1
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Yared MJ, Yoluç Y, Catala M, Tisné C, Kaiser S, Barraud P. Different modification pathways for m1A58 incorporation in yeast elongator and initiator tRNAs. Nucleic Acids Res 2023; 51:10653-10667. [PMID: 37650648 PMCID: PMC10602860 DOI: 10.1093/nar/gkad722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/18/2023] [Indexed: 09/01/2023] Open
Abstract
As essential components of the protein synthesis machinery, tRNAs undergo a tightly controlled biogenesis process, which include the incorporation of numerous posttranscriptional modifications. Defects in these tRNA maturation steps may lead to the degradation of hypomodified tRNAs by the rapid tRNA decay (RTD) and nuclear surveillance pathways. We previously identified m1A58 as a late modification introduced after modifications Ψ55 and T54 in yeast elongator tRNAPhe. However, previous reports suggested that m1A58 is introduced early during the tRNA modification process, in particular on primary transcripts of initiator tRNAiMet, which prevents its degradation by RNA decay pathways. Here, aiming to reconcile this apparent inconsistency on the temporality of m1A58 incorporation, we examined its introduction into yeast elongator and initiator tRNAs. We used specifically modified tRNAs to report on the molecular aspects controlling the Ψ55 → T54 → m1A58 modification circuit in elongator tRNAs. We also show that m1A58 is efficiently introduced on unmodified tRNAiMet, and does not depend on prior modifications. Finally, we show that m1A58 has major effects on the structural properties of initiator tRNAiMet, so that the tRNA elbow structure is only properly assembled when this modification is present. This observation provides a structural explanation for the degradation of hypomodified tRNAiMet lacking m1A58 by the nuclear surveillance and RTD pathways.
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Affiliation(s)
- Marcel-Joseph Yared
- Expression génétique microbienne, Université Paris Cité, CNRS, Institut de biologie physico-chimique, Paris, France
| | - Yasemin Yoluç
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
| | - Marjorie Catala
- Expression génétique microbienne, Université Paris Cité, CNRS, Institut de biologie physico-chimique, Paris, France
| | - Carine Tisné
- Expression génétique microbienne, Université Paris Cité, CNRS, Institut de biologie physico-chimique, Paris, France
| | - Stefanie Kaiser
- Department of Chemistry, Ludwig Maximilians University, Munich, Germany
- Institute of Pharmaceutical Chemistry, Goethe-University, Frankfurt, Germany
| | - Pierre Barraud
- Expression génétique microbienne, Université Paris Cité, CNRS, Institut de biologie physico-chimique, Paris, France
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2
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Schultz SK, Kothe U. Fluorescent labeling of tRNA for rapid kinetic interaction studies with tRNA-binding proteins. Methods Enzymol 2023; 692:103-126. [PMID: 37925176 DOI: 10.1016/bs.mie.2023.05.007] [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] [Indexed: 11/06/2023]
Abstract
Transfer RNA (tRNA) plays a critical role during translation and interacts with numerous proteins during its biogenesis, functional cycle and degradation. In particular, tRNA is extensively post-transcriptionally modified by various tRNA modifying enzymes which each target a specific nucleotide at different positions within tRNAs to introduce different chemical modifications. Fluorescent assays can be used to study the interaction between a protein and tRNA. Moreover, rapid mixing fluorescence stopped-flow assays provide insights into the kinetics of the tRNA-protein interaction in order to elucidate the tRNA binding mechanism for the given protein. A prerequisite for these studies is a fluorescently labeled molecule, such as fluorescent tRNA, wherein a change in fluorescence occurs upon protein binding. In this chapter, we discuss the utilization of tRNA modifications in order to introduce fluorophores at particular positions within tRNAs. Particularly, we focus on in vitro thiolation of a uridine at position 8 within tRNAs using the tRNA modification enzyme ThiI, followed by labeling of the thiol group with fluorescein. As such, this fluorescently labeled tRNA is primarily unmodified, with the exception of the thiolation modification to which the fluorophore is attached, and can be used as a substrate to study the binding of different tRNA-interacting factors. Herein, we discuss the example of studying the tRNA binding mechanism of the tRNA modifying enzymes TrmB and DusA using internally fluorescein-labeled tRNA.
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Affiliation(s)
- Sarah K Schultz
- Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada; Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Ute Kothe
- Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada; Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada.
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3
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Schultz SK, Meadows K, Kothe U. Molecular mechanism of tRNA binding by the Escherichia coli N7 guanosine methyltransferase TrmB. J Biol Chem 2023; 299:104612. [PMID: 36933808 PMCID: PMC10130221 DOI: 10.1016/j.jbc.2023.104612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/11/2023] [Accepted: 03/12/2023] [Indexed: 03/18/2023] Open
Abstract
Among the large and diverse collection of tRNA modifications, 7-methylguanosine (m7G) is frequently found in the tRNA variable loop at position 46. This modification is introduced by the TrmB enzyme, which is conserved in bacteria and eukaryotes. However, the molecular determinants and the mechanism for tRNA recognition by TrmB are not well understood. Complementing the report of various phenotypes for different organisms lacking TrmB homologs, we report here hydrogen peroxide sensitivity for the Escherichia coli ΔtrmB knockout strain. To gain insight into the molecular mechanism of tRNA binding by E. coli TrmB in real-time, we developed a new assay based on introducing a 4-thiouridine modification at position 8 of in vitro transcribed tRNAPhe enabling us to fluorescently label this unmodified tRNA. Using rapid kinetic stopped-flow measurements with this fluorescent tRNA, we examined the interaction of wildtype and single substitution variants of TrmB with tRNA. Our results reveal the role of SAM for rapid and stable tRNA binding, the rate-limiting nature of m7G46 catalysis for tRNA release, and the importance of residues R26, T127 and R155 across the entire surface of TrmB for tRNA binding.
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Affiliation(s)
- Sarah K Schultz
- Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada; Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kieran Meadows
- Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Ute Kothe
- Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada; Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada.
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4
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Kiss DJ, Oláh J, Tóth G, Varga M, Stirling A, Menyhárd DK, Ferenczy GG. The Structure-Derived Mechanism of Box H/ACA Pseudouridine Synthase Offers a Plausible Paradigm for Programmable RNA Editing. ACS Catal 2022. [DOI: 10.1021/acscatal.1c04870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Dóra Judit Kiss
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - Julianna Oláh
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Műegyetem rakpart 3, H-1111 Budapest, Hungary
| | - Gergely Tóth
- Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány P. stny. 1/a, H-1117 Budapest, Hungary
| | - Máté Varga
- Department of Genetics, ELTE Eötvös Loránd University, Pázmány P. stny. 1/c, H-1117 Budapest, Hungary
| | - András Stirling
- Theoretical Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - Dóra K. Menyhárd
- MTA-ELTE Protein Modelling Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány P. stny. 1/a, H-1117 Budapest, Hungary
| | - György G. Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary
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5
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Purchal MK, Eyler DE, Tardu M, Franco MK, Korn MM, Khan T, McNassor R, Giles R, Lev K, Sharma H, Monroe J, Mallik L, Koutmos M, Koutmou KS. Pseudouridine synthase 7 is an opportunistic enzyme that binds and modifies substrates with diverse sequences and structures. Proc Natl Acad Sci U S A 2022; 119:e2109708119. [PMID: 35058356 PMCID: PMC8794802 DOI: 10.1073/pnas.2109708119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 11/17/2021] [Indexed: 12/13/2022] Open
Abstract
Pseudouridine (Ψ) is a ubiquitous RNA modification incorporated by pseudouridine synthase (Pus) enzymes into hundreds of noncoding and protein-coding RNA substrates. Here, we determined the contributions of substrate structure and protein sequence to binding and catalysis by pseudouridine synthase 7 (Pus7), one of the principal messenger RNA (mRNA) modifying enzymes. Pus7 is distinct among the eukaryotic Pus proteins because it modifies a wider variety of substrates and shares limited homology with other Pus family members. We solved the crystal structure of Saccharomyces cerevisiae Pus7, detailing the architecture of the eukaryotic-specific insertions thought to be responsible for the expanded substrate scope of Pus7. Additionally, we identified an insertion domain in the protein that fine-tunes Pus7 activity both in vitro and in cells. These data demonstrate that Pus7 preferentially binds substrates possessing the previously identified UGUAR (R = purine) consensus sequence and that RNA secondary structure is not a strong requirement for Pus7-binding. In contrast, the rate constants and extent of Ψ incorporation are more influenced by RNA structure, with Pus7 modifying UGUAR sequences in less-structured contexts more efficiently both in vitro and in cells. Although less-structured substrates were preferred, Pus7 fully modified every transfer RNA, mRNA, and nonnatural RNA containing the consensus recognition sequence that we tested. Our findings suggest that Pus7 is a promiscuous enzyme and lead us to propose that factors beyond inherent enzyme properties (e.g., enzyme localization, RNA structure, and competition with other RNA-binding proteins) largely dictate Pus7 substrate selection.
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Affiliation(s)
- Meredith K Purchal
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| | - Daniel E Eyler
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Mehmet Tardu
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Monika K Franco
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| | - Megan M Korn
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Taslima Khan
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| | - Ryan McNassor
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Rachel Giles
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Katherine Lev
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| | - Hari Sharma
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Jeremy Monroe
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Leena Mallik
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109
| | - Markos Koutmos
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109;
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109
| | - Kristin S Koutmou
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109;
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
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6
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Vos TJ, Kothe U. Synergistic interaction network between the snR30 RNP, Utp23, and ribosomal RNA during ribosome synthesis. RNA Biol 2022; 19:764-773. [PMID: 35648701 PMCID: PMC9176245 DOI: 10.1080/15476286.2022.2078092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/28/2022] [Accepted: 05/11/2022] [Indexed: 11/19/2022] Open
Abstract
snR30/U17 is a highly conserved H/ACA RNA that is required for maturation of the small ribosomal subunit in eukaryotes. By base-pairing to the expansion segment 6 (ES6) of 18S ribosomal RNA (rRNA), the snR30 H/ACA Ribonucleoprotein (RNP) indirectly facilitates processing of the precursor rRNA (pre-rRNA) together with other proteins such as Utp23 and other RNAs acting as ribosome assembly factors. However, the details of the molecular interaction network of snR30 and its binding partners and how these interactions contribute to pre-rRNA processing remains unknown. Here, we report the in vitro reconstitution of a Saccharomyces cerevisiae snR30 RNP and quantitative characterization of the interactions of snR30, H/ACA proteins, the Utp23 protein and ES6 of the 18S rRNA. The snR30 RNA is bound tightly by both H/ACA proteins and Utp23. We dissected the importance of different 18S rRNA regions for snR30 RNP binding and demonstrated that the snR30 complex is tightly anchored on the pre-rRNA through base-pairing to ES6 whereas other reported rRNA binding sites do not contribute to the affinity of the snR30 RNP. On its own, the ribosome assembly factor Utp23 binds in a tight, but unspecific manner to RNA. However, in complex with the snR30 RNP, Utp23 increases the affinity of the RNP for rRNA revealing synergies between snR30 RNP and Utp23 which are enhancing specificity and affinity for rRNA, respectively. Together, these findings provide mechanistic insights how the snR30 RNP and Utp23 cooperate to interact tightly and specifically with rRNA during the early stages of ribosome biogenesis.
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Affiliation(s)
- Timothy J. Vos
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
- Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Ute Kothe
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
- Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
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7
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Kouvela A, Zaravinos A, Stamatopoulou V. Adaptor Molecules Epitranscriptome Reprograms Bacterial Pathogenicity. Int J Mol Sci 2021; 22:8409. [PMID: 34445114 PMCID: PMC8395126 DOI: 10.3390/ijms22168409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/31/2021] [Accepted: 08/02/2021] [Indexed: 11/16/2022] Open
Abstract
The strong decoration of tRNAs with post-transcriptional modifications provides an unprecedented adaptability of this class of non-coding RNAs leading to the regulation of bacterial growth and pathogenicity. Accumulating data indicate that tRNA post-transcriptional modifications possess a central role in both the formation of bacterial cell wall and the modulation of transcription and translation fidelity, but also in the expression of virulence factors. Evolutionary conserved modifications in tRNA nucleosides ensure the proper folding and stability redounding to a totally functional molecule. However, environmental factors including stress conditions can cause various alterations in tRNA modifications, disturbing the pathogen homeostasis. Post-transcriptional modifications adjacent to the anticodon stem-loop, for instance, have been tightly linked to bacterial infectivity. Currently, advances in high throughput methodologies have facilitated the identification and functional investigation of such tRNA modifications offering a broader pool of putative alternative molecular targets and therapeutic avenues against bacterial infections. Herein, we focus on tRNA epitranscriptome shaping regarding modifications with a key role in bacterial infectivity including opportunistic pathogens of the human microbiome.
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Affiliation(s)
- Adamantia Kouvela
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece;
| | - Apostolos Zaravinos
- Department of Life Sciences, School of Sciences, European University Cyprus, Nicosia 2404, Cyprus
- Cancer Genetics, Genomics and Systems Biology Group, Basic and Translational Cancer Research Center (BTCRC), Nicosia 1516, Cyprus
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8
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Partially modified tRNAs for the study of tRNA maturation and function. Methods Enzymol 2021; 658:225-250. [PMID: 34517948 DOI: 10.1016/bs.mie.2021.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Transfer RNA (tRNA) is the most highly and diversely modified class of RNA in all domains of life. However, we still have only a limited understanding of the concerted action of the many enzymes that modify tRNA during tRNA maturation and the synergistic functions of tRNA modifications for protein synthesis. Here, we describe the preparation of in vitro transcribed tRNAs with a partial set of defined modifications and the use of partially modified tRNAs in biochemical assays. By comparing the affinity and activity of tRNA modification enzymes for partially modified and unmodified tRNAs, we gain insight into the preferred pathways of tRNA maturation. Additionally, partially modified tRNAs will be highly useful to investigate the importance of tRNA modifications for tRNA function during translation including the interaction with aminoacyl-tRNA synthases, translation factors and the ribosome. Thereby, the methods described here lay the foundation for understanding the mechanistic function of tRNA modifications.
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9
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Porat J, Kothe U, Bayfield MA. Revisiting tRNA chaperones: New players in an ancient game. RNA (NEW YORK, N.Y.) 2021; 27:rna.078428.120. [PMID: 33593999 PMCID: PMC8051267 DOI: 10.1261/rna.078428.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/10/2021] [Indexed: 05/03/2023]
Abstract
tRNAs undergo an extensive maturation process including post-transcriptional modifications that influence secondary and tertiary interactions. Precursor and mature tRNAs lacking key modifications are often recognized as aberrant and subsequently targeted for decay, illustrating the importance of modifications in promoting structural integrity. tRNAs also rely on tRNA chaperones to promote the folding of misfolded substrates into functional conformations. The best characterized tRNA chaperone is the La protein, which interacts with nascent RNA polymerase III transcripts to promote folding and offers protection from exonucleases. More recently, certain tRNA modification enzymes have also been demonstrated to possess tRNA folding activity distinct from their catalytic activity, suggesting that they may act as tRNA chaperones. In this review, we will discuss pioneering studies relating post-transcriptional modification to tRNA stability and decay pathways, present recent advances into the mechanism by which the RNA chaperone La assists pre-tRNA maturation, and summarize emerging research directions aimed at characterizing modification enzymes as tRNA chaperones. Together, these findings shed light on the importance of tRNA folding and how tRNA chaperones, in particular, increase the fraction of nascent pre-tRNAs that adopt a folded, functional conformation.
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10
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Czekay DP, Schultz SK, Kothe U. Assaying the Molecular Determinants and Kinetics of RNA Pseudouridylation by H/ACA snoRNPs and Stand-Alone Pseudouridine Synthases. Methods Mol Biol 2021; 2298:357-378. [PMID: 34085255 DOI: 10.1007/978-1-0716-1374-0_21] [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] [Indexed: 11/06/2023]
Abstract
Posttranscriptional modifications of RNA play an important role in promoting the maturation and functional diversity of many RNA species. Accordingly, understanding the enzymes and mechanisms that underlie RNA modifications is an important aspect in advancing our knowledge of the continually expanding RNA modification field. However, of the more than 160 currently identified RNA modifications, a large portion remains without quantitative detection assays for their biochemical characterization. Here, we describe the tritium release assay as a convenient tool allowing for the quantitative assessment of in vitro RNA pseudouridylation by stand-alone or box H/ACA RNA-guided pseudouridine synthases. This assay enables quantification of RNA pseudouridylation over a time course to effectively compare pseudouridylation activity between different substrates and/or different recombinant enzymes as well as to determine kinetic parameters. With the help of a quench-flow apparatus, the tritium release assay can be adapted for rapid kinetic measurements under single-turnover conditions to dissect reaction mechanisms. As examples, we show the formation of pseudouridines by a reconstituted Saccharomyces cerevisiae H/ACA small ribonucleoprotein (snoRNP) and an Escherichia coli stand-alone pseudouridine synthase.
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Affiliation(s)
- Dominic P Czekay
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada
| | - Sarah K Schultz
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada
| | - Ute Kothe
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, AB, Canada.
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11
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Kurimoto R, Chiba T, Ito Y, Matsushima T, Yano Y, Miyata K, Yashiro Y, Suzuki T, Tomita K, Asahara H. The tRNA pseudouridine synthase TruB1 regulates the maturation of let-7 miRNA. EMBO J 2020; 39:e104708. [PMID: 32926445 PMCID: PMC7560213 DOI: 10.15252/embj.2020104708] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 12/14/2022] Open
Abstract
Let-7 is an evolutionary conserved microRNA that mediates post-transcriptional gene silencing to regulate a wide range of biological processes, including development, differentiation, and tumor suppression. Let-7 biogenesis is tightly regulated by several RNA-binding proteins, including Lin28A/B, which represses let-7 maturation. To identify new regulators of let-7, we devised a cell-based functional screen of RNA-binding proteins using a let-7 sensor luciferase reporter and identified the tRNA pseudouridine synthase, TruB1. TruB1 enhanced maturation specifically of let-7 family members. Rather than inducing pseudouridylation of the miRNAs, high-throughput sequencing crosslinking immunoprecipitation (HITS-CLIP) and biochemical analyses revealed direct binding between endogenous TruB1 and the stem-loop structure of pri-let-7, which also binds Lin28A/B. TruB1 selectively enhanced the interaction between pri-let-7 and the microprocessor DGCR8, which mediates miRNA maturation. Finally, TruB1 suppressed cell proliferation, which was mediated in part by let-7. Altogether, we reveal an unexpected function for TruB1 in promoting let-7 maturation.
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Affiliation(s)
- Ryota Kurimoto
- Department of Systems BioMedicineGraduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Tomoki Chiba
- Department of Systems BioMedicineGraduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Yoshiaki Ito
- Department of Systems BioMedicineGraduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
- Research CoreResearch Facility ClusterInstitute of ResearchTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Takahide Matsushima
- Department of Systems BioMedicineGraduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Yuki Yano
- Department of Systems BioMedicineGraduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Kohei Miyata
- Department Obstetrics and GynecologyFaculty of MedicineFukuoka UniversityFukuokaJapan
| | - Yuka Yashiro
- Department of Computational Biology and Medical SciencesGraduate School of Frontier SciencesThe University of TokyoKashiwaChibaJapan
| | - Tsutomu Suzuki
- Department of Chemistry and BiotechnologyGraduate School of EngineeringUniversity of TokyoTokyoJapan
| | - Kozo Tomita
- Department of Computational Biology and Medical SciencesGraduate School of Frontier SciencesThe University of TokyoKashiwaChibaJapan
| | - Hiroshi Asahara
- Department of Systems BioMedicineGraduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
- Department of Molecular and Experimental MedicineThe Scripps Research InstituteSan DiegoCAUSA
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12
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Keffer-Wilkes LC, Soon EF, Kothe U. The methyltransferase TrmA facilitates tRNA folding through interaction with its RNA-binding domain. Nucleic Acids Res 2020; 48:7981-7990. [PMID: 32597953 PMCID: PMC7641329 DOI: 10.1093/nar/gkaa548] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/29/2020] [Accepted: 06/17/2020] [Indexed: 11/12/2022] Open
Abstract
tRNAs are the most highly modified RNAs in all cells, and formation of 5-methyluridine (m5U) at position 54 in the T arm is a common RNA modification found in all tRNAs. The m5U modification is generated by the methyltransferase TrmA. Here, we test and prove the hypothesis that Escherichia coli TrmA has dual functions, acting both as a methyltransferase and as a tRNA chaperone. We identify two conserved residues, F106 and H125, in the RNA-binding domain of TrmA, which interact with the tRNA elbow and are critical for tRNA binding. Co-culture competition assays reveal that the catalytic activity of TrmA is important for cellular fitness, and that substitutions of F106 or H125 impair cellular fitness. We directly show that TrmA enhances tRNA folding in vitro independent of its catalytic activity. In conclusion, our study suggests that F106 and H125 in the RNA-binding domain of TrmA act as a wedge disrupting tertiary interactions between tRNA’s D arm and T arm; this tRNA unfolding is the mechanistic basis for TrmA’s tRNA chaperone activity. TrmA is the second tRNA modifying enzyme next to the pseudouridine synthase TruB shown to act as a tRNA chaperone supporting a functional link between RNA modification and folding.
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Affiliation(s)
- Laura Carole Keffer-Wilkes
- University of Lethbridge, Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, Lethbridge, AB T1K 3M4, Canada
| | - Emily F Soon
- University of Lethbridge, Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, Lethbridge, AB T1K 3M4, Canada
| | - Ute Kothe
- University of Lethbridge, Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, Lethbridge, AB T1K 3M4, Canada
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13
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Schultz SKL, Kothe U. tRNA elbow modifications affect the tRNA pseudouridine synthase TruB and the methyltransferase TrmA. RNA (NEW YORK, N.Y.) 2020; 26:1131-1142. [PMID: 32385137 PMCID: PMC7430675 DOI: 10.1261/rna.075473.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/04/2020] [Indexed: 05/20/2023]
Abstract
tRNAs constitute the most highly modified class of RNA. Every tRNA contains a unique set of modifications, and Ψ55, m5U54, and m7G46 are frequently found within the elbow of the tRNA structure. Despite the abundance of tRNA modifications, we are only beginning to understand the orchestration of modification enzymes during tRNA maturation. Here, we investigated whether pre-existing modifications impact the binding affinity or catalysis by tRNA elbow modification enzymes. Specifically, we focused on the Escherichia coli enzymes TruB, TrmA, and TrmB which generate Ψ55, m5U54, and m7G46, respectively. tRNAs containing a single modification were prepared, and the binding and activity preferences of purified E. coli TrmA, TruB, and TrmB were examined in vitro. TruB preferentially binds and modifies unmodified tRNA. TrmA prefers to modify unmodified tRNA, but binds most tightly to tRNA that already contains Ψ55. In contrast, binding and modification by TrmB is insensitive to the tRNA modification status. Our results suggest that TrmA and TruB are likely to act on mostly unmodified tRNA precursors during the early stages of tRNA maturation whereas TrmB presumably acts on later tRNA intermediates that are already partially modified. In conclusion, we uncover the mechanistic basis for the preferred modification order in the E. coli tRNA elbow region.
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Affiliation(s)
- Sarah Kai-Leigh Schultz
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada T1K 3M4
| | - Ute Kothe
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada T1K 3M4
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14
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Tillault AS, Schultz SK, Wieden HJ, Kothe U. Molecular Determinants for 23S rRNA Recognition and Modification by the E. coli Pseudouridine Synthase RluE. J Mol Biol 2018; 430:1284-1294. [PMID: 29555553 DOI: 10.1016/j.jmb.2018.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/25/2018] [Accepted: 03/13/2018] [Indexed: 11/18/2022]
Abstract
The isomerization of uridine to pseudouridine is the most common type of RNA modification found in RNAs across all domains of life and is performed by RNA-dependent and RNA-independent enzymes. The Escherichia coli pseudouridine synthase RluE acts as a stand-alone, highly specific enzyme forming the universally conserved pseudouridine at position 2457, located in helix 89 (H89) of the 23S rRNA in the peptidyltransferase center. Here, we conduct a detailed structure-function analysis to determine the structural elements both in RluE and in 23S rRNA required for RNA-protein interaction and pseudouridine formation. We determined that RluE recognizes a large part of 23S rRNA comprising both H89 and the single-stranded flanking regions which explains the high substrate specificity of RluE. Within RluE, the target RNA is recognized through sequence-specific contacts with loop L7-8 as well as interactions with loop L1-2 and the flexible N-terminal region. We demonstrate that RluE is a faster pseudouridine synthase than other enzymes which likely enables it to act in the early stages of ribosome formation. In summary, our biochemical characterization of RluE provides detailed insight into the molecular mechanism of RluE forming a highly conserved pseudouridine during ribosome biogenesis.
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Affiliation(s)
- Anne-Sophie Tillault
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Sarah K Schultz
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Hans-Joachim Wieden
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Ute Kothe
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada.
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15
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Caton EA, Kelly EK, Kamalampeta R, Kothe U. Efficient RNA pseudouridylation by eukaryotic H/ACA ribonucleoproteins requires high affinity binding and correct positioning of guide RNA. Nucleic Acids Res 2018; 46:905-916. [PMID: 29177505 PMCID: PMC5778458 DOI: 10.1093/nar/gkx1167] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 10/31/2017] [Accepted: 11/07/2017] [Indexed: 12/19/2022] Open
Abstract
H/ACA ribonucleoproteins (H/ACA RNPs) are responsible for introducing many pseudouridines into RNAs, but are also involved in other cellular functions. Utilizing a purified and reconstituted yeast H/ACA RNP system that is active in pseudouridine formation under physiological conditions, we describe here the quantitative characterization of H/ACA RNP formation and function. This analysis reveals a surprisingly tight interaction of H/ACA guide RNA with the Cbf5p-Nop10p-Gar1p trimeric protein complex whereas Nhp2p binds comparably weakly to H/ACA guide RNA. Substrate RNA is bound to H/ACA RNPs with nanomolar affinity which correlates with the GC content in the guide-substrate RNA base pairing. Both Nhp2p and the conserved Box ACA element in guide RNA are required for efficient pseudouridine formation, but not for guide RNA or substrate RNA binding. These results suggest that Nhp2p and the Box ACA motif indirectly facilitate loading of the substrate RNA in the catalytic site of Cbf5p by correctly positioning the upper and lower parts of the H/ACA guide RNA on the H/ACA proteins. In summary, this study provides detailed insight into the molecular mechanism of H/ACA RNPs.
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Affiliation(s)
- Evan A Caton
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Erin K Kelly
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Rajashekhar Kamalampeta
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Ute Kothe
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
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16
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Abstract
All types of nucleic acids in cells undergo naturally occurring chemical modifications, including DNA, rRNA, mRNA, snRNA, and most prominently tRNA. Over 100 different modifications have been described and every position in the purine and pyrimidine bases can be modified; often the sugar is also modified [1]. In tRNA, the function of modifications varies; some modulate global and/or local RNA structure, and others directly impact decoding and may be essential for viability. Whichever the case, the overall importance of modifications is highlighted by both their evolutionary conservation and the fact that organisms use a substantial portion of their genomes to encode modification enzymes, far exceeding what is needed for the de novo synthesis of the canonical nucleotides themselves [2]. Although some modifications occur at exactly the same nucleotide position in tRNAs from the three domains of life, many can be found at various positions in a particular tRNA and their location may vary between and within different tRNAs. With this wild array of chemical diversity and substrate specificities, one of the big challenges in the tRNA modification field has been to better understand at a molecular level the modes of substrate recognition by the different modification enzymes; in this realm RNA binding rests at the heart of the problem. This chapter will focus on several examples of modification enzymes where their mode of RNA binding is well understood; from these, we will try to draw general conclusions and highlight growing themes that may be applicable to the RNA modification field at large.
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17
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Abstract
Cellular RNAs are chemically modified by many RNA modification enzymes; however, often the functions of modifications remain unclear, such as for pseudouridine formation in the tRNA TΨC arm by the bacterial tRNA pseudouridine synthase TruB. Here we test the hypothesis that RNA modification enzymes also act as RNA chaperones. Using TruB as a model, we demonstrate that TruB folds tRNA independent of its catalytic activity, thus increasing the fraction of tRNA that can be aminoacylated. By rapid kinetic stopped-flow analysis, we identified the molecular mechanism of TruB's RNA chaperone activity: TruB binds and unfolds both misfolded and folded tRNAs thereby providing misfolded tRNAs a second chance at folding. Previously, it has been shown that a catalytically inactive TruB variant has no phenotype when expressed in an Escherichia coli truB KO strain [Gutgsell N, et al. (2000) RNA 6(12):1870-1881]. However, here we uncover that E. coli strains expressing a TruB variant impaired in tRNA binding and in in vitro tRNA folding cannot compete with WT E. coli. Consequently, the tRNA chaperone activity of TruB is critical for bacterial fitness. In conclusion, we prove the tRNA chaperone activity of the pseudouridine synthase TruB, reveal its molecular mechanism, and demonstrate its importance for cellular fitness. We discuss the likelihood that other RNA modification enzymes are also RNA chaperones.
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18
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Veerareddygari GR, Singh SK, Mueller EG. The Pseudouridine Synthases Proceed through a Glycal Intermediate. J Am Chem Soc 2016; 138:7852-5. [PMID: 27292228 PMCID: PMC4929527 DOI: 10.1021/jacs.6b04491] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
The pseudouridine
synthases isomerize (U) in RNA to pseudouridine
(Ψ), and the mechanism that they follow has long been a question
of interest. The recent elucidation of a product of the mechanistic
probe 5-fluorouridine that had been epimerized to the arabino isomer suggested that the Ψ synthases might operate through
a glycal intermediate formed by deprotonation of C2′. When
that position in substrate U is deuterated, a primary kinetic isotope
effect is observed, which indisputably indicates that the proposed
deprotonation occurs during the isomerization of U to Ψ and
establishes the mechanism followed by the Ψ synthases.
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Affiliation(s)
| | - Sanjay K Singh
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40205, United States
| | - Eugene G Mueller
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40205, United States
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19
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Saliou JM, Manival X, Tillault AS, Atmanene C, Bobo C, Branlant C, Van Dorsselaer A, Charpentier B, Cianférani S. Combining native MS approaches to decipher archaeal box H/ACA ribonucleoprotein particle structure and activity. Proteomics 2015; 15:2851-61. [DOI: 10.1002/pmic.201400529] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Revised: 02/06/2015] [Accepted: 02/24/2015] [Indexed: 12/23/2022]
Affiliation(s)
- Jean-Michel Saliou
- BioOrganic Mass Spectrometry Laboratory (LSMBO); IPHC; Université de Strasbourg; Strasbourg France
- IPHC; CNRS UMR 7178; Strasbourg France
| | - Xavier Manival
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA); UMR 7365 CNRS Université de Lorraine; Biopôle Vandœuvre-lès-Nancy France
| | - Anne-Sophie Tillault
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA); UMR 7365 CNRS Université de Lorraine; Biopôle Vandœuvre-lès-Nancy France
| | - Cédric Atmanene
- BioOrganic Mass Spectrometry Laboratory (LSMBO); IPHC; Université de Strasbourg; Strasbourg France
- IPHC; CNRS UMR 7178; Strasbourg France
| | - Claude Bobo
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA); UMR 7365 CNRS Université de Lorraine; Biopôle Vandœuvre-lès-Nancy France
| | - Christiane Branlant
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA); UMR 7365 CNRS Université de Lorraine; Biopôle Vandœuvre-lès-Nancy France
| | - Alain Van Dorsselaer
- BioOrganic Mass Spectrometry Laboratory (LSMBO); IPHC; Université de Strasbourg; Strasbourg France
- IPHC; CNRS UMR 7178; Strasbourg France
| | - Bruno Charpentier
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA); UMR 7365 CNRS Université de Lorraine; Biopôle Vandœuvre-lès-Nancy France
| | - Sarah Cianférani
- BioOrganic Mass Spectrometry Laboratory (LSMBO); IPHC; Université de Strasbourg; Strasbourg France
- IPHC; CNRS UMR 7178; Strasbourg France
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20
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Spenkuch F, Hinze G, Kellner S, Kreutz C, Micura R, Basché T, Helm M. Dye label interference with RNA modification reveals 5-fluorouridine as non-covalent inhibitor. Nucleic Acids Res 2014; 42:12735-45. [PMID: 25300485 PMCID: PMC4227767 DOI: 10.1093/nar/gku908] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The interest in RNA modification enzymes surges due to their involvement in epigenetic phenomena. Here we present a particularly informative approach to investigate the interaction of dye-labeled RNA with modification enzymes. We investigated pseudouridine (Ψ) synthase TruB interacting with an alleged suicide substrate RNA containing 5-fluorouridine (5FU). A longstanding dogma, stipulating formation of a stable covalent complex was challenged by discrepancies between the time scale of complex formation and enzymatic turnover. Instead of classic mutagenesis, we used differentially positioned fluorescent labels to modulate substrate properties in a range of enzymatic conversion between 6% and 99%. Despite this variegation, formation of SDS-stable complexes occurred instantaneously for all 5FU-substrates. Protein binding was investigated by advanced fluorescence spectroscopy allowing unprecedented simultaneous detection of change in fluorescence lifetime, anisotropy decay, as well as emission and excitation maxima. Determination of Kd values showed that introduction of 5FU into the RNA substrate increased protein affinity by 14× at most. Finally, competition experiments demonstrated reversibility of complex formation for 5FU-RNA. Our results lead us to conclude that the hitherto postulated long-term covalent interaction of TruB with 5FU tRNA is based on the interpretation of artifacts. This is likely true for the entire class of pseudouridine synthases.
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Affiliation(s)
- Felix Spenkuch
- Institute of Pharmacy and Biochemistry, University of Mainz, Staudingerweg 5, D-55128 Mainz, Germany
| | - Gerald Hinze
- Institute of Physical Chemistry, University of Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Stefanie Kellner
- Institute of Pharmacy and Biochemistry, University of Mainz, Staudingerweg 5, D-55128 Mainz, Germany
| | - Christoph Kreutz
- Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52A, A-60230 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Chemistry and Biomedicine - CCB, University of Innsbruck, Innrain 80/82, A-60230 Innsbruck, Austria
| | - Thomas Basché
- Institute of Physical Chemistry, University of Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, University of Mainz, Staudingerweg 5, D-55128 Mainz, Germany
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21
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Boschi-Muller S, Motorin Y. Chemistry enters nucleic acids biology: enzymatic mechanisms of RNA modification. BIOCHEMISTRY (MOSCOW) 2014; 78:1392-404. [PMID: 24490730 DOI: 10.1134/s0006297913130026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Modified nucleotides are universally conserved in all living kingdoms and are present in almost all types of cellular RNAs, including tRNA, rRNA, sn(sno)RNA, and mRNA and in recently discovered regulatory RNAs. Altogether, over 110 chemically distinct RNA modifications have been characterized and localized in RNA by various analytical methods. However, this impressive list of known modified nucleotides is certainly incomplete, mainly due to difficulties in identification and characterization of these particular residues in low abundance cellular RNAs. In DNA, modified residues are formed by both enzymatic reactions (like DNA methylations, for example) and by spontaneous chemical reactions resulting from oxidative damage. In contrast, all modified residues characterized in cellular RNA molecules are formed by specific action of dedicated RNA-modification enzymes, which recognize their RNA substrate with high specificity. These RNA-modification enzymes display a great diversity in terms of the chemical reaction and use various low molecular weight cofactors (or co-substrates) in enzymatic catalysis. Depending on the nature of the target base and of the co-substrate, precise chemical mechanisms are used for appropriate activation of the base and the co-substrate in the enzyme active site. In this review, we give an extended summary of the enzymatic mechanisms involved in formation of different methylated nucleotides in RNA, as well as pseudouridine residues, which are almost universally conserved in all living organisms. Other interesting mechanisms include thiolation of uridine residues by ThiI and the reaction of guanine exchange catalyzed by TGT. The latter implies the reversible cleavage of the N-glycosidic bond in order to replace the initially encoded guanine by an aza-guanosine base. Despite the extensive studies of RNA modification and RNA-modification machinery during the last 20 years, our knowledge on the exact chemical steps involved in catalysis of RNA modification remains very limited. Recent discoveries of radical mechanisms involved in base methylation clearly demonstrate that numerous possibilities are used in Nature for these difficult reactions. Future studies are certainly required for better understanding of the enzymatic mechanisms of RNA modification, and this knowledge is crucial not only for basic research, but also for development of new therapeutic molecules.
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Affiliation(s)
- S Boschi-Muller
- Université de Lorraine, Laboratoire IMoPA, UMR 7365 CNRS-UL, Faculté de Médecine de Nancy, BP 184, Vandoeuvre les Nancy, 54505, France.
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22
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Friedt J, Leavens FMV, Mercier E, Wieden HJ, Kothe U. An arginine-aspartate network in the active site of bacterial TruB is critical for catalyzing pseudouridine formation. Nucleic Acids Res 2014; 42:3857-70. [PMID: 24371284 PMCID: PMC3973310 DOI: 10.1093/nar/gkt1331] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 11/27/2013] [Accepted: 11/30/2013] [Indexed: 11/12/2022] Open
Abstract
Pseudouridine synthases introduce the most common RNA modification and likely use the same catalytic mechanism. Besides a catalytic aspartate residue, the contributions of other residues for catalysis of pseudouridine formation are poorly understood. Here, we have tested the role of a conserved basic residue in the active site for catalysis using the bacterial pseudouridine synthase TruB targeting U55 in tRNAs. Substitution of arginine 181 with lysine results in a 2500-fold reduction of TruB's catalytic rate without affecting tRNA binding. Furthermore, we analyzed the function of a second-shell aspartate residue (D90) that is conserved in all TruB enzymes and interacts with C56 of tRNA. Site-directed mutagenesis, biochemical and kinetic studies reveal that this residue is not critical for substrate binding but influences catalysis significantly as replacement of D90 with glutamate or asparagine reduces the catalytic rate 30- and 50-fold, respectively. In agreement with molecular dynamics simulations of TruB wild type and TruB D90N, we propose an electrostatic network composed of the catalytic aspartate (D48), R181 and D90 that is important for catalysis by fine-tuning the D48-R181 interaction. Conserved, negatively charged residues similar to D90 are found in a number of pseudouridine synthases, suggesting that this might be a general mechanism.
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Affiliation(s)
- Jenna Friedt
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge AB T1K 3M4, Canada
| | - Fern M. V. Leavens
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge AB T1K 3M4, Canada
| | - Evan Mercier
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge AB T1K 3M4, Canada
| | - Hans-Joachim Wieden
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge AB T1K 3M4, Canada
| | - Ute Kothe
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge AB T1K 3M4, Canada
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23
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Spenkuch F, Motorin Y, Helm M. Pseudouridine: still mysterious, but never a fake (uridine)! RNA Biol 2014; 11:1540-54. [PMID: 25616362 PMCID: PMC4615568 DOI: 10.4161/15476286.2014.992278] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 09/23/2014] [Accepted: 10/10/2014] [Indexed: 01/15/2023] Open
Abstract
Pseudouridine (Ψ) is the most abundant of >150 nucleoside modifications in RNA. Although Ψ was discovered as the first modified nucleoside more than half a century ago, neither the enzymatic mechanism of its formation, nor the function of this modification are fully elucidated. We present the consistent picture of Ψ synthases, their substrates and their substrate positions in model organisms of all domains of life as it has emerged to date and point out the challenges that remain concerning higher eukaryotes and the elucidation of the enzymatic mechanism.
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MESH Headings
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Humans
- Intramolecular Transferases/genetics
- Intramolecular Transferases/metabolism
- Isoenzymes/genetics
- Isoenzymes/metabolism
- Nucleic Acid Conformation
- Pseudouridine/metabolism
- RNA/genetics
- RNA/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Mitochondrial
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Transfer, Amino Acid-Specific/chemistry
- RNA, Transfer, Amino Acid-Specific/genetics
- RNA, Transfer, Amino Acid-Specific/metabolism
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Ribosomes/chemistry
- Ribosomes/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Uridine/metabolism
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Felix Spenkuch
- Institute of Pharmacy and Biochemistry; Johannes Gutenberg-University of Mainz; Mainz, Germany
| | - Yuri Motorin
- Laboratoire IMoPA; Ingénierie Moléculaire et Physiopathologie Articulaire; BioPôle de l'Université de Lorraine; Campus Biologie-Santé; Faculté de Médecine; Vandoeuvre-les-Nancy Cedex, France
| | - Mark Helm
- Institute of Pharmacy and Biochemistry; Johannes Gutenberg-University of Mainz; Mainz, Germany
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24
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Kamalampeta R, Keffer-Wilkes LC, Kothe U. tRNA binding, positioning, and modification by the pseudouridine synthase Pus10. J Mol Biol 2013; 425:3863-74. [PMID: 23743107 DOI: 10.1016/j.jmb.2013.05.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 05/17/2013] [Accepted: 05/22/2013] [Indexed: 10/26/2022]
Abstract
Pus10 is the most recently identified pseudouridine synthase found in archaea and higher eukaryotes. It modifies uridine 55 in the TΨC arm of tRNAs. Here, we report the first quantitative biochemical analysis of tRNA binding and pseudouridine formation by Pyrococcus furiosus Pus10. The affinity of Pus10 for both substrate and product tRNA is high (Kd of 30nM), and product formation occurs with a Km of 400nM and a kcat of 0.9s(-1). Site-directed mutagenesis was used to demonstrate that the thumb loop in the catalytic domain is important for efficient catalysis; we propose that the thumb loop positions the tRNA within the active site. Furthermore, a new catalytic arginine residue was identified (arginine 208), which is likely responsible for triggering flipping of the target uridine into the active site of Pus10. Lastly, our data support the proposal that the THUMP-containing domain, found in the N-terminus of Pus10, contributes to binding of tRNA. Together, our findings are consistent with the hypothesis that tRNA binding by Pus10 occurs through an induced-fit mechanism, which is a prerequisite for efficient pseudouridine formation.
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Affiliation(s)
- Rajashekhar Kamalampeta
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB, T1K 3M4, Canada.
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25
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Abstract
BACKGROUND The endoribonuclease RNase-L is a type-I interferon (IFN)-regulated component of the innate immune response that functions in antiviral, antibacterial, and antiproliferative activities. RNase-L produces RNA agonists of RIG-I-like receptors, sensors of cytosolic pathogen-associated RNAs that induce cytokines including IFN-β. IFN-β and RIG-I-like receptors signaling mediate protective responses against experimental colitis and colitis-associated cancer and contribute to gastrointestinal homeostasis. Therefore, we investigated a role for RNase-L in murine colitis and colitis-associated cancer and its association with RIG-I-like receptors signaling in response to bacterial RNA. METHODS Colitis was induced in wild type-deficient and RNase-L-deficient mice (RNase-L⁻/⁻) by administration of dextran sulfate sodium (DSS). Colitis-associated cancer was induced by DSS and azoxymethane (AOM). Histological analysis and immunohistochemistry were performed on colon tissue to analyze immune cell infiltration and tissue damage after induction of colitis. Expression of cytokines was measured by quantitative real-time-PCR and ELISA. RESULTS DSS-treated RNase-L⁻/⁻ mice exhibited a significantly higher clinical score, delayed leukocyte infiltration, reduced expression of IFN-β, tumor necrosis factor α, interleukin-1β, and interleukin-18 at early times post-DSS exposure, and increased mortality as compared with wild-type mice. DSS/AOM-treated RNase-L⁻/⁻ mice displayed an increased tumor burden. Bacterial RNA triggered IFN-β production in an RNase-L-dependent manner and provided a potential mechanism by which RNase-L contributes to the gastrointestinal immune response to microbiota and protects against experimental colitis and colitis-associated cancer. CONCLUSIONS RNase-L promotes the innate immune response to intestinal damage and ameliorates murine colitis and colitis-associated cancer. The RNase-L-dependent production of IFN-β stimulated by bacterial RNA may be a mechanism to protect against gastrointestinal inflammatory disease.
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26
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Yang X, Duan J, Li S, Wang P, Ma S, Ye K, Zhao XS. Kinetic and thermodynamic characterization of the reaction pathway of box H/ACA RNA-guided pseudouridine formation. Nucleic Acids Res 2012; 40:10925-36. [PMID: 23012266 PMCID: PMC3510513 DOI: 10.1093/nar/gks882] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 08/29/2012] [Accepted: 08/30/2012] [Indexed: 12/20/2022] Open
Abstract
The box H/ACA RNA-guided pseudouridine synthase is a complicated ribonucleoprotein enzyme that recruits substrate via both the guide RNA and the catalytic subunit Cbf5. Structural studies have revealed multiple conformations of the enzyme, but a quantitative description of the reaction pathway is still lacking. Using fluorescence correlation spectroscopy, we here measured the equilibrium dissociation constants and kinetic association and dissociation rates of substrate and product complexes mimicking various reaction intermediate states. These data support a sequential model for substrate loading and product release regulated by the thumb loop of Cbf5. The uridine substrate is first bound primarily through interaction with the guide RNA and then loaded into the active site while progressively interacted with the thumb. After modification, the subtle chemical structure change from uridine to pseudouridine at the target site triggers the release of the thumb, resulting in an intermediate complex with the product bound mainly by the guide RNA. By dissecting the role of Gar1 in individual steps of substrate turnover, we show that Gar1 plays a major role in catalysis and also accelerates product release about 2-fold. Our biophysical results integrate with previous structural knowledge into a coherent reaction pathway of H/ACA RNA-guided pseudouridylation.
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Affiliation(s)
- Xinxing Yang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871 and National Institute of Biological Sciences, Beijing 102206, China
| | - Jingqi Duan
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871 and National Institute of Biological Sciences, Beijing 102206, China
| | - Shuang Li
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871 and National Institute of Biological Sciences, Beijing 102206, China
| | - Peng Wang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871 and National Institute of Biological Sciences, Beijing 102206, China
| | - Shoucai Ma
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871 and National Institute of Biological Sciences, Beijing 102206, China
| | - Keqiong Ye
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871 and National Institute of Biological Sciences, Beijing 102206, China
| | - Xin Sheng Zhao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University, Beijing 100871 and National Institute of Biological Sciences, Beijing 102206, China
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27
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Kamalampeta R, Kothe U. Archaeal proteins Nop10 and Gar1 increase the catalytic activity of Cbf5 in pseudouridylating tRNA. Sci Rep 2012; 2:663. [PMID: 22993689 PMCID: PMC3443816 DOI: 10.1038/srep00663] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 09/03/2012] [Indexed: 02/05/2023] Open
Abstract
Cbf5 is a pseudouridine synthase that usually acts in a guide RNA-dependent manner as part of H/ACA small ribonucleoproteins; however archaeal Cbf5 can also act independently of guide RNA in modifying uridine 55 in tRNA. This guide-independent activity of Cbf5 is enhanced by proteins Nop10 and Gar1 which are also found in H/ACA small ribonucleoproteins. Here, we analyzed the specific contribution of Nop10 and Gar1 for Cbf5-catalyzed pseudouridylation of tRNA. Interestingly, both Nop10 and Gar1 not only increase Cbf5's affinity for tRNA, but they also directly enhance Cbf5's catalytic activity by increasing the k(cat) of the reaction. In contrast to the guide RNA-dependent reaction, Gar1 is not involved in product release after tRNA modification. These results in conjunction with structural information suggest that Nop10 and Gar1 stabilize Cbf5 in its active conformation; we hypothesize that this might also be true for guide-RNA dependent pseudouridine formation by Cbf5.
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Affiliation(s)
- Rajashekhar Kamalampeta
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Ute Kothe
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
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