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Benoni B, Potužník J, Škríba A, Benoni R, Trylcova J, Tulpa M, Spustová K, Grab K, Mititelu MB, Pačes J, Weber J, Stanek D, Kowalska J, Bednarova L, Keckesova Z, Vopalensky P, Gahurova L, Cahova H. HIV-1 Infection Reduces NAD Capping of Host Cell snRNA and snoRNA. ACS Chem Biol 2024; 19:1243-1249. [PMID: 38747804 PMCID: PMC11197007 DOI: 10.1021/acschembio.4c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 06/22/2024]
Abstract
Nicotinamide adenine dinucleotide (NAD) is a critical component of the cellular metabolism and also serves as an alternative 5' cap on various RNAs. However, the function of the NAD RNA cap is still under investigation. We studied NAD capping of RNAs in HIV-1-infected cells because HIV-1 is responsible for the depletion of the NAD/NADH cellular pool and causing intracellular pellagra. By applying the NAD captureSeq protocol to HIV-1-infected and uninfected cells, we revealed that four snRNAs (e.g., U1) and four snoRNAs lost their NAD cap when infected with HIV-1. Here, we provide evidence that the presence of the NAD cap decreases the stability of the U1/HIV-1 pre-mRNA duplex. Additionally, we demonstrate that reducing the quantity of NAD-capped RNA by overexpressing the NAD RNA decapping enzyme DXO results in an increase in HIV-1 infectivity. This suggests that NAD capping is unfavorable for HIV-1 and plays a role in its infectivity.
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Affiliation(s)
- Barbora Benoni
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
- First
Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague, Czechia
| | - Jiří
František Potužník
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
- Faculty
of Science, Department of Cell Biology, Charles University, Viničná 7, 121 08 Prague 2, Czechia
| | - Anton Škríba
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
| | - Roberto Benoni
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
| | - Jana Trylcova
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
| | - Matouš Tulpa
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
- Faculty
of Science, Department of Physical and Macromolecular Chemistry, Charles University, Hlavova 8, 121 08 Prague 2, Czechia
| | - Kristína Spustová
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
| | - Katarzyna Grab
- Division
of Biophysics, Faculty of Physics, University
of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Maria-Bianca Mititelu
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
- Faculty
of Science, Department of Cell Biology, Charles University, Viničná 7, 121 08 Prague 2, Czechia
| | - Jan Pačes
- Institute
of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czechia
| | - Jan Weber
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
| | - David Stanek
- Institute
of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czechia
| | - Joanna Kowalska
- Division
of Biophysics, Faculty of Physics, University
of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Lucie Bednarova
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
| | - Zuzana Keckesova
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
| | - Pavel Vopalensky
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
| | - Lenka Gahurova
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
- Department
of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czechia
| | - Hana Cahova
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
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František Potužník J, Nešuta O, Škríba A, Voleníková B, Mititelu MB, Mancini F, Serianni V, Fernandez H, Spustová K, Trylčová J, Vopalensky P, Cahová H. Diadenosine Tetraphosphate (Ap 4 A) Serves as a 5' RNA Cap in Mammalian Cells. Angew Chem Int Ed Engl 2024; 63:e202314951. [PMID: 37934413 DOI: 10.1002/anie.202314951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/08/2023]
Abstract
The recent expansion of the field of RNA chemical modifications has changed our understanding of post-transcriptional gene regulation. Apart from internal nucleobase modifications, 7-methylguanosine was long thought to be the only eukaryotic RNA cap. However, the discovery of non-canonical RNA caps in eukaryotes revealed a new niche of previously undetected RNA chemical modifications. We are the first to report the existence of a new non-canonical RNA cap, diadenosine tetraphosphate (Ap4 A), in human and rat cell lines. Ap4 A is the most abundant dinucleoside polyphosphate in eukaryotic cells and can be incorporated into RNA by RNA polymerases as a non-canonical initiating nucleotide (NCIN). Using liquid chromatography-mass spectrometry (LC-MS), we show that the amount of capped Ap4 A-RNA is independent of the cellular concentration of Ap4 A. A decapping enzyme screen identifies two enzymes cleaving Ap4 A-RNA,NUDT2 and DXO, both of which also cleave other substrate RNAs in vitro. We further assess the translatability and immunogenicity of Ap4 A-RNA and show that although it is not translated, Ap4 A-RNA is recognized as self by the cell and does not elicit an immune response, making it a natural component of the transcriptome. Our findings open a previously unexplored area of eukaryotic RNA regulation.
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Affiliation(s)
- Jiří František Potužník
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 2, Czechia
| | - Ondřej Nešuta
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Anton Škríba
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Barbora Voleníková
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Maria-Bianca Mititelu
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 2, Czechia
| | - Flaminia Mancini
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 2, Czechia
| | - Valentina Serianni
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 2, Czechia
| | - Henri Fernandez
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Kristína Spustová
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Jana Trylčová
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Pavel Vopalensky
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Hana Cahová
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
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Potužník JF, Cahova H. If the 5' cap fits (wear it) - Non-canonical RNA capping. RNA Biol 2024; 21:1-13. [PMID: 39007883 PMCID: PMC11253889 DOI: 10.1080/15476286.2024.2372138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024] Open
Abstract
RNA capping is a prominent RNA modification that influences RNA stability, metabolism, and function. While it was long limited to the study of the most abundant eukaryotic canonical m7G cap, the field recently went through a large paradigm shift with the discovery of non-canonical RNA capping in bacteria and ultimately all domains of life. The repertoire of non-canonical caps has expanded to encompass metabolite caps, including NAD, FAD, CoA, UDP-Glucose, and ADP-ribose, alongside alarmone dinucleoside polyphosphate caps, and methylated phosphate cap-like structures. This review offers an introduction into the field, presenting a summary of the current knowledge about non-canonical RNA caps. We highlight the often still enigmatic biological roles of the caps together with their processing enzymes, focusing on the most recent discoveries. Furthermore, we present the methods used for the detection and analysis of these non-canonical RNA caps and thus provide an introduction into this dynamic new field.
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Affiliation(s)
- Jiří František Potužník
- Institute of Organic Chemistry and Biochemistry of the CAS, Prague 6, Czechia
- Department of Cell Biology, Charles University, Faculty of Science, Prague 2, Czechia
| | - Hana Cahova
- Institute of Organic Chemistry and Biochemistry of the CAS, Prague 6, Czechia
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Mattay J. Noncanonical metabolite RNA caps: Classification, quantification, (de)capping, and function. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1730. [PMID: 35675554 DOI: 10.1002/wrna.1730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 06/15/2023]
Abstract
The 5' cap of eukaryotic mRNA is a hallmark for cellular functions from mRNA stability to translation. However, the discovery of novel 5'-terminal RNA caps derived from cellular metabolites has challenged this long-standing singularity in both eukaryotes and prokaryotes. Reminiscent of the 7-methylguanosine (m7G) cap structure, these noncanonical caps originate from abundant coenzymes such as NAD, FAD, or CoA and from metabolites like dinucleoside polyphosphates (NpnN). As of now, the significance of noncanonical RNA caps is elusive: they differ for individual transcripts, occur in distinct types of RNA, and change in response to environmental stimuli. A thorough comparison of their prevalence, quantity, and characteristics is indispensable to define the distinct classes of metabolite-capped RNAs. This is achieved by a structured analysis of all present studies covering functional, quantitative, and sequencing data which help to uncover their biological impact. The biosynthetic strategies of noncanonical RNA capping and the elaborate decapping machinery reveal the regulation and turnover of metabolite-capped RNAs. With noncanonical capping being a universal and ancient phenomenon, organisms have developed diverging strategies to adapt metabolite-derived caps to their metabolic needs, but ultimately to establish noncanonical RNA caps as another intriguing layer of RNA regulation. This article is categorized under: RNA Processing > Capping and 5' End Modifications RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Johanna Mattay
- Institute of Biochemistry, University of Münster, Münster, Germany
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Depaix A, Grudzien-Nogalska E, Fedorczyk B, Kiledjian M, Jemielity J, Kowalska J. Preparation of RNAs with non-canonical 5' ends using novel di- and trinucleotide reagents for co-transcriptional capping. Front Mol Biosci 2022; 9:854170. [PMID: 36060251 PMCID: PMC9437278 DOI: 10.3389/fmolb.2022.854170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 07/06/2022] [Indexed: 12/04/2022] Open
Abstract
Many eukaryotic and some bacterial RNAs are modified at the 5' end by the addition of cap structures. In addition to the classic 7-methylguanosine 5' cap in eukaryotic mRNA, several non-canonical caps have recently been identified, including NAD-linked, FAD-linked, and UDP-glucose-linked RNAs. However, studies of the biochemical properties of these caps are impaired by the limited access to in vitro transcribed RNA probes of high quality, as the typical capping efficiencies with NAD or FAD dinucleotides achieved in the presence of T7 polymerase rarely exceed 50%, and pyrimidine derivatives are not incorporated because of promoter sequence limitations. To address this issue, we developed a series of di- and trinucleotide capping reagents and in vitro transcription conditions to provide straightforward access to unconventionally capped RNAs with improved 5'-end homogeneity. We show that because of the transcription start site flexibility of T7 polymerase, R1ppApG-type structures (where R1 is either nicotinamide riboside or riboflavin) are efficiently incorporated into RNA during transcription from dsDNA templates containing both φ 6.5 and φ 2.5 promoters and enable high capping efficiencies (∼90%). Moreover, uridine-initiated RNAs are accessible by transcription from templates containing the φ 6.5 promoter performed in the presence of R2ppUpG-type initiating nucleotides (where R2 is a sugar or phosphate moiety). We successfully employed this strategy to obtain several nucleotide-sugar-capped and uncapped RNAs. The capping reagents developed herein provide easy access to chemical probes to elucidate the biological roles of non-canonical RNA 5' capping.
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Affiliation(s)
- Anaïs Depaix
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Ewa Grudzien-Nogalska
- Department of Cell Biology and Neuroscience, Rutgers University, New York, NJ, United States
| | | | - Megerditch Kiledjian
- Department of Cell Biology and Neuroscience, Rutgers University, New York, NJ, United States
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
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Benoni R, Krafcikova P, Baranowski MR, Kowalska J, Boura E, Cahová H. Substrate Specificity of SARS-CoV-2 Nsp10-Nsp16 Methyltransferase. Viruses 2021; 13:v13091722. [PMID: 34578302 PMCID: PMC8472550 DOI: 10.3390/v13091722] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/20/2021] [Accepted: 08/21/2021] [Indexed: 01/18/2023] Open
Abstract
The ongoing COVID-19 pandemic exemplifies the general need to better understand viral infections. The positive single-strand RNA genome of its causative agent, the SARS coronavirus 2 (SARS-CoV-2), encodes all viral enzymes. In this work, we focused on one particular methyltransferase (MTase), nsp16, which, in complex with nsp10, is capable of methylating the first nucleotide of a capped RNA strand at the 2′-O position. This process is part of a viral capping system and is crucial for viral evasion of the innate immune reaction. In light of recently discovered non-canonical RNA caps, we tested various dinucleoside polyphosphate-capped RNAs as substrates for nsp10-nsp16 MTase. We developed an LC-MS-based method and discovered four types of capped RNA (m7Gp3A(G)- and Gp3A(G)-RNA) that are substrates of the nsp10-nsp16 MTase. Our technique is an alternative to the classical isotope labelling approach for the measurement of 2′-O-MTase activity. Further, we determined the IC50 value of sinefungin to illustrate the use of our approach for inhibitor screening. In the future, this approach may be an alternative technique to the radioactive labelling method for screening inhibitors of any type of 2′-O-MTase.
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Affiliation(s)
- Roberto Benoni
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 16610 Prague, Czech Republic; (R.B.); (P.K.)
| | - Petra Krafcikova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 16610 Prague, Czech Republic; (R.B.); (P.K.)
| | - Marek R. Baranowski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093 Warsaw, Poland; (M.R.B.); (J.K.)
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093 Warsaw, Poland; (M.R.B.); (J.K.)
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 16610 Prague, Czech Republic; (R.B.); (P.K.)
- Correspondence: (E.B.); (H.C.)
| | - Hana Cahová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 16610 Prague, Czech Republic; (R.B.); (P.K.)
- Correspondence: (E.B.); (H.C.)
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Schauerte M, Pozhydaieva N, Höfer K. Shaping the Bacterial Epitranscriptome-5'-Terminal and Internal RNA Modifications. Adv Biol (Weinh) 2021; 5:e2100834. [PMID: 34121369 DOI: 10.1002/adbi.202100834] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/07/2021] [Indexed: 11/11/2022]
Abstract
All domains of life utilize a diverse set of modified ribonucleotides that can impact the sequence, structure, function, stability, and the fate of RNAs, as well as their interactions with other molecules. Today, more than 160 different RNA modifications are known that decorate the RNA at the 5'-terminus or internal RNA positions. The boost of next-generation sequencing technologies sets the foundation to identify and study the functional role of RNA modifications. The recent advances in the field of RNA modifications reveal a novel regulatory layer between RNA modifications and proteins, which is central to developing a novel concept called "epitranscriptomics." The majority of RNA modifications studies focus on the eukaryotic epitranscriptome. In contrast, RNA modifications in prokaryotes are poorly characterized. This review outlines the current knowledge of the prokaryotic epitranscriptome focusing on mRNA modifications. Here, it is described that several internal and 5'-terminal RNA modifications either present or likely present in prokaryotic mRNA. Thereby, the individual techniques to identify these epitranscriptomic modifications, their writers, readers and erasers, and their proposed functions are explored. Besides that, still unanswered questions in the field of prokaryotic epitranscriptomics are pointed out, and its future perspectives in the dawn of next-generation sequencing technologies are outlined.
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Affiliation(s)
- Maik Schauerte
- Max-Planck-Institute for terrestrial Microbiology, Marburg, Hessen, 35043, Germany
| | - Nadiia Pozhydaieva
- Max-Planck-Institute for terrestrial Microbiology, Marburg, Hessen, 35043, Germany
| | - Katharina Höfer
- Max-Planck-Institute for terrestrial Microbiology, Marburg, Hessen, 35043, Germany
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