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Choi SY, Chung IY, Bae HW, Cho YH. Autolysis of Pseudomonas aeruginosa Quorum-Sensing Mutant Is Suppressed by Staphylococcus aureus through Iron-Dependent Metabolism. J Microbiol Biotechnol 2024; 34:795-803. [PMID: 38303126 DOI: 10.4014/jmb.2312.12028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 02/03/2024]
Abstract
Microorganisms usually coexist as a multifaceted polymicrobial community in the natural habitats and at mucosal sites of the human body. Two opportunistic human pathogens, Pseudomonas aeruginosa and Staphylococcus aureus commonly coexist in the bacterial infections for hospitalized and/or immunocompromised patients. Here, we observed that autolysis of the P. aeruginosa quorum-sensing (QS) mutant (lasRmvfR) was suppressed by the presence of the S. aureus cells in vitro. The QS mutant still displayed killing against S. aureus cells, suggesting the link between the S. aureus-killing activity and the autolysis suppression. Independent screens of the P. aeruginosa transposon mutants defective in the S. aureus-killing and the S. aureus transposon mutants devoid of the autolysis suppression revealed the genetic link between both phenotypes, suggesting that the iron-dependent metabolism involving S. aureus exoproteins might be central to both phenotypes. The autolysis was suppressed by iron treatment as well. These results suggest that the interaction between P. aeruginosa and S. aureus might be governed by mechanisms that necessitate the QS circuitry as well as the metabolism involving the extracellular iron resources during the polymicrobial infections in the human airway.
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Affiliation(s)
- Shin-Yae Choi
- Program of Biopharmaceutical Science and Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Republic of Korea
| | - In-Young Chung
- Program of Biopharmaceutical Science and Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Republic of Korea
| | - Hee-Won Bae
- Program of Biopharmaceutical Science and Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Republic of Korea
| | - You-Hee Cho
- Program of Biopharmaceutical Science and Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Republic of Korea
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2
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Grünberg S, Doyle LA, Wolf EJ, Dai N, Corrêa IR, Yigit E, Stoddard BL. The structural basis of mRNA recognition and binding by yeast pseudouridine synthase PUS1. PLoS One 2023; 18:e0291267. [PMID: 37939088 PMCID: PMC10631681 DOI: 10.1371/journal.pone.0291267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/25/2023] [Indexed: 11/10/2023] Open
Abstract
The chemical modification of RNA bases represents a ubiquitous activity that spans all domains of life. Pseudouridylation is the most common RNA modification and is observed within tRNA, rRNA, ncRNA and mRNAs. Pseudouridine synthase or 'PUS' enzymes include those that rely on guide RNA molecules and others that function as 'stand-alone' enzymes. Among the latter, several have been shown to modify mRNA transcripts. Although recent studies have defined the structural requirements for RNA to act as a PUS target, the mechanisms by which PUS1 recognizes these target sequences in mRNA are not well understood. Here we describe the crystal structure of yeast PUS1 bound to an RNA target that we identified as being a hot spot for PUS1-interaction within a model mRNA at 2.4 Å resolution. The enzyme recognizes and binds both strands in a helical RNA duplex, and thus guides the RNA containing the target uridine to the active site for subsequent modification of the transcript. The study also allows us to show the divergence of related PUS1 enzymes and their corresponding RNA target specificities, and to speculate on the basis by which PUS1 binds and modifies mRNA or tRNA substrates.
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Affiliation(s)
| | - Lindsey A. Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Eric J. Wolf
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Nan Dai
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Ivan R. Corrêa
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Erbay Yigit
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Barry L. Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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3
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Mendoza HG, Beal PA. Chemical Modifications in RNA: Elucidating the Chemistry of dsRNA-Specific Adenosine Deaminases (ADARs). Acc Chem Res 2023; 56:2489-2499. [PMID: 37665999 PMCID: PMC10826463 DOI: 10.1021/acs.accounts.3c00390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
The term RNA editing refers to any structural change in an RNA molecule (e.g. insertion, deletion, or base modification) that changes its coding properties and is not a result of splicing. An important class of enzymes involved in RNA editing is the ADAR family (adenosine deaminases acting on RNA), which facilitate the deamination of adenosine (A) to inosine (I) in double-stranded RNA (dsRNA). Inosines are decoded as guanosines (G) in most cellular processes; hence, A-to-I editing can be considered an A-to-G substitution. Among the RNA editing enzymes, ADARs are of particular interest because a large portion of RNA editing events are due to A-to-I editing by the two catalytically active human ADARs (ADAR1 and ADAR2). ADARs have diverse roles in RNA processing, gene expression regulation, and innate immunity; and mutations in the ADAR genes and dysregulated ADAR activity have been associated with cancer, autoimmune diseases, and neurological disorders. A-to-I editing is also currently being explored for correcting disease-causing mutations in the RNA, where therapeutic guide oligonucleotides complementary to the target transcript are used to form a dsRNA substrate and site-specifically direct ADAR editing. Knowledge of the mechanism of ADAR-catalyzed reaction and the origin of its substrate selectivity will allow understanding of ADAR’s role in disease biology and expedite the process of developing ADAR-targeted therapeutics. Chemically modified oligonucleotides provide a versatile platform for modulating the activity and interrogating the structure, function, and selectivity of nucleic acid binding or modifying proteins. In this account, we provide an overview of oligonucleotide modifications that have allowed us to gain deeper understanding of ADAR’s molecular mechanisms, which we utilize in the rational design and optimization of ADAR activity modulators. First, we describe the use of the nucleoside analog 8-azanebularine (8-azaN) to generate high-affinity ADAR-RNA complexes for biochemical and biophysical studies with ADARs, with particular emphasis on X-ray crystallography. We then discuss key observations derived from the crystal structures of ADAR bound to 8-azaN-modified RNA duplexes and describe how these findings provided insight into ADAR editing optimization by introducing nucleoside modifications at various positions in synthetic guide strands. We also present the informed design of 8-azaN-modified RNA duplexes that selectively bind and inhibit ADAR1 but not the closely-related ADAR2 enzyme. Finally, we conclude with some open questions on ADAR structure and substrate recognition and share our current endeavors in the development of ADAR guide oligonucleotides and inhibitors.
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Affiliation(s)
- Herra G. Mendoza
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - Peter A. Beal
- Department of Chemistry, University of California, Davis, CA 95616 USA
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4
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Pomaville MM, He C. Advances in targeting RNA modifications for anticancer therapy. Trends Cancer 2023:S2405-8033(23)00059-6. [PMID: 37147166 DOI: 10.1016/j.trecan.2023.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 05/07/2023]
Abstract
Numerous strategies are employed by cancer cells to control gene expression and facilitate tumorigenesis. In the study of epitranscriptomics, a diverse set of modifications to RNA represent a new player of gene regulation in disease and in development. N6-methyladenosine (m6A) is the most common modification on mammalian messenger RNA and tends to be aberrantly placed in cancer. Recognized by a series of reader proteins that dictate the fate of the RNA, m6A-modified RNA could promote tumorigenesis by driving protumor gene expression signatures and altering the immunologic response to tumors. Preclinical evidence suggests m6A writer, reader, and eraser proteins are attractive therapeutic targets. First-in-human studies are currently testing small molecule inhibition against the methyltransferase-like 3 (METTL3)/methyltransferase-like 14 (METTL14) methyltransferase complex. Additional modifications to RNA are adopted by cancers to drive tumor development and are under investigation.
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Affiliation(s)
- Monica M Pomaville
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL, USA; Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA.
| | - Chuan He
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA; Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
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Jia Z, Meng F, Chen H, Zhu G, Li X, He Y, Zhang L, He X, Zhan H, Chen M, Ji Y, Wang M, Guan MX. Human TRUB1 is a highly conserved pseudouridine synthase responsible for the formation of Ψ55 in mitochondrial tRNAAsn, tRNAGln, tRNAGlu and tRNAPro. Nucleic Acids Res 2022; 50:9368-9381. [PMID: 36018806 PMCID: PMC9458420 DOI: 10.1093/nar/gkac698] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 07/26/2022] [Accepted: 07/30/2022] [Indexed: 12/24/2022] Open
Abstract
Pseudouridine (Ψ) at position 55 in tRNAs plays an important role in their structure and function. This modification is catalyzed by TruB/Pus4/Cbf5 family of pseudouridine synthases in bacteria and yeast. However, the mechanism of TRUB family underlying the formation of Ψ55 in the mammalian tRNAs is largely unknown. In this report, the CMC/reverse transcription assays demonstrated the presence of Ψ55 in the human mitochondrial tRNAAsn, tRNAGln, tRNAGlu, tRNAPro, tRNAMet, tRNALeu(UUR) and tRNASer(UCN). TRUB1 knockout (KO) cell lines generated by CRISPR/Cas9 technology exhibited the loss of Ψ55 modification in mitochondrial tRNAAsn, tRNAGln, tRNAGlu and tRNAPro but did not affect other 18 mitochondrial tRNAs. An in vitro assay revealed that recombinant TRUB1 protein can catalyze the efficient formation of Ψ55 in tRNAAsn and tRNAGln, but not in tRNAMet and tRNAArg. Notably, the overexpression of TRUB1 cDNA reversed the deficient Ψ55 modifications in these tRNAs in TRUB1KO HeLa cells. TRUB1 deficiency affected the base-pairing (18A/G-Ψ55), conformation and stability but not aminoacylation capacity of these tRNAs. Furthermore, TRUB1 deficiency impacted mitochondrial translation and biogenesis of oxidative phosphorylation system. Our findings demonstrated that human TRUB1 is a highly conserved mitochondrial pseudouridine synthase responsible for the Ψ55 modification in the mitochondrial tRNAAsn, tRNAGln, tRNAGlu and tRNAPro.
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Affiliation(s)
| | | | | | - Gao Zhu
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xincheng Li
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yunfan He
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Liyao Zhang
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiao He
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Huisen Zhan
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Mengquan Chen
- Department of Lab Medicine, Wenzhou Hospital of Traditional Chinese Medicine, Wenzhou, Zhejiang, China
| | - Yanchun Ji
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Meng Wang
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Min-Xin Guan
- To whom correspondence should be addressed. Tel: +571 88206916; Fax: +571 88982377;
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6
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Frazier MN, Wilson IM, Krahn JM, Butay KJ, Dillard LB, Borgnia MJ, Stanley RE. Flipped over U: structural basis for dsRNA cleavage by the SARS-CoV-2 endoribonuclease. Nucleic Acids Res 2022; 50:8290-8301. [PMID: 35801916 DOI: 10.1093/nar/gkac589] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 01/13/2023] Open
Abstract
Coronaviruses generate double-stranded (ds) RNA intermediates during viral replication that can activate host immune sensors. To evade activation of the host pattern recognition receptor MDA5, coronaviruses employ Nsp15, which is a uridine-specific endoribonuclease. Nsp15 is proposed to associate with the coronavirus replication-transcription complex within double-membrane vesicles to cleave these dsRNA intermediates. How Nsp15 recognizes and processes dsRNA is poorly understood because previous structural studies of Nsp15 have been limited to small single-stranded (ss) RNA substrates. Here we present cryo-EM structures of SARS-CoV-2 Nsp15 bound to a 52nt dsRNA. We observed that the Nsp15 hexamer forms a platform for engaging dsRNA across multiple protomers. The structures, along with site-directed mutagenesis and RNA cleavage assays revealed critical insight into dsRNA recognition and processing. To process dsRNA Nsp15 utilizes a base-flipping mechanism to properly orient the uridine within the active site for cleavage. Our findings show that Nsp15 is a distinctive endoribonuclease that can cleave both ss- and dsRNA effectively.
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Affiliation(s)
- Meredith N Frazier
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Isha M Wilson
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Juno M Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Kevin John Butay
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Lucas B Dillard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
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7
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Frazier MN, Wilson IM, Krahn JM, Butay KJ, Dillard LB, Borgnia MJ, Stanley RE. Flipped Over U: Structural Basis for dsRNA Cleavage by the SARS-CoV-2 Endoribonuclease. bioRxiv 2022:2022.03.02.480688. [PMID: 35262076 PMCID: PMC8902873 DOI: 10.1101/2022.03.02.480688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Coronaviruses generate double-stranded (ds) RNA intermediates during viral replication that can activate host immune sensors. To evade activation of the host pattern recognition receptor MDA5, coronaviruses employ Nsp15, which is uridine-specific endoribonuclease. Nsp15 is proposed to associate with the coronavirus replication-transcription complex within double-membrane vesicles to cleave these dsRNA intermediates. How Nsp15 recognizes and processes dsRNA is poorly understood because previous structural studies of Nsp15 have been limited to small single-stranded (ss) RNA substrates. Here we present cryo-EM structures of SARS-CoV-2 Nsp15 bound to a 52nt dsRNA. We observed that the Nsp15 hexamer forms a platform for engaging dsRNA across multiple protomers. The structures, along with site-directed mutagenesis and RNA cleavage assays revealed critical insight into dsRNA recognition and processing. To process dsRNA Nsp15 utilizes a base-flipping mechanism to properly orient the uridine within the active site for cleavage. Our findings show that Nsp15 is a distinctive endoribonuclease that can cleave both ss- and dsRNA effectively.
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Affiliation(s)
- Meredith N. Frazier
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Isha M. Wilson
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Juno M. Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Kevin John Butay
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Lucas B. Dillard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Mario J. Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Robin E. Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Garus A, Autexier C. Dyskerin: an essential pseudouridine synthase with multifaceted roles in ribosome biogenesis, splicing, and telomere maintenance. RNA 2021; 27:1441-1458. [PMID: 34556550 PMCID: PMC8594475 DOI: 10.1261/rna.078953.121] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Dyskerin and its homologs are ancient and conserved enzymes that catalyze the most common post-transcriptional modification found in cells, pseudouridylation. The resulting pseudouridines provide stability to RNA molecules and regulate ribosome biogenesis and splicing events. Dyskerin does not act independently-it is the core component of a protein heterotetramer, which associates with RNAs that contain the H/ACA motif. The variety of H/ACA RNAs that guide the function of this ribonucleoprotein (RNP) complex highlights the diversity of cellular processes in which dyskerin participates. When associated with small nucleolar (sno) RNAs, it regulates ribosomal (r) RNAs and ribosome biogenesis. By interacting with small Cajal body (sca) RNAs, it targets small nuclear (sn) RNAs to regulate pre-mRNA splicing. As a component of the telomerase holoenzyme, dyskerin binds to the telomerase RNA to modulate telomere maintenance. In a disease context, dyskerin malfunction can result in multiple detrimental phenotypes. Mutations in DKC1, the gene that encodes dyskerin, cause the premature aging syndrome X-linked dyskeratosis congenita (X-DC), a still incurable disorder that typically leads to bone marrow failure. In this review, we present the classical and most recent findings on this essential protein, discussing the evolutionary, structural, and functional aspects of dyskerin and the H/ACA RNP. The latest research underscores the role that dyskerin plays in the regulation of gene expression, translation efficiency, and telomere maintenance, along with the impacts that defective dyskerin has on aging, cell proliferation, haematopoietic potential, and cancer.
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Affiliation(s)
- Alexandre Garus
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada
- Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada
| | - Chantal Autexier
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada
- Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada
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10
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Lin TY, Mehta R, Glatt S. Pseudouridines in RNAs: switching atoms means shifting paradigms. FEBS Lett 2021; 595:2310-2322. [PMID: 34468991 PMCID: PMC9290505 DOI: 10.1002/1873-3468.14188] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/18/2021] [Accepted: 08/22/2021] [Indexed: 01/21/2023]
Abstract
The structure, stability, and function of various coding and noncoding RNAs are influenced by chemical modifications. Pseudouridine (Ψ) is one of the most abundant post‐transcriptional RNA base modifications and has been detected at individual positions in tRNAs, rRNAs, mRNAs, and snRNAs, which are referred to as Ψ‐sites. By allowing formation of additional bonds with neighboring atoms, Ψ strengthens RNA–RNA and RNA–protein interactions. Although many aspects of the underlying modification reactions remain unclear, the advent of new transcriptome‐wide methods to quantitatively detect Ψ‐sites has recently changed our perception of the functional roles and importance of Ψ. For instance, it is now clear that the occurrence of Ψs appears to be directly linked to the lifetime and the translation efficiency of a given mRNA molecule. Furthermore, the administration of Ψ‐containing RNAs reduces innate immune responses, which appears strikingly advantageous for the development of generations of mRNA‐based vaccines. In this review, we aim to comprehensively summarize recent discoveries that highlight the impact of Ψ on various types of RNAs and outline possible novel biomedical applications of Ψ.
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Affiliation(s)
- Ting-Yu Lin
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Rahul Mehta
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
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11
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Pujari N, Saundh SL, Acquah FA, Mooers BHM, Ferré-D’Amaré AR, Leung AKW. Engineering Crystal Packing in RNA Structures I: Past and Future Strategies for Engineering RNA Packing in Crystals. Crystals (Basel) 2021; 11:952. [PMID: 34745656 PMCID: PMC8570644 DOI: 10.3390/cryst11080952] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
X-ray crystallography remains a powerful method to gain atomistic insights into the catalytic and regulatory functions of RNA molecules. However, the technique requires the preparation of diffraction-quality crystals. This is often a resource- and time-consuming venture because RNA crystallization is hindered by the conformational heterogeneity of RNA, as well as the limited opportunities for stereospecific intermolecular interactions between RNA molecules. The limited success at crystallization explains in part the smaller number of RNA-only structures in the Protein Data Bank. Several approaches have been developed to aid the formation of well-ordered RNA crystals. The majority of these are construct-engineering techniques that aim to introduce crystal contacts to favor the formation of well-diffracting crystals. A typical example is the insertion of tetraloop-tetraloop receptor pairs into non-essential RNA segments to promote intermolecular association. Other methods of promoting crystallization involve chaperones and crystallization-friendly molecules that increase RNA stability and improve crystal packing. In this review, we discuss the various techniques that have been successfully used to facilitate crystal packing of RNA molecules, recent advances in construct engineering, and directions for future research in this vital aspect of RNA crystallography.
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Affiliation(s)
- Narsimha Pujari
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Stephanie L. Saundh
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Francis A. Acquah
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Blaine H. M. Mooers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Adrian R. Ferré-D’Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
| | - Adelaine Kwun-Wai Leung
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
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12
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Stephan NC, Ries AB, Boehringer D, Ban N. Structural basis of successive adenosine modifications by the conserved ribosomal methyltransferase KsgA. Nucleic Acids Res 2021; 49:6389-6398. [PMID: 34086932 PMCID: PMC8216452 DOI: 10.1093/nar/gkab430] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/09/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
Biogenesis of ribosomal subunits involves enzymatic modifications of rRNA that fine-tune functionally important regions. The universally conserved prokaryotic dimethyltransferase KsgA sequentially modifies two universally conserved adenosine residues in helix 45 of the small ribosomal subunit rRNA, which is in proximity of the decoding site. Here we present the cryo-EM structure of Escherichia coli KsgA bound to an E. coli 30S at a resolution of 3.1 Å. The high-resolution structure reveals how KsgA recognizes immature rRNA and binds helix 45 in a conformation where one of the substrate nucleotides is flipped-out into the active site. We suggest that successive processing of two adjacent nucleotides involves base-flipping of the rRNA, which allows modification of the second substrate nucleotide without dissociation of the enzyme. Since KsgA is homologous to the essential eukaryotic methyltransferase Dim1 involved in 40S maturation, these results have also implications for understanding eukaryotic ribosome maturation.
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Affiliation(s)
- Niklas C Stephan
- Institute of Molecular Biology and Biophysics, ETH Zurich (Swiss Federal Institute of Technology), Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland
| | - Anne B Ries
- Institute of Molecular Biology and Biophysics, ETH Zurich (Swiss Federal Institute of Technology), Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland
| | - Daniel Boehringer
- Institute of Molecular Biology and Biophysics, ETH Zurich (Swiss Federal Institute of Technology), Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland
| | - Nenad Ban
- Institute of Molecular Biology and Biophysics, ETH Zurich (Swiss Federal Institute of Technology), Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland
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13
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Wilson KA, Kung RW, D'souza S, Wetmore SD. Anatomy of noncovalent interactions between the nucleobases or ribose and π-containing amino acids in RNA-protein complexes. Nucleic Acids Res 2021; 49:2213-2225. [PMID: 33544852 PMCID: PMC7913691 DOI: 10.1093/nar/gkab008] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/22/2021] [Indexed: 01/07/2023] Open
Abstract
A set of >300 nonredundant high-resolution RNA–protein complexes were rigorously searched for π-contacts between an amino acid side chain (W, H, F, Y, R, E and D) and an RNA nucleobase (denoted π–π interaction) or ribose moiety (denoted sugar–π). The resulting dataset of >1500 RNA–protein π-contacts were visually inspected and classified based on the interaction type, and amino acids and RNA components involved. More than 80% of structures searched contained at least one RNA–protein π-interaction, with π–π contacts making up 59% of the identified interactions. RNA–protein π–π and sugar–π contacts exhibit a range in the RNA and protein components involved, relative monomer orientations and quantum mechanically predicted binding energies. Interestingly, π–π and sugar–π interactions occur more frequently with RNA (4.8 contacts/structure) than DNA (2.6). Moreover, the maximum stability is greater for RNA–protein contacts than DNA–protein interactions. In addition to highlighting distinct differences between RNA and DNA–protein binding, this work has generated the largest dataset of RNA–protein π-interactions to date, thereby underscoring that RNA–protein π-contacts are ubiquitous in nature, and key to the stability and function of RNA–protein complexes.
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Affiliation(s)
- Katie A Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Ryan W Kung
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Simmone D'souza
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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14
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Affiliation(s)
- Seung Hun Han
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Korea
| | - Junho Choe
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Korea
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15
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Porat J, Kothe U, Bayfield MA. Revisiting tRNA chaperones: New players in an ancient game. RNA 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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Abstract
C-Analogues of the canonical N-nucleosides have considerable importance in medicinal chemistry and are promising building blocks of xenobiotic nucleic acids (XNA) in synthetic biology. Although well established for synthesis of N-nucleosides, biocatalytic methods are lacking in C-nucleoside synthetic chemistry. Here, we identify pseudouridine monophosphate C-glycosidase for selective 5-β-C-glycosylation of uracil and derivatives thereof from pentose 5-phosphate (D-ribose, 2-deoxy-D-ribose, D-arabinose, D-xylose) substrates. Substrate requirements of the enzymatic reaction are consistent with a Mannich-like addition between the pyrimidine nucleobase and the iminium intermediate of enzyme (Lys166) and open-chain pentose 5-phosphate. β-Elimination of the lysine and stereoselective ring closure give the product. We demonstrate phosphorylation-glycosylation cascade reactions for efficient, one-pot synthesis of C-nucleoside phosphates (yield: 33 - 94%) from unprotected sugar and nucleobase. We show incorporation of the enzymatically synthesized C-nucleotide triphosphates into nucleic acids by RNA polymerase. Collectively, these findings implement biocatalytic methodology for C-nucleotide synthesis which can facilitate XNA engineering for synthetic biology applications.
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Affiliation(s)
- Martin Pfeiffer
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010, Graz, Austria
- Austrian Centre of Industrial Biotechnology (acib), Petersgasse 14, 8010, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010, Graz, Austria.
- Austrian Centre of Industrial Biotechnology (acib), Petersgasse 14, 8010, Graz, Austria.
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17
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Abstract
Following its transcription, RNA can be modified by >170 chemically distinct types of modifications - the epitranscriptome. In recent years, there have been substantial efforts to uncover and characterize the modifications present on mRNA, motivated by the potential of such modifications to regulate mRNA fate and by discoveries and advances in our understanding of N 6-methyladenosine (m6A). Here, we review our knowledge regarding the detection, distribution, abundance, biogenesis, functions and possible mechanisms of action of six of these modifications - pseudouridine (Ψ), 5-methylcytidine (m5C), N 1-methyladenosine (m1A), N 4-acetylcytidine (ac4C), ribose methylations (Nm) and N 7-methylguanosine (m7G). We discuss the technical and analytical aspects that have led to inconsistent conclusions and controversies regarding the abundance and distribution of some of these modifications. We further highlight shared commonalities and important ways in which these modifications differ with respect to m6A, based on which we speculate on their origin and their ability to acquire functions over evolutionary timescales.
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18
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Donsbach P, Yee BA, Sanchez-Hevia D, Berenguer J, Aigner S, Yeo GW, Klostermeier D. The Thermus thermophilus DEAD-box protein Hera is a general RNA binding protein and plays a key role in tRNA metabolism. RNA 2020; 26:1557-1574. [PMID: 32669294 PMCID: PMC7566566 DOI: 10.1261/rna.075580.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/05/2020] [Indexed: 06/11/2023]
Abstract
RNA helicases catalyze the ATP-dependent destabilization of RNA duplexes. DEAD-box helicases share a helicase core that mediates ATP binding and hydrolysis, RNA binding and unwinding. Most members of this family contain domains flanking the core that can confer RNA substrate specificity and guide the helicase to a specific RNA. However, the in vivo RNA substrates of most helicases are currently not defined. The DEAD-box helicase Hera from Thermus thermophilus contains a helicase core, followed by a dimerization domain and an RNA binding domain that folds into an RNA recognition motif (RRM). The RRM mediates high affinity binding to an RNA hairpin, and an adjacent duplex is then unwound by the helicase core. Hera is a cold-shock protein, and has been suggested to act as an RNA chaperone under cold-shock conditions. Using crosslinking immunoprecipitation of Hera/RNA complexes and sequencing, we show that Hera binds to a large fraction of T. thermophilus RNAs under normal-growth and cold-shock conditions without a strong sequence preference, in agreement with a structure-specific recognition of RNAs and a general function in RNA metabolism. Under cold-shock conditions, Hera is recruited to RNAs with high propensities to form stable secondary structures. We show that selected RNAs identified, including a set of tRNAs, bind to Hera in vitro, and activate the Hera helicase core. Gene ontology analysis reveals an enrichment of genes related to translation, including mRNAs of ribosomal proteins, tRNAs, tRNA ligases, and tRNA-modifying enzymes, consistent with a key role of Hera in ribosome and tRNA metabolism.
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Affiliation(s)
- Pascal Donsbach
- University of Muenster, Institute for Physical Chemistry, 48149 Muenster, Germany
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Dione Sanchez-Hevia
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - José Berenguer
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Dagmar Klostermeier
- University of Muenster, Institute for Physical Chemistry, 48149 Muenster, Germany
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19
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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: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Schultz SKL, Kothe U. tRNA elbow modifications affect the tRNA pseudouridine synthase TruB and the methyltransferase TrmA. RNA 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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Abstract
Recent advances in pseudouridine detection reveal a complex pseudouridine landscape that includes messenger RNA and diverse classes of noncoding RNA in human cells. The known molecular functions of pseudouridine, which include stabilizing RNA conformations and destabilizing interactions with varied RNA-binding proteins, suggest that RNA pseudouridylation could have widespread effects on RNA metabolism and gene expression. Here, we emphasize how much remains to be learned about the RNA targets of human pseudouridine synthases, their basis for recognizing distinct RNA sequences, and the mechanisms responsible for regulated RNA pseudouridylation. We also examine the roles of noncoding RNA pseudouridylation in splicing and translation and point out the potential effects of mRNA pseudouridylation on protein production, including in the context of therapeutic mRNAs.
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Affiliation(s)
- Erin K Borchardt
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
| | - Nicole M Martinez
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
| | - Wendy V Gilbert
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
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22
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Dégut C, Roovers M, Barraud P, Brachet F, Feller A, Larue V, Al Refaii A, Caillet J, Droogmans L, Tisné C. Structural characterization of B. subtilis m1A22 tRNA methyltransferase TrmK: insights into tRNA recognition. Nucleic Acids Res 2019; 47:4736-4750. [PMID: 30931478 PMCID: PMC6511850 DOI: 10.1093/nar/gkz230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/04/2019] [Accepted: 03/26/2019] [Indexed: 12/21/2022] Open
Abstract
1-Methyladenosine (m1A) is a modified nucleoside found at positions 9, 14, 22 and 58 of tRNAs, which arises from the transfer of a methyl group onto the N1-atom of adenosine. The yqfN gene of Bacillus subtilis encodes the methyltransferase TrmK (BsTrmK) responsible for the formation of m1A22 in tRNA. Here, we show that BsTrmK displays a broad substrate specificity, and methylates seven out of eight tRNA isoacceptor families of B. subtilis bearing an A22. In addition to a non-Watson–Crick base-pair between the target A22 and a purine at position 13, the formation of m1A22 by BsTrmK requires a full-length tRNA with intact tRNA elbow and anticodon stem. We solved the crystal structure of BsTrmK showing an N-terminal catalytic domain harbouring the typical Rossmann-like fold of Class-I methyltransferases and a C-terminal coiled-coil domain. We used NMR chemical shift mapping to drive the docking of BstRNASer to BsTrmK in complex with its methyl-donor cofactor S-adenosyl-L-methionine (SAM). In this model, validated by methyltransferase activity assays on BsTrmK mutants, both domains of BsTrmK participate in tRNA binding. BsTrmK recognises tRNA with very few structural changes in both partner, the non-Watson–Crick R13–A22 base-pair positioning the A22 N1-atom close to the SAM methyl group.
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Affiliation(s)
- Clément Dégut
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Sorbonne Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France
| | | | - Pierre Barraud
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Sorbonne Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France.,Laboratoire d'Expression génétique microbienne, CNRS, Univ. Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Franck Brachet
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Sorbonne Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France
| | - André Feller
- Laboratoire de Microbiologie, Université libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Valéry Larue
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Sorbonne Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France
| | - Abdalla Al Refaii
- Laboratoire de Microbiologie, Université libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Joël Caillet
- Laboratoire d'Expression génétique microbienne, CNRS, Univ. Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Louis Droogmans
- Laboratoire de Microbiologie, Université libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Carine Tisné
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Sorbonne Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France.,Laboratoire d'Expression génétique microbienne, CNRS, Univ. Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
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23
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Barraud P, Tisné C. To be or not to be modified: Miscellaneous aspects influencing nucleotide modifications in tRNAs. IUBMB Life 2019; 71:1126-1140. [PMID: 30932315 PMCID: PMC6850298 DOI: 10.1002/iub.2041] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/10/2019] [Indexed: 12/12/2022]
Abstract
Transfer RNAs (tRNAs) are essential components of the cellular protein synthesis machineries, but are also implicated in many roles outside translation. To become functional, tRNAs, initially transcribed as longer precursor tRNAs, undergo a tightly controlled biogenesis process comprising the maturation of their extremities, removal of intronic sequences if present, addition of the 3'-CCA amino-acid accepting sequence, and aminoacylation. In addition, the most impressive feature of tRNA biogenesis consists in the incorporation of a large number of posttranscriptional chemical modifications along its sequence. The chemical nature of these modifications is highly diverse, with more than hundred different modifications identified in tRNAs to date. All functions of tRNAs in cells are controlled and modulated by modifications, making the understanding of the mechanisms that determine and influence nucleotide modifications in tRNAs an essential point in tRNA biology. This review describes the different aspects that determine whether a certain position in a tRNA molecule is modified or not. We describe how sequence and structural determinants, as well as the presence of prior modifications control modification processes. We also describe how environmental factors and cellular stresses influence the level and/or the nature of certain modifications introduced in tRNAs, and report situations where these dynamic modulations of tRNA modification levels are regulated by active demodification processes. © 2019 IUBMB Life, 71(8):1126-1140, 2019.
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Affiliation(s)
- Pierre Barraud
- Expression génétique microbienneInstitut de biologie physico‐chimique (IBPC), UMR 8261, CNRS, Université Paris DiderotParisFrance
| | - Carine Tisné
- Expression génétique microbienneInstitut de biologie physico‐chimique (IBPC), UMR 8261, CNRS, Université Paris DiderotParisFrance
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24
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Abstract
tRNAs are short noncoding RNAs required for protein translation. The human genome includes more than 600 putative tRNA genes, many of which are considered redundant. tRNA transcripts are subject to tightly controlled, multistep maturation processes that lead to the removal of flanking sequences and the addition of nontemplated nucleotides. Furthermore, tRNAs are highly structured and posttranscriptionally modified. Together, these unique features have impeded the adoption of modern genomics and transcriptomics technologies for tRNA studies. Nevertheless, it has become apparent from human neurogenetic research that many tRNA biogenesis proteins cause brain abnormalities and other neurological disorders when mutated. The cerebral cortex, cerebellum, and peripheral nervous system show defects, impairment, and degeneration upon tRNA misregulation, suggesting that they are particularly sensitive to changes in tRNA expression or function. An integrated approach to identify tRNA species and contextually characterize tRNA function will be imperative to drive future tool development and novel therapeutic design for tRNA-associated disorders.
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Affiliation(s)
- Ashleigh E Schaffer
- Department of Genetics and Genome Sciences and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio 44106, USA;
| | - Otis Pinkard
- Department of Genetics and Genome Sciences and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio 44106, USA;
| | - Jeffery M Coller
- Department of Genetics and Genome Sciences and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio 44106, USA;
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25
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Abstract
Thermus thermophilus is an extreme-thermophilic bacterium that can grow at a wide range of temperatures (50-83°C). To enable T. thermophilus to grow at high temperatures, several biomolecules including tRNA and tRNA modification enzymes show extreme heat-resistance. Therefore, the modified nucleosides in tRNA from T. thermophilus have been studied mainly from the view point of tRNA stabilization at high temperatures. Such studies have shown that several modifications stabilize the structure of tRNA and are essential for survival of the organism at high temperatures. Together with tRNA modification enzymes, the modified nucleosides form a network that regulates the extent of different tRNA modifications at various temperatures. In this review, I describe this network, as well as the tRNA recognition mechanism of individual tRNA modification enzymes. Furthermore, I summarize the roles of other tRNA stabilization factors such as polyamines and metal ions.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Sciences and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
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26
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Adachi H, De Zoysa MD, Yu YT. Post-transcriptional pseudouridylation in mRNA as well as in some major types of noncoding RNAs. Biochim Biophys Acta Gene Regul Mech 2018; 1862:230-239. [PMID: 30414851 DOI: 10.1016/j.bbagrm.2018.11.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/29/2018] [Accepted: 11/02/2018] [Indexed: 01/13/2023]
Abstract
Pseudouridylation is a post-transcriptional isomerization reaction that converts a uridine to a pseudouridine (Ψ) within an RNA chain. Ψ has chemical properties that are distinct from that of uridine and any other known nucleotides. Experimental data accumulated thus far have indicated that Ψ is present in many different types of RNAs, including coding and noncoding RNAs. Ψ is particularly concentrated in rRNA and spliceosomal snRNAs, and plays an important role in protein translation and pre-mRNA splicing, respectively. Ψ has also been found in mRNA, but its function there remains essentially unknown. In this review, we discuss the mechanisms and functions of RNA pseudouridylation, focusing on rRNA, snRNA and mRNA. We also discuss the methods, which have been developed to detect Ψs in RNAs. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
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Affiliation(s)
- Hironori Adachi
- University of Rochester Medical Center, Department of Biochemistry and Biophysics, Center for RNA Biology, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Meemanage D De Zoysa
- University of Rochester Medical Center, Department of Biochemistry and Biophysics, Center for RNA Biology, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Yi-Tao Yu
- University of Rochester Medical Center, Department of Biochemistry and Biophysics, Center for RNA Biology, 601 Elmwood Avenue, Rochester, NY 14642, USA.
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Ryu H, Grove TL, Almo SC, Kim J. Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine. Nucleic Acids Res 2018; 46:9160-9169. [PMID: 29982645 PMCID: PMC6158493 DOI: 10.1093/nar/gky592] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/14/2018] [Accepted: 06/20/2018] [Indexed: 11/13/2022] Open
Abstract
Derivatives of 5-hydroxyuridine (ho5U), such as 5-methoxyuridine (mo5U) and 5-oxyacetyluridine (cmo5U), are ubiquitous modifications of the wobble position of bacterial tRNA that are believed to enhance translational fidelity by the ribosome. In gram-negative bacteria, the last step in the biosynthesis of cmo5U from ho5U involves the unique metabolite carboxy S-adenosylmethionine (Cx-SAM) and the carboxymethyl transferase CmoB. However, the equivalent position in the tRNA of Gram-positive bacteria is instead mo5U, where the methyl group is derived from SAM and installed by an unknown methyltransferase. By utilizing a cmoB-deficient strain of Escherichia coli as a host and assaying for the formation of mo5U in total RNA isolates with methyltransferases of unknown function from Bacillus subtilis, we found that this modification is installed by the enzyme TrmR (formerly known as YrrM). Furthermore, X-ray crystal structures of TrmR with and without the anticodon stemloop of tRNAAla have been determined, which provide insight into both sequence and structure specificity in the interactions of TrmR with tRNA.
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Affiliation(s)
- Huijeong Ryu
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Tyler L Grove
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jungwook Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
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Morena F, Argentati C, Bazzucchi M, Emiliani C, Martino S. Above the Epitranscriptome: RNA Modifications and Stem Cell Identity. Genes (Basel) 2018; 9:E329. [PMID: 29958477 PMCID: PMC6070936 DOI: 10.3390/genes9070329] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 06/15/2018] [Accepted: 06/25/2018] [Indexed: 02/07/2023] Open
Abstract
Sequence databases and transcriptome-wide mapping have revealed different reversible and dynamic chemical modifications of the nitrogen bases of RNA molecules. Modifications occur in coding RNAs and noncoding-RNAs post-transcriptionally and they can influence the RNA structure, metabolism, and function. The result is the expansion of the variety of the transcriptome. In fact, depending on the type of modification, RNA molecules enter into a specific program exerting the role of the player or/and the target in biological and pathological processes. Many research groups are exploring the role of RNA modifications (alias epitranscriptome) in cell proliferation, survival, and in more specialized activities. More recently, the role of RNA modifications has been also explored in stem cell biology. Our understanding in this context is still in its infancy. Available evidence addresses the role of RNA modifications in self-renewal, commitment, and differentiation processes of stem cells. In this review, we will focus on five epitranscriptomic marks: N6-methyladenosine, N1-methyladenosine, 5-methylcytosine, Pseudouridine (Ψ) and Adenosine-to-Inosine editing. We will provide insights into the function and the distribution of these chemical modifications in coding RNAs and noncoding-RNAs. Mainly, we will emphasize the role of epitranscriptomic mechanisms in the biology of naïve, primed, embryonic, adult, and cancer stem cells.
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Affiliation(s)
- Francesco Morena
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06126 Perugia, Italy.
| | - Chiara Argentati
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06126 Perugia, Italy.
| | - Martina Bazzucchi
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06126 Perugia, Italy.
| | - Carla Emiliani
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06126 Perugia, Italy.
- CEMIN, Center of Excellence of Nanostructured Innovative Materials, University of Perugia, 06126 Perugia, Italy.
| | - Sabata Martino
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06126 Perugia, Italy.
- CEMIN, Center of Excellence of Nanostructured Innovative Materials, University of Perugia, 06126 Perugia, Italy.
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Zhao Y, Dunker W, Yu YT, Karijolich J. The Role of Noncoding RNA Pseudouridylation in Nuclear Gene Expression Events. Front Bioeng Biotechnol 2018; 6:8. [PMID: 29473035 PMCID: PMC5809436 DOI: 10.3389/fbioe.2018.00008] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/22/2018] [Indexed: 12/23/2022] Open
Abstract
Pseudouridine is the most abundant internal RNA modification in stable noncoding RNAs (ncRNAs). It can be catalyzed by both RNA-dependent and RNA-independent mechanisms. Pseudouridylation impacts both the biochemical and biophysical properties of RNAs and thus influences RNA-mediated cellular processes. The investigation of nuclear-ncRNA pseudouridylation has demonstrated that it is critical for the proper control of multiple stages of gene expression regulation. Here, we review how nuclear-ncRNA pseudouridylation contributes to transcriptional regulation and pre-mRNA splicing.
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Affiliation(s)
- Yang Zhao
- Department of Pathology, Microbiology, and Immunology, School of Medicine, Vanderbilt University, Nashville, TN, United States
| | - William Dunker
- Department of Pathology, Microbiology, and Immunology, School of Medicine, Vanderbilt University, Nashville, TN, United States
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, United States
| | - John Karijolich
- Department of Pathology, Microbiology, and Immunology, School of Medicine, Vanderbilt University, Nashville, TN, United States.,Vanderbilt-Ingram Cancer Center, Nashville, TN, United States
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Fitzek E, Joardar A, Gupta R, Geisler M. Evolution of Eukaryal and Archaeal Pseudouridine Synthase Pus10. J Mol Evol 2018; 86:77-89. [PMID: 29349599 DOI: 10.1007/s00239-018-9827-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/03/2018] [Indexed: 10/18/2022]
Abstract
In archaea, pseudouridine (Ψ) synthase Pus10 modifies uridine (U) to Ψ at positions 54 and 55 of tRNA. In contrast, Pus10 is not found in bacteria, where modifications at those two positions are carried out by TrmA (U54 to m5U54) and TruB (U55 to Ψ55). Many eukaryotes have an apparent redundancy; their genomes contain orthologs of archaeal Pus10 and bacterial TrmA and TruB. Although eukaryal Pus10 genes share a conserved catalytic domain with archaeal Pus10 genes, their biological roles are not clear for the two reasons. First, experimental evidence suggests that human Pus10 participates in apoptosis induced by the tumor necrosis factor-related apoptosis-inducing ligand. Whether the function of human Pus10 is in place or in addition to of Ψ synthesis in tRNA is unknown. Second, Pus10 is found in earlier evolutionary branches of fungi (such as chytrid Batrachochytrium) but is absent in all dikaryon fungi surveyed (Ascomycetes and Basidiomycetes). We did a comprehensive analysis of sequenced genomes and found that orthologs of Pus10, TrmA, and TruB were present in all the animals, plants, and protozoa surveyed. This indicates that the common eukaryotic ancestor possesses all the three genes. Next, we examined 116 archaeal and eukaryotic Pus10 protein sequences to find that Pus10 existed as a single copy gene in all the surveyed genomes despite ancestral whole genome duplications had occurred. This indicates a possible deleterious gene dosage effect. Our results suggest that functional redundancy result in gene loss or neofunctionalization in different evolutionary lineages.
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Liu RJ, Long T, Li J, Li H, Wang ED. Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6. Nucleic Acids Res 2017; 45:6684-6697. [PMID: 28531330 PMCID: PMC5499824 DOI: 10.1093/nar/gkx473] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 05/12/2017] [Indexed: 12/20/2022] Open
Abstract
5-methylcytosine (m5C) modifications of RNA are ubiquitous in nature and play important roles in many biological processes such as protein translational regulation, RNA processing and stress response. Aberrant expressions of RNA:m5C methyltransferases are closely associated with various human diseases including cancers. However, no structural information for RNA-bound RNA:m5C methyltransferase was available until now, hindering elucidation of the catalytic mechanism behind RNA:m5C methylation. Here, we have solved the structures of NSun6, a human tRNA:m5C methyltransferase, in the apo form and in complex with a full-length tRNA substrate. These structures show a non-canonical conformation of the bound tRNA, rendering the base moiety of the target cytosine accessible to the enzyme for methylation. Further biochemical assays reveal the critical, but distinct, roles of two conserved cysteine residues for the RNA:m5C methylation. Collectively, for the first time, we have solved the complex structure of a RNA:m5C methyltransferase and addressed the catalytic mechanism of the RNA:m5C methyltransferase family, which may allow for structure-based drug design toward RNA:m5C methyltransferase–related diseases.
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Affiliation(s)
- Ru-Juan Liu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China
| | - Tao Long
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China.,University of Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Jing Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China.,University of Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Hao Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China.,University of Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China.,University of Chinese Academy of Sciences, Beijing 100039, P. R. China.,School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, P. R. China
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Dezi V, Ivanov C, Haussmann IU, Soller M. Nucleotide modifications in messenger RNA and their role in development and disease. Biochem Soc Trans 2016; 44:1385-93. [PMID: 27911721 DOI: 10.1042/BST20160110] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 05/20/2016] [Accepted: 05/26/2016] [Indexed: 11/17/2022]
Abstract
Modified nucleotides in messenger RNA (mRNA) have been discovered over 40 years ago, but until recently little was known about which transcripts contain them and what their function is. High-throughput sequencing approaches revealed a dynamic landscape of the 'Epitranscriptome' for many mRNA modifications in various organisms from yeast to humans. Meanwhile, also many genes encoding mRNA-modifying enzymes and auxiliary proteins have been identified yielding functional insights by reverse genetics into their role in development and disease.
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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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Abstract
Pseudouridine (Ψ) is the most abundant posttranscriptional modification in noncoding RNAs. Pseudouridines are often clustered in important regions of rRNAs (ribosomal RNAs), snRNAs (small nuclear RNAs), and tRNAs (transfer RNAs), contributing to RNA function. Pseudouridylation is governed by two independent mechanisms. The first involves single protein enzymes called pseudouridine synthases (PUSs) that alone recognize the substrate and catalyze the isomerization of uridine to pseudouridine (RNA-independent pseudouridylation). The second is an RNA-guided pseudouridylation by a family of box H/ACA RNPs (ribonucleoproteins), each of which consists of a unique RNA (box H/ACA RNA) and four common core proteins (Cbf5/NAP57/Dyskerin, Nhp2/L7Ae, Nop10, and Gar1). The RNA component serves as a guide that base pairs with the substrate RNA and directs the enzyme (Cbf5) to carry out the pseudouridylation reaction at a specific site. The crystal structures of many PUSs have been solved in numerous organisms including E. coli and human. Several partial and complete crystal structures of archaea and yeast box H/ACA RNPs are available, providing a rich source of information regarding the molecular interactions between protein components and box H/ACA RNA. Over the years, several experimental systems have been developed to study the mechanism and function of pseudouridylation. Apart from noncoding RNA pseudouridylation, recent experiments have provided evidence of mRNA pseudouridylation as well. Despite remarkable progress, there is a need to accelerate efforts in order to understand the detailed mechanisms and functions of RNA pseudouridylation.
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Affiliation(s)
- Meemanage D De Zoysa
- University of Rochester Medical Center, Center for RNA Biology, Rochester, NY, United States
| | - Yi-Tao Yu
- University of Rochester Medical Center, Center for RNA Biology, Rochester, NY, United States.
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Kilin V, Gavvala K, Barthes NPF, Michel BY, Shin D, Boudier C, Mauffret O, Yashchuk V, Mousli M, Ruff M, Granger F, Eiler S, Bronner C, Tor Y, Burger A, Mély Y. Dynamics of Methylated Cytosine Flipping by UHRF1. J Am Chem Soc 2017; 139:2520-2528. [PMID: 28112929 PMCID: PMC5335914 DOI: 10.1021/jacs.7b00154] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA methylation patterns, which are critical for gene expression, are replicated by DNA methyltransferase 1 (DNMT1) and ubiquitin-like containing PHD and RING finger domains 1 (UHRF1) proteins. This replication is initiated by the recognition of hemimethylated CpG sites and further flipping of methylated cytosines (mC) by the Set and Ring Associated (SRA) domain of UHRF1. Although crystallography has shed light on the mechanism of mC flipping by SRA, tools are required to monitor in real time how SRA reads DNA and flips the modified nucleobase. To accomplish this aim, we have utilized two distinct fluorescent nucleobase surrogates, 2-thienyl-3-hydroxychromone nucleoside (3HCnt) and thienoguanosine (thG), incorporated at different positions into hemimethylated (HM) and nonmethylated (NM) DNA duplexes. Large fluorescence changes were associated with mC flipping in HM duplexes, showing the outstanding sensitivity of both nucleobase surrogates to the small structural changes accompanying base flipping. Importantly, the nucleobase surrogates marginally affected the structure of the duplex and its affinity for SRA at positions where they were responsive to base flipping, illustrating their promise as nonperturbing probes for monitoring such events. Stopped-flow studies using these two distinct tools revealed the fast kinetics of SRA binding and sliding to NM duplexes, consistent with its reader role. In contrast, the kinetics of mC flipping was found to be much slower in HM duplexes, substantially increasing the lifetime of CpG-bound UHRF1, and thus the probability of recruiting DNMT1 to faithfully duplicate the DNA methylation profile. The fluorescence-based approach using these two different fluorescent nucleoside surrogates advances the mechanistic understanding of the UHRF1/DNMT1 tandem and the development of assays for the identification of base flipping inhibitors.
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Affiliation(s)
- Vasyl Kilin
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Universitéde Strasbourg, Facultéde pharmacie, 74 Route du Rhin, 67401 Illkirch, France
| | - Krishna Gavvala
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Universitéde Strasbourg, Facultéde pharmacie, 74 Route du Rhin, 67401 Illkirch, France
| | - Nicolas P. F. Barthes
- Institut de Chimie de Nice, UMR 7272 CNRS, UniversitéCôte d’Azur, Parc Valrose, 06108 Nice Cedex 2, France
| | - Benoît Y. Michel
- Institut de Chimie de Nice, UMR 7272 CNRS, UniversitéCôte d’Azur, Parc Valrose, 06108 Nice Cedex 2, France
| | - Dongwon Shin
- TriLink BioTechnologies, LLC., San Diego, California 92121, United States
| | - Christian Boudier
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Universitéde Strasbourg, Facultéde pharmacie, 74 Route du Rhin, 67401 Illkirch, France
| | - Olivier Mauffret
- LBPA, UMR 8113 CNRS, ENS Paris-Saclay, Université Paris Saclay, 94235 Cachan Cedex, France
| | - Valeriy Yashchuk
- Department of Physics, Kiev National Taras Shevchenko University, Kiev 01601, Ukraine
| | - Marc Mousli
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Universitéde Strasbourg, Facultéde pharmacie, 74 Route du Rhin, 67401 Illkirch, France
| | - Marc Ruff
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 CNRS UMR 7104, Université de Strasbourg, Illkirch 67000, France
| | - Florence Granger
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 CNRS UMR 7104, Université de Strasbourg, Illkirch 67000, France
| | - Sylvia Eiler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 CNRS UMR 7104, Université de Strasbourg, Illkirch 67000, France
| | - Christian Bronner
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 CNRS UMR 7104, Université de Strasbourg, Illkirch 67000, France
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, United States
| | - Alain Burger
- Institut de Chimie de Nice, UMR 7272 CNRS, UniversitéCôte d’Azur, Parc Valrose, 06108 Nice Cedex 2, France
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Universitéde Strasbourg, Facultéde pharmacie, 74 Route du Rhin, 67401 Illkirch, France
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Safra M, Nir R, Farouq D, Vainberg Slutskin I, Schwartz S. TRUB1 is the predominant pseudouridine synthase acting on mammalian mRNA via a predictable and conserved code. Genome Res 2017; 27:393-406. [PMID: 28073919 DOI: 10.1101/gr.207613.116] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 12/15/2016] [Indexed: 12/21/2022]
Abstract
Following synthesis, RNA can be modified with over 100 chemically distinct modifications, which can potentially regulate RNA expression post-transcriptionally. Pseudouridine (Ψ) was recently established to be widespread and dynamically regulated on yeast mRNA, but less is known about Ψ presence, regulation, and biogenesis in mammalian mRNA. Here, we sought to characterize the Ψ landscape on mammalian mRNA, to identify the main Ψ-synthases (PUSs) catalyzing Ψ formation, and to understand the factors governing their specificity toward selected targets. We first developed a framework allowing analysis, evaluation, and integration of Ψ mappings, which we applied to >2.5 billion reads from 30 human samples. These maps, complemented with genetic perturbations, allowed us to uncover TRUB1 and PUS7 as the two key PUSs acting on mammalian mRNA and to computationally model the sequence and structural elements governing the specificity of TRUB1, achieving near-perfect prediction of its substrates (AUC = 0.974). We then validated and extended these maps and the inferred specificity of TRUB1 using massively parallel reporter assays in which we monitored Ψ levels at thousands of synthetically designed sequence variants comprising either the sequences surrounding pseudouridylation targets or systematically designed mutants perturbing RNA sequence and structure. Our findings provide an extensive and high-quality characterization of the transcriptome-wide distribution of pseudouridine in human and the factors governing it and provide an important resource for the community, paving the path toward functional and mechanistic dissection of this emerging layer of post-transcriptional regulation.
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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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Zhao M, Zhang H, Liu G, Wang L, Wang J, Gao Z, Dong Y, Zhang L, Gong Y. Structural Insights into the Methylation of C1402 in 16S rRNA by Methyltransferase RsmI. PLoS One 2016; 11:e0163816. [PMID: 27711192 PMCID: PMC5053481 DOI: 10.1371/journal.pone.0163816] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/14/2016] [Indexed: 11/18/2022] Open
Abstract
RsmI and RsmH are conserved S-Adenosylmethionine (AdoMet)-dependent methyltransferases (MTases) that are responsible for the 2'-O-methylation and N4-methylation of C1402 in bacterial 16S rRNA, respectively. Methylation of m4Cm1402 plays a role in fine-tuning the shape and functions of the P-site to increase the decoding fidelity, and was recently found to contribute to the virulence of Staphylococcus aureus in host animals. Here we report the 2.20-Å crystal structure of homodimeric RsmI from Escherichia coli in complex with the cofactor AdoMet. RsmI consists of an N-terminal putative RNA-binding domain (NTD) and a C-terminal catalytic domain (CTD) with a Rossmann-like fold, and belongs to the class III MTase family. AdoMet is specifically bound into a negatively charged deep pocket formed by both domains by making extensive contacts. Structure-based mutagenesis and isothermal titration calorimetry (ITC) assays revealed Asp100 and Ala124 are vital for AdoMet-binding. Although the overall fold of RsmI shows remarkable similarities to the characterized MTases involved in vitamin B12 biosynthesis, it exhibits a distinct charge distribution especially around the AdoMet-binding pocket because of different substrate specificity. The docking model of RsmI-AdoMet-RNA ternary complex suggested a possible base-flipping mechanism of the substrate RNA that has been observed in several known RNA MTases. Our structural and biochemical studies provide novel insights into the catalytic mechanism of C1402 methylation in 16S rRNA.
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Affiliation(s)
- Mohan Zhao
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Heng Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Guangfeng Liu
- National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Li Wang
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Jian Wang
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Zengqiang Gao
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Yuhui Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Linbo Zhang
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Yong Gong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
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Majumder M, Bosmeny MS, Gupta R. Structure-function relationships of archaeal Cbf5 during in vivo RNA-guided pseudouridylation. RNA 2016; 22:1604-1619. [PMID: 27539785 PMCID: PMC5029457 DOI: 10.1261/rna.057547.116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 07/25/2016] [Indexed: 05/31/2023]
Abstract
In Eukarya and Archaea, in addition to protein-only pseudouridine (Ψ) synthases, complexes containing one guide RNA and four proteins can also produce Ψ. Cbf5 protein is the Ψ synthase in the complex. Previously, we showed that Ψ's at positions 1940, 1942, and 2605 of Haloferax volcanii 23S rRNA are absent in a cbf5-deleted strain, and a plasmid-borne copy of cbf5 can rescue the synthesis of these Ψ's. Based on published reports of the structure of archaeal Cbf5 complexed with other proteins and RNAs, we identified several potential residues and structures in H. volcanii Cbf5, which were expected to play important roles in pseudouridylation. We mutated these structures and determined their effects on Ψ production at the three rRNA positions under in vivo conditions. Mutations of several residues in the catalytic domain and certain residues in the thumb loop either abolished Ψ's or produced partial modification; the latter indicates a slower rate of Ψ formation. The universal catalytic aspartate of Ψ synthases could be replaced by glutamate in Cbf5. A conserved histidine, which is common to Cbf5 and TruB is not needed, but another conserved histidine of Cbf5 is required for the in vivo RNA-guided Ψ formation. We also identified a previously unreported novelty in the pseudouridylation activity of Cbf5 where a single stem-loop of a guide H/ACA RNA is used to produce two closely placed Ψ's and mutations of certain residues of Cbf5 abolished one of these two Ψ's. In summary, this first in vivo study identifies several structures of an archaeal Cbf5 protein that are important for its RNA-guided pseudouridylation activity.
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Affiliation(s)
- Mrinmoyee Majumder
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
| | - Michael S Bosmeny
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
| | - Ramesh Gupta
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
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41
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Addepalli B, Limbach PA. Pseudouridine in the Anticodon of Escherichia coli tRNATyr(QΨA) Is Catalyzed by the Dual Specificity Enzyme RluF. J Biol Chem 2016; 291:22327-22337. [PMID: 27551044 DOI: 10.1074/jbc.m116.747865] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Indexed: 02/02/2023] Open
Abstract
Pseudouridine is found in almost all cellular ribonucleic acids (RNAs). Of the multiple characteristics attributed to pseudouridine, making messenger RNAs (mRNAs) highly translatable and non-immunogenic is one such feature that directly implicates this modification in protein synthesis. We report the existence of pseudouridine in the anticodon of Escherichia coli tyrosine transfer RNAs (tRNAs) at position 35. Pseudouridine was verified by multiple detection methods, which include pseudouridine-specific chemical derivatization and gas phase dissociation of RNA during liquid chromatography tandem mass spectrometry (LC-MS/MS). Analysis of total tRNA isolated from E. coli pseudouridine synthase knock-out mutants identified RluF as the enzyme responsible for this modification. Furthermore, the absence of this modification compromises the translational ability of a luciferase reporter gene coding sequence when it is preceded by multiple tyrosine codons. This effect has implications for the translation of mRNAs that are rich in tyrosine codons in bacterial expression systems.
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Affiliation(s)
- Balasubrahmanyam Addepalli
- From the Department of Chemistry, Rieveschl Laboratories for Mass Spectrometry, University of Cincinnati, Cincinnati, Ohio 45221
| | - Patrick A Limbach
- From the Department of Chemistry, Rieveschl Laboratories for Mass Spectrometry, University of Cincinnati, Cincinnati, Ohio 45221
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42
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Wu G, Radwan MK, Xiao M, Adachi H, Fan J, Yu YT. The TOR signaling pathway regulates starvation-induced pseudouridylation of yeast U2 snRNA. RNA 2016; 22:1146-52. [PMID: 27268497 PMCID: PMC4931107 DOI: 10.1261/rna.056796.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/05/2016] [Indexed: 05/28/2023]
Abstract
Pseudouridine (Ψ) has been identified in various types of RNAs, including mRNA, rRNA, tRNA, snRNA, and many other noncoding RNAs. We have previously shown that RNA pseudouridylation, like DNA and protein modifications, can be induced by stress. For instance, growing yeast cells to saturation induces the formation of Ψ93 in U2 snRNA. Here, we further investigate this inducible RNA modification. We show that switching yeast cells from nutrient-rich medium to different nutrient-deprived media (including water) results in the formation of Ψ93 in U2 snRNA. Using gene deletion/conditional depletion as well as rapamycin treatment, we further show that the TOR signaling pathway, which controls cell entry into stationary phase, regulates Ψ93 formation. The RAS/cAMP signaling pathway, which parallels the TOR pathway, plays no role in this inducible modification.
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Affiliation(s)
- Guowei Wu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Mohamed K Radwan
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Mu Xiao
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Hironori Adachi
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Jason Fan
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
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43
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Abstract
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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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44
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Matthews MM, Thomas JM, Zheng Y, Tran K, Phelps KJ, Scott AI, Havel J, Fisher AJ, Beal PA. Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity. Nat Struct Mol Biol 2016; 23:426-33. [PMID: 27065196 DOI: 10.1038/nsmb.3203] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/11/2016] [Indexed: 12/20/2022]
Abstract
ADARs (adenosine deaminases acting on RNA) are editing enzymes that convert adenosine (A) to inosine (I) in duplex RNA, a modification reaction with wide-ranging consequences on RNA function. Our understanding of the ADAR reaction mechanism, origin of editing site selectivity and effect of mutations is limited by the lack of high-resolution structural data for complexes of ADARs bound to substrate RNAs. Here we describe four crystal structures of the deaminase domain of human ADAR2 bound to RNA duplexes bearing a mimic of the deamination reaction intermediate. These structures, together with structure-guided mutagenesis and RNA-modification experiments, explain the basis for ADAR deaminase domain’s dsRNA specificity, its base-flipping mechanism, and nearest neighbor preferences. In addition, an ADAR2-specific RNA-binding loop was identified near the enzyme active site rationalizing differences in selectivity observed between different ADARs. Finally, our results provide a structural framework for understanding the effects of ADAR mutations associated with human disease.
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45
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Zhang J, Ferré-DAmaré AR. Trying on tRNA for Size: RNase P and the T-box Riboswitch as Molecular Rulers. Biomolecules 2016; 6:biom6020018. [PMID: 27043647 PMCID: PMC4919913 DOI: 10.3390/biom6020018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 03/23/2016] [Accepted: 03/25/2016] [Indexed: 12/27/2022] Open
Abstract
Length determination is a fundamental problem in biology and chemistry. Numerous proteins measure distances on linear biopolymers to exert effects with remarkable spatial precision. Recently, ruler-like devices made of noncoding RNAs have been structurally and biochemically characterized. Two prominent examples are the RNase P ribozyme and the T-box riboswitch. Both act as molecular calipers. The two RNAs clamp onto the elbow of tRNA (or pre-tRNA) and make distance measurements orthogonal to each other. Here, we compare and contrast the molecular ruler characteristics of these RNAs. RNase P appears pre-configured to measure a fixed distance on pre-tRNA to ensure the fidelity of its maturation. RNase P is a multiple-turnover ribozyme, and its rigid structure efficiently selects pre-tRNAs, cleaves, and releases them. In contrast, the T-box is flexible and segmented, an architecture that adapts to the intrinsically flexible tRNA. The tripartite T-box inspects the overall shape, anticodon sequence, and aminoacylation status of an incoming tRNA while it folds co-transcriptionally, leading to a singular, conditional genetic switching event. The elucidation of the structures and mechanisms of action of these two RNA molecular rulers may augur the discovery of new RNA measuring devices in noncoding and viral transcriptomes, and inform the design of artificial RNA rulers.
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Affiliation(s)
- Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Bethesda, MD 20892, USA.
| | - Adrian R Ferré-DAmaré
- Laboratory of RNA Biophysics and Cellular Physiology, National Heart, Lung and Blood Institute, 50 South Drive, Bethesda, MD 20892, USA.
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46
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Connor DO, Zantow J, Hust M, Bier FF, von Nickisch-Rosenegk M. Identification of Novel Immunogenic Proteins of Neisseria gonorrhoeae by Phage Display. PLoS One 2016; 11:e0148986. [PMID: 26859666 PMCID: PMC4747489 DOI: 10.1371/journal.pone.0148986] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/26/2016] [Indexed: 12/14/2022] Open
Abstract
Neisseria gonorrhoeae is one of the most prevalent sexually transmitted diseases worldwide with more than 100 million new infections per year. A lack of intense research over the last decades and increasing resistances to the recommended antibiotics call for a better understanding of gonococcal infection, fast diagnostics and therapeutic measures against N. gonorrhoeae. Therefore, the aim of this work was to identify novel immunogenic proteins as a first step to advance those unresolved problems. For the identification of immunogenic proteins, pHORF oligopeptide phage display libraries of the entire N. gonorrhoeae genome were constructed. Several immunogenic oligopeptides were identified using polyclonal rabbit antibodies against N. gonorrhoeae. Corresponding full-length proteins of the identified oligopeptides were expressed and their immunogenic character was verified by ELISA. The immunogenic character of six proteins was identified for the first time. Additional 13 proteins were verified as immunogenic proteins in N. gonorrhoeae.
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Affiliation(s)
- Daniel O. Connor
- Department of Bioanalytics and Biosensorics, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Jonas Zantow
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Hust
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Frank F. Bier
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Department of Biosystem Integration and Automation, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Markus von Nickisch-Rosenegk
- Department of Bioanalytics and Biosensorics, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
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47
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Zhang J, Ferré-D'Amaré AR. The tRNA Elbow in Structure, Recognition and Evolution. Life (Basel) 2016; 6:E3. [PMID: 26771646 DOI: 10.3390/life6010003] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/04/2016] [Accepted: 01/06/2016] [Indexed: 01/07/2023] Open
Abstract
Prominent in the L-shaped three-dimensional structure of tRNAs is the "elbow" where their two orthogonal helical stacks meet. It has a conserved structure arising from the interaction of the terminal loops of the D- and T-stem-loops, and presents to solution a flat face of a tertiary base pair between the D- and T-loops. In addition to the ribosome, which interacts with the elbow in all three of its tRNA binding sites, several cellular RNAs and many proteins are known to recognize the elbow. At least three classes of non-coding RNAs, namely 23S rRNA, ribonuclease P, and the T-box riboswitches, recognize the tRNA elbow employing an identical structural motif consisting of two interdigitated T-loops. In contrast, structural solutions to tRNA-elbow recognition by proteins are varied. Some enzymes responsible for post-transcriptional tRNA modification even disrupt the elbow structure in order to access their substrate nucleotides. The evolutionary origin of the elbow is mysterious, but, because it does not explicitly participate in the flow of genetic information, it has been proposed to be a late innovation. Regardless, it is biologically essential. Even some viruses that hijack the cellular machinery using tRNA decoys have convergently evolved near-perfect mimics of the tRNA elbow.
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48
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Madan B, Kasprzak JM, Tuszynska I, Magnus M, Szczepaniak K, Dawson WK, Bujnicki JM. Modeling of Protein-RNA Complex Structures Using Computational Docking Methods. Methods Mol Biol 2016; 1414:353-372. [PMID: 27094302 DOI: 10.1007/978-1-4939-3569-7_21] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A significant part of biology involves the formation of RNA-protein complexes. X-ray crystallography has added a few solved RNA-protein complexes to the repertoire; however, it remains challenging to capture these complexes and often only the unbound structures are available. This has inspired a growing interest in finding ways to predict these RNA-protein complexes. In this study, we show ways to approach this problem by computational docking methods, either with a fully automated NPDock server or with a workflow of methods for generation of many alternative structures followed by selection of the most likely solution. We show that by introducing experimental information, the structure of the bound complex is rendered far more likely to be within reach. This study is meant to help the user of docking software understand how to grapple with a typical realistic problem in RNA-protein docking, understand what to expect in the way of difficulties, and recognize the current limitations.
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Affiliation(s)
- Bharat Madan
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland
| | - Joanna M Kasprzak
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland
- Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland
| | - Irina Tuszynska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland
- Institute of Informatics, University of Warsaw, ul. Banacha 2, 02-097, Warsaw, Poland
| | - Marcin Magnus
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland
| | - Krzysztof Szczepaniak
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland
| | - Wayne K Dawson
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland.
- Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland.
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49
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Laptev IG, Golovina AY, Sergiev PV, Dontsova OA. Posttranscriptional modification of messenger RNAs in eukaryotes. Mol Biol 2015; 49:825-836. [PMID: 32214475 PMCID: PMC7088549 DOI: 10.1134/s002689331506014x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 06/25/2015] [Indexed: 11/30/2022]
Abstract
Transcriptome-wide mapping of posttranscriptional modifications in eukaryotic RNA revealed tens of thousands of modification sites. Modified nucleotides include 6-methyladenosine, 5-methylcytidine, pseudouridine, inosine, etc. Many modification sites are conserved, and many are regulated. The function is known for a minor subset of modified nucleotides, while the role of their majority is still obscure. In view of the global character of mRNA modification, RNA epigenetics arose as a new field of molecular biology. The review considers posttranscriptional modification of eukaryotic mRNA, focusing on the major modified nucleotides, the role they play in the cell, the methods to detect them, and the enzymes responsible for modification.
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Affiliation(s)
- I G Laptev
- 1Department of Chemistry, Moscow State University, Moscow, 119991 Russia
| | - A Ya Golovina
- 2Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119992 Russia
| | - P V Sergiev
- 1Department of Chemistry, Moscow State University, Moscow, 119991 Russia.,2Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119992 Russia
| | - O A Dontsova
- 1Department of Chemistry, Moscow State University, Moscow, 119991 Russia.,2Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119992 Russia
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50
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Nomura Y, Ohno S, Nishikawa K, Yokogawa T. Correlation between the stability of tRNA tertiary structure and the catalytic efficiency of a tRNA-modifying enzyme, archaeal tRNA-guanine transglycosylase. Genes Cells 2015; 21:41-52. [PMID: 26663416 DOI: 10.1111/gtc.12317] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 10/22/2015] [Indexed: 11/29/2022]
Abstract
In many archaeal tRNAs, archaeosine is found at position 15. During archaeosine biosynthesis, archaeal tRNA-guanine transglycosylase (ArcTGT) first replaces the guanine base at position 15 with 7-cyano-7-deazaguanine (preQ0). In this study, we investigated whether modified nucleosides in tRNA substrates would affect ArcTGT incorporation of preQ0. We prepared a series of hypomodified tRNAs(Ser)(GGA) from Escherichia coli strains lacking each tRNA-modifying enzyme. Measurement of ArcTGT kinetic parameters with the various tRNAs(Ser)(GGA) as substrates showed that the Km decreased due to the lack of modified nucleosides. The tRNAs(Ser)(GGA) melting profiles resulted in experimental evidence showing that each modified nucleoside in tRNA(Ser)(GGA) enhanced tRNA stability. Furthermore, the ArcTGT K(m) strongly correlated with the melting temperature (T(m)), suggesting that the unstable tRNA containing fewer modified nucleosides served as a better ArcTGT substrate. These results show that preQ0 incorporation into tRNA by ArcTGT takes place early in the archaeal tRNA modification process.
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Affiliation(s)
- Yuichiro Nomura
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Satoshi Ohno
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Kazuya Nishikawa
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Takashi Yokogawa
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
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