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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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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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Kim SC, Sekhon SS, Shin WR, Ahn G, Cho BK, Ahn JY, Kim YH. Modifications of mRNA vaccine structural elements for improving mRNA stability and translation efficiency. Mol Cell Toxicol 2021; 18:1-8. [PMID: 34567201 PMCID: PMC8450916 DOI: 10.1007/s13273-021-00171-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [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] [Accepted: 09/13/2021] [Indexed: 01/15/2023]
Abstract
Background mRNA vaccines hold great potential as therapeutic techniques against viral infections due to their efficacy, safety,
and large-scale production. mRNA vaccines offer flexibility in development as any protein can be produced from
mRNA without altering the production or application process. Objective This review highlights the iterative optimization of mRNA vaccine structural elements that impact the type,
specificity, and intensity of immune responses leading to higher translational potency and intracellular stability. Results Modifying the mRNA structural elements particularly the 5′ cap, 5′-and 3′-untranslated regions (UTRs), the coding region, and polyadenylation tail help reduce the excessive mRNA immunogenicity and consistently improve its
intracellular stability and translational efficiency. Conclusion Further studies regarding mRNA-structural elements and their optimization are needed to create new opportunities
for engineering mRNA vaccines.
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Affiliation(s)
- Sun Chang Kim
- Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 South Korea
| | - Simranjeet Singh Sekhon
- School of Biological Sciences, Chungbuk National University, Chungdae-ro, Seowon-gu, Cheongju, 28644 South Korea
| | - Woo-Ri Shin
- School of Biological Sciences, Chungbuk National University, Chungdae-ro, Seowon-gu, Cheongju, 28644 South Korea.,Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk 28644 South Korea
| | - Gna Ahn
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk 28644 South Korea
| | - Byung-Kwan Cho
- Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 South Korea
| | - Ji-Young Ahn
- School of Biological Sciences, Chungbuk National University, Chungdae-ro, Seowon-gu, Cheongju, 28644 South Korea.,Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk 28644 South Korea
| | - Yang-Hoon Kim
- School of Biological Sciences, Chungbuk National University, Chungdae-ro, Seowon-gu, Cheongju, 28644 South Korea.,Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk 28644 South Korea
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Abstract
Methyltransferases that methylate the guanine-N7 position of the mRNA 5' cap structure are ubiquitous among eukaryotes and commonly encoded by viruses. Here we provide a detailed protocol for the biochemical analysis of RNA cap methyltransferase activity of biological samples. This assay involves incubation of cap-methyltransferase-containing samples with a [32P]G-capped RNA substrate and S-adenosylmethionine (SAM) to produce RNAs with N7-methylated caps. The extent of cap methylation is then determined by P1 nuclease digestion, thin-layer chromatography (TLC), and phosphorimaging. The protocol described here includes additional steps for generating the [32P]G-capped RNA substrate and for preparing nuclear and cytoplasmic extracts from mammalian cells. This assay is also applicable to analyzing the cap methyltransferase activity of other biological samples, including recombinant protein preparations and fractions from analytical separations and immunoprecipitation/pulldown experiments.
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Affiliation(s)
- Jackson B Trotman
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA.,Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio, USA.,Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA
| | - Daniel R Schoenberg
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA.,Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio, USA
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Weiss B, Curran JA. CAP(+) selection: A combined chemical-enzymatic strategy for efficient eukaryotic messenger RNA enrichment via the 5' cap. Anal Biochem 2015; 484:72-4. [PMID: 25963893 DOI: 10.1016/j.ab.2015.04.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 04/29/2015] [Accepted: 04/30/2015] [Indexed: 10/23/2022]
Abstract
Eukaryotic messenger RNAs (mRNAs) are generally enriched using oligo(dT) selection. However, a significant fraction of mRNAs contain either short or no poly(A). Our technique permits the isolation of mRNAs via their unique biochemical feature, the 5' cap. It involves RNA extraction, blocking of the 3' ribose cis-diol by cordycepin, oxidation of the 5' cis-diol of the CAP to a dialdehyde, coupling to a biotinylated linker, and enrichment on a streptavidin affinity matrix. We demonstrate that it efficiently pulls out a synthetic capped and non-polyadenylated transcript used to spike total cell RNA as well as endogenous histone 3c mRNA reported to be poly(A) negative.
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Affiliation(s)
- Benjamin Weiss
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Joseph A Curran
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, CH-1211 Geneva, Switzerland; Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, CH-1211 Geneva, Switzerland.
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