1
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Zhou J, Han Y, Hou R. Potential role of N6-methyladenosine modification in the development of Parkinson's disease. Front Cell Dev Biol 2023; 11:1321995. [PMID: 38155838 PMCID: PMC10753761 DOI: 10.3389/fcell.2023.1321995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 12/04/2023] [Indexed: 12/30/2023] Open
Abstract
N6-methyladenosine (m6A) represents the most abundant modification of messenger RNA (mRNA) and is regulated by methyltransferases (writers), demethylases (erasers), and m6A-binding proteins (readers). A dynamic modification process is implicated in nearly every critical stage of RNA metabolism, including mRNA stability, transcription, translation, splicing, nuclear export, and decay. Notably, m6A methylation is significantly enriched in the brain and has recently been shown to be associated with neurodevelopmental disorders and the development of Parkinson's disease (PD). In this review, we summarize the proteins involved in the process of m6A modification and elucidate the emerging role of m6A modification in PD, which could illuminate alternative strategies for the prevention and treatment of PD.
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Affiliation(s)
- Jiale Zhou
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yang Han
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Ruizhe Hou
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, China
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2
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Parsons MF, Allan MF, Li S, Shepherd TR, Ratanalert S, Zhang K, Pullen KM, Chiu W, Rouskin S, Bathe M. 3D RNA-scaffolded wireframe origami. Nat Commun 2023; 14:382. [PMID: 36693871 PMCID: PMC9872083 DOI: 10.1038/s41467-023-36156-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Hybrid RNA:DNA origami, in which a long RNA scaffold strand folds into a target nanostructure via thermal annealing with complementary DNA oligos, has only been explored to a limited extent despite its unique potential for biomedical delivery of mRNA, tertiary structure characterization of long RNAs, and fabrication of artificial ribozymes. Here, we investigate design principles of three-dimensional wireframe RNA-scaffolded origami rendered as polyhedra composed of dual-duplex edges. We computationally design, fabricate, and characterize tetrahedra folded from an EGFP-encoding messenger RNA and de Bruijn sequences, an octahedron folded with M13 transcript RNA, and an octahedron and pentagonal bipyramids folded with 23S ribosomal RNA, demonstrating the ability to make diverse polyhedral shapes with distinct structural and functional RNA scaffolds. We characterize secondary and tertiary structures using dimethyl sulfate mutational profiling and cryo-electron microscopy, revealing insight into both global and local, base-level structures of origami. Our top-down sequence design strategy enables the use of long RNAs as functional scaffolds for complex wireframe origami.
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Affiliation(s)
- Molly F Parsons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Matthew F Allan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Shanshan Li
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Tyson R Shepherd
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Inscripta, Inc., Boulder, CO, 80027, USA
| | - Sakul Ratanalert
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kaiming Zhang
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Krista M Pullen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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3
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Tian C, Chai J, Liu W, Zhang X, Li Y, Zuo H, Yuan G, Zhang H, Liu H, Chen Z. Role of the Demethylase AlkB Homolog H5 in the Promotion of Dentinogenesis. Front Physiol 2022; 13:923185. [PMID: 35784864 PMCID: PMC9240783 DOI: 10.3389/fphys.2022.923185] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/23/2022] [Indexed: 11/25/2022] Open
Abstract
Dentinogenesis is a key process in tooth formation and is regulated by a series of pre- and post-transcriptional regulations. N6-methyl-adenosine (m6A), which is the most prevalent internal chemical modification that can be removed by the RNA demethylase AlkB homolog H5 (ALKBH5), has recently been reported to be involved in several biological processes. However, the exact function of ALKBH5-mediated m6A modification in tooth development remains unclear. Here, we showed that Alkbh5 was expressed in pre-odontoblasts, polarizing odontoblasts, and secretory odontoblasts. Alkbh5 overexpression in the mouse dental papilla cell line mDPC6T promoted odontoblastic differentiation. Conditional knockout of Alkbh5 in Dmp1-expressing odontoblasts led to a decrease in number of odontoblasts and increased pre-dentin formation. Mechanistically, RNA sequencing and m6A sequencing of Alkbh5-overexpressing mDPC6T cells revealed that Alkbh5 promoted odontoblast differentiation by prolonging the half-life of Runx2 transcripts in an m6A-dependent manner and by activating the phosphatidylinositol 3-kinase/protein kinase B pathway. Notably, the loss of Alkbh5 expression in odontoblasts impaired tertiary dentin formation in vivo. These results suggested that the RNA demethylase ALKBH5 plays a role in dentinogenesis.
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Affiliation(s)
- Cheng Tian
- The State Key Laboratory Breeding Base of Basic Sciences of Stomatology, Key Laboratory of Oral Biomedicine, Ministry of Education (Hubei-MOST KLOS & KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jihua Chai
- The State Key Laboratory Breeding Base of Basic Sciences of Stomatology, Key Laboratory of Oral Biomedicine, Ministry of Education (Hubei-MOST KLOS & KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Weidong Liu
- The State Key Laboratory Breeding Base of Basic Sciences of Stomatology, Key Laboratory of Oral Biomedicine, Ministry of Education (Hubei-MOST KLOS & KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Xinye Zhang
- The State Key Laboratory Breeding Base of Basic Sciences of Stomatology, Key Laboratory of Oral Biomedicine, Ministry of Education (Hubei-MOST KLOS & KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yashu Li
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, China
| | - Huanyan Zuo
- The State Key Laboratory Breeding Base of Basic Sciences of Stomatology, Key Laboratory of Oral Biomedicine, Ministry of Education (Hubei-MOST KLOS & KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Guohua Yuan
- The State Key Laboratory Breeding Base of Basic Sciences of Stomatology, Key Laboratory of Oral Biomedicine, Ministry of Education (Hubei-MOST KLOS & KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Haojian Zhang
- The State Key Laboratory Breeding Base of Basic Sciences of Stomatology, Key Laboratory of Oral Biomedicine, Ministry of Education (Hubei-MOST KLOS & KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, China
| | - Huan Liu
- The State Key Laboratory Breeding Base of Basic Sciences of Stomatology, Key Laboratory of Oral Biomedicine, Ministry of Education (Hubei-MOST KLOS & KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Periodontology, School and Hospital of Stomatology, Wuhan University, Wuhan, China
- *Correspondence: Huan Liu, ; Zhi Chen,
| | - Zhi Chen
- The State Key Laboratory Breeding Base of Basic Sciences of Stomatology, Key Laboratory of Oral Biomedicine, Ministry of Education (Hubei-MOST KLOS & KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Cariology and Endodontics, School and Hospital of Stomatology, Wuhan University, Wuhan, China
- *Correspondence: Huan Liu, ; Zhi Chen,
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4
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Liljeruhm J, Leppik M, Bao L, Truu T, Calvo-Noriega M, Freyer NS, Liiv A, Wang J, Blanco RC, Ero R, Remme J, Forster AC. Plasticity and conditional essentiality of modification enzymes for domain V of Escherichia coli 23S ribosomal RNA. RNA (NEW YORK, N.Y.) 2022; 28:796-807. [PMID: 35260421 PMCID: PMC9074899 DOI: 10.1261/rna.079096.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/18/2022] [Indexed: 06/03/2023]
Abstract
Escherichia coli rRNAs are post-transcriptionally modified at 36 positions but their modification enzymes are dispensable individually for growth, bringing into question their significance. However, a major growth defect was reported for deletion of the RlmE enzyme, which abolished a 2'O methylation near the peptidyl transferase center (PTC) of the 23S rRNA. Additionally, an adjacent 80-nt "critical region" around the PTC had to be modified to yield significant peptidyl transferase activity in vitro. Surprisingly, we discovered that an absence of just two rRNA modification enzymes is conditionally lethal (at 20°C): RlmE and RluC. At a permissive temperature (37°C), this double knockout was shown to abolish four modifications and be defective in ribosome assembly, though not more so than the RlmE single knockout. However, the double knockout exhibited an even lower rate of tripeptide synthesis than did the single knockout, suggesting an even more defective ribosomal translocation. A combination knockout of the five critical-region-modifying enzymes RluC, RlmKL, RlmN, RlmM, and RluE (not RlmE), which synthesize five of the seven critical-region modifications and 14 rRNA and tRNA modifications altogether, was viable (minor growth defect at 37°C, major at 20°C). This was surprising based on prior in vitro studies. This five-knockout combination had minimal effects on ribosome assembly and frameshifting at 37°C, but greater effects on ribosome assembly and in vitro peptidyl transferase activity at cooler temperatures. These results establish the conditional essentiality of bacterial rRNA modification enzymes and also reveal unexpected plasticity of modification of the PTC region in vivo.
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Affiliation(s)
- Josefine Liljeruhm
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | - Margus Leppik
- Department of Molecular Biology, University of Tartu, 51010 Tartu, Estonia
| | - Letian Bao
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | - Triin Truu
- Department of Molecular Biology, University of Tartu, 51010 Tartu, Estonia
| | - Maria Calvo-Noriega
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | - Nicola S Freyer
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | - Aivar Liiv
- Department of Molecular Biology, University of Tartu, 51010 Tartu, Estonia
| | - Jinfan Wang
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | - Rubén Crespo Blanco
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | - Rya Ero
- Department of Molecular Biology, University of Tartu, 51010 Tartu, Estonia
| | - Jaanus Remme
- Department of Molecular Biology, University of Tartu, 51010 Tartu, Estonia
| | - Anthony C Forster
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
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5
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Meynier V, Iannazzo L, Catala M, Oerum S, Braud E, Atdjian C, Barraud P, Fonvielle M, Tisné C, Ethève-Quelquejeu M. Synthesis of RNA-cofactor conjugates and structural exploration of RNA recognition by an m6A RNA methyltransferase. Nucleic Acids Res 2022; 50:5793-5806. [PMID: 35580049 PMCID: PMC9178011 DOI: 10.1093/nar/gkac354] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/22/2022] [Accepted: 05/10/2022] [Indexed: 11/14/2022] Open
Abstract
Chemical synthesis of RNA conjugates has opened new strategies to study enzymatic mechanisms in RNA biology. To gain insights into poorly understood RNA nucleotide methylation processes, we developed a new method to synthesize RNA-conjugates for the study of RNA recognition and methyl-transfer mechanisms of SAM-dependent m6A RNA methyltransferases. These RNA conjugates contain a SAM cofactor analogue connected at the N6-atom of an adenosine within dinucleotides, a trinucleotide or a 13mer RNA. Our chemical route is chemo- and regio-selective and allows flexible modification of the RNA length and sequence. These compounds were used in crystallization assays with RlmJ, a bacterial m6A rRNA methyltransferase. Two crystal structures of RlmJ in complex with RNA–SAM conjugates were solved and revealed the RNA-specific recognition elements used by RlmJ to clamp the RNA substrate in its active site. From these structures, a model of a trinucleotide bound in the RlmJ active site could be built and validated by methyltransferase assays on RlmJ mutants. The methyl transfer by RlmJ could also be deduced. This study therefore shows that RNA-cofactor conjugates are potent molecular tools to explore the active site of RNA modification enzymes.
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Affiliation(s)
- Vincent Meynier
- Expression Génétique Microbienne, UMR 8261, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique (IBPC), 75005, Paris, France
| | - Laura Iannazzo
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601, CNRS, Université Paris Cité, 75006, Paris, France
| | - Marjorie Catala
- Expression Génétique Microbienne, UMR 8261, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique (IBPC), 75005, Paris, France
| | - Stephanie Oerum
- Expression Génétique Microbienne, UMR 8261, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique (IBPC), 75005, Paris, France
| | - Emmanuelle Braud
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601, CNRS, Université Paris Cité, 75006, Paris, France
| | - Colette Atdjian
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601, CNRS, Université Paris Cité, 75006, Paris, France
| | - Pierre Barraud
- Expression Génétique Microbienne, UMR 8261, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique (IBPC), 75005, Paris, France
| | - Matthieu Fonvielle
- Sorbonne Université, Université Paris Cité, Centre de recherche des Cordeliers, 75006, Paris, France
| | - Carine Tisné
- Expression Génétique Microbienne, UMR 8261, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique (IBPC), 75005, Paris, France
| | - Mélanie Ethève-Quelquejeu
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601, CNRS, Université Paris Cité, 75006, Paris, France
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6
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Jeong H, Lee Y, Kim J. Structural and functional characterization of TrmM in m 6 A modification of bacterial tRNA. Protein Sci 2022; 31:e4319. [PMID: 35481631 PMCID: PMC9045083 DOI: 10.1002/pro.4319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/29/2022] [Accepted: 04/06/2022] [Indexed: 01/14/2023]
Abstract
N6 -methyladenosine (m6 A), widely distributed in both coding and noncoding RNAs, regulates the epigenetic signals and RNA metabolism in eukaryotes. Although this posttranscriptional modification is frequently observed in messenger and ribosomal RNA, it is relatively rare in transfer RNA. In Escherichia coli, TrmM encoded by yfiC is the tRNA-specific N6 methyltransferase, which modifies the A37 residue of tRNAVal (cmo5 UAC) using S-adenosyl-l-methionine as a methyl donor. However, the structure-function relationship of this enzyme is not completely understood. In this report, we determined two x-ray crystal structures of Mycoplasma capricolum TrmM with and without S-adenosyl-l-homocysteine, which is a reaction product. We also demonstrated the cellular and in vitro activities of this enzyme in the m6 A modification of tRNA and the requirement of a divalent metal ion for its function, which is unprecedented in other RNA N6 methyltransferases, including the E. coli TrmM. Our results reveal that the dimeric form of M. capricolum TrmM is important for efficient tRNA binding and catalysis, thereby offering insights into the distinct substrate specificity of the monomeric E. coli homolog.
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Affiliation(s)
- Hyeonju Jeong
- Department of ChemistryGwangju Institute of Science and TechnologyGwangjuKorea
| | - Yeji Lee
- Department of ChemistryGwangju Institute of Science and TechnologyGwangjuKorea
| | - Jungwook Kim
- Department of ChemistryGwangju Institute of Science and TechnologyGwangjuKorea
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7
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Oerum S, Meynier V, Catala M, Tisné C. A comprehensive review of m6A/m6Am RNA methyltransferase structures. Nucleic Acids Res 2021; 49:7239-7255. [PMID: 34023900 PMCID: PMC8287941 DOI: 10.1093/nar/gkab378] [Citation(s) in RCA: 210] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023] Open
Abstract
Gene expression is regulated at many levels including co- or post-transcriptionally, where chemical modifications are added to RNA on riboses and bases. Expression control via RNA modifications has been termed 'epitranscriptomics' to keep with the related 'epigenomics' for DNA modification. One such RNA modification is the N6-methylation found on adenosine (m6A) and 2'-O-methyladenosine (m6Am) in most types of RNA. The N6-methylation can affect the fold, stability, degradation and cellular interaction(s) of the modified RNA, implicating it in processes such as splicing, translation, export and decay. The multiple roles played by this modification explains why m6A misregulation is connected to multiple human cancers. The m6A/m6Am writer enzymes are RNA methyltransferases (MTases). Structures are available for functionally characterized m6A RNA MTases from human (m6A mRNA, m6A snRNA, m6A rRNA and m6Am mRNA MTases), zebrafish (m6Am mRNA MTase) and bacteria (m6A rRNA MTase). For each of these MTases, we describe their overall domain organization, the active site architecture and the substrate binding. We identify areas that remain to be investigated, propose yet unexplored routes for structural characterization of MTase:substrate complexes, and highlight common structural elements that should be described for future m6A/m6Am RNA MTase structures.
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Affiliation(s)
- Stephanie Oerum
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France
| | - Vincent Meynier
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France
| | - Marjorie Catala
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France
| | - Carine Tisné
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France
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8
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Mahdavi-Amiri Y, Chung Kim Chung K, Hili R. Single-nucleotide resolution of N 6-adenine methylation sites in DNA and RNA by nitrite sequencing. Chem Sci 2020; 12:606-612. [PMID: 34163791 PMCID: PMC8179008 DOI: 10.1039/d0sc03509b] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A single-nucleotide resolution sequencing method of N6-adenine methylation sites in DNA and RNA is described. Using sodium nitrite under acidic conditions, chemoselective deamination of unmethylated adenines readily occurs, without competing deamination of N6-adenine sites. The deamination of adenines results in the formation of hypoxanthine bases, which are read by polymerases and reverse transcriptases as guanine; the methylated adenine sites resist deamination and are read as adenine. The approach, when coupled with high-throughput DNA sequencing and mutational analysis, enables the identification of N6-adenine sites in RNA and DNA within various sequence contexts. Chemoselective deamination of adenine in the presence of N6-methyladenine using nitrite enables single-nucleotide resolution sequencing of N6-adenine methylation sites in DNA and RNA.![]()
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Affiliation(s)
- Yasaman Mahdavi-Amiri
- Department of Chemistry, Centre for Research on Biomolecular Interactions, York University 4700 Keele Street Toronto ON M3J 1P3 Canada www.yorku.ca/rhili
| | - Kimberley Chung Kim Chung
- Department of Chemistry, Centre for Research on Biomolecular Interactions, York University 4700 Keele Street Toronto ON M3J 1P3 Canada www.yorku.ca/rhili
| | - Ryan Hili
- Department of Chemistry, Centre for Research on Biomolecular Interactions, York University 4700 Keele Street Toronto ON M3J 1P3 Canada www.yorku.ca/rhili
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9
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Crystal structure of ErmE - 23S rRNA methyltransferase in macrolide resistance. Sci Rep 2019; 9:14607. [PMID: 31601908 PMCID: PMC6787224 DOI: 10.1038/s41598-019-51174-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 09/25/2019] [Indexed: 12/14/2022] Open
Abstract
Pathogens often receive antibiotic resistance genes through horizontal gene transfer from bacteria that produce natural antibiotics. ErmE is a methyltransferase (MTase) from Saccharopolyspora erythraea that dimethylates A2058 in 23S rRNA using S-adenosyl methionine (SAM) as methyl donor, protecting the ribosomes from macrolide binding. To gain insights into the mechanism of macrolide resistance, the crystal structure of ErmE was determined to 1.75 Å resolution. ErmE consists of an N-terminal Rossmann-like α/ß catalytic domain and a C-terminal helical domain. Comparison with ErmC’ that despite only 24% sequence identity has the same function, reveals highly similar catalytic domains. Accordingly, superposition with the catalytic domain of ErmC’ in complex with SAM suggests that the cofactor binding site is conserved. The two structures mainly differ in the C-terminal domain, which in ErmE contains a longer loop harboring an additional 310 helix that interacts with the catalytic domain to stabilize the tertiary structure. Notably, ErmE also differs from ErmC’ by having long disordered extensions at its N- and C-termini. A C-terminal disordered region rich in arginine and glycine is also a present in two other MTases, PikR1 and PikR2, which share about 30% sequence identity with ErmE and methylate the same nucleotide in 23S rRNA.
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10
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Oerum S, Catala M, Atdjian C, Brachet F, Ponchon L, Barraud P, Iannazzo L, Droogmans L, Braud E, Ethève-Quelquejeu M, Tisné C. Bisubstrate analogues as structural tools to investigate m 6A methyltransferase active sites. RNA Biol 2019; 16:798-808. [PMID: 30879411 PMCID: PMC6546350 DOI: 10.1080/15476286.2019.1589360] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/24/2019] [Accepted: 02/27/2019] [Indexed: 12/20/2022] Open
Abstract
RNA methyltransferases (MTases) catalyse the transfer of a methyl group to their RNA substrates using most-often S-adenosyl-L-methionine (SAM) as cofactor. Only few RNA-bound MTases structures are currently available due to the difficulties in crystallising RNA:protein complexes. The lack of complex structures results in poorly understood RNA recognition patterns and methylation reaction mechanisms. On the contrary, many cofactor-bound MTase structures are available, resulting in well-understood protein:cofactor recognition, that can guide the design of bisubstrate analogues that mimic the state at which both the substrate and the cofactor is bound. Such bisubstrate analogues were recently synthesized for proteins monomethylating the N6-atom of adenine (m6A). These proteins include, amongst others, RlmJ in E. coli and METLL3:METT14 and METTL16 in human. As a proof-of-concept, we here test the ability of the bisubstrate analogues to mimic the substrate:cofactor bound state during catalysis by studying their binding to RlmJ using differential scanning fluorimetry, isothermal titration calorimetry and X-ray crystallography. We find that the methylated adenine base binds in the correct pocket, and thus these analogues could potentially be used broadly to study the RNA recognition and catalytic mechanism of m6A MTases. Two bisubstrate analogues bind RlmJ with micro-molar affinity, and could serve as starting scaffolds for inhibitor design against m6A RNA MTases. The same analogues cause changes in the melting temperature of the m1A RNA MTase, TrmK, indicating non-selective protein:compound complex formation. Thus, optimization of these molecular scaffolds for m6A RNA MTase inhibition should aim to increase selectivity, as well as affinity.
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Affiliation(s)
- Stephanie Oerum
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
| | - Marjorie Catala
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
| | - Colette Atdjian
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Franck Brachet
- Institut de Biologie Physico-Chimique, IBPC, CNRS, Paris, France
| | - Luc Ponchon
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Paris, France
| | - Pierre Barraud
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
| | - Laura Iannazzo
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Louis Droogmans
- Laboratoire de Microbiologie, Université libre de Bruxelles (ULB), Gosselies, Belgium
| | - Emmanuelle Braud
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Mélanie Ethève-Quelquejeu
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Carine Tisné
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
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11
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Wamhoff EC, Banal JL, Bricker WP, Shepherd TR, Parsons MF, Veneziano R, Stone MB, Jun H, Wang X, Bathe M. Programming Structured DNA Assemblies to Probe Biophysical Processes. Annu Rev Biophys 2019; 48:395-419. [PMID: 31084582 PMCID: PMC7035826 DOI: 10.1146/annurev-biophys-052118-115259] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Structural DNA nanotechnology is beginning to emerge as a widely accessible research tool to mechanistically study diverse biophysical processes. Enabled by scaffolded DNA origami in which a long single strand of DNA is weaved throughout an entire target nucleic acid assembly to ensure its proper folding, assemblies of nearly any geometric shape can now be programmed in a fully automatic manner to interface with biology on the 1-100-nm scale. Here, we review the major design and synthesis principles that have enabled the fabrication of a specific subclass of scaffolded DNA origami objects called wireframe assemblies. These objects offer unprecedented control over the nanoscale organization of biomolecules, including biomolecular copy numbers, presentation on convex or concave geometries, and internal versus external functionalization, in addition to stability in physiological buffer. To highlight the power and versatility of this synthetic structural biology approach to probing molecular and cellular biophysics, we feature its application to three leading areas of investigation: light harvesting and nanoscale energy transport, RNA structural biology, and immune receptor signaling, with an outlook toward unique mechanistic insight that may be gained in these areas in the coming decade.
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Affiliation(s)
- Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - James L Banal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - William P Bricker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Tyson R Shepherd
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Molly F Parsons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Rémi Veneziano
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Matthew B Stone
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Hyungmin Jun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Xiao Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
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12
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Lence T, Paolantoni C, Worpenberg L, Roignant JY. Mechanistic insights into m6A RNA enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:222-229. [DOI: 10.1016/j.bbagrm.2018.10.014] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/27/2018] [Indexed: 12/09/2022]
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13
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Mettl3 Regulates Osteogenic Differentiation and Alternative Splicing of Vegfa in Bone Marrow Mesenchymal Stem Cells. Int J Mol Sci 2019; 20:ijms20030551. [PMID: 30696066 PMCID: PMC6387109 DOI: 10.3390/ijms20030551] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 01/20/2019] [Accepted: 01/25/2019] [Indexed: 12/16/2022] Open
Abstract
Bone mesenchymal stem cells (BMSCs) can be a useful cell resource for developing biological treatment strategies for bone repair and regeneration, and their therapeutic applications hinge on an understanding of their physiological characteristics. N6-methyl-adenosine (m6A) is the most prevalent internal chemical modification of mRNAs and has recently been reported to play important roles in cell lineage differentiation and development. However, little is known about the role of m6A modification in the cell differentiation of BMSCs. To address this issue, we investigated the expression of N6-adenosine methyltransferases (Mettl3 and Mettl14) and demethylases (Fto and Alkbh5) and found that Mettl3 was upregulated in BMSCs undergoing osteogenic induction. Furthermore, we knocked down Mettl3 and demonstrated that Mettl3 knockdown decreased the expression of bone formation-related genes, such as Runx2 and Osterix. The alkaline phosphatase (ALP) activity and the formation of mineralized nodules also decreased after Mettl3 knockdown. RNA sequencing analysis revealed that a vast number of genes affected by Mettl3 knockdown were associated with osteogenic differentiation and bone mineralization. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis revealed that the phosphatidylinositol 3-kinase/AKT (PI3K-Akt) signaling pathway appeared to be one of the most enriched pathways, and Western blotting results showed that Akt phosphorylation was significantly reduced after Mettl3 knockdown. Mettl3 has been reported to play an important role in regulating alternative splicing of mRNA in previous research. In this study, we found that Mettl3 knockdown not only reduced the expression of Vegfa but also decreased the level of its splice variants, vegfa-164 and vegfa-188, in Mettl3-deficient BMSCs. These findings might contribute to novel progress in understanding the role of epitranscriptomic regulation in the osteogenic differentiation of BMSCs and provide a promising perspective for new therapeutic strategies for bone regeneration.
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14
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Ma H, Wang X, Cai J, Dai Q, Natchiar SK, Lv R, Chen K, Lu Z, Chen H, Shi YG, Lan F, Fan J, Klaholz BP, Pan T, Shi Y, He C. N 6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation. Nat Chem Biol 2018; 15:88-94. [PMID: 30531910 DOI: 10.1038/s41589-018-0184-3] [Citation(s) in RCA: 247] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/30/2018] [Indexed: 01/09/2023]
Abstract
N6-Methyladenosine (m6A) RNA modification is present in messenger RNAs (mRNA), ribosomal RNAs (rRNA), and spliceosomal RNAs (snRNA) in humans. Although mRNA m6A modifications have been extensively studied and shown to play critical roles in many cellular processes, the identity of m6A methyltransferases for rRNAs and the function of rRNA m6A modifications are unknown. Here we report a new m6A methyltransferase, ZCCHC4, which primarily methylates human 28S rRNA and also interacts with a subset of mRNAs. ZCCHC4 knockout eliminates m6A4220 modification in 28S rRNA, reduces global translation, and inhibits cell proliferation. We also find that ZCCHC4 protein is overexpressed in hepatocellular carcinoma tumors, and ZCCHC4 knockout significantly reduces tumor size in a xenograft mouse model. Our results highlight the functional significance of an rRNA m6A modification in translation and in tumor biology.
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Affiliation(s)
- Honghui Ma
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Xiaoyun Wang
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Jiabin Cai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, China
| | - Qing Dai
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - S Kundhavai Natchiar
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), CNRS, Inserm, Université de Strasbourg, Illkirch, France
| | - Ruitu Lv
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Kai Chen
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Zhike Lu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Hao Chen
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yujiang Geno Shi
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China.,Endocrinology Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Fei Lan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, China
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), CNRS, Inserm, Université de Strasbourg, Illkirch, France
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
| | - Yang Shi
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China. .,Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA. .,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA. .,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
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15
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Kellici TF, Mavromoustakos T, Jendrossek D, Papageorgiou AC. Crystal structure analysis, covalent docking, and molecular dynamics calculations reveal a conformational switch in PhaZ7 PHB depolymerase. Proteins 2017; 85:1351-1361. [DOI: 10.1002/prot.25296] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 03/14/2017] [Accepted: 03/27/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Tahsin F. Kellici
- Department of Chemistry; National and Kapodistrian University of Athens; Athens 15784 Greece
- Department of Chemistry; University of Ioannina; Ioannina 45110 Greece
| | - Thomas Mavromoustakos
- Department of Chemistry; National and Kapodistrian University of Athens; Athens 15784 Greece
- Department of Chemistry; York College and the Graduate Center of the City University of New York; 94-20 Guy R. Brewer Blvd Jamaica New York 11451
| | - Dieter Jendrossek
- Institut für Mikrobiologie, Universität Stuttgart; Allmandring 31 Stuttgart 70550 Germany
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16
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Ou B, Chen L, Song Y, Yang Y, Zhang Q, Yang Y, Li L, Tham WL, Francis DH, Zhu G. Impact of acquisition of 16S rRNA methylase RmtB on the fitness of Escherichia coli. J Glob Antimicrob Resist 2016; 6:32-38. [PMID: 27530836 DOI: 10.1016/j.jgar.2016.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 02/21/2016] [Accepted: 02/23/2016] [Indexed: 10/22/2022] Open
Abstract
The aim of this study was to elucidate the biological phenotypes of 16S rRNA methylase RmtB in Escherichia coli and the impact of RmtB acquisition on the fitness of the target bacterium. An rmtB in-frame deletion mutant in E. coli was constructed using a suicide vector (pDMS197)-based double crossover allelic exchange, and its corresponding complemented strain was established. Combined studies of microdilution susceptibility testing, conjugation experiments, growth kinetics assays, competitive experiments, biofilm formation tests and motility assays were performed to study the rmtB-mediated fitness among the prototype E. coli strain, its isogenic mutant and the corresponding complemented strain. The minimum inhibitory concentrations (MICs) of 4,6-disubstituted 2-deoxystreptamines for the rmtB wild-type strain, its isogenic mutant and the complemented strain were ≥1024, ≤2 and ≥1024mg/L, respectively. Both the growth rates and the competitive abilities of the wild-type and complemented strains were relatively inferior to the ΔrmtB mutant. There was no significant difference in biofilm formation and motility among the three strains. In conclusion, the data presented here suggest that acquisition of the 16S rRNA methylase gene rmtB in E. coli can exact a fitness cost on the bacteria, subsequently reducing the growth rate slightly and decreasing the competitive capacity of the bacterium, whereas it does not affect biofilm formation or motility.
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Affiliation(s)
- Bingming Ou
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
| | - Lin Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Jiangsu Agri-animal Husbandry Vocational College, Taizhou 225300, China
| | - Yujie Song
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
| | - Ying Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
| | - Qian Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
| | - Yi Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
| | - Luan Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Wai Liang Tham
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - David H Francis
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China.
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17
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Sergiev PV, Golovina AY, Osterman IA, Nesterchuk MV, Sergeeva OV, Chugunova AA, Evfratov SA, Andreianova ES, Pletnev PI, Laptev IG, Petriukov KS, Navalayeu TI, Koteliansky VE, Bogdanov AA, Dontsova OA. N6-Methylated Adenosine in RNA: From Bacteria to Humans. J Mol Biol 2015; 428:2134-45. [PMID: 26707202 DOI: 10.1016/j.jmb.2015.12.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 12/14/2015] [Accepted: 12/16/2015] [Indexed: 12/11/2022]
Abstract
N6-methyladenosine (m(6)A) is ubiquitously present in the RNA of living organisms from Escherichia coli to humans. Methyltransferases that catalyze adenosine methylation are drastically different in specificity from modification of single residues in bacterial ribosomal or transfer RNA to modification of thousands of residues spread among eukaryotic mRNA. Interactions that are formed by m(6)A residues range from RNA-RNA tertiary contacts to RNA-protein recognition. Consequences of the modification loss might vary from nearly negligible to complete reprogramming of regulatory pathways and lethality. In this review, we summarized current knowledge on enzymes that introduce m(6)A modification, ways to detect m(6)A presence in RNA and the functional role of this modification everywhere it is present, from bacteria to humans.
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Affiliation(s)
- Petr V Sergiev
- Department of Chemistry, Department of Bioengineering and Bioinformatics and A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.
| | - Anna Ya Golovina
- Department of Chemistry, Department of Bioengineering and Bioinformatics and A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Ilya A Osterman
- Department of Chemistry, Department of Bioengineering and Bioinformatics and A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | | | - Olga V Sergeeva
- Skolkovo Institute for Science and Technology, Moscow 143025, Russia
| | | | - Sergey A Evfratov
- Department of Chemistry, Department of Bioengineering and Bioinformatics and A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Ekaterina S Andreianova
- Department of Chemistry, Department of Bioengineering and Bioinformatics and A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Philipp I Pletnev
- Department of Chemistry, Department of Bioengineering and Bioinformatics and A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Ivan G Laptev
- Department of Chemistry, Department of Bioengineering and Bioinformatics and A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Kirill S Petriukov
- Department of Chemistry, Department of Bioengineering and Bioinformatics and A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Tsimafei I Navalayeu
- Department of Chemistry, Department of Bioengineering and Bioinformatics and A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | | | - Alexey A Bogdanov
- Department of Chemistry, Department of Bioengineering and Bioinformatics and A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Olga A Dontsova
- Department of Chemistry, Department of Bioengineering and Bioinformatics and A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
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18
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Dégut C, Ponchon L, Folly-Klan M, Barraud P, Tisné C. The m1A(58) modification in eubacterial tRNA: An overview of tRNA recognition and mechanism of catalysis by TrmI. Biophys Chem 2015; 210:27-34. [PMID: 26189113 DOI: 10.1016/j.bpc.2015.06.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/16/2015] [Accepted: 06/27/2015] [Indexed: 01/23/2023]
Abstract
The enzymes of the TrmI family catalyze the formation of the m(1)A58 modification in tRNA. We previously solved the crystal structure of the Thermus thermophilus enzyme and conducted a biophysical study to characterize the interaction between TrmI and tRNA. TrmI enzymes are active as a tetramer and up to two tRNAs can bind to TrmI simultaneously. In this paper, we present the structures of two TrmI mutants (D170A and Y78A). These residues are conserved in the active site of TrmIs and their mutations result in a dramatic alteration of TrmI activity. Both structures of TrmI mutants revealed the flexibility of the N-terminal domain that is probably important to bind tRNA. The structure of TrmI Y78A catalytic domain is unmodified regarding the binding of the SAM co-factor and the conformation of residues potentially interacting with the substrate adenine. This structure reinforces the previously proposed role of Y78, i.e. stabilize the conformation of the A58 ribose needed to hold the adenosine in the active site. The structure of the D170A mutant shows a flexible active site with one loop occupying in part the place of the co-factor and the second loop moving at the entrance to the active site. This structure and recent data confirms the central role of D170 residue binding the amino moiety of SAM and the exocyclic amino group of adenine. Possible mechanisms for methyl transfer are then discussed.
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Affiliation(s)
- Clément Dégut
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Paris Sorbonne Cité, 4 avenue de l'Observatoire, 75006, Paris
| | - Luc Ponchon
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Paris Sorbonne Cité, 4 avenue de l'Observatoire, 75006, Paris
| | - Marcia Folly-Klan
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Paris Sorbonne Cité, 4 avenue de l'Observatoire, 75006, Paris
| | - Pierre Barraud
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Paris Sorbonne Cité, 4 avenue de l'Observatoire, 75006, Paris
| | - Carine Tisné
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Paris Sorbonne Cité, 4 avenue de l'Observatoire, 75006, Paris.
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19
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Aranda J, Zinovjev K, Roca M, Tuñón I. Dynamics and Reactivity in Thermus aquaticus N6-Adenine Methyltransferase. J Am Chem Soc 2014; 136:16227-39. [DOI: 10.1021/ja5077124] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Juan Aranda
- Departament de Química
Física, Universitat de València, 46100 Burjassot, Spain
| | - Kirill Zinovjev
- Departament de Química
Física, Universitat de València, 46100 Burjassot, Spain
| | - Maite Roca
- Departament de Química
Física, Universitat de València, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament de Química
Física, Universitat de València, 46100 Burjassot, Spain
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