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Probst-Rüd S, Nyangaresi PO, Adeyeye AA, Ackermann M, Beck SE, McNeill K. Synergistic effect of UV-A and UV-C light is traced to UV-induced damage of the transfer RNA. WATER RESEARCH 2024; 252:121189. [PMID: 38295454 DOI: 10.1016/j.watres.2024.121189] [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: 10/16/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/02/2024]
Abstract
UV light emitting diodes (LEDs) are considered the new frontier of UV water disinfection. As UV technologies continue to evolve, so does the need to understand disinfection mechanisms to ensure that UV treatment continues to adequately protect public health. In this research, two Escherichia coli (E. coli) strains (the wild type K12 MG1655 and K12 SP11 (ThiI E342K)) were irradiated with UV-C at 268 nm both independently and after exposure to UV-A (365 nm). A synergistic effect was found on the viability of the wild type E. coli K12 strain when UV-A irradiation was applied prior to UV-C. Sublethal UV-A doses, which had a negligible effect on cell viability alone, enhanced UV-C inactivation by several orders of magnitude. This indicated a specific cellular response mechanism to UV-A irradiation, which was traced to direct photolysis of the transfer RNA (tRNA), which are critical links in the translation of messenger RNA to proteins. The wild type K12 strain MG1655, containing tRNAs with a thiolated uridine, directly absorbs the UV-A light, which leads to a reduction in protein synthesis, making them more susceptible to UV-C induced damage. However, the K12 strain SP11 (ThiI E342K), with a point mutation in the thiI gene that prevents a post-transcriptional modification of tRNA, experienced less inactivation upon subsequent irradiation by UV-C. The growth rate of cells, which was inhibited by sublethal UV-A doses, was not inhibited in this mutant strain with the modified tRNA. Time-lapse microscopy with microfluidics showed that sub-lethal UV-A caused a transient, reversible, growth arrest in E. coli. However, once the growth resumed, the cell division time resembled that of unirradiated cells. Damage induced by UV-A impaired the recovery of damage induced by UV-C. Depending on the UV-A dose applied, the synergistic effect remained even when there was a time delay of several hours between UV-A and UV-C exposures. The effect of sublethal UV-A was reversible over time; therefore, the synergistic effect was strongest when UV-C was applied immediately after UV-A. Combining UV-A and UV-C irradiation may serve as a practical tool to increase UV disinfection efficacy, which could potentially reduce costs while still adequately protecting public health.
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Affiliation(s)
- Sandra Probst-Rüd
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zurich, Zurich, Switzerland; Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dubendorf, Switzerland
| | | | - Adefolawe A Adeyeye
- Department of Civil Engineering, University of British Columbia, Vancouver, Canada
| | - Martin Ackermann
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zurich, Zurich, Switzerland; Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dubendorf, Switzerland
| | - Sara E Beck
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dubendorf, Switzerland; Department of Civil Engineering, University of British Columbia, Vancouver, Canada.
| | - Kristopher McNeill
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zurich, Zurich, Switzerland.
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Hertler J, Slama K, Schober B, Özrendeci Z, Marchand V, Motorin Y, Helm M. Synthesis of point-modified mRNA. Nucleic Acids Res 2022; 50:e115. [PMID: 36062567 PMCID: PMC9723659 DOI: 10.1093/nar/gkac719] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 07/20/2022] [Accepted: 08/15/2022] [Indexed: 12/24/2022] Open
Abstract
Synthetic mRNA has recently moved into the focus of therapeutic and vaccination efforts. Incorporation of modified nucleotides during in vitro transcription can improve translation and attenuate immunogenicity, but is limited to triphosphate nucleotides which are accepted by RNA polymerases, and their incorporation is either random or complete. In contrast, site-specific modification, herein termed 'point modification' in analogy to point mutations, holds significant technical challenge. We developed fundamental techniques for isolation of long, translatable and internally point-modified mRNAs. Enabling concepts include three-way-one-pot splint ligations, and isolation of mRNA by real-time elution from agarose gels. The use of blue light permitted visualization of mRNA in pre-stained gels without the photochemical damage associated with the use of hard UV-radiation. This allowed visualization of the mRNA through its migration in the agarose gel, which in turn, was a prerequisite for its recovery by electroelution into precast troughs. Co-eluting agarose particles were quantified and found to not be detrimental to mRNA translation in vitro. Translation of EGFP-coding mRNA into functional protein was quantified by incorporation of 35S-labelled methionine and by in-gel EGFP fluorescence. This enabled the functional analysis of point modifications, specifically of ribose methylations in the middle of a 1371 nt long mRNA.
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Affiliation(s)
| | | | - Benedikt Schober
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Zeynep Özrendeci
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Virginie Marchand
- IMoPA UMR7365 CNRS-UL, BioPole Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Yuri Motorin
- IMoPA UMR7365 CNRS-UL, BioPole Université de Lorraine, Vandœuvre-lès-Nancy, France,Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, UMS2008 IBSLor (CNRS-UL)/US40 (INSERM), Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Mark Helm
- To whom correspondence should be addressed. Tel: +49 6131 392 5731; Fax: +49 6131 392 0373;
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Thakur P, Atway J, Limbach PA, Addepalli B. RNA Cleavage Properties of Nucleobase-Specific RNase MC1 and Cusativin Are Determined by the Dinucleotide-Binding Interactions in the Enzyme-Active Site. Int J Mol Sci 2022; 23:7021. [PMID: 35806025 PMCID: PMC9266746 DOI: 10.3390/ijms23137021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 02/05/2023] Open
Abstract
Knowledge of the cleavage specificity of ribonucleases is critical for their application in RNA modification mapping or RNA-protein binding studies. Here, we detail the cleavage specificity and efficiency of ribonuclease MC1 and cusativin using a customized RNA sequence that contained all dinucleotide combinations and homopolymer sequences. The sequencing of the oligonucleotide digestion products by a semi-quantitative liquid chromatography coupled with mass spectrometry (LC-MS) analysis documented as little as 0.5-1% cleavage levels for a given dinucleotide sequence combination. While RNase MC1 efficiently cleaved the [A/U/C]pU dinucleotide bond, no cleavage was observed for the GpU bond. Similarly, cusativin efficiently cleaved Cp[U/A/G] dinucleotide combinations along with UpA and [A/U]pU, suggesting a broader specificity of dinucleotide preferences. The molecular interactions between the substrate and active site as determined by the dinucleotide docking studies of protein models offered additional evidence and support for the observed substrate specificity. Targeted alteration of the key amino acid residues in the nucleotide-binding site confirms the utility of this in silico approach for the identification of key interactions. Taken together, the use of bioanalytical and computational approaches, involving LC-MS and ligand docking of tertiary structural models, can form a powerful combination to help explain the RNA cleavage behavior of RNases.
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Affiliation(s)
| | | | | | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (P.T.); (J.A.); (P.A.L.)
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Seixas AF, Quendera AP, Sousa JP, Silva AFQ, Arraiano CM, Andrade JM. Bacterial Response to Oxidative Stress and RNA Oxidation. Front Genet 2022; 12:821535. [PMID: 35082839 PMCID: PMC8784731 DOI: 10.3389/fgene.2021.821535] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/21/2021] [Indexed: 01/03/2023] Open
Abstract
Bacteria have to cope with oxidative stress caused by distinct Reactive Oxygen Species (ROS), derived not only from normal aerobic metabolism but also from oxidants present in their environments. The major ROS include superoxide O2−, hydrogen peroxide H2O2 and radical hydroxide HO•. To protect cells under oxidative stress, bacteria induce the expression of several genes, namely the SoxRS, OxyR and PerR regulons. Cells are able to tolerate a certain number of free radicals, but high levels of ROS result in the oxidation of several biomolecules. Strikingly, RNA is particularly susceptible to this common chemical damage. Oxidation of RNA causes the formation of strand breaks, elimination of bases or insertion of mutagenic lesions in the nucleobases. The most common modification is 8-hydroxyguanosine (8-oxo-G), an oxidized form of guanosine. The structure and function of virtually all RNA species (mRNA, rRNA, tRNA, sRNA) can be affected by RNA oxidation, leading to translational defects with harmful consequences for cell survival. However, bacteria have evolved RNA quality control pathways to eliminate oxidized RNA, involving RNA-binding proteins like the members of the MutT/Nudix family and the ribonuclease PNPase. Here we summarize the current knowledge on the bacterial stress response to RNA oxidation, namely we present the different ROS responsible for this chemical damage and describe the main strategies employed by bacteria to fight oxidative stress and control RNA damage.
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Affiliation(s)
- André F Seixas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ana P Quendera
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - João P Sousa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Alda F Q Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - José M Andrade
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Thakur P, Abernathy S, Limbach PA, Addepalli B. Locating chemical modifications in RNA sequences through ribonucleases and LC-MS based analysis. Methods Enzymol 2021; 658:1-24. [PMID: 34517943 PMCID: PMC9680040 DOI: 10.1016/bs.mie.2021.06.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Knowledge of the structural information is essential for understanding the functional details of modified RNA. Cellular non-coding RNA such as rRNA, tRNA and even viral RNAs contain a number of post-transcriptional modifications with varied degree of diversity and density. In this chapter, we discuss the use of a combination of biochemical and analytical tools such as ribonucleases and liquid chromatography coupled with mass spectrometry approaches for characterization of modified RNA. We present the protocols and alternate strategies for obtaining confident modified sequence information to facilitate the understanding of function.
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Affiliation(s)
- Priti Thakur
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
| | - Scott Abernathy
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
| | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States.
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Estevez M, Valesyan S, Jora M, Limbach PA, Addepalli B. Oxidative Damage to RNA is Altered by the Presence of Interacting Proteins or Modified Nucleosides. Front Mol Biosci 2021; 8:697149. [PMID: 34277707 PMCID: PMC8281250 DOI: 10.3389/fmolb.2021.697149] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/21/2021] [Indexed: 12/15/2022] Open
Abstract
Oxidative stress triggered by the Fenton reaction (chemical) or UVR exposure (photo) can damage cellular biomolecules including RNA through oxidation of nucleotides. Besides such xenobiotic chemical modifications, RNA also contains several post-transcriptional nucleoside modifications that are installed by enzymes to modulate structure, RNA-protein interactions, and biochemical functions. We examined the extent of oxidative damage to naturally modified RNA which is required for cellular protein synthesis under two different contexts. The extent of oxidative damage is higher when RNA is not associated with proteins, but the degree of damage is lower when the RNA is presented in the form of a ribonucleoprotein complex, such as an intact ribosome. Our studies also indicate that absence of methylations in ribosomal RNA at specific positions could make it more susceptible to photooxidative stress. However, the extent of guanosine oxidation varied with the position at which the modification is deficient, indicating position-dependent structural effects. Further, an E. coli strain deficient in 5-methylaminomethyl-2-thiouridine (mnm5s2U) (found in lysine and glutamate tRNA anticodon) is more vulnerable to oxidative RNA damage compared to its wildtype strain suggesting an auxiliary function for the mnm5s2U modification. These studies indicate that oxidative damage to RNA is altered by the presence of enzymatic modified nucleosides or protein association inside the cell.
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Affiliation(s)
- Mariana Estevez
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
| | - Satenik Valesyan
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
| | - Manasses Jora
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
| | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
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