglycosides induces a very similar ground state structure in the RNA, however, only neomycin can efficiently repress translation initiation. The molecular origin of these differences has been traced back to differences in the dynamics of the ligand:riboswitch complexes. Here, we combine five complementary fluorine based NMR methods to accurately quantify seconds to microseconds dynamics in the three riboswitch complexes. Our data reveal complex exchange processes with up to four structurally different states. We interpret our findings in a model that shows an interplay between different chemical groups in the antibiotics and specific bases in the riboswitch. More generally, our data underscore the potential of 19 F NMR methods to characterize complex exchange processes with multiple excited states.
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Affiliation(s)
- Jan H. Overbeck
- Department of Biophysics IRegensburg Center for BiochemistryUniversity of RegensburgUniversitätsstrasse 3193051RegensburgGermany
| | - Jennifer Vögele
- Institute for Molecular BiosciencesGoethe-University FrankfurtMax-von-Laue-Str. 960438Frankfurt/M.Germany
| | - Felix Nussbaumer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnsbruckAustria
| | - Elke Duchardt‐Ferner
- Institute for Molecular BiosciencesGoethe-University FrankfurtMax-von-Laue-Str. 960438Frankfurt/M.Germany
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnsbruckAustria
| | - Jens Wöhnert
- Institute for Molecular BiosciencesGoethe-University FrankfurtMax-von-Laue-Str. 960438Frankfurt/M.Germany
| | - Remco Sprangers
- Department of Biophysics IRegensburg Center for BiochemistryUniversity of RegensburgUniversitätsstrasse 3193051RegensburgGermany
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7
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Krempl C, Wurm JP, Beck Erlach M, Kremer W, Sprangers R. Insights into the Structure of Invisible Conformations of Large Methyl Group Labeled Molecular Machines from High Pressure NMR. J Mol Biol 2023; 435:167922. [PMID: 37330282 DOI: 10.1016/j.jmb.2022.167922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 06/19/2023]
Abstract
Most proteins are highly flexible and can adopt conformations that deviate from the energetically most favorable ground state. Structural information on these lowly populated, alternative conformations is often lacking, despite the functional importance of these states. Here, we study the pathway by which the Dcp1:Dcp2 mRNA decapping complex exchanges between an autoinhibited closed and an open conformation. We make use of methyl Carr-Purcell-Meiboom-Gill (CPMG) NMR relaxation dispersion (RD) experiments that report on the population of the sparsely populated open conformation as well as on the exchange rate between the two conformations. To obtain volumetric information on the open conformation as well as on the transition state structure we made use of RD measurements at elevated pressures. We found that the open Dcp1:Dcp2 conformation has a lower molecular volume than the closed conformation and that the transition state is close in volume to the closed state. In the presence of ATP the volume change upon opening of the complex increases and the volume of the transition state lies in-between the volumes of the closed and open state. These findings show that ATP has an effect on the volume changes that are associated with the opening-closing pathway of the complex. Our results highlight the strength of pressure dependent NMR methods to obtain insights into structural features of protein conformations that are not directly observable. As our work makes use of methyl groups as NMR probes we conclude that the applied methodology is also applicable to high molecular weight complexes.
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Affiliation(s)
- Christina Krempl
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Jan Philip Wurm
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Markus Beck Erlach
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Werner Kremer
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Remco Sprangers
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany.
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8
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Krempl C, Sprangers R. Assessing the applicability of 19F labeled tryptophan residues to quantify protein dynamics. JOURNAL OF BIOMOLECULAR NMR 2023; 77:55-67. [PMID: 36639431 PMCID: PMC10149471 DOI: 10.1007/s10858-022-00411-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/20/2022] [Indexed: 05/03/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited to study the dynamics of biomolecules in solution. Most NMR studies exploit the spins of proton, carbon and nitrogen isotopes, as these atoms are highly abundant in proteins and nucleic acids. As an alternative and complementary approach, fluorine atoms can be introduced into biomolecules at specific sites of interest. These labels can then be used as sensitive probes for biomolecular structure, dynamics or interactions. Here, we address if the replacement of tryptophan with 5-fluorotryptophan residues has an effect on the overall dynamics of proteins and if the introduced fluorine probe is able to accurately report on global exchange processes. For the four different model proteins (KIX, Dcp1, Dcp2 and DcpS) that we examined, we established that 15N CPMG relaxation dispersion or EXSY profiles are not affected by the 5-fluorotryptophan, indicating that this replacement of a proton with a fluorine has no effect on the protein motions. However, we found that the motions that the 5-fluorotryptophan reports on can be significantly faster than the backbone motions. This implies that care needs to be taken when interpreting fluorine relaxation data in terms of global protein motions. In summary, our results underscore the great potential of fluorine NMR methods, but also highlight potential pitfalls that need to be considered.
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Affiliation(s)
- Christina Krempl
- Department of Biophysics I, Regensburg Center for Biochemistry, University of Regensburg, 93053, Regensburg, Germany
| | - Remco Sprangers
- Department of Biophysics I, Regensburg Center for Biochemistry, University of Regensburg, 93053, Regensburg, Germany.
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Deng M, Wang X, Xiong Z, Tang P. Control of RNA degradation in cell fate decision. Front Cell Dev Biol 2023; 11:1164546. [PMID: 37025171 PMCID: PMC10070868 DOI: 10.3389/fcell.2023.1164546] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/03/2023] [Indexed: 04/08/2023] Open
Abstract
Cell fate is shaped by a unique gene expression program, which reflects the concerted action of multilayered precise regulation. Substantial research attention has been paid to the contribution of RNA biogenesis to cell fate decisions. However, increasing evidence shows that RNA degradation, well known for its function in RNA processing and the surveillance of aberrant transcripts, is broadly engaged in cell fate decisions, such as maternal-to-zygotic transition (MZT), stem cell differentiation, or somatic cell reprogramming. In this review, we first look at the diverse RNA degradation pathways in the cytoplasm and nucleus. Then, we summarize how selective transcript clearance is regulated and integrated into the gene expression regulation network for the establishment, maintenance, and exit from a special cellular state.
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Affiliation(s)
- Mingqiang Deng
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiwei Wang
- Guangzhou Laboratory, Guangzhou, Guangdong, China
| | - Zhi Xiong
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou, China
| | - Peng Tang
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- *Correspondence: Peng Tang,
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