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Yilmaz Demirel N, Weber M, Höfer K. Bridging the gap: RNAylation conjugates RNAs to proteins. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119826. [PMID: 39182583 DOI: 10.1016/j.bbamcr.2024.119826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 08/04/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024]
Abstract
In nature, the majority of known RNA-protein interactions are transient. Our recent study has depicted a novel mechanism known as RNAylation, which covalently links proteins and RNAs. This novel modification bridges the realms of RNA and protein modifications. This review specifically explores RNAylation catalyzed by bacteriophage T4 ADP-ribosyltransferase ModB, with a focus on its protein targets and RNA substrates in the context of Escherichia coli-bacteriophage T4 interaction. Additionally, we discuss the biological significance of RNAylation and present perspectives on RNAylation as a versatile bioconjugation strategy for RNAs and proteins.
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Affiliation(s)
- Nurseda Yilmaz Demirel
- Max-Planck-Institute for Terrestrial Microbiology and Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Moritz Weber
- Max-Planck-Institute for Terrestrial Microbiology and Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Katharina Höfer
- Max-Planck-Institute for Terrestrial Microbiology and Center for Synthetic Microbiology, 35043 Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany.
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Wang X, Yu D, Yu J, Hu H, Hang R, Amador Z, Chen Q, Chai J, Chen X. Toll/interleukin-1 receptor (TIR) domain-containing proteins have NAD-RNA decapping activity. Nat Commun 2024; 15:2261. [PMID: 38480720 PMCID: PMC10937652 DOI: 10.1038/s41467-024-46499-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/29/2024] [Indexed: 03/17/2024] Open
Abstract
The occurrence of NAD+ as a non-canonical RNA cap has been demonstrated in diverse organisms. TIR domain-containing proteins present in all kingdoms of life act in defense responses and can have NADase activity that hydrolyzes NAD+. Here, we show that TIR domain-containing proteins from several bacterial and one archaeal species can remove the NAM moiety from NAD-capped RNAs (NAD-RNAs). We demonstrate that the deNAMing activity of AbTir (from Acinetobacter baumannii) on NAD-RNA specifically produces a cyclic ADPR-RNA, which can be further decapped in vitro by known decapping enzymes. Heterologous expression of the wild-type but not a catalytic mutant AbTir in E. coli suppressed cell propagation and reduced the levels of NAD-RNAs from a subset of genes before cellular NAD+ levels are impacted. Collectively, the in vitro and in vivo analyses demonstrate that TIR domain-containing proteins can function as a deNAMing enzyme of NAD-RNAs, raising the possibility of TIR domain proteins acting in gene expression regulation.
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Affiliation(s)
- Xufeng Wang
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China
- Beijing Advanced Center of RNA Biology (BEACON), Peking University, Beijing, 100871, China
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Dongli Yu
- Institute of Biochemistry, University of Cologne, Cologne, 50674, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Jiancheng Yu
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Hao Hu
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China
- Beijing Advanced Center of RNA Biology (BEACON), Peking University, Beijing, 100871, China
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Runlai Hang
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China
- Beijing Advanced Center of RNA Biology (BEACON), Peking University, Beijing, 100871, China
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Zachary Amador
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Qi Chen
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
- Molecular Medicine Program, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Jijie Chai
- Institute of Biochemistry, University of Cologne, Cologne, 50674, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Xuemei Chen
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China.
- Beijing Advanced Center of RNA Biology (BEACON), Peking University, Beijing, 100871, China.
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Wolfram-Schauerte M, Pozhydaieva N, Grawenhoff J, Welp LM, Silbern I, Wulf A, Billau FA, Glatter T, Urlaub H, Jäschke A, Höfer K. A viral ADP-ribosyltransferase attaches RNA chains to host proteins. Nature 2023; 620:1054-1062. [PMID: 37587340 PMCID: PMC10468400 DOI: 10.1038/s41586-023-06429-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/12/2023] [Indexed: 08/18/2023]
Abstract
The mechanisms by which viruses hijack the genetic machinery of the cells they infect are of current interest. When bacteriophage T4 infects Escherichia coli, it uses three different adenosine diphosphate (ADP)-ribosyltransferases (ARTs) to reprogram the transcriptional and translational apparatus of the host by ADP-ribosylation using nicotinamide adenine dinucleotide (NAD) as a substrate1,2. NAD has previously been identified as a 5' modification of cellular RNAs3-5. Here we report that the T4 ART ModB accepts not only NAD but also NAD-capped RNA (NAD-RNA) as a substrate and attaches entire RNA chains to acceptor proteins in an 'RNAylation' reaction. ModB specifically RNAylates the ribosomal proteins rS1 and rL2 at defined Arg residues, and selected E. coli and T4 phage RNAs are linked to rS1 in vivo. T4 phages that express an inactive mutant of ModB have a decreased burst size and slowed lysis of E. coli. Our findings reveal a distinct biological role for NAD-RNA, namely the activation of the RNA for enzymatic transfer to proteins. The attachment of specific RNAs to ribosomal proteins might provide a strategy for the phage to modulate the host's translation machinery. This work reveals a direct connection between RNA modification and post-translational protein modification. ARTs have important roles far beyond viral infections6, so RNAylation may have far-reaching implications.
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Affiliation(s)
- Maik Wolfram-Schauerte
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | | | - Julia Grawenhoff
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Luisa M Welp
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center, Göttingen, Germany
| | - Ivan Silbern
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center, Göttingen, Germany
| | - Alexander Wulf
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Franziska A Billau
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Timo Glatter
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Georg-August-University, Göttingen, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
| | - Katharina Höfer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany.
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Wolfram-Schauerte M, Höfer K. NAD-capped RNAs - a redox cofactor meets RNA. Trends Biochem Sci 2023; 48:142-155. [PMID: 36068130 DOI: 10.1016/j.tibs.2022.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 01/25/2023]
Abstract
RNA modifications immensely expand the diversity of the transcriptome, thereby influencing the function, localization, and stability of RNA. One prominent example of an RNA modification is the eukaryotic cap located at the 5' terminus of mRNAs. Interestingly, the redox cofactor NAD can be incorporated into RNA by RNA polymerase in vitro. The existence of NAD-modified RNAs in vivo was confirmed using liquid chromatography and mass spectrometry (LC-MS). In the past few years novel technologies and methods have characterized NAD as a cap-like RNA structure and enabled the investigation of NAD-capped RNAs (NAD-RNAs) in a physiological context. We highlight the identification of NAD-RNAs as well as the regulation and functions of this epitranscriptomic mark in all domains of life.
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Affiliation(s)
| | - Katharina Höfer
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, 35043, Hessen, Germany.
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