1
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Weissenboeck F, Klöcker N, Špaček P, Hüwel S, Rentmeister A. Stabilized 5' Cap Analogue for Optochemical Activation of mRNA Translation. ACS Omega 2024; 9:12810-12816. [PMID: 38524462 PMCID: PMC10955689 DOI: 10.1021/acsomega.3c08505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/02/2024] [Accepted: 01/19/2024] [Indexed: 03/26/2024]
Abstract
The 5' cap is a distinguishing feature of transcripts made by polymerase II and characterized by an N7-methylated guanosine (m7G) linked to the first transcribed nucleotide by a 5'-5' triphosphate bridge. It stabilizes eukaryotic mRNAs and plays a crucial role in translation initiation. Its importance in mRNA processing, translation, and turnover makes the 5' cap a privileged structure for engineering by non-natural modifications. A photocleavable group at the 5' cap of guanosine was recently used to mute translation of exogenous mRNAs. Its removal by light enabled direct control of protein production at the posttranscriptional level. Modifications in the triphosphate bridge impede degradation by specific decapping enzymes and maintain translation. Here, we combined 5' cap modifications at different positions and investigated how they impact 5' cap-dependent processes in distinct manners. We synthesized 5' cap analogues with a photocleavable group at the N2-position of m7G in addition to a medronate in the triphosphate bridge to obtain a photoactivatable 5' cap analogue featuring a methylene group between the β and γ phosphates. The resulting Medronate-FlashCap transiently or permanently impeded distinct crucial interactions of the 5' cap required for translation and degradation. We show that the Medronate-FlashCap is compatible with in vitro transcription to generate muted mRNA and that light can be used to activate translation in cells. After light-induced removal of the photocleavable group, the Medronate-FlashCap remained stable against degradation by the decapping enzyme DcpS. The additional methylene group renders the 5' cap resistant to DcpS, while maintaining the interaction with cap-binding proteins.
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Affiliation(s)
| | - Nils Klöcker
- Institute of Biochemistry, University of Münster, Münster 48149, Germany
| | - Petr Špaček
- Institute of Biochemistry, University of Münster, Münster 48149, Germany
| | - Sabine Hüwel
- Institute of Biochemistry, University of Münster, Münster 48149, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, University of Münster, Münster 48149, Germany
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2
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Bollu A, Schepers H, Klöcker N, Erguven M, Lawrence-Dörner AM, Rentmeister A. Visible Light Activates Coumarin-Caged mRNA for Cytoplasmic Cap Methylation in Cells. Chemistry 2024; 30:e202303174. [PMID: 37883670 DOI: 10.1002/chem.202303174] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 10/28/2023]
Abstract
Protein synthesis is important and regulated by various mechanisms in the cell. Translation initiation in eukaryotes starts at the 5' cap and is the most complex of the three phases of mRNA translation. It requires methylation of the N7 position of the terminal guanosine (m7 G). The canonical capping occurs in the nucleus, however, cytoplasmic recapping has been discovered. It functions in switching mRNAs between translating and non-translating states, but the individual steps are difficult to dissect. We targeted cytoplasmic cap methylation as the ultimate step of cytoplasmic recapping. We present an N7G photocaged 5' cap that can be activated for cytoplasmic methylation by visible light. We report chemical and chemo-enzymatic synthesis of this 5' cap with 7-(diethylamino)-4-methyl-coumarin (DEACM) at the N7G and validate that it is not bound by translation initiation factor 4E (eIF4E). We demonstrate incorporation into mRNA, the release of unmethylated cap analog and enzymatic remethylation to functional cap 0 after irradiation at 450 nm. In cells, irradiation triggers translation of mRNAs with the N7G photocaged 5' cap via cytoplasmic cap methylation.
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Affiliation(s)
- Amarnath Bollu
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Helena Schepers
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Nils Klöcker
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Mehmet Erguven
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149, Münster, Germany
- Cells in Motion Interfaculty Centre, University of Münster, Waldeyerstraße 15, 48149, Münster, Germany
| | - Ann-Marie Lawrence-Dörner
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149, Münster, Germany
- Cells in Motion Interfaculty Centre, University of Münster, Waldeyerstraße 15, 48149, Münster, Germany
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3
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Helm M, Bohnsack MT, Carell T, Dalpke A, Entian KD, Ehrenhofer-Murray A, Ficner R, Hammann C, Höbartner C, Jäschke A, Jeltsch A, Kaiser S, Klassen R, Leidel SA, Marx A, Mörl M, Meier JC, Meister G, Rentmeister A, Rodnina M, Roignant JY, Schaffrath R, Stadler P, Stafforst T. Experience with German Research Consortia in the Field of Chemical Biology of Native Nucleic Acid Modifications. ACS Chem Biol 2023; 18:2441-2449. [PMID: 37962075 DOI: 10.1021/acschembio.3c00586] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The chemical biology of native nucleic acid modifications has seen an intense upswing, first concerning DNA modifications in the field of epigenetics and then concerning RNA modifications in a field that was correspondingly rebaptized epitranscriptomics by analogy. The German Research Foundation (DFG) has funded several consortia with a scientific focus in these fields, strengthening the traditionally well-developed nucleic acid chemistry community and inciting it to team up with colleagues from the life sciences and data science to tackle interdisciplinary challenges. This Perspective focuses on the genesis, scientific outcome, and downstream impact of the DFG priority program SPP1784 and offers insight into how it fecundated further consortia in the field. Pertinent research was funded from mid-2015 to 2022, including an extension related to the coronavirus pandemic. Despite being a detriment to research activity in general, the pandemic has resulted in tremendously boosted interest in the field of RNA and RNA modifications as a consequence of their widespread and successful use in vaccination campaigns against SARS-CoV-2. Funded principal investigators published over 250 pertinent papers with a very substantial impact on the field. The program also helped to redirect numerous laboratories toward this dynamic field. Finally, SPP1784 spawned initiatives for several funded consortia that continue to drive the fields of nucleic acid modification.
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Affiliation(s)
- Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Alexander Dalpke
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Karl-Dieter Entian
- Institute for Molecular Biosciences, Goethe-University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | | | - Ralf Ficner
- Institute for Microbiology and Genetics, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Christian Hammann
- Department of Medicine, HMU Health and Medical University, 14471 Potsdam, Germany
| | - Claudia Höbartner
- Institute for Organic Chemistry, Julius-Maximilians-University of Würzburg, 97074 Würzburg, Germany
| | - Andres Jäschke
- Institute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-University Heidelberg, 69120 Heidelberg, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Stefanie Kaiser
- Institute for Pharmaceutical Chemistry, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Roland Klassen
- Institute for Biology - Microbiology, University of Kassel, 34132 Kassel, Germany
| | - Sebastian A Leidel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Andreas Marx
- Department of Chemistry - Organic/Cellular Chemistry, University of Constance, 78457 Constance, Germany
| | - Mario Mörl
- Institute of Biochemistry, University of Leipzig, 04103 Leipzig, Germany
| | - Jochen C Meier
- Department of Cell Physiology, Technical University of Braunschweig, 38106 Brunswick, Germany
| | - Gunter Meister
- Institute of Biochemistry, Genetics and Microbiology - Biochemistry I, University of Regensburg, 93053 Regensburg, Germany
| | - Andrea Rentmeister
- Institute for Biochemistry, Westphalian Wilhelms University Münster, 48149 Münster, Germany
| | - Marina Rodnina
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Jean-Yves Roignant
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
- Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Raffael Schaffrath
- Institute for Biology - Microbiology, University of Kassel, 34132 Kassel, Germany
| | - Peter Stadler
- Institute for Computer Science - Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Thorsten Stafforst
- Interfaculty Institute for Biochemistry, Eberhard Karls University Tübingen, 72074 Tübingen, Germany
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Hartstock K, Kueck NA, Spacek P, Ovcharenko A, Hüwel S, Cornelissen NV, Bollu A, Dieterich C, Rentmeister A. MePMe-seq: antibody-free simultaneous m 6A and m 5C mapping in mRNA by metabolic propargyl labeling and sequencing. Nat Commun 2023; 14:7154. [PMID: 37935679 PMCID: PMC10630376 DOI: 10.1038/s41467-023-42832-z] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 10/23/2023] [Indexed: 11/09/2023] Open
Abstract
Internal modifications of mRNA have emerged as widespread and versatile regulatory mechanism to control gene expression at the post-transcriptional level. Most of these modifications are methyl groups, making S-adenosyl-L-methionine (SAM) a central metabolic hub. Here we show that metabolic labeling with a clickable metabolic precursor of SAM, propargyl-selenohomocysteine (PSH), enables detection and identification of various methylation sites. Propargylated A, C, and G nucleosides form at detectable amounts via intracellular generation of the corresponding SAM analogue. Integration into next generation sequencing enables mapping of N6-methyladenosine (m6A) and 5-methylcytidine (m5C) sites in mRNA with single nucleotide precision (MePMe-seq). Analysis of the termination profiles can be used to distinguish m6A from 2'-O-methyladenosine (Am) and N1-methyladenosine (m1A) sites. MePMe-seq overcomes the problems of antibodies for enrichment and sequence-motifs for evaluation, which was limiting previous methodologies. Metabolic labeling via clickable SAM facilitates the joint evaluation of methylation sites in RNA and potentially DNA and proteins.
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Affiliation(s)
- Katja Hartstock
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Nadine A Kueck
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Petr Spacek
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Anna Ovcharenko
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Sabine Hüwel
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Nicolas V Cornelissen
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Amarnath Bollu
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Berlin, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany.
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Cornelissen NV, Rentmeister A. Ribozyme for stabilized SAM analogue modifies RNA in cells. Nat Chem 2023; 15:1486-1487. [PMID: 37907605 DOI: 10.1038/s41557-023-01354-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
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6
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Cornelissen NV, Mineikaitė R, Erguven M, Muthmann N, Peters A, Bartels A, Rentmeister A. Post-synthetic benzylation of the mRNA 5' cap via enzymatic cascade reactions. Chem Sci 2023; 14:10962-10970. [PMID: 37829022 PMCID: PMC10566477 DOI: 10.1039/d3sc03822j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 08/28/2023] [Indexed: 10/14/2023] Open
Abstract
mRNAs are emerging modalities for vaccination and protein replacement therapy. Increasing the amount of protein produced by stabilizing the transcript or enhancing translation without eliciting a strong immune response are major steps towards overcoming the present limitations and improving their therapeutic potential. The 5' cap is a hallmark of mRNAs and non-natural modifications can alter the properties of the entire transcript selectively. Here, we developed a versatile enzymatic cascade for regioselective benzylation of various biomolecules and applied it for post-synthetic modification of mRNA at the 5' cap to demonstrate its potential. Starting from six synthetic methionine analogues bearing (hetero-)benzyl groups, S-adenosyl-l-methionine analogues are formed and utilized for N7G-cap modification of mRNAs. This post-synthetic enzymatic modification exclusively modifies mRNAs at the terminal N7G, producing mRNAs with functional 5' caps. It avoids the wrong orientation of the 5' cap-a problem in common co-transcriptional capping. In the case of the 4-chlorobenzyl group, protein production was increased to 139% during in vitro translation and to 128-150% in four different cell lines. This 5' cap modification did not activate cytosolic pathogen recognition receptors TLR3, TLR7 or TLR8 significantly more than control mRNAs, underlining its potential to contribute to the development of future mRNA therapeutics.
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Affiliation(s)
- N V Cornelissen
- University of Münster, Department of Chemistry, Institute of Biochemistry Corrensstr. 36 48149 Münster Germany
| | - R Mineikaitė
- University of Münster, Department of Chemistry, Institute of Biochemistry Corrensstr. 36 48149 Münster Germany
| | - M Erguven
- University of Münster, Department of Chemistry, Institute of Biochemistry Corrensstr. 36 48149 Münster Germany
- University of Münster, Cells in Motion Interfaculty Centre Waldeyerstr. 15 48149 Münster Germany
| | - N Muthmann
- University of Münster, Department of Chemistry, Institute of Biochemistry Corrensstr. 36 48149 Münster Germany
| | - A Peters
- University of Münster, Department of Chemistry, Institute of Biochemistry Corrensstr. 36 48149 Münster Germany
| | - A Bartels
- University of Münster, Department of Chemistry, Institute of Biochemistry Corrensstr. 36 48149 Münster Germany
| | - A Rentmeister
- University of Münster, Department of Chemistry, Institute of Biochemistry Corrensstr. 36 48149 Münster Germany
- University of Münster, Cells in Motion Interfaculty Centre Waldeyerstr. 15 48149 Münster Germany
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7
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Hoffmann A, Schülke KH, Hammer SC, Rentmeister A, Cornelissen NV. Comparative S-adenosyl-L-methionine analogue generation for selective biocatalytic Friedel-Crafts alkylation. Chem Commun (Camb) 2023; 59:5463-5466. [PMID: 37070635 DOI: 10.1039/d3cc01036h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Methyltransferases provide excellent specificity in late-stage alkylation of biomolecules. Their dependence on S-adenosyl-L-methionine (SAM) mandates efficient access to SAM analogues for biocatalytic applications. We directly compared halide methyltransferase (HMT) and methionine adenosyltransferase (MAT) to access SAM analogues and explored their utility in cascade reactions with NovO for regioselective, late-stage Friedel-Crafts alkylation of a coumarin. The HMT cascade efficiently provided SAM for methylation, while the MAT cascade also supplied high levels of SAM analogues for alkylation reactions.
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Affiliation(s)
- Arne Hoffmann
- University of Muenster, Institute of Biochemistry, Corrensstr. 36, Muenster D-48149, Germany.
| | - Kai H Schülke
- Bielefeld University, Faculty of Chemistry, Organic Chemistry and Biocatalysis Universitätsstraße 25, Bielefeld D-33615, Germany.
| | - Stephan C Hammer
- Bielefeld University, Faculty of Chemistry, Organic Chemistry and Biocatalysis Universitätsstraße 25, Bielefeld D-33615, Germany.
| | - Andrea Rentmeister
- University of Muenster, Institute of Biochemistry, Corrensstr. 36, Muenster D-48149, Germany.
| | - Nicolas V Cornelissen
- University of Muenster, Institute of Biochemistry, Corrensstr. 36, Muenster D-48149, Germany.
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8
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Gericke L, Mhaindarkar D, Karst LC, Jahn S, Kuge M, Mohr MKF, Gagsteiger J, Cornelissen NV, Wen X, Mordhorst S, Jessen HJ, Rentmeister A, Seebeck FP, Layer G, Loenarz C, Andexer JN. Biomimetic S-Adenosylmethionine Regeneration Starting from Multiple Byproducts Enables Biocatalytic Alkylation with Radical SAM Enzymes. Chembiochem 2023; 24:e202300133. [PMID: 36942622 DOI: 10.1002/cbic.202300133] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 03/23/2023]
Abstract
S-Adenosylmethionine (SAM) is an enzyme cofactor involved in methylation, aminopropyl transfer, and radical reactions. This versatility renders SAM-dependent enzymes of great interest in biocatalysis. The usage of SAM analogues adds to this diversity. However, high cost and instability of the cofactor impedes the investigation and usage of these enzymes. While SAM regeneration protocols from the methyltransferase (MT) byproduct S-adenosylhomocysteine are available, aminopropyl transferases and radical SAM enzymes are not covered. Here, we report a set of efficient one-pot systems to supply or regenerate SAM and SAM analogues for all three enzyme classes. The systems' flexibility is showcased by the transfer of an ethyl group with a cobalamin-dependent radical SAM MT using S-adenosylethionine as a cofactor. This shows the potential of SAM (analogue) supply and regeneration for the application of diverse chemistry, as well as for mechanistic studies using cofactor analogues.
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Affiliation(s)
- Lukas Gericke
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, GERMANY
| | - Dipali Mhaindarkar
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, GERMANY
| | - Lukas C Karst
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, GERMANY
| | - Sören Jahn
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, GERMANY
| | - Marco Kuge
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, GERMANY
| | - Michael K F Mohr
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, GERMANY
| | - Jana Gagsteiger
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, GERMANY
| | - Nicolas V Cornelissen
- University of Münster: Westfalische Wilhelms-Universitat Munster, Institute of Biochemistry, GERMANY
| | - Xiaojin Wen
- University of Basel: Universitat Basel, Department of Chemistry, SWITZERLAND
| | - Silja Mordhorst
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, GERMANY
| | - Henning J Jessen
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Organic Chemistry, GERMANY
| | - Andrea Rentmeister
- University of Munster: Westfalische Wilhelms-Universitat Munster, Institute of Biochemistry, GERMANY
| | - Florian P Seebeck
- University of Basel: Universitat Basel, Department of Chemistry, SWITZERLAND
| | - Gunhild Layer
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, GERMANY
| | - Christoph Loenarz
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, GERMANY
| | - Jennifer Nina Andexer
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, Albertstr. 25, 79104, Freiburg, GERMANY
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9
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Weissenboeck FP, Schepers H, Rentmeister A. Optochemical control of mRNA translation in eukaryotes. Angew Chem Int Ed Engl 2023; 62:e202301778. [PMID: 36929624 DOI: 10.1002/anie.202301778] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/18/2023]
Abstract
A major stage in the expression of genes is the translation of messenger RNA (mRNA), and the regulation of this process is essential for protein production in cells. How tightly controlled gene expression can be spatially and temporally, is particularly evident in polar cells and embryonic development. We need tools to dissect these complex processes, if we wish to understand the underlying links, especially the difficulties brought on by malfunction. External bioorthogonal triggers are very helpful in this area, if they let us precisely control where and when a process is started. Equipping nucleic acids with light-responsive groups has proven to be an effective approach to examine the dynamic regulatory route of mRNA translation in living cells. In this review, we present an overview of the most recent methods for optochemically controlling translation, focusing on cis-acting technologies.
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Affiliation(s)
- Florian P Weissenboeck
- Westfälische Wilhelms-Universität Münster: Westfalische Wilhelms-Universitat Munster, Institute of Biochemistry, GERMANY
| | - Helena Schepers
- Westfälische Wilhelms-Universität Münster: Westfalische Wilhelms-Universitat Munster, Institute of Biochemistry, GERMANY
| | - Andrea Rentmeister
- Westfälische Wilhelms-Universität Münster: Westfalische Wilhelms-Universitat Munster, Department of Chemistry, Institute for Biochemistry, Corrensstraße 36, 48149, Muenster, GERMANY
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10
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Weissenboeck FP, Schepers H, Rentmeister A. Optochemical control of mRNA translation in eukaryotes. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202301778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Affiliation(s)
- Florian P. Weissenboeck
- Westfälische Wilhelms-Universität Münster: Westfalische Wilhelms-Universitat Munster Institute of Biochemistry GERMANY
| | - Helena Schepers
- Westfälische Wilhelms-Universität Münster: Westfalische Wilhelms-Universitat Munster Institute of Biochemistry GERMANY
| | - Andrea Rentmeister
- Westfälische Wilhelms-Universität Münster: Westfalische Wilhelms-Universitat Munster Department of Chemistry, Institute for Biochemistry Corrensstraße 36 48149 Muenster GERMANY
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11
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Cornelissen NV, Hoffmann A, Rentmeister A. DNA‐Methyltransferasen und AdoMet‐Analoga als Werkzeuge für die Molekularbiologie und Biotechnologie. CHEM-ING-TECH 2023. [DOI: 10.1002/cite.202200174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- Nicolas V. Cornelissen
- Westfälische Wilhelms-Universität Münster Institut für Biochemie, Fachbereich Chemie und Pharmazie Corrensstraße 36 48149 Münster Deutschland
| | - Arne Hoffmann
- Westfälische Wilhelms-Universität Münster Institut für Biochemie, Fachbereich Chemie und Pharmazie Corrensstraße 36 48149 Münster Deutschland
| | - Andrea Rentmeister
- Westfälische Wilhelms-Universität Münster Institut für Biochemie, Fachbereich Chemie und Pharmazie Corrensstraße 36 48149 Münster Deutschland
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12
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Bollu A, Klöcker N, Špaček P, P Weissenboeck F, Hüwel S, Rentmeister A. Light-Activated Translation of Different mRNAs in Cells via Wavelength-Dependent Photouncaging. Angew Chem Int Ed Engl 2023; 62:e202209975. [PMID: 36417319 PMCID: PMC10107135 DOI: 10.1002/anie.202209975] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/20/2022] [Accepted: 11/23/2022] [Indexed: 11/24/2022]
Abstract
The 5' cap is a hallmark of eukaryotic mRNA involved in the initiation of translation. Its modification with a single photo-cleavable group can bring translation of mRNA under the control of light. However, UV irradiation causes cell stress and downregulation of translation. Furthermore, complex processes often involve timed expression of more than one gene. The approach would thus greatly benefit from the ability to photo-cleave by blue light and to control more than one mRNA at a time. We report the synthesis of a 5' cap modified with a 7-(diethylamino)coumarin (CouCap) and adapted conditions for in vitro transcription. Translation of the resulting CouCap-mRNA is muted in vitro and in mammalian cells, and can be initiated by irradiation with 450 nm. The native cap is restored and no non-natural residues nor sequence alterations remain in the mRNA. Multiplexing for two different mRNAs was achieved by combining cap analogs with coumarin- and ortho-nitrobenzyl-based photo-cleavable groups.
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Affiliation(s)
- Amarnath Bollu
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Nils Klöcker
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Petr Špaček
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Florian P Weissenboeck
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Sabine Hüwel
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
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13
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Muthmann N, Albers M, Rentmeister A. CAPturAM, a Chemo-Enzymatic Strategy for Selective Enrichment and Detection of Physiological CAPAM-Targets. Angew Chem Int Ed Engl 2023; 62:e202211957. [PMID: 36282111 PMCID: PMC10107118 DOI: 10.1002/anie.202211957] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 11/07/2022]
Abstract
Modified nucleotides impact all aspects of eukaryotic mRNAs and contribute to regulation of gene expression at the transcriptional and translational level. At the 5' cap, adenosine as first transcribed nucleotide is often N6 -methyl-2'-O-methyl adenosine (m6 Am ). This modification is tissue dependent and reversible, pointing to a regulatory function. CAPAM was recently identified as methyltransferase responsible for m6 Am formation, however, the direct assignment of its target transcripts proves difficult. Antibodies do not discriminate between internal N6 -methyl adenosine (m6 A) and m6 Am . Here we present CAPturAM, an antibody-free chemical biology approach for direct enrichment and probing of physiological CAPAM-targets. We harness CAPAM's cosubstrate promiscuity to install propargyl groups on its targets. Subsequent functionalization with an affinity handle allows for their enrichment. Using wildtype and CAPAM-/- cells, we successfully applied CAPturAM to confirm or disprove CAPAM-targets, facilitating the verification and identification of CAPAM targets.
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Affiliation(s)
- Nils Muthmann
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstrasse 36, 48149, Münster, Germany
| | - Marvin Albers
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstrasse 36, 48149, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstrasse 36, 48149, Münster, Germany
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14
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Klöcker N, Anhäuser L, Rentmeister A. Enzymatic Modification of the 5' Cap with Photocleavable ONB-Derivatives Using GlaTgs V34A. Chembiochem 2023; 24:e202200522. [PMID: 36408753 PMCID: PMC10108117 DOI: 10.1002/cbic.202200522] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 11/22/2022]
Abstract
The 5' cap of mRNA plays a critical role in mRNA processing, quality control and turnover. Enzymatic availability of the 5' cap governs translation and could be a tool to investigate cell fate decisions and protein functions or develop protein replacement therapies. We have previously reported on the chemical synthesis of 5' cap analogues with photocleavable groups for this purpose. However, the synthesis is complex and post-synthetic enzymatic installation may make the technique more applicable to biological researchers. Common 5' cap analogues, like the cap 0, are commercially available and routinely used for in vitro transcription. Here, we report a facile enzymatic approach to attach photocleavable groups site-specifically to the N2 position of m7 G of the 5' cap. By expanding the substrate scope of the methyltransferase variant GlaTgs V34A and using synthetic co-substrate analogues, we could enzymatically photocage the 5' cap and recover it after irradiation.
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Affiliation(s)
- Nils Klöcker
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, Münster, Germany
| | - Lea Anhäuser
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, Münster, Germany
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15
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Dittmar M, Weissenböck FP, Rentmeister A. Lichtgesteuerte Translation von mRNA in Eukaryoten. Biospektrum (Heidelb) 2023; 29:31-34. [PMID: 36845577 PMCID: PMC9942070 DOI: 10.1007/s12268-023-1881-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Messenger RNA (mRNA) shows great potential for medical applications, as recently demonstrated by the mRNA-based vaccines against the coronavirus. In addition, it has long been used for ectopic gene expression in cells and model organisms. While numerous methodologies are available for controlling gene expression at the level of transcription, approaches to control translation are scarce. Here we review strategies for direct light-mediated activation of mRNA translation via photocleavable groups and their potential to achieve spatial and temporal control of protein production.
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Affiliation(s)
- Maria Dittmar
- Institut für Biochemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, D-48149 Münster, Deutschland
| | - Florian Peter Weissenböck
- Institut für Biochemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, D-48149 Münster, Deutschland
| | - Andrea Rentmeister
- Institut für Biochemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, D-48149 Münster, Deutschland
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16
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Erguven M, Cornelissen NV, Peters A, Karaca E, Rentmeister A. Enzymatic Generation of Double-Modified AdoMet Analogues and Their Application in Cascade Reactions with Different Methyltransferases. Chembiochem 2022; 23:e202200511. [PMID: 36288101 PMCID: PMC10100234 DOI: 10.1002/cbic.202200511] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/26/2022] [Indexed: 01/25/2023]
Abstract
Methyltransferases (MTases) have become an important tool for site-specific alkylation and biomolecular labelling. In biocatalytic cascades with methionine adenosyltransferases (MATs), transfer of functional moieties has been realized starting from methionine analogues and ATP. However, the widespread use of S-adenosyl-l-methionine (AdoMet) and the abundance of MTases accepting sulfonium centre modifications limit selective modification in mixtures. AdoMet analogues with additional modifications at the nucleoside moiety bear potential for acceptance by specific MTases. Here, we explored the generation of double-modified AdoMets by an engineered Methanocaldococcus jannaschii MAT (PC-MjMAT), using 19 ATP analogues in combination with two methionine analogues. This substrate screening was extended to cascade reactions and to MTase competition assays. Our results show that MTase targeting selectivity can be improved by using bulky substituents at the N6 of adenine. The facile access to >10 new AdoMet analogues provides the groundwork for developing MAT-MTase cascades for orthogonal biomolecular labelling.
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Affiliation(s)
- Mehmet Erguven
- Department of Chemistry and PharmacyInstitute of BiochemistryUniversity of MünsterCorrensstr. 36, 48149MünsterGermany
- Cells in Motion Interfaculty CentreUniversity of MünsterWaldeyerstraße 1548149MünsterGermany
| | - Nicolas V. Cornelissen
- Department of Chemistry and PharmacyInstitute of BiochemistryUniversity of MünsterCorrensstr. 36, 48149MünsterGermany
| | - Aileen Peters
- Department of Chemistry and PharmacyInstitute of BiochemistryUniversity of MünsterCorrensstr. 36, 48149MünsterGermany
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center35330IzmirTurkey
- Izmir International Biomedicine and Genome InstituteDokuz Eylul University, 35340 Izmir (Turkey)
| | - Andrea Rentmeister
- Department of Chemistry and PharmacyInstitute of BiochemistryUniversity of MünsterCorrensstr. 36, 48149MünsterGermany
- Cells in Motion Interfaculty CentreUniversity of MünsterWaldeyerstraße 1548149MünsterGermany
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17
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Bollu A, Klöcker N, Špaček P, Weissenböck FP, Hüwel S, Rentmeister A. Light‐Activated Translation of Different mRNAs in Cells via Wavelength‐Dependent Photouncaging. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202209975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Amarnath Bollu
- Westfälische Wilhelms-Universität Münster: Westfalische Wilhelms-Universitat Munster Deparment of Chemistry GERMANY
| | - Nils Klöcker
- Westfälische Wilhelms-Universität Münster: Westfalische Wilhelms-Universitat Munster Department of Chemistry GERMANY
| | - Petr Špaček
- Westfälische Wilhelms-Universität Münster: Westfalische Wilhelms-Universitat Munster Department of Chemistry GERMANY
| | - Florian Peter Weissenböck
- Westfälische Wilhelms-Universität Münster: Westfalische Wilhelms-Universitat Munster Deparment of Chemistry GERMANY
| | - Sabine Hüwel
- Westfälische Wilhelms-Universität Münster: Westfalische Wilhelms-Universitat Munster Deparment of Chemistry GERMANY
| | - Andrea Rentmeister
- Westfälische Wilhelms-Universität Münster: Westfalische Wilhelms-Universitat Munster Department of Chemistry, Institute for Biochemistry Corrensstraße 36 48149 Muenster GERMANY
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18
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Muthmann N, Albers M, Rentmeister A. CAPturAM, a Chemo‐Enzymatic Strategy for Selective Enrichment and Detection of Physiological CAPAM‐Targets. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202211957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nils Muthmann
- Westfalische Wilhelms Universität Munster: Westfalische Wilhelms-Universitat Munster Institute of Biochemistry GERMANY
| | - Marvin Albers
- Westfalische Wilhelms Universität Munster: Westfalische Wilhelms-Universitat Munster Institute of Biochemistry GERMANY
| | - Andrea Rentmeister
- Westfälische Wilhelms-Universität Münster: Westfalische Wilhelms-Universitat Munster Department of Chemistry, Institute for Biochemistry Corrensstraße 36 48149 Muenster GERMANY
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19
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Rösner L, Reichert D, Rau K, Muthmann N, Rentmeister A. Sequence-specific targeting of RNA. Methods 2022; 205:73-82. [PMID: 35764247 DOI: 10.1016/j.ymeth.2022.06.007] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/10/2022] [Accepted: 06/23/2022] [Indexed: 11/30/2022] Open
Abstract
Post-transcriptional modifications play an important role in several processes, including translation, splicing, and RNA degradation in eukaryotic cells. To investigate the function of specific modifications it is of high interest to develop tools for sequence-specific RNA-targeting. This work focuses on two abundant modifications of eukaryotic mRNA, namely methylation of the guanine-N7 position of the 5'-cap and internal N6-methyladenosine (m6A). We describe the sequence-specific targeting of model RNA transcripts via RNA-binding proteins, such as nuclease-deficient RNA-targeting Cas9 (RCas9) and the Pumilio homology domain (PumHD) fused to two different effector enzymes, the dioxygenase FTO and the guanine-N7 methyltransferase Ecm1. With this tool, we were able to install and remove the methylation at the respective positions with high specificity.
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Affiliation(s)
- Lukas Rösner
- University of Münster, Department of Chemistry, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany
| | - Dennis Reichert
- University of Münster, Department of Chemistry, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany; Cells in Motion Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Kristina Rau
- University of Münster, Department of Chemistry, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany
| | - Nils Muthmann
- University of Münster, Department of Chemistry, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany
| | - Andrea Rentmeister
- University of Münster, Department of Chemistry, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany; Cells in Motion Interfaculty Center, University of Münster, 48149 Münster, Germany
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20
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Rösner L, Konken CP, Depke DA, Rentmeister A, Schäfers M. Covalent labeling of immune cells. Curr Opin Chem Biol 2022; 68:102144. [DOI: 10.1016/j.cbpa.2022.102144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/06/2022] [Accepted: 03/11/2022] [Indexed: 12/15/2022]
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21
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Abstract
The central dogma of molecular biology hinges on messenger RNA (mRNA), which presents a blueprint of the genetic information encoded in the DNA and serves as a template for translation into proteins. In addition to its fundamental importance in basic research, this class of biomolecules has recently become the first approved Covid vaccine, underscoring its utility in medical applications.Eukaryotic mRNA is heavily processed, including the 5' cap as the primary hallmark. This 5' cap protects mRNA from degradation by exoribonucleases but also interacts specifically with several proteins and enzymes to ensure mRNA turnover and processing, like splicing, export from the nucleus to the cytoplasm, and initiation of translation. The absence of a 5' cap leads to a strong immune response, and the methylation status contributes to distinguishing self from non-self RNA.Non-natural modifications of the 5' cap provide an avenue to label mRNAs and make them accessible to analyses, which is important to study their cellular localization, trafficking, and binding partners. They bear potential to engineer mRNAs, e.g., more stable or immunogenic mRNAs that are still translated, by impacting select interactions in a distinct manner. The modification of the 5' cap itself is powerful as it can be applied to make long mRNAs (∼1000 nt, not directly accessible by solid-phase synthesis) by in vitro transcription.This Account describes our contribution to the field of chemo-enzymatic modification of mRNA at the 5' cap. Our approach relies on RNA methyltransferases (MTases) with promiscuous activity on analogues of their natural cosubstrate S-adenosyl-L-methionine (AdoMet). We will describe how RNA MTases in combination with non-natural cosubstrates provide access to site-specific modification of different positions of the 5' cap, namely, the N2 and N7 position of guanosine and the N6 position of adenosine as the transcription start nucleotide (TSN) and exemplify strategies to make long mRNAs with modified 5' caps.We will compare the chemical and enzymatic synthesis of the AdoMet analogues used for this purpose. We could overcome previous limitations in methionine adenosyltransferase (MAT) substrate scope by engineering variants (termed PC-MATs) with the ability to convert methionine analogues with benzylic and photocaging groups at the sulfonium ion.The final part of this Account will highlight applications of the modified mRNAs. Like in many chemo-enzymatic approaches, a versatile strategy is to install small functional groups enzymatically and use them as handles in subsequent bioorthogonal reactions. We showed fluorescent labeling of mRNAs via different types of click chemistry in vitro and in cells. In a second line of applications, we used the handles to make mRNAs amenable for analyses, most notably next-generation sequencing. In the case of extremely promiscuous enzymes, the direct installation of photo-cross-linking groups was successful also and provided a way to covalently bind protein-interaction partners. Finally, the non-natural modifications of mRNAs can also modulate the properties of mRNAs. Propargylation of Am as the transcription start nucleotide at its N6 position maintained the translation of mRNAs but increased their immunogenicity. The installation of photocaging groups provides a way to revert these effects and control interactions by light.
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Affiliation(s)
- Amarnath Bollu
- Department of Chemistry and Pharmacy, Institute of Biochemistry Westfälische Wilhelms-Universität Münster, University of Münster, Corrensstrasse 36, 48149 Münster, Germany
| | - Aileen Peters
- Department of Chemistry and Pharmacy, Institute of Biochemistry Westfälische Wilhelms-Universität Münster, University of Münster, Corrensstrasse 36, 48149 Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry and Pharmacy, Institute of Biochemistry Westfälische Wilhelms-Universität Münster, University of Münster, Corrensstrasse 36, 48149 Münster, Germany
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22
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Reichert D, Schepers H, Simke J, Lechner H, Dörner W, Höcker B, Ravoo BJ, Rentmeister A. Computational design and experimental characterization of a photo-controlled mRNA-cap guanine-N7 methyltransferase. RSC Chem Biol 2021; 2:1484-1490. [PMID: 34704053 PMCID: PMC8495969 DOI: 10.1039/d1cb00109d] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 05/14/2021] [Accepted: 06/25/2021] [Indexed: 11/21/2022] Open
Abstract
The spatial and temporal control of gene expression at the post-transcriptional level is essential in eukaryotic cells and developing multicellular organisms. In recent years optochemical and optogenetic tools have enabled the manipulation and investigation of many steps in the involved processes. However, examples for light-mediated control of eukaryotic mRNA processing and the responsible enzymes are still rare. In particular, methylation of the 5′ cap of mRNA is required for ribosome assembly, and the responsible guanine-N7 methyltransferase (MTase) from E. cuniculi (Ecm1) proved suitable for activating translation. Here, we report on a photoswitchable MTase obtained by bridging the substrate-binding cleft of Ecm1 with a tetra-ortho-methoxy-azobenzene. This azobenzene derivative is characterized by efficient trans-to-cis isomerization using red light at 615 nm. Starting from a cysteine-free Ecm1 variant (ΔCys), we used a computational approach to identify suitable conjugation sites for the azobenzene moiety. We created and characterized the four best-ranked variants, each featuring two appropriately positioned cysteines close to the substrate-binding cleft. Conjugating and crosslinking the azobenzene between C149/C155 in a designed Ecm1 variant (VAR3-Az) enabled light-dependent modulation of the MTase activity and showed a 50% higher activity for the cis form than the trans-form of the azobenzene conjugated to VAR3-Az. Guided by computational design, we engineered a light-dependent 5' cap guanine-N7 methyltransferase by bridging the substrate-binding cleft with an azobenzene derivative.![]()
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Affiliation(s)
- Dennis Reichert
- Institute of Biochemistry, University of Münster, Correnstraße 36 Münster 48149 Germany .,Cells in Motion Interfaculty Center, University of Münster Münster 48149 Germany
| | - Helena Schepers
- Institute of Biochemistry, University of Münster, Correnstraße 36 Münster 48149 Germany
| | - Julian Simke
- Organic Chemistry Institute, University of Münster, Corrensstraße 36 Münster 48149 Germany
| | - Horst Lechner
- Department for Biochemistry, University of Bayreuth, Universitätsstraße 30 Bayreuth 95447 Germany.,Institute of Biochemistry, Graz University of Technology, Petersgasse 10-12/II Graz 8010 Austria
| | - Wolfgang Dörner
- Institute of Biochemistry, University of Münster, Correnstraße 36 Münster 48149 Germany
| | - Birte Höcker
- Department for Biochemistry, University of Bayreuth, Universitätsstraße 30 Bayreuth 95447 Germany
| | - Bart Jan Ravoo
- Cells in Motion Interfaculty Center, University of Münster Münster 48149 Germany.,Organic Chemistry Institute, University of Münster, Corrensstraße 36 Münster 48149 Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, University of Münster, Correnstraße 36 Münster 48149 Germany .,Cells in Motion Interfaculty Center, University of Münster Münster 48149 Germany
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23
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Peters A, Herrmann E, Cornelissen NV, Klöcker N, Kümmel D, Rentmeister A. Visible-Light Removable Photocaging Groups Accepted by MjMAT Variant: Structural Basis and Compatibility with DNA and RNA Methyltransferases. Chembiochem 2021; 23:e202100437. [PMID: 34606675 PMCID: PMC9298006 DOI: 10.1002/cbic.202100437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 08/20/2021] [Revised: 10/01/2021] [Indexed: 12/20/2022]
Abstract
Methylation and demethylation of DNA, RNA and proteins constitutes a major regulatory mechanism in epigenetic processes. Investigations would benefit from the ability to install photo‐cleavable groups at methyltransferase target sites that block interactions with reader proteins until removed by non‐damaging light in the visible spectrum. Engineered methionine adenosyltransferases (MATs) have been exploited in cascade reactions with methyltransferases (MTases) to modify biomolecules with non‐natural groups, including first evidence for accepting photo‐cleavable groups. We show that an engineered MAT from Methanocaldococcus jannaschii (PC‐MjMAT) is 308‐fold more efficient at converting ortho‐nitrobenzyl‐(ONB)‐homocysteine than the wildtype enzyme. PC‐MjMAT is active over a broad range of temperatures and compatible with MTases from mesophilic organisms. We solved the crystal structures of wildtype and PC‐MjMAT in complex with AdoONB and a red‐shifted derivative thereof. These structures reveal that aromatic stacking interactions within the ligands are key to accommodating the photocaging groups in PC‐MjMAT. The enlargement of the binding pocket eliminates steric clashes to enable AdoMet analogue binding. Importantly, PC‐MjMAT exhibits remarkable activity on methionine analogues with red‐shifted ONB‐derivatives enabling photo‐deprotection of modified DNA by visible light.
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Affiliation(s)
- Aileen Peters
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Eric Herrmann
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Nicolas V Cornelissen
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Nils Klöcker
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Daniel Kümmel
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
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24
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Depke DA, Konken CP, Rösner L, Hermann S, Schäfers M, Rentmeister A. A novel 18F-labeled clickable substrate for targeted imaging of SNAP-tag expressing cells by PET in vivo. Chem Commun (Camb) 2021; 57:9850-9853. [PMID: 34490435 DOI: 10.1039/d1cc03871k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bioorthogonal covalent labeling with self-labeling enzymes like SNAP-tag bears a high potential for specific targeting of cells for imaging in vitro and also in vivo. To this end, fluorescent SNAP substrates have been established and used in microscopy and fluorescence imaging while radioactive substrates for the highly sensitive and whole-body positron emission tomography (PET) have been lacking. Here, we show for the first time successful and high-contrast PET imaging of subcutaneous SNAP-tag expressing tumor xenografts by bioorthogonal covalent targeting with a novel 18F-based radioligand in vivo.
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Affiliation(s)
- Dominic Alexej Depke
- European Institute for Molecular Imaging (EIMI), University of Münster, Germany.
| | - Christian Paul Konken
- European Institute for Molecular Imaging (EIMI), University of Münster, Germany. .,Department of Nuclear Medicine, University Hospital Münster, Germany
| | - Lukas Rösner
- Institute of Biochemistry, University of Münster, Germany.
| | - Sven Hermann
- European Institute for Molecular Imaging (EIMI), University of Münster, Germany.
| | - Michael Schäfers
- European Institute for Molecular Imaging (EIMI), University of Münster, Germany. .,Department of Nuclear Medicine, University Hospital Münster, Germany
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25
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Rickhoff J, Cornelissen NV, Beuse T, Rentmeister A, Jan Ravoo B. Multiresponsive hydrogels and organogels based on photocaged cysteine. Chem Commun (Camb) 2021; 57:5913-5916. [PMID: 34008646 DOI: 10.1039/d1cc01363g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Here we present the readily accessible amino acid 4,5-dimethoxy-2-nitrobenzyl-l-cysteine (DNC), as an ultra-low molecular weight gelator (MW = 316 g mol-1). Sonication of DNC in water or organic solvents as well as pH adjustment in water trigger gelation. A diverse set of stimuli (UV irradiation, oxidation, heat or pH change) induce a gel-sol transition. Moreover, the photo-triggered gel-sol transition was used to obtain a controlled cysteine release from the hydrogel.
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Affiliation(s)
- Jonas Rickhoff
- Organic Chemistry Institute, University of Muenster, Corrensstr. 36, D-48149 Muenster, Germany.
| | - Nicolas V Cornelissen
- Institute of Biochemistry, University of Muenster, Corrensstr. 36, D-48149 Muenster, Germany.
| | - Thomas Beuse
- MEET Battery Research Center, Institute of Physical Chemistry, University of Muenster, Corrensstr. 46, D-48149 Muenster, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, University of Muenster, Corrensstr. 36, D-48149 Muenster, Germany.
| | - Bart Jan Ravoo
- Organic Chemistry Institute, University of Muenster, Corrensstr. 36, D-48149 Muenster, Germany.
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26
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Abstract
Supramolecular nanogels are an emerging class of polymer nanocarriers for intracellular delivery, due to their straightforward preparation, biocompatibility, and capability to spontaneously encapsulate biologically active components such as DNA. A completely biodegradable three-component cationic supramolecular nanogel was designed exploiting the multivalent host-guest interaction of cyclodextrin and adamantane attached to a polypeptide backbone. While cyclodextrin was conjugated to linear poly-L-lysine, adamantane was grafted to linear as well as star shaped poly-L-lysine. Size control of nanogels was obtained with the increase in the length of the host and guest polymer. Moreover, smaller nanogels were obtained using the star shaped polymers because of the compact nature of star polymers compared to linear polymers. Nanogels were loaded with anionic model cargoes, pyranine and carboxyfluorescein, and their enzyme responsive release was studied using protease trypsin. Confocal microscopy revealed successful transfection of mammalian HeLa cells and intracellular release of pyranine and plasmid DNA, as quantified using a luciferase assay, showing that supramolecular polypeptide nanogels have significant potential in gene therapy applications.
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Affiliation(s)
- Sharafudheen Pottanam Chali
- Organic Chemistry Institute and Centre for Soft NanoscienceWestfälische Wilhelms-Universität MünsterCorrensstrasse 3648149MünsterGermany
| | - Sabine Hüwel
- Institute of BiochemistryWestfälische Wilhelms-Universität MünsterCorrensstrasse 3648149MünsterGermany
| | - Andrea Rentmeister
- Institute of BiochemistryWestfälische Wilhelms-Universität MünsterCorrensstrasse 3648149MünsterGermany
| | - Bart Jan Ravoo
- Organic Chemistry Institute and Centre for Soft NanoscienceWestfälische Wilhelms-Universität MünsterCorrensstrasse 3648149MünsterGermany
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27
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Kueck NA, Ovcharenko A, Hartstock K, Cornelissen NV, Rentmeister A. Chemoenzymatic labeling of RNA to enrich, detect and identify methyltransferase-target sites. Methods Enzymol 2021; 658:161-190. [PMID: 34517946 DOI: 10.1016/bs.mie.2021.06.006] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The RNA methyltransferase (MTase) complex METTL3-METTL14 transfers methyl groups from S-adenosyl-l-methionine (AdoMet) to the N6-position of adenosines within its consensus sequence, the DRACH motif (D=A, G, U; R=A, G; H=A, C, U). Interestingly, this MTase complex shows remarkable promiscuity regarding the cosubstrate. This can be exploited to install nonnatural modifications, like clickable or photocaging groups. Clickable groups are widely used for subsequent functionalization and open a broad range of possibilities for downstream applications. Here, we elaborate on click chemistry for coupling of RNA to biotin to enrich MTase targets via streptavidin-coated magnetic beads. Importantly, after clicking and coupling to beads the modification becomes sterically demanding and stalls reverse transcriptases, leading to termination adjacent to the MTase target site. Using radioactively labeled primers in the reverse transcription, the modified position can be precisely identified on a sequencing gel via phosphor imaging.
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Affiliation(s)
- Nadine A Kueck
- Department of Chemistry, Institute of Biochemistry, University of Münster, Münster, Germany
| | - Anna Ovcharenko
- Department of Chemistry, Institute of Biochemistry, University of Münster, Münster, Germany
| | - Katja Hartstock
- Department of Chemistry, Institute of Biochemistry, University of Münster, Münster, Germany
| | - Nicolas V Cornelissen
- Department of Chemistry, Institute of Biochemistry, University of Münster, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster, Münster, Germany; Cells in Motion Interfaculty Center, University of Münster, Münster, Germany.
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van Dülmen M, Muthmann N, Rentmeister A. Chemo-Enzymatic Modification of the 5' Cap Maintains Translation and Increases Immunogenic Properties of mRNA. Angew Chem Int Ed Engl 2021; 60:13280-13286. [PMID: 33751748 PMCID: PMC8250829 DOI: 10.1002/anie.202100352] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 01/08/2021] [Indexed: 12/19/2022]
Abstract
Eukaryotic mRNAs are emerging modalities for protein replacement therapy and vaccination. Their 5' cap is important for mRNA translation and immune response and can be naturally methylated at different positions by S-adenosyl-l-methionine (AdoMet)-dependent methyltransferases (MTases). We report on the cosubstrate scope of the MTase CAPAM responsible for methylation at the N6 -position of adenosine start nucleotides using synthetic AdoMet analogs. The chemo-enzymatic propargylation enabled production of site-specifically modified reporter-mRNAs. These cap-propargylated mRNAs were efficiently translated and showed ≈3-fold increased immune response in human cells. The same effects were observed when the receptor binding domain (RBD) of SARS-CoV-2-a currently tested epitope for mRNA vaccination-was used. Site-specific chemo-enzymatic modification of eukaryotic mRNA may thus be a suitable strategy to modulate translation and immune response of mRNAs for future therapeutic applications.
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Affiliation(s)
- Melissa van Dülmen
- Department of Chemistry and PharmacyInstitute of BiochemistryCorrensstrasse 3648149MünsterGermany
| | - Nils Muthmann
- Department of Chemistry and PharmacyInstitute of BiochemistryCorrensstrasse 3648149MünsterGermany
| | - Andrea Rentmeister
- Department of Chemistry and PharmacyInstitute of BiochemistryCorrensstrasse 3648149MünsterGermany
- Cells in Motion Interfaculty CenterUniversity of MünsterGermany
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29
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Dülmen M, Muthmann N, Rentmeister A. Eine chemo‐enzymatische Modifizierung der 5′‐Kappe erhält die Translation und erhöht die Immunogenität der mRNA. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Melissa Dülmen
- Fachbereich Chemie und Pharmazie Institut für Biochemie Corrensstrasse 36 48149 Münster Deutschland
| | - Nils Muthmann
- Fachbereich Chemie und Pharmazie Institut für Biochemie Corrensstrasse 36 48149 Münster Deutschland
| | - Andrea Rentmeister
- Fachbereich Chemie und Pharmazie Institut für Biochemie Corrensstrasse 36 48149 Münster Deutschland
- Cells in Motion Interfaculty Center Westfälische Wilhelms-Universität Münster Deutschland
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30
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Mattay J, Dittmar M, Rentmeister A. Chemoenzymatic strategies for RNA modification and labeling. Curr Opin Chem Biol 2021; 63:46-56. [PMID: 33690011 DOI: 10.1016/j.cbpa.2021.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/20/2021] [Accepted: 01/31/2021] [Indexed: 12/17/2022]
Abstract
RNA is a central molecule in numerous cellular processes, including transcription, translation, and regulation of gene expression. To reveal the numerous facets of RNA function and metabolism in cells, labeling has become indispensable and enables the visualization, isolation, characterization, and even quantification of certain RNA species. In this review, we will cover chemoenzymatic approaches for covalent RNA labeling. These approaches rely on an enzymatic step to introduce an RNA modification before conjugation with a label for detection or isolation. We start with in vitro manipulation of RNA, sorted according to the enzymatic reaction exploited. Then, metabolic approaches for co- and post-transcriptional RNA labeling will be treated. We focus on recent advances in the field and highlight the most relevant applications for cellular imaging, RNA isolation and sequencing.
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Affiliation(s)
- Johanna Mattay
- Department of Chemistry, Institute of Biochemistry, University of Münster, Correnstr. 36, 48149, Münster, Germany
| | - Maria Dittmar
- Department of Chemistry, Institute of Biochemistry, University of Münster, Correnstr. 36, 48149, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster, Correnstr. 36, 48149, Münster, Germany; Cells in Motion Interfaculty Center, University of Münster, 48149, Münster, Germany.
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31
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Abstract
The mRNA modification N6 -methyladenosine (m6 A) is associated with multiple roles in cell function and disease. The methyltransferases METTL3-METTL14 and METTL16 act as "writers" for different target transcripts and sequence motifs. The modification is perceived by dedicated "reader" and "eraser" proteins, but not by polymerases. We report that METTL3-14 shows remarkable cosubstrate promiscuity, enabling sequence-specific internal labeling of RNA without additional guide RNAs. The transfer of ortho-nitrobenzyl and 6-nitropiperonyl groups allowed enzymatic photocaging of RNA in the consensus motif, which impaired polymerase-catalyzed primer extension in a reversible manner. METTL16 was less promiscuous but suitable for chemo-enzymatic labeling using different types of click chemistry. Since both enzymes act on distinct sequence motifs, their combination allowed orthogonal chemo-enzymatic modification of different sites in a single RNA.
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Affiliation(s)
- Anna Ovcharenko
- Department of ChemistryInstitute of BiochemistryUniversity of Münster, Corrensstrasse 3648149MünsterGermany
- Cells in Motion Interfaculty CenterUniversity of MünsterWaldeyerstraße 1548149MünsterGermany
| | - Florian P. Weissenboeck
- Department of ChemistryInstitute of BiochemistryUniversity of Münster, Corrensstrasse 3648149MünsterGermany
- Cells in Motion Interfaculty CenterUniversity of MünsterWaldeyerstraße 1548149MünsterGermany
| | - Andrea Rentmeister
- Department of ChemistryInstitute of BiochemistryUniversity of Münster, Corrensstrasse 3648149MünsterGermany
- Cells in Motion Interfaculty CenterUniversity of MünsterWaldeyerstraße 1548149MünsterGermany
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32
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Abstract
Gene expression is tightly regulated in all domains of life, with post-transcriptional regulation being more pronounced in higher eukaryotes. Optochemical and optogenetic approaches enable the actuation of many underlying processes by light, which is an excellent tool to exert spatio-temporal control. However, light-mediated control of eukaryotic mRNA processing and the respective enzymes has not been reported. We used genetic code expansion to install a photo-caged tyrosine (Y) in the active site of the cap methyltransferase Ecm1. This enzyme is responsible for guanine N7 methylation of the 5′ cap, which is required for translation. Substituting Y284 with the photocaged ortho-nitrobenzyl-tyrosine (ONBY) almost completely abrogated the methylation activity of Ecm1. Irradiation with light removed the ONB group, restoring the native tyrosine and Ecm1 activity, yielding up to 97% conversion of the minimal substrate GpppA within 60 min after activation. Using luciferase- and eGFP-mRNAs as reporters, we could show that light actuates translation by inducing activation of Ecm1 ONBY284 in a eukaryotic in vitro translation system. A tyrosine in the active site of the 5′ cap methyltransferase Ecm1 was photocaged. Translation of mRNA could be triggered by light in eukaryotic cell lysate.![]()
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Affiliation(s)
- Dennis Reichert
- Department of Chemistry, Institute of Biochemistry, University of Münster Correnstr. 36 48149 Münster Germany .,Cells in Motion Interfaculty Center, University of Münster 48149 Münster Germany
| | - Henning D Mootz
- Department of Chemistry, Institute of Biochemistry, University of Münster Correnstr. 36 48149 Münster Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster Correnstr. 36 48149 Münster Germany .,Cells in Motion Interfaculty Center, University of Münster 48149 Münster Germany
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33
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Michailidou F, Rentmeister A. Harnessing methylation and AdoMet-utilising enzymes for selective modification in cascade reactions. Org Biomol Chem 2021; 19:3756-3762. [PMID: 33949607 DOI: 10.1039/d1ob00354b] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Enzyme-mediated methylation is a very important reaction in nature, yielding a wide range of modified natural products, diversifying small molecules and fine-tuning the activity of biomacromolecules. The field has attracted much attention over the recent years and interesting applications of the dedicated enzymes in biocatalysis and biomolecular labelling have emerged. In this review article, we summarise the concepts and recent advances in developing (chemo)-enzymatic cascades for selective methylation, alkylation and photocaging as tools to study biological methylation and as biotransformations to generate site-specifically alkylated products.
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Affiliation(s)
- Freideriki Michailidou
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 481\49 Münster, Germany.
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 481\49 Münster, Germany.
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34
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Affiliation(s)
- Anna Ovcharenko
- Department of Chemistry Institute of Biochemistry University of Münster, Corrensstrasse 36 48149 Münster Germany
- Cells in Motion Interfaculty Center University of Münster Waldeyerstraße 15 48149 Münster Germany
| | - Florian P. Weissenboeck
- Department of Chemistry Institute of Biochemistry University of Münster, Corrensstrasse 36 48149 Münster Germany
- Cells in Motion Interfaculty Center University of Münster Waldeyerstraße 15 48149 Münster Germany
| | - Andrea Rentmeister
- Department of Chemistry Institute of Biochemistry University of Münster, Corrensstrasse 36 48149 Münster Germany
- Cells in Motion Interfaculty Center University of Münster Waldeyerstraße 15 48149 Münster Germany
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35
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Michailidou F, Klöcker N, Cornelissen NV, Singh RK, Peters A, Ovcharenko A, Kümmel D, Rentmeister A. Cover Picture: Engineered SAM Synthetases for Enzymatic Generation of AdoMet Analogs with Photocaging Groups and Reversible DNA Modification in Cascade Reactions (Angew. Chem. Int. Ed. 1/2021). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/anie.202015604] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Freideriki Michailidou
- Department of Chemistry Institute of Biochemistry University of Münster Corrensstr. 36 48149 Münster Germany
- Current address: ETH Zürich Department of Chemistry and Applied Biosciences Laboratory of Organic Chemistry Vladimir-Prelog-Weg 1–5/10 8093 Zürich Switzerland
| | - Nils Klöcker
- Department of Chemistry Institute of Biochemistry University of Münster Corrensstr. 36 48149 Münster Germany
| | - Nicolas V. Cornelissen
- Department of Chemistry Institute of Biochemistry University of Münster Corrensstr. 36 48149 Münster Germany
| | - Rohit K. Singh
- Department of Chemistry Institute of Biochemistry University of Münster Corrensstr. 36 48149 Münster Germany
| | - Aileen Peters
- Department of Chemistry Institute of Biochemistry University of Münster Corrensstr. 36 48149 Münster Germany
| | - Anna Ovcharenko
- Department of Chemistry Institute of Biochemistry University of Münster Corrensstr. 36 48149 Münster Germany
| | - Daniel Kümmel
- Department of Chemistry Institute of Biochemistry University of Münster Corrensstr. 36 48149 Münster Germany
| | - Andrea Rentmeister
- Department of Chemistry Institute of Biochemistry University of Münster Corrensstr. 36 48149 Münster Germany
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36
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Michailidou F, Klöcker N, Cornelissen NV, Singh RK, Peters A, Ovcharenko A, Kümmel D, Rentmeister A. Titelbild: Maßgeschneiderte SAM‐Synthetasen zur enzymatischen Herstellung von AdoMet‐Analoga mit Photoschutzgruppen und zur reversiblen DNA‐Modifizierung in Kaskadenreaktionen (Angew. Chem. 1/2021). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202015604] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Freideriki Michailidou
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
- Derzeitige Adresse: ETH Zürich Fachbereich Chemie und angewandte Biowissenschaften Laboratorium für Organische Chemie Vladimir-Prelog-Weg 1–5/10 8093 Zürich Schweiz
| | - Nils Klöcker
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Nicolas V. Cornelissen
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Rohit K. Singh
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Aileen Peters
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Anna Ovcharenko
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Daniel Kümmel
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Andrea Rentmeister
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
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Abstract
Labeling of nucleic acids is required for many studies aiming to elucidate their functions and dynamics in vitro and in cells. Out of the numerous labeling concepts that have been devised, covalent labeling provides the most stable linkage, an unrivaled choice of small and highly fluorescent labels and - thanks to recent advances in click chemistry - an incredible versatility. Depending on the approach, site-, sequence- and cell-specificity can be achieved. DNA and RNA labeling are rapidly developing fields that bring together multiple areas of research: on the one hand, synthetic and biophysical chemists develop new fluorescent labels and isomorphic nucleobases as well as faster and more selective bioorthogonal reactions. On the other hand, the number of enzymes that can be harnessed for post-synthetic and site-specific labeling of nucleic acids has increased significantly. Together with protein engineering and genetic manipulation of cells, intracellular and cell-specific labeling has become possible. In this review, we provide a structured overview of covalent labeling approaches for nucleic acids and highlight notable developments, in particular recent examples. The majority of this review will focus on fluorescent labeling; however, the principles can often be readily applied to other labels. We will start with entirely chemical approaches, followed by chemo-enzymatic strategies and ribozymes, and finish with metabolic labeling of nucleic acids. Each section is subdivided into direct (or one-step) and two-step labeling approaches and will start with DNA before treating RNA.
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Affiliation(s)
- Nils Klöcker
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, D-48149 Münster, Germany.
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38
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Michailidou F, Klöcker N, Cornelissen NV, Singh RK, Peters A, Ovcharenko A, Kümmel D, Rentmeister A. Maßgeschneiderte SAM‐Synthetasen zur enzymatischen Herstellung von AdoMet‐Analoga mit Photoschutzgruppen und zur reversiblen DNA‐Modifizierung in Kaskadenreaktionen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202012623] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Freideriki Michailidou
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
- Derzeitige Adresse: ETH Zürich Fachbereich Chemie und angewandte Biowissenschaften Laboratorium für Organische Chemie Vladimir-Prelog-Weg 1–5/10 8093 Zürich Schweiz
| | - Nils Klöcker
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Nicolas V. Cornelissen
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Rohit K. Singh
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Aileen Peters
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Anna Ovcharenko
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Daniel Kümmel
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Andrea Rentmeister
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
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39
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Michailidou F, Klöcker N, Cornelissen NV, Singh RK, Peters A, Ovcharenko A, Kümmel D, Rentmeister A. Engineered SAM Synthetases for Enzymatic Generation of AdoMet Analogs with Photocaging Groups and Reversible DNA Modification in Cascade Reactions. Angew Chem Int Ed Engl 2020; 60:480-485. [PMID: 33017502 PMCID: PMC7839696 DOI: 10.1002/anie.202012623] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 09/17/2020] [Indexed: 12/17/2022]
Abstract
Methylation and demethylation of DNA, RNA and proteins has emerged as a major regulatory mechanism. Studying the function of these modifications would benefit from tools for their site‐specific inhibition and timed removal. S‐Adenosyl‐L‐methionine (AdoMet) analogs in combination with methyltransferases (MTases) have proven useful to map or block and release MTase target sites, however their enzymatic generation has been limited to aliphatic groups at the sulfur atom. We engineered a SAM synthetase from Cryptosporidium hominis (PC‐ChMAT) for efficient generation of AdoMet analogs with photocaging groups that are not accepted by any WT MAT reported to date. The crystal structure of PC‐ChMAT at 1.87 Å revealed how the photocaged AdoMet analog is accommodated and guided engineering of a thermostable MAT from Methanocaldococcus jannaschii. PC‐MATs were compatible with DNA‐ and RNA‐MTases, enabling sequence‐specific modification (“writing”) of plasmid DNA and light‐triggered removal (“erasing”).
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Affiliation(s)
- Freideriki Michailidou
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany.,Current address: ETH Zürich, Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Nils Klöcker
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Nicolas V Cornelissen
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Rohit K Singh
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Aileen Peters
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Anna Ovcharenko
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Daniel Kümmel
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
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41
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Abstract
Melanoma is a life-threatening disease caused by mutations in pigment-producing cells. Numerous treatments for melanoma have been approved in the past several decades; however, they often cause severe side effects and in most cases do not result in a complete cure. mRNA (messenger RNA) as a therapeutic agent provides a new avenue for melanoma treatment and several advantages over conventional treatments. The first mRNA drugs for melanoma treatment are currently in clinical trials, and approval of mRNA drugs by the Food and Drug Administration seems to be within reach. This new class of drugs can be readily adapted to other diseases, raising the hope of providing a new therapeutic option for various diseases.
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Affiliation(s)
- Melissa van Dülmen
- Department of Chemistry and Pharmacy, Institute for Biochemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149 Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry and Pharmacy, Institute for Biochemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149 Münster, Germany.,Cells in Motion Interfaculty Center, Waldeyerstraße 15, 48149 Münster, Germany
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42
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Westerich KJ, Chandrasekaran KS, Gross-Thebing T, Kueck N, Raz E, Rentmeister A. Bioorthogonal mRNA labeling at the poly(A) tail for imaging localization and dynamics in live zebrafish embryos. Chem Sci 2020; 11:3089-3095. [PMID: 33623655 PMCID: PMC7879197 DOI: 10.1039/c9sc05981d] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 11/26/2019] [Accepted: 02/21/2020] [Indexed: 12/14/2022] Open
Abstract
Live imaging of mRNA in cells and organisms is important for understanding the dynamic aspects underlying its function.
Live imaging of mRNA in cells and organisms is important for understanding the dynamic aspects underlying its function. Ideally, labeling of mRNA should not alter its structure or function, nor affect the biological system. However, most methods applied in vivo make use of genetically encoded tags and reporters that significantly enhance the size of the mRNA of interest. Alternately, we utilize the 3′ poly(A) tail as a non-coding repetitive hallmark to covalently label mRNAs via bioorthogonal chemistry with different fluorophores from a wide range of spectra without significantly changing the size. We demonstrate that the labeled mRNAs can be visualized in cells and zebrafish embryos, and that they are efficiently translated. Importantly, the labeled mRNAs acquired the proper subcellular localization in developing zebrafish embryos and their dynamics could be tracked in vivo.
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Affiliation(s)
- Kim J Westerich
- Institute of Cell Biology Center for Molecular Biology of Inflammation , University of Münster , D-48149 Münster , Germany .
| | - Karthik S Chandrasekaran
- Institut für Biochemie , Westfälische Wilhelms-Universität Münster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - Theresa Gross-Thebing
- Institute of Cell Biology Center for Molecular Biology of Inflammation , University of Münster , D-48149 Münster , Germany .
| | - Nadine Kueck
- Institut für Biochemie , Westfälische Wilhelms-Universität Münster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - Erez Raz
- Cells in Motion Interfaculty Centre (CiMIC) , Waldeyerstraße 15 , D-48149 Münster , Germany.,Institute of Cell Biology Center for Molecular Biology of Inflammation , University of Münster , D-48149 Münster , Germany .
| | - Andrea Rentmeister
- Cells in Motion Interfaculty Centre (CiMIC) , Waldeyerstraße 15 , D-48149 Münster , Germany.,Institut für Biochemie , Westfälische Wilhelms-Universität Münster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
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43
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Cornelissen NV, Michailidou F, Muttach F, Rau K, Rentmeister A. Nucleoside-modified AdoMet analogues for differential methyltransferase targeting. Chem Commun (Camb) 2020; 56:2115-2118. [PMID: 31970375 PMCID: PMC7030947 DOI: 10.1039/c9cc07807j] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 12/27/2022]
Abstract
Methyltransferases (MTases) modify a wide range of biomolecules using S-adenosyl-l-methionine (AdoMet) as the cosubstrate. Synthetic AdoMet analogues are powerful tools to site-specifically introduce a variety of functional groups and exhibit potential to be converted only by distinct MTases. Extending the size of the substituent at the sulfur/selenium atom provides selectivity among MTases but is insufficient to discriminate between promiscuous MTases. We present a panel of AdoMet analogues differing in the nucleoside moiety (NM-AdoMets). These NM-AdoMets were efficiently produced by a previously uncharacterized methionine adenosyltransferase (MAT) from methionine and ATP analogues, such as ITP and N6-propargyl-ATP. The N6-modification changed the relative activity of three representative MTases up to 13-fold resulting in discrimination of substrates for the methyl transfer and could also be combined with transfer of allyl and propargyl groups.
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Affiliation(s)
- Nicolas V Cornelissen
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
| | - Freideriki Michailidou
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
| | - Fabian Muttach
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
| | - Kristina Rau
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
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44
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Anhäuser L, Klöcker N, Muttach F, Mäsing F, Špaček P, Studer A, Rentmeister A. A Benzophenone-Based Photocaging Strategy for the N7 Position of Guanosine. Angew Chem Int Ed Engl 2020; 59:3161-3165. [PMID: 31747109 PMCID: PMC7012642 DOI: 10.1002/anie.201914573] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [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: 11/14/2019] [Indexed: 12/11/2022]
Abstract
Selective modification of nucleobases with photolabile caging groups enables the study and control of processes and interactions of nucleic acids. Numerous positions on nucleobases have been targeted, but all involve formal substitution of a hydrogen atom with a photocaging group. Nature, however, also uses ring-nitrogen methylation, such as m7 G and m1 A, to change the electronic structure and properties of RNA and control biomolecular interactions essential for translation and turnover. We report that aryl ketones such as benzophenone and α-hydroxyalkyl ketone are photolabile caging groups if installed at the N7 position of guanosine or the N1 position of adenosine. Common photocaging groups derived from the ortho-nitrobenzyl moiety were not suitable. Both chemical and enzymatic methods for site-specific modification of N7G in nucleosides, dinucleotides, and RNA were developed, thereby opening the door to studying the molecular interactions of m7 G and m1 A with spatiotemporal control.
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Affiliation(s)
- Lea Anhäuser
- Institut für BiochemieWestfälische Wilhelms-Universität MünsterWilhelm-Klemm-Str. 248149MünsterGermany
| | - Nils Klöcker
- Institut für BiochemieWestfälische Wilhelms-Universität MünsterWilhelm-Klemm-Str. 248149MünsterGermany
| | - Fabian Muttach
- Institut für BiochemieWestfälische Wilhelms-Universität MünsterWilhelm-Klemm-Str. 248149MünsterGermany
| | - Florian Mäsing
- Organisch-Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstrasse 4048149MünsterGermany
| | - Petr Špaček
- Institut für BiochemieWestfälische Wilhelms-Universität MünsterWilhelm-Klemm-Str. 248149MünsterGermany
| | - Armido Studer
- Organisch-Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstrasse 4048149MünsterGermany
| | - Andrea Rentmeister
- Institut für BiochemieWestfälische Wilhelms-Universität MünsterWilhelm-Klemm-Str. 248149MünsterGermany
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Kurmayer R, Entfellner E, Weisse T, Offterdinger M, Rentmeister A, Deng L. Chemically labeled toxins or bioactive peptides show a heterogeneous intracellular distribution and low spatial overlap with autofluorescence in bloom-forming cyanobacteria. Sci Rep 2020; 10:2781. [PMID: 32066776 PMCID: PMC7026079 DOI: 10.1038/s41598-020-59381-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 01/21/2020] [Indexed: 11/08/2022] Open
Abstract
Harmful algal blooms formed by colony-forming cyanobacteria deteriorate water resources by producing cyanotoxins, which frequently occur at high intracellular concentrations. We aimed to localize toxic microcystins (MCs) and bioactive anabaenopeptins (APs) at the subcellular level under noninvasive conditions. Since both metabolites are synthesized nonribosomally, the relaxed specificity of key enzymes catalyzing substrate activation allowed chemical labeling through a standard copper-catalyzed click chemistry reaction. The genera Planktothrix and Microcystis specifically incorporated unnatural amino acids such as N-propargyloxy-carbonyl-L-lysine or O-propargyl-L-tyrosine, resulting in modified AP or MC peptides carrying the incorporated alkyne moiety. The labeled cells were quantitatively differentiated from the unlabeled control cells. MCs and APs occurred intracellularly as distinct entities showing a cell-wide distribution but a lowered spatial overlap with natural autofluorescence. Using the immunofluorescence technique, colocalization with markers of individual organelles was utilized to relate the distribution of labeled MCs to cellular compartments, e.g., using RbcL and FtsZ (cytosol) and PsbA (thylakoids). The colocalization correlation coefficients calculated pairwise between organelles and autofluorescence were highly positive as opposed to the relatively low positive indices derived from labeled MCs. The lower correlation coefficients imply that only a portion of the labeled MC molecules were related spatially to the organelles in the cell.
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Affiliation(s)
- Rainer Kurmayer
- University of Innsbruck, Research Department for Limnology, Mondseestrasse 9, 5310, Mondsee, Austria.
| | - Elisabeth Entfellner
- University of Innsbruck, Research Department for Limnology, Mondseestrasse 9, 5310, Mondsee, Austria
| | - Thomas Weisse
- University of Innsbruck, Research Department for Limnology, Mondseestrasse 9, 5310, Mondsee, Austria
| | - Martin Offterdinger
- Innsbruck Medical University, Division of Neurobiochemistry, Biooptics Core Facility, Innrain 80, 6020, Innsbruck, Austria
| | - Andrea Rentmeister
- University of Muenster, Department of Chemistry, Institute of Biochemistry, Wilhelm-Klemm-Strasse 2, 48149, Muenster, Germany
| | - Li Deng
- Helmholtz Centre Munich, Institute of Virology, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
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46
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Anhäuser L, Klöcker N, Muttach F, Mäsing F, Špaček P, Studer A, Rentmeister A. Eine auf dem Benzophenongerüst basierende Strategie für die Photoschützung der N7‐Position des Guanosins. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201914573] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Lea Anhäuser
- Institut für Biochemie Westfälische Wilhelms-Universität Münster Wilhelm-Klemm-Str. 2 48149 Münster Deutschland
| | - Nils Klöcker
- Institut für Biochemie Westfälische Wilhelms-Universität Münster Wilhelm-Klemm-Str. 2 48149 Münster Deutschland
| | - Fabian Muttach
- Institut für Biochemie Westfälische Wilhelms-Universität Münster Wilhelm-Klemm-Str. 2 48149 Münster Deutschland
| | - Florian Mäsing
- Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstrasse 40 48149 Münster Deutschland
| | - Petr Špaček
- Institut für Biochemie Westfälische Wilhelms-Universität Münster Wilhelm-Klemm-Str. 2 48149 Münster Deutschland
| | - Armido Studer
- Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstrasse 40 48149 Münster Deutschland
| | - Andrea Rentmeister
- Institut für Biochemie Westfälische Wilhelms-Universität Münster Wilhelm-Klemm-Str. 2 48149 Münster Deutschland
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47
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Abstract
Eukaryotic mRNAs possess 5′ caps that are determinants for their function. A structural characteristic of 5′ caps is methylation, with this feature already present in early eukaryotes such as Trypanosoma. While the common cap‐0 (m7GpppN) shows a rather simple methylation pattern, the Trypanosoma cap‐4 displays seven distinguished additional methylations within the first four nucleotides. The study of essential biological functions mediated by these unique structural features of the cap‐4 and thereby of the metabolism of an important class of human pathogenic parasites is hindered by the lack of reliable preparation methods. Herein we describe the synthesis of custom‐made nucleoside phosphoramidite building blocks for m62Am and m3Um, their incorporation into short RNAs, the efficient construction of the 5′‐to‐5′ triphosphate bridge to guanosine by using a solid‐phase approach, the selective enzymatic methylation at position N7 of the inverted guanosine, and enzymatic ligation to generate trypanosomatid mRNAs of up to 40 nucleotides in length. This study introduces a reliable synthetic strategy to the much‐needed cap‐4 RNA probes for integrated structural biology studies, using a combination of chemical and enzymatic steps.
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Affiliation(s)
- Josef Leiter
- University of Innsbruck, Institute of Organic Chemistry and Center for Molecular Biosciences, Innrain 80-82, 6020, Innsbruck, Austria
| | - Dennis Reichert
- University of Münster, Department of Chemistry, Institute of Biochemistry, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany
| | - Andrea Rentmeister
- University of Münster, Department of Chemistry, Institute of Biochemistry, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany
| | - Ronald Micura
- University of Innsbruck, Institute of Organic Chemistry and Center for Molecular Biosciences, Innrain 80-82, 6020, Innsbruck, Austria
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Anhäuser L, Hüwel S, Zobel T, Rentmeister A. Multiple covalent fluorescence labeling of eukaryotic mRNA at the poly(A) tail enhances translation and can be performed in living cells. Nucleic Acids Res 2019; 47:e42. [PMID: 30726958 PMCID: PMC6468298 DOI: 10.1093/nar/gkz084] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 01/24/2019] [Accepted: 01/31/2019] [Indexed: 12/22/2022] Open
Abstract
Post-transcriptional regulation of gene expression occurs by multiple mechanisms, including subcellular localization of mRNA and alteration of the poly(A) tail length. These mechanisms play crucial roles in the dynamics of cell polarization and embryonic development. Furthermore, mRNAs are emerging therapeutics and chemical alterations to increase their translational efficiency are highly sought after. We show that yeast poly(A) polymerase can be used to install multiple azido-modified adenosine nucleotides to luciferase and eGFP-mRNAs. These mRNAs can be efficiently reacted in a bioorthogonal click reaction with fluorescent reporters without degradation and without sequence alterations in their coding or untranslated regions. Importantly, the modifications in the poly(A) tail impact positively on the translational efficiency of reporter-mRNAs in vitro and in cells. Therefore, covalent fluorescent labeling at the poly(A) tail presents a new way to increase the amount of reporter protein from exogenous mRNA and to label genetically unaltered and translationally active mRNAs.
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Affiliation(s)
- Lea Anhäuser
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149 Münster, Germany
| | - Sabine Hüwel
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149 Münster, Germany
| | - Thomas Zobel
- Cells-in-Motion Cluster of Excellence (EXC1003-CiM), University of Münster, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149 Münster, Germany.,Cells-in-Motion Cluster of Excellence (EXC1003-CiM), University of Münster, Germany
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49
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Abstract
N6-methyladenosine (m6A) is the most common internal modification in eukaryotic mRNA and associated with numerous cellular processes in health and disease. Up- and down-regulation of its "writer" or "eraser" proteins alter the global m6A level; however, modifying distinct m6A sites has remained elusive. We genetically fused the dioxygenase FTO responsible for m6A demethylation to RCas9 as an RNA-targeting module. The resulting RCas9-FTO retained demethylation activity and bound to RNA in a sequence-specific manner depending on the sgRNA and PAMmer. Using SCARLET analysis, we quantified the m6A level at a specific site and analyzed the effect of the PAM-to-m6A distance on activity. Sequence-specific demethylation by RCas9-FTO was tested on different RNA combinations and showed up to 15-fold sequence preference for target RNA compared to off-target RNA. Taken together, RCas9-FTO represents a new tool for sequence-specific demethylation of m6A in RNA that can be readily adapted to any given RNA sequence and opens the door to studying the function of distinct m6A sites.
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Affiliation(s)
- Kristina Rau
- Institute of Biochemistry, Department of Chemistry, University of Münster, 48149 Münster, Germany
| | - Lukas Rösner
- Institute of Biochemistry, Department of Chemistry, University of Münster, 48149 Münster, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, Department of Chemistry, University of Münster, 48149 Münster, Germany
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50
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Muthmann N, Hartstock K, Rentmeister A. Chemo-enzymatic treatment of RNA to facilitate analyses. Wiley Interdiscip Rev RNA 2019; 11:e1561. [PMID: 31392842 DOI: 10.1002/wrna.1561] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/17/2019] [Accepted: 07/04/2019] [Indexed: 12/11/2022]
Abstract
Labeling RNA is a recurring problem to make RNA compatible with state-of-the-art methodology and comes in many flavors. Considering only cellular applications, the spectrum still ranges from site-specific labeling of individual transcripts, for example, for live-cell imaging of mRNA trafficking, to metabolic labeling in combination with next generation sequencing to capture dynamic aspects of RNA metabolism on a transcriptome-wide scale. Combining the specificity of RNA-modifying enzymes with non-natural substrates has emerged as a valuable strategy to modify RNA site- or sequence-specifically with functional groups suitable for subsequent bioorthogonal reactions and thus label RNA with reporter moieties such as affinity or fluorescent tags. In this review article, we will cover chemo-enzymatic approaches (a) for in vitro labeling of RNA for application in cells, (b) for treatment of total RNA, and (c) for metabolic labeling of RNA. This article is categorized under: RNA Processing < RNA Editing and Modification RNA Methods < RNA Analyses in vitro and In Silico RNA Methods < RNA Analyses in Cells.
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Affiliation(s)
- Nils Muthmann
- Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Katja Hartstock
- Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
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