1
|
Rahm M, Kwast H, Wessels HJCT, Noga MJ, Lefeber DJ. Mixed-phase weak anion-exchange/reversed-phase LC-MS/MS for analysis of nucleotide sugars in human fibroblasts. Anal Bioanal Chem 2024:10.1007/s00216-024-05313-w. [PMID: 38676823 DOI: 10.1007/s00216-024-05313-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/29/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024]
Abstract
Nucleotide sugars (NS) fulfil important roles in all living organisms and in humans, related defects result in severe clinical syndromes. NS can be seen as the "activated" sugars used for biosynthesis of a wide range of glycoconjugates and serve as substrates themselves for the synthesis of other nucleotide sugars. NS analysis is complicated by the presence of multiple stereoisomers without diagnostic transition ions, therefore requiring separation by liquid chromatography. In this paper, we explored weak anion-exchange/reversed-phase chromatography on a hybrid column for the separation of 17 nucleotide sugars that can occur in humans. A robust and reproducible method was established with intra- and inter-day coefficients of variation below 10% and a linear range spanning three orders of magnitude. Application to patient fibroblasts with genetic defects in mannose-1-phosphate guanylyltransferase beta, CDP-L-ribitol pyrophosphorylase A, and UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase showed abnormal levels of guanosine-5'-diphosphate-α-D-mannose (GDP-Man), cytidine-5'-diphosphate-L-ribitol (CDP-ribitol), and cytidine-5'-monophosphate-N-acetyl-β-D-neuraminic acid (CMP-Neu5Ac), respectively, in consonance with expectations based on the diagnosis. In conclusion, a novel, semi-quantitative method was established for the analysis of nucleotide sugars that can be applied to diagnose several genetic glycosylation disorders in fibroblasts and beyond.
Collapse
Affiliation(s)
- Moritz Rahm
- Department of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Hanneke Kwast
- Translational Metabolic Laboratory (TML), Department of Human Genetics, Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525 GA, Nijmegen, The Netherlands
| | - Hans J C T Wessels
- Translational Metabolic Laboratory (TML), Department of Human Genetics, Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525 GA, Nijmegen, The Netherlands
| | - Marek J Noga
- Laboratory of Clinical Genetics, Inborn Errors of Metabolism, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Dirk J Lefeber
- Department of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
- Translational Metabolic Laboratory (TML), Department of Human Genetics, Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525 GA, Nijmegen, The Netherlands.
| |
Collapse
|
2
|
Shu S, Tsutsui Y, Nathawat R, Mi W. Dual function of LapB (YciM) in regulating Escherichia coli lipopolysaccharide synthesis. Proc Natl Acad Sci U S A 2024; 121:e2321510121. [PMID: 38635633 PMCID: PMC11046580 DOI: 10.1073/pnas.2321510121] [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: 12/06/2023] [Accepted: 03/21/2024] [Indexed: 04/20/2024] Open
Abstract
Levels of lipopolysaccharide (LPS), an essential glycolipid on the surface of most gram-negative bacteria, are tightly controlled-making LPS synthesis a promising target for developing new antibiotics. Escherichia coli adaptor protein LapB (YciM) plays an important role in regulating LPS synthesis by promoting degradation of LpxC, a deacetylase that catalyzes the first committed step in LPS synthesis. Under conditions where LPS is abundant, LapB recruits LpxC to the AAA+ protease FtsH for degradation. LapB achieves this by simultaneously interacting with FtsH through its transmembrane helix and LpxC through its cytoplasmic domain. Here, we describe a cryo-EM structure of the complex formed between LpxC and the cytoplasmic domain of LapB (LapBcyto). The structure reveals how LapB exploits both its tetratricopeptide repeat (TPR) motifs and rubredoxin domain to interact with LpxC. Through both in vitro and in vivo analysis, we show that mutations at the LapBcyto/LpxC interface prevent LpxC degradation. Unexpectedly, binding to LapBcyto also inhibits the enzymatic activity of LpxC through allosteric effects reminiscent of LpxC activation by MurA in Pseudomonas aeruginosa. Our findings argue that LapB regulates LPS synthesis in two steps: In the first step, LapB inhibits the activity of LpxC, and in the second step, it commits LpxC to degradation by FtsH.
Collapse
Affiliation(s)
- Sheng Shu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520
| | - Yuko Tsutsui
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520
- Cancer Biology Institute, Yale University, West Haven, CT06516
| | - Rajkanwar Nathawat
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520
| | - Wei Mi
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06520
| |
Collapse
|
3
|
Rady T, Erb S, Deddouche-Grass S, Morales R, Chaubet G, Cianférani S, Basse N, Wagner A. Targeted delivery of immune-stimulating bispecific RNA, inducing apoptosis and anti-tumor immunity in cancer cells. iScience 2024; 27:109068. [PMID: 38380254 PMCID: PMC10877685 DOI: 10.1016/j.isci.2024.109068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 07/18/2023] [Accepted: 01/25/2024] [Indexed: 02/22/2024] Open
Abstract
Double-stranded RNAs (dsRNA)-based strategies appeared as promising therapies to induce an inflammation in the tumor microenvironment. However, currently described systems generally lack active targeting of tissues, and their clinical translation is thus limited to intratumoral injection. Herein, we developed an antibody-siRNA-5'triphosphate conjugate with multiple modes of action, combining cell surface EphA2-specific internalization, leading to a simultaneous gene silencing and activation of the receptor retinoic acid-inducible gene I (RIG-I). Recognition of cytosolic siRNA-5'triphosphate by RIG-I triggers the expression of interferons and pro-inflammatory cytokines, inducing an inflammation of the tumor environment and activating neighboring immune cells. In addition, these RIG-I-specific effects synergized with siRNA-mediated PLK1 silencing to promote cancer cell death by apoptosis. Altogether, such immune-stimulating antibody-RNA conjugate opens a novel modality to overcome some limitations encountered by dsRNA molecules currently in clinical trials.
Collapse
Affiliation(s)
- Tony Rady
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
- Sanofi, 13 Quai Jules Guesde, 94400 Vitry-sur-Seine, France
| | - Stéphane Erb
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI – FR2048, 67087 Strasbourg, France
| | | | - Renaud Morales
- Sanofi, 13 Quai Jules Guesde, 94400 Vitry-sur-Seine, France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI – FR2048, 67087 Strasbourg, France
| | - Nicolas Basse
- Sanofi, 13 Quai Jules Guesde, 94400 Vitry-sur-Seine, France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| |
Collapse
|
4
|
Lowenthal MS, Antonishek AS, Phinney KW. Quantification of mRNA in Lipid Nanoparticles Using Mass Spectrometry. Anal Chem 2024; 96:1214-1222. [PMID: 38189247 PMCID: PMC10809213 DOI: 10.1021/acs.analchem.3c04406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/26/2023] [Accepted: 12/26/2023] [Indexed: 01/09/2024]
Abstract
Lipid nanoparticle-encapsulated mRNA (LNP-mRNA) holds great promise as a novel modality for treating a broad range of diseases. The ability to quantify mRNA accurately in therapeutic products helps to ensure consistency and safety. Here, we consider a central aspect of accuracy, measurement traceability, which establishes trueness in quantity. In this study, LNP-mRNA is measured in situ using a novel liquid chromatography-mass spectrometry (LC-MS) approach with traceable quantification. Previous works established that oligonucleotide quantification is possible through the accounting of an oligomer's fundamental nucleobases, with traceability established through common nucleobase calibrators. This sample preparation does not require mRNA extraction, detergents, or enzymes and can be achieved through direct acid hydrolysis of an LNP-mRNA product prior to an isotope dilution strategy. This results in an accurate quantitative analysis of mRNA, independent of time or place. Acid hydrolysis LC-MS is demonstrated to be amenable to measuring mRNA as both an active substance or a formulated mRNA drug product.
Collapse
Affiliation(s)
- Mark S. Lowenthal
- Biomolecular Measurement
Division, Material Measurement Lab, National
Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899, United States
| | - Abigail S. Antonishek
- Biomolecular Measurement
Division, Material Measurement Lab, National
Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899, United States
| | - Karen W. Phinney
- Biomolecular Measurement
Division, Material Measurement Lab, National
Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899, United States
| |
Collapse
|
5
|
Raoof GFA, El-Anssary AA, Younis EA, Aly HF. Metabolomic Analysis and in Vitro Investigation of the Biological Properties of a By-Product Derived from Vicia faba. Chem Biodivers 2023; 20:e202301095. [PMID: 37878681 DOI: 10.1002/cbdv.202301095] [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: 07/26/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 10/27/2023]
Abstract
By-products from plant sources are recently regarded as a valuable source of bioactive compounds. In this regard, the present study aims to assess the bioactivities of the 70 % MeOH extract obtained from Vicia faba peels and analyze its metabolomic profile. Acetylcholinesterase and carbohydrate metabolizing enzymes inhibitory activities of the plant extract were assayed using quantitative colorimetric tests. Antioxidant activity was estimated by DPPH assay, and cytotoxic activity was evaluated against normal fibroblast skin cells (1-BJ1). Ninety-one metabolites were tentatively identified using ultra-high-performance liquid chromatography (UHPLC) hyphenated with quadrupole-time-of-flight tandem mass spectrometry (QTOF-MS). Most of these compounds were described for the first time in the plant. In addition, catechin, rutin, quercitrin, and rhamnetin were isolated from the plant extract. The plant extract and the isolated compounds possessed no cytotoxic activity on (1-BJ1), while they exhibited anticholinesterase with the highest activity for 70 % MeOH extract (IC50 =120.11 mg/L), antioxidant potential with the highest activity for rutin (90.54±0.73 %), and carbohydrate metabolizing inhibitory activities with the highest activity for rutin. These discoveries imply that V. faba peels might serve as an efficient antioxidant, exhibit anticholinesterase properties, and have the potential for use in managing diabetes, all while avoiding cytotoxicity in normal cells.
Collapse
Affiliation(s)
- Gehan F Abdel Raoof
- Pharmacognosy Department, Pharmaceutical and Drug Research Industries Institute, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Amira A El-Anssary
- Pharmacognosy Department, Pharmaceutical and Drug Research Industries Institute, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Eman A Younis
- Department of Therapeutic Chemistry, National Research Centre, Dokki, P.O. 12622, Giza, Egypt
| | - Hanan F Aly
- Department of Therapeutic Chemistry, National Research Centre, Dokki, P.O. 12622, Giza, Egypt
| |
Collapse
|
6
|
Mattioli G, Schürmann R, Nicolafrancesco C, Giuliani A, Milosavljević AR. Effect of Protonation on the Molecular Structure of Adenosine 5'-Triphosphate: A Combined Theoretical and Near Edge X-ray Absorption Fine Structure Study. J Phys Chem Lett 2023; 14:10173-10180. [PMID: 37925744 PMCID: PMC10658619 DOI: 10.1021/acs.jpclett.3c01666] [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: 06/18/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
The present work combines the near edge X-ray absorption mass spectrometry of a protonated adenosine 5'-triphosphate (ATP) molecule isolated in an ion trap with (time-dependent) density functional theory calculations. Our study unravels the effect of protonation on the ATP structure and its spectral properties, providing structure-property relationships at atomistic resolution for protonated ATP (ATPH) isolated in the gas-phase conditions. On the other hand, the present C and N K-edge X-ray absorption spectra of isolated ATPH appear closely like those previously reported for solvated ATP at low pH. Therefore, the present work should be relevant for further investigation and modeling of structure-function properties of protonated adenine and ATP in complex biological environments.
Collapse
Affiliation(s)
- Giuseppe Mattioli
- Istituto
di Struttura della Materia (ISM), Consiglio
Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1, CP 10, 00016 Monterotondo Scalo, Italy
| | - Robin Schürmann
- Synchrotron
SOLEIL, L’Orme
de Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette Cedex, France
- Institute
of Chemistry, University of Potsdam, 14476 Potsdam, Germany
| | | | - Alexandre Giuliani
- Synchrotron
SOLEIL, L’Orme
de Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette Cedex, France
- INRAE,
UAR1008, Transform Department, Rue de la Géraudière, BP 71627, 44316 Nantes, France
| | | |
Collapse
|
7
|
Wang J, Chew BLA, Lai Y, Dong H, Xu L, Liu Y, Fu XY, Lin Z, Shi PY, Lu TK, Luo D, Jaffrey SR, Dedon PC. A systems-level mass spectrometry-based technique for accurate and sensitive quantification of the RNA cap epitranscriptome. Nat Protoc 2023; 18:2671-2698. [PMID: 37567932 DOI: 10.1038/s41596-023-00857-0] [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: 08/11/2021] [Accepted: 04/26/2023] [Indexed: 08/13/2023]
Abstract
Chemical modifications of transcripts with a 5' cap occur in all organisms and function in many aspects of RNA metabolism. To facilitate analysis of RNA caps, we developed a systems-level mass spectrometry-based technique, CapQuant, for accurate and sensitive quantification of the cap epitranscriptome. The protocol includes the addition of stable isotope-labeled cap nucleotides (CNs) to RNA, enzymatic hydrolysis of endogenous RNA to release CNs, and off-line enrichment of CNs by ion-pairing high-pressure liquid chromatography, followed by a 17 min chromatography-coupled tandem quadrupole mass spectrometry run for the identification and quantification of individual CNs. The total time required for the protocol can be up to 7 d. In this approach, 26 CNs can be quantified in eukaryotic poly(A)-tailed RNA, bacterial total RNA and viral RNA. This protocol can be modified to analyze other types of RNA and RNA from in vitro sources. CapQuant stands out from other methods in terms of superior specificity, sensitivity and accuracy, and it is not limited to individual caps nor does it require radiolabeling. Thanks to its unique capability of accurately and sensitively quantifying RNA caps on a systems level, CapQuant can reveal both the RNA cap landscape and the transcription start site distribution of capped RNA in a broad range of settings.
Collapse
Affiliation(s)
- Jin Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, People's Republic of China.
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore.
- Institute of Biomedical Sciences, Inner Mongolia University, Hohhot, China.
| | - Bing Liang Alvin Chew
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- NTU Institute of Health Technologies, Interdisciplinary Graduate Programme, Nanyang Technological University, Singapore, Singapore
| | - Yong Lai
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong, China
| | | | - Luang Xu
- Cancer Science Institute of Singapore, Singapore, Singapore
- School of Life Science and Technology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai, China
| | - Yu Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, People's Republic of China
| | - Xin-Yuan Fu
- Cancer Science Institute of Singapore, Singapore, Singapore
- Generos Pharmaceutical Co. Ltd, Hangzhou, China
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO, USA
| | - Pei-Yong Shi
- Departments of Biochemistry & Molecular Biology and Pharmacology & Toxicology, and Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
- GlaxoSmithKline, Rockville, MD, USA
| | - Timothy K Lu
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
- Synthetic Biology Center, Departments of Biological Engineering and Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Senti Bio, San Francisco, CA, USA
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY, USA
| | - Peter C Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore.
- Dept. of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
8
|
Leiva LE, Zegarra V, Bange G, Ibba M. At the Crossroad of Nucleotide Dynamics and Protein Synthesis in Bacteria. Microbiol Mol Biol Rev 2023; 87:e0004422. [PMID: 36853029 PMCID: PMC10029340 DOI: 10.1128/mmbr.00044-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Nucleotides are at the heart of the most essential biological processes in the cell, be it as key protagonists in the dogma of molecular biology or by regulating multiple metabolic pathways. The dynamic nature of nucleotides, the cross talk between them, and their constant feedback to and from the cell's metabolic state position them as a hallmark of adaption toward environmental and growth challenges. It has become increasingly clear how the activity of RNA polymerase, the synthesis and maintenance of tRNAs, mRNA translation at all stages, and the biogenesis and assembly of ribosomes are fine-tuned by the pools of intracellular nucleotides. With all aspects composing protein synthesis involved, the ribosome emerges as the molecular hub in which many of these nucleotides encounter each other and regulate the state of the cell. In this review, we aim to highlight intracellular nucleotides in bacteria as dynamic characters permanently cross talking with each other and ultimately regulating protein synthesis at various stages in which the ribosome is mainly the principal character.
Collapse
Affiliation(s)
- Lorenzo Eugenio Leiva
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Victor Zegarra
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Michael Ibba
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| |
Collapse
|
9
|
Frańska M, Stȩżycka O, Jankowski W, Hoffmann M. Gas-Phase Internal Ribose Residue Loss from Mg-ATP and Mg-ADP Complexes: Experimental and Theoretical Evidence for Phosphate-Mg-Adenine Interaction. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1474-1479. [PMID: 35796751 PMCID: PMC9354248 DOI: 10.1021/jasms.2c00071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Gas-phase decompositions of magnesium complexes with adenosine-5'-triphosphate (ATP) and adenosine-5'-diphosphate (ADP) were studied by using electrospray ionization-collision-induced dissociation-tandem mass spectrometry, in the negative ion mode. The loss of internal ribose residue was observed and was found to occur directly from the [ADP-3H+Mg]- ion. The occurrence of this process indicates the presence of a strong phosphate-Mg-adenine interaction. The performed quantum mechanics calculations confirmed the occurrence of this interaction in the [ADP-3H+Mg]- ion, namely the presence of Mg-N7 bond and hydrogen bond between the phosphate oxygen atom and amino group. Although the finding concerns the gas phase, it indicates that phosphate-Mg-adenine interaction may be also of importance for biological processes. The loss of an internal ribose residue was also observed for calcium and zinc complexes with ATP/ADP as well as for magnesium complexes with guanosine-5'-triphosphate (GTP) or guanosine-5'-diphosphate (GDP). Therefore, it is reasonable to conclude that the presence of the phosphate-metal-nucleobase interaction is a feature of gas phase [NDP-3H+metal]- ion (NDP, nucleoside-5'-diphosphate) and may also be important for biological processes.
Collapse
Affiliation(s)
- Magdalena Frańska
- Institute
of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965 Poznań, Poland
| | - Olga Stȩżycka
- Institute
of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965 Poznań, Poland
| | - Wojciech Jankowski
- Faculty of
Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego
8, 61-614 Poznań, Poland
| | - Marcin Hoffmann
- Faculty of
Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego
8, 61-614 Poznań, Poland
| |
Collapse
|
10
|
Stochastic dynamic quantitative and 3D structural matrix assisted laser desorption/ionization mass spectrometric analyses of mixture of nucleosides. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
11
|
Flamme M, Hanlon S, Marzuoli I, Püntener K, Sladojevich F, Hollenstein M. Evaluation of 3'-phosphate as a transient protecting group for controlled enzymatic synthesis of DNA and XNA oligonucleotides. Commun Chem 2022; 5:68. [PMID: 36697944 PMCID: PMC9814670 DOI: 10.1038/s42004-022-00685-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/12/2022] [Indexed: 01/28/2023] Open
Abstract
Chemically modified oligonucleotides have advanced as important therapeutic tools as reflected by the recent advent of mRNA vaccines and the FDA-approval of various siRNA and antisense oligonucleotides. These sequences are typically accessed by solid-phase synthesis which despite numerous advantages is restricted to short sequences and displays a limited tolerance to functional groups. Controlled enzymatic synthesis is an emerging alternative synthetic methodology that circumvents the limitations of traditional solid-phase synthesis. So far, most approaches strived to improve controlled enzymatic synthesis of canonical DNA and no potential routes to access xenonucleic acids (XNAs) have been reported. In this context, we have investigated the possibility of using phosphate as a transient protecting group for controlled enzymatic synthesis of DNA and locked nucleic acid (LNA) oligonucleotides. Phosphate is ubiquitously employed in natural systems and we demonstrate that this group displays most characteristics required for controlled enzymatic synthesis. We have devised robust synthetic pathways leading to these challenging compounds and we have discovered a hitherto unknown phosphatase activity of various DNA polymerases. These findings open up directions for the design of protected DNA and XNA nucleoside triphosphates for controlled enzymatic synthesis of chemically modified nucleic acids.
Collapse
Affiliation(s)
- Marie Flamme
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université de Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724 Paris Cedex 15, Paris, France
| | - Steven Hanlon
- grid.417570.00000 0004 0374 1269Pharmaceutical Devision, Synthetic Molecules Technical Development, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Irene Marzuoli
- grid.417570.00000 0004 0374 1269Pharmaceutical Devision, Synthetic Molecules Technical Development, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Kurt Püntener
- grid.417570.00000 0004 0374 1269Pharmaceutical Devision, Synthetic Molecules Technical Development, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Filippo Sladojevich
- grid.417570.00000 0004 0374 1269Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Marcel Hollenstein
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université de Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724 Paris Cedex 15, Paris, France
| |
Collapse
|
12
|
Kubacka D, Kozarski M, Baranowski MR, Wojcik R, Panecka-Hofman J, Strzelecka D, Basquin J, Jemielity J, Kowalska J. Substrate-Based Design of Cytosolic Nucleotidase IIIB Inhibitors and Structural Insights into Inhibition Mechanism. Pharmaceuticals (Basel) 2022; 15:ph15050554. [PMID: 35631380 PMCID: PMC9144445 DOI: 10.3390/ph15050554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/26/2022] Open
Abstract
Cytosolic nucleotidases (cNs) catalyze dephosphorylation of nucleoside 5’-monophosphates and thereby contribute to the regulation of nucleotide levels in cells. cNs have also been shown to dephosphorylate several therapeutically relevant nucleotide analogues. cN-IIIB has shown in vitro a distinctive activity towards 7-mehtylguanosine monophosphate (m7GMP), which is one key metabolites of mRNA cap. Consequently, it has been proposed that cN-IIIB participates in mRNA cap turnover and prevents undesired accumulation and salvage of m7GMP. Here, we sought to develop molecular tools enabling more advanced studies on the cellular role of cN-IIIB. To that end, we performed substrate and inhibitor property profiling using a library of 41 substrate analogs. The most potent hit compounds (identified among m7GMP analogs) were used as a starting point for structure–activity relationship studies. As a result, we identified several 7-benzylguanosine 5’-monophosphate (Bn7GMP) derivatives as potent, unhydrolyzable cN-IIIB inhibitors. The mechanism of inhibition was elucidated using X-ray crystallography and molecular docking. Finally, we showed that compounds that potently inhibit recombinant cN-IIIB have the ability to inhibit m7GMP decay in cell lysates.
Collapse
Affiliation(s)
- Dorota Kubacka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; (D.K.); (M.K.); (M.R.B.); (J.P.-H.); (D.S.)
| | - Mateusz Kozarski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; (D.K.); (M.K.); (M.R.B.); (J.P.-H.); (D.S.)
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland;
| | - Marek R. Baranowski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; (D.K.); (M.K.); (M.R.B.); (J.P.-H.); (D.S.)
| | - Radoslaw Wojcik
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland;
| | - Joanna Panecka-Hofman
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; (D.K.); (M.K.); (M.R.B.); (J.P.-H.); (D.S.)
| | - Dominika Strzelecka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; (D.K.); (M.K.); (M.R.B.); (J.P.-H.); (D.S.)
| | - Jerome Basquin
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany;
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland;
- Correspondence: (J.J.); (J.K.); Tel.: +4822-5543-774
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; (D.K.); (M.K.); (M.R.B.); (J.P.-H.); (D.S.)
- Correspondence: (J.J.); (J.K.); Tel.: +4822-5543-774
| |
Collapse
|
13
|
Yoshida Y, Ti Z, Tanabe W, Tomoike F, Hashiya F, Suzuki T, Hirota S, Saiki Y, Horii A, Hirayama A, Soga T, Kimura Y, Abe H. Development of Fluorophosphoramidate as a New Biocompatible Transformable Functional Group and its Application as a Phosphate Prodrug for Nucleoside Analogs. ChemMedChem 2022; 17:e202200188. [PMID: 35393747 DOI: 10.1002/cmdc.202200188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Indexed: 11/12/2022]
Abstract
Synthetic phosphate-derived functional groups are important for controlling the function of bioactive molecules in vivo . Herein we describe the development of a new type of biocompatible phosphate analog, a fluorophosphoramidate (FPA) functional group that has characteristic P-F and P-N bonds. We found that FPA with a primary amino group was relatively unstable in aqueous solution and was converted to a monophosphate, while FPA with a secondary amino group was stable. Furthermore, by improving the molecular design of FPA, we developed a reaction in which a secondary amino group is converted to a primary amino group in the intracellular environment, and clarified that the FPA group functions as a phosphate prodrug of nucleoside. Various FPA-gemcitabine derivatives were synthesized and their anticancer activities were evaluated. One of the FPA-gemcitabine derivatives showed superior anticancer activity compared with gemcitabine and its ProTide prodrug, which methodology is widely used in various nucleoside analogs, including anti-cancer and anti-virus drugs.
Collapse
Affiliation(s)
- Yuki Yoshida
- Nagoya University: Nagoya Daigaku, Graduate School of Science, JAPAN
| | - Zheng Ti
- Nagoya University: Nagoya Daigaku, Graduate School of Science, JAPAN
| | - Wataru Tanabe
- Nagoya University: Nagoya Daigaku, Graduate School of Science, JAPAN
| | - Fumiaki Tomoike
- Gakushuin University: Gakushuin Daigaku, Graduate School of Science, JAPAN
| | - Fumitaka Hashiya
- Nagoya University: Nagoya Daigaku, Research Center for Material Science, JAPAN
| | | | - Shuto Hirota
- Tohoku University: Tohoku Daigaku, School of Medicine, JAPAN
| | - Yuriko Saiki
- Tohoku University: Tohoku Daigaku, School of Medicine, JAPAN
| | - Akira Horii
- Tohoku University: Tohoku Daigaku, School of Medicine, JAPAN
| | - Akiyoshi Hirayama
- Keio University: Keio Gijuku Daigaku, Institute for Biosciences, JAPAN
| | - Tomoyoshi Soga
- Keio University: Keio Gijuku Daigaku, Institute for Advance Biosciences, JAPAN
| | - Yasuaki Kimura
- Nagoya University: Nagoya Daigaku, Graduate School of Science, JAPAN
| | - Hiroshi Abe
- Nagoya University, Department of Chemistry, Graduate School of Science, Furo, Chikusa, 464-8602, Nagoya, JAPAN
| |
Collapse
|
14
|
Farid MM, Ibrahim FM, Ragheb AY, Mohammed RS, Hegazi NM, Shabrawy MOEL, Kawashty SA, Marzouk MM. Comprehensive Phytochemical Characterization of Raphanus raphanistrum L.: In Vitro Antioxidant and Antihyperglycemic Evaluation. SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2022.e01154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
|
15
|
Sisley EK, Hale OJ, Styles IB, Cooper HJ. Native Ambient Mass Spectrometry Imaging of Ligand-Bound and Metal-Bound Proteins in Rat Brain. J Am Chem Soc 2022; 144:2120-2128. [DOI: 10.1021/jacs.1c10032] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Emma K. Sisley
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Oliver J. Hale
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, U.K
| | - Iain B. Styles
- School of Computer Science, University of Birmingham, Birmingham, B15 2TT, U.K
- The Alan Turing Institute, London, NW1 2DB, U.K
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, B15 2TT, U.K
- University of Nottingham, Midlands, NG7 2RD, U.K
| | - Helen J. Cooper
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, U.K
| |
Collapse
|
16
|
Quantification of mRNA cap-modifications by means of LC-QqQ-MS. Methods 2021; 203:196-206. [PMID: 34058305 PMCID: PMC7612805 DOI: 10.1016/j.ymeth.2021.05.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 12/24/2022] Open
Abstract
Enzymatic modification of the 5'-cap is a versatile approach to modulate the properties of mRNAs. Transfer of methyl groups from S-adenosyl-l-methionine (AdoMet) or functional moieties from non-natural analogs by methyltransferases (MTases) allows for site-specific modifications at the cap. These modifications have been used to tune translation or control it in a temporal manner and even influence immunogenicity of mRNA. For quantification of the MTase-mediated cap modification, liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) provides the required sensitivity and accuracy. Here, we describe the complete workflow starting from in vitro transcription to produce mRNAs, via their enzymatic modification at the cap with natural or non-natural moieties to the quantification of these cap-modifications by LC-QqQ-MS.
Collapse
|
17
|
Straube H, Witte CP, Herde M. Analysis of Nucleosides and Nucleotides in Plants: An Update on Sample Preparation and LC-MS Techniques. Cells 2021; 10:689. [PMID: 33804650 PMCID: PMC8003640 DOI: 10.3390/cells10030689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Nucleotides fulfill many essential functions in plants. Compared to non-plant systems, these hydrophilic metabolites have not been adequately investigated in plants, especially the less abundant nucleotide species such as deoxyribonucleotides and modified or damaged nucleotides. Until recently, this was mainly due to a lack of adequate methods for in-depth analysis of nucleotides and nucleosides in plants. In this review, we focus on the current state-of-the-art of nucleotide analysis in plants with liquid chromatography coupled to mass spectrometry and describe recent major advances. Tissue disruption, quenching, liquid-liquid and solid-phase extraction, chromatographic strategies, and peculiarities of nucleotides and nucleosides in mass spectrometry are covered. We describe how the different steps of the analytical workflow influence each other, highlight the specific challenges of nucleotide analysis, and outline promising future developments. The metabolite matrix of plants is particularly complex. Therefore, it is likely that nucleotide analysis methods that work for plants can be applied to other organisms as well. Although this review focuses on plants, we also discuss advances in nucleotide analysis from non-plant systems to provide an overview of the analytical techniques available for this challenging class of metabolites.
Collapse
Affiliation(s)
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, 30419 Hannover, Germany;
| | - Marco Herde
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, 30419 Hannover, Germany;
| |
Collapse
|
18
|
Identification of New Markers of Alcohol-Derived DNA Damage in Humans. Biomolecules 2021; 11:biom11030366. [PMID: 33673538 PMCID: PMC7997542 DOI: 10.3390/biom11030366] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/16/2021] [Accepted: 02/21/2021] [Indexed: 12/13/2022] Open
Abstract
Alcohol consumption is a risk factor for the development of several cancers, including those of the head and neck and the esophagus. The underlying mechanisms of alcohol-induced carcinogenesis remain unclear; however, at these sites, alcohol-derived acetaldehyde seems to play a major role. By reacting with DNA, acetaldehyde generates covalent modifications (adducts) that can lead to mutations. Previous studies have shown a dose dependence between levels of a major acetaldehyde-derived DNA adduct and alcohol exposure in oral-cell DNA. The goal of this study was to optimize a mass spectrometry (MS)-based DNA adductomic approach to screen for all acetaldehyde-derived DNA adducts to more comprehensively characterize the genotoxic effects of acetaldehyde in humans. A high-resolution/-accurate-mass data-dependent constant-neutral-loss-MS3 methodology was developed to profile acetaldehyde-DNA adducts in purified DNA. This resulted in the identification of 22 DNA adducts. In addition to the expected N2-ethyldeoxyguanosine (after NaBH3CN reduction), two previously unreported adducts showed prominent signals in the mass spectra. MSn fragmentation spectra and accurate mass were used to hypothesize the structure of the two new adducts, which were then identified as N6-ethyldeoxyadenosine and N4-ethyldeoxycytidine by comparison with synthesized standards. These adducts were quantified in DNA isolated from oral cells collected from volunteers exposed to alcohol, revealing a significant increase after the exposure. In addition, 17 of the adducts identified in vitro were detected in these samples confirming our ability to more comprehensively characterize the DNA damage deriving from alcohol exposures.
Collapse
|
19
|
Alqarni MH, Foudah AI, Muharram MM, Budurian H, Labrou NE. Probing the Role of the Conserved Arg174 in Formate Dehydrogenase by Chemical Modification and Site-Directed Mutagenesis. Molecules 2021; 26:molecules26051222. [PMID: 33668802 PMCID: PMC7956174 DOI: 10.3390/molecules26051222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 11/22/2022] Open
Abstract
The reactive adenosine derivative, adenosine 5′-O-[S-(4-hydroxy-2,3-dioxobutyl)]-thiophosphate (AMPS-HDB), contains a dicarbonyl group linked to the purine nucleotide at a position equivalent to the pyrophosphate region of NAD+. AMPS-HDB was used as a chemical label towards Candida boidinii formate dehydrogenase (CbFDH). AMPS-HDB reacts covalently with CbFDH, leading to complete inactivation of the enzyme activity. The inactivation kinetics of CbFDH fit the Kitz and Wilson model for time-dependent, irreversible inhibition (KD = 0.66 ± 0.15 mM, first order maximum rate constant k3 = 0.198 ± 0.06 min−1). NAD+ and NADH protects CbFDH from inactivation by AMPS-HDB, showing the specificity of the reaction. Molecular modelling studies revealed Arg174 as a candidate residue able to be modified by the dicarbonyl group of AMPS-HDB. Arg174 is a strictly conserved residue among FDHs and is located at the Rossmann fold, the common mononucleotide-binding motif of dehydrogenases. Arg174 was replaced by Asn, using site-directed mutagenesis. The mutant enzyme CbFDHArg174Asn was showed to be resistant to inactivation by AMPS-HDB, confirming that the guanidinium group of Arg174 is the target for AMPS-HDB. The CbFDHArg174Asn mutant enzyme exhibited substantial reduced affinity for NAD+ and lower thermostability. The results of the study underline the pivotal and multifunctional role of Arg174 in catalysis, coenzyme binding and structural stability of CbFDH.
Collapse
Affiliation(s)
- Mohammed Hamed Alqarni
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia;
- Correspondence: (M.H.A.); (N.E.L.)
| | - Ahmed Ibrahim Foudah
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia;
| | - Magdy Mohamed Muharram
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia;
- Department of Microbiology, College of Science, Al-Azhar University, Nasr City, Cairo 11884, Egypt
| | - Haritium Budurian
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 Athens, Greece;
| | - Nikolaos E. Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 Athens, Greece;
- Correspondence: (M.H.A.); (N.E.L.)
| |
Collapse
|
20
|
Strzelecka D, Smietanski M, Sikorski PJ, Warminski M, Kowalska J, Jemielity J. Phosphodiester modifications in mRNA poly(A) tail prevent deadenylation without compromising protein expression. RNA (NEW YORK, N.Y.) 2020; 26:1815-1837. [PMID: 32820035 PMCID: PMC7668260 DOI: 10.1261/rna.077099.120] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/13/2020] [Indexed: 06/07/2023]
Abstract
Chemical modifications enable preparation of mRNAs with augmented stability and translational activity. In this study, we explored how chemical modifications of 5',3'-phosphodiester bonds in the mRNA body and poly(A) tail influence the biological properties of eukaryotic mRNA. To obtain modified and unmodified in vitro transcribed mRNAs, we used ATP and ATP analogs modified at the α-phosphate (containing either O-to-S or O-to-BH3 substitutions) and three different RNA polymerases-SP6, T7, and poly(A) polymerase. To verify the efficiency of incorporation of ATP analogs in the presence of ATP, we developed a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for quantitative assessment of modification frequency based on exhaustive degradation of the transcripts to 5'-mononucleotides. The method also estimated the average poly(A) tail lengths, thereby providing a versatile tool for establishing a structure-biological property relationship for mRNA. We found that mRNAs containing phosphorothioate groups within the poly(A) tail were substantially less susceptible to degradation by 3'-deadenylase than unmodified mRNA and were efficiently expressed in cultured cells, which makes them useful research tools and potential candidates for future development of mRNA-based therapeutics.
Collapse
Affiliation(s)
- Dominika Strzelecka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | | | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| |
Collapse
|
21
|
Maity C, Ghosh D, Guha S. Assays for Intracellular Cyclic Adenosine Monophosphate (cAMP) and Lysosomal Acidification. Methods Mol Biol 2020; 1996:161-178. [PMID: 31127555 DOI: 10.1007/978-1-4939-9488-5_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cyclic adenosine monophosphate (3',5'-cAMP) is a multifunctional second messenger which controls extremely diverse and physiologically important biochemical pathways. Among its myriad roles, 3',5'-cAMP functions as an intracellular regulator of lysosomal pH, which is essential for the activity of acidic lysosomal enzymes. Defects in lysosomal acidification are attributed to many diseases like macular degeneration, Parkinson's, Alzheimer's, and cystic fibrosis. Strategic re-acidification of defective lysosomes by pharmacological increase of intracellular cAMP offers exciting therapeutic potential in these diseases. Modular assays for accurate assessment of intracellular cAMP and lysosomal pH are a critical component of this research. We describe label-free targeted metabolomics for quantitating intracellular cAMP and integrated assays for measuring lysosomal pH. These hybrid assays offer fast, unbiased information on intracellular cAMP concentrations and lysosomal pH that can be applied to many cell types and putative drug screening strategies.
Collapse
Affiliation(s)
- Chiranjit Maity
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Dipankar Ghosh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Sonia Guha
- Stein Eye Institute, University of California Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
22
|
Calderisi G, Glasner H, Breuker K. Radical Transfer Dissociation for De Novo Characterization of Modified Ribonucleic Acids by Mass Spectrometry. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Giovanni Calderisi
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität Innsbruck Innrain 80/82 6020 Innsbruck Austria
| | - Heidelinde Glasner
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität Innsbruck Innrain 80/82 6020 Innsbruck Austria
| | - Kathrin Breuker
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität Innsbruck Innrain 80/82 6020 Innsbruck Austria
| |
Collapse
|
23
|
Calderisi G, Glasner H, Breuker K. Radical Transfer Dissociation for De Novo Characterization of Modified Ribonucleic Acids by Mass Spectrometry. Angew Chem Int Ed Engl 2020; 59:4309-4313. [PMID: 31867820 PMCID: PMC7065001 DOI: 10.1002/anie.201914275] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Indexed: 12/20/2022]
Abstract
Mass spectrometry (MS) can reliably detect and localize all mass-altering modifications of ribonucleic acids (RNA), but current MS approaches that allow for simultaneous de novo sequencing and modification analysis generally require specialized instrumentation. Here we report a novel RNA dissociation technique, radical transfer dissociation (RTD), that can be used for the comprehensive de novo characterization of ribonucleic acids and their posttranscriptional or synthetic modifications. We demonstrate full sequence coverage for RNA consisting of up to 39 nucleotides and show that RTD is especially useful for RNA with highly labile modifications such as 5-hydroxymethylcytidine and 5-formylcytidine.
Collapse
Affiliation(s)
- Giovanni Calderisi
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität InnsbruckInnrain 80/826020InnsbruckAustria
| | - Heidelinde Glasner
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität InnsbruckInnrain 80/826020InnsbruckAustria
| | - Kathrin Breuker
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI)Universität InnsbruckInnrain 80/826020InnsbruckAustria
| |
Collapse
|
24
|
Franco A, Ascenso JR, Ilharco L, Silva JALD. Synthesis of ribonucleotides from the corresponding ribonucleosides under plausible prebiotic conditions within self-assembled supramolecular structures. NEW J CHEM 2020. [DOI: 10.1039/c9nj05601g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abiotic synthesis of ribonucleotides, mainly at the 5′ position, from the corresponding ribonucleosides within guanosine:borate hydrogels in the temperature range of 70–90 °C, using urea and a phosphate source (K2HPO4 or hydroxyapatite).
Collapse
Affiliation(s)
- A. Franco
- Centro de Química Estrutural
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisboa
- Portugal
| | - J. R. Ascenso
- Centro de Química Estrutural
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisboa
- Portugal
| | - L. Ilharco
- IBB
- Instituto de Bioengenharia e Biociências
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisboa
| | - J. A. L. da Silva
- Centro de Química Estrutural
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisboa
- Portugal
| |
Collapse
|
25
|
Development and validation of a rapid LC–MS/MS method for determination of methylated nucleosides and nucleobases in urine. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1128:121775. [DOI: 10.1016/j.jchromb.2019.121775] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/12/2019] [Accepted: 08/20/2019] [Indexed: 12/11/2022]
|
26
|
Nakamura M, Matsuda K, Nakamura M, Yamashita K, Suzuki T, Inouye S. Enzymatic Conversion of Cypridina Luciferyl Sulfate to Cypridina Luciferin with Coenzyme A as a Sulfate Acceptor in Cypridina (Vargula) hilgendorfii. Photochem Photobiol 2019; 95:1376-1386. [PMID: 31230356 DOI: 10.1111/php.13137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/07/2019] [Accepted: 06/13/2019] [Indexed: 01/09/2023]
Abstract
In the luminous ostracod Cypridina (presently Vargula) hilgendorfii, Cypridina luciferyl sulfate (3-enol sulfate of Cypridina luciferin) is converted to Cypridina luciferin by a sulfotransferase with 3'-phosphoadenosine-5'-phosphate (PAP) as a sulfate acceptor. The resultant Cypridina luciferin is used for the luciferase-luciferin reaction of Cypridina to emit blue light. The luminescence stimulation with major organic cofactors was examined using the crude extracts of Cypridina specimens, and we found that the addition of coenzyme A (CoA) to the crude extracts significantly stimulated luminescence intensity. Further, the light-emitting source in the crude extracts stimulated with CoA was identified as Cypridina luciferyl sulfate, and we demonstrated that CoA could act as a sulfate acceptor from Cypridina luciferyl sulfate. In addition, the sulfate group of Cypridina luciferyl sulfate was also transferred to adenosine 5'-monophosphate (5'-AMP) and adenosine 3'-monophosphate (3'-AMP) by a sulfotransferase. The sulfated products corresponding to CoA, 5'-AMP and 3'-AMP were identified using mass spectrometry. This is the first report that CoA can act as a sulfate acceptor in a sulfotransferase reaction.
Collapse
Affiliation(s)
- Mitsuhiro Nakamura
- Graduate School of Science and Technology, Tokushima University, Tokushima, Japan.,Graduate School of Integrated Arts and Sciences, Tokushima University, Tokushima, Japan
| | - Kazuo Matsuda
- Graduate School of Integrated Arts and Sciences, Tokushima University, Tokushima, Japan
| | - Misaki Nakamura
- Graduate School of Integrated Arts and Sciences, Tokushima University, Tokushima, Japan
| | - Kyohei Yamashita
- Graduate School of Integrated Arts and Sciences, Tokushima University, Tokushima, Japan
| | - Tomoko Suzuki
- Graduate School of Integrated Arts and Sciences, Tokushima University, Tokushima, Japan
| | - Satoshi Inouye
- Yokohama Research Center, JNC Corporation, Yokohama, Japan
| |
Collapse
|
27
|
|
28
|
Secondary‐Ion Mass Spectrometry Images Cardiolipins and Phosphatidylethanolamines at the Subcellular Level. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814256] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
29
|
Tian H, Sparvero LJ, Blenkinsopp P, Amoscato AA, Watkins SC, Bayır H, Kagan VE, Winograd N. Secondary-Ion Mass Spectrometry Images Cardiolipins and Phosphatidylethanolamines at the Subcellular Level. Angew Chem Int Ed Engl 2019; 58:3156-3161. [PMID: 30680861 DOI: 10.1002/anie.201814256] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Indexed: 12/22/2022]
Abstract
Millions of diverse molecules constituting the lipidome act as important signals within cells. Of these, cardiolipin (CL) and phosphatidylethanolamine (PE) participate in apoptosis and ferroptosis, respectively. Their subcellular distribution is largely unknown. Imaging mass spectrometry is capable of deciphering the spatial distribution of multiple lipids at subcellular levels. Here we report the development of a unique 70 keV gas-cluster ion beam that consists of (CO2 )n + (n>10 000) projectiles. Coupled with direct current beam buncher-time-of-flight secondary-ion mass spectrometry, it is optimized for sensitivity towards high-mass species (up to m/z 3000) at high spatial resolution (1 μm). In combination with immunohistochemistry, phospholipids, including PE and CL, have been assessed in subcellular compartments of mouse hippocampal neuronal cells and rat brain tissue.
Collapse
Affiliation(s)
- Hua Tian
- Department of Chemistry, Pennsylvania State University, 209 Chemistry Bldg., University Park, PA, 16802, USA
| | - Louis J Sparvero
- Department of Environmental and Occupational Health and Center for Free Radical and Antioxidant Health, University of Pittsburgh, USA
| | - Paul Blenkinsopp
- Ionoptika Ltd., Unit B6, Millbrook Cl, Chandler's Ford, Eastleigh, SO53 4BZ, UK
| | - Andrew A Amoscato
- Department of Environmental and Occupational Health and Center for Free Radical and Antioxidant Health, University of Pittsburgh, USA
| | | | - Hülya Bayır
- Department of Chemistry, Pennsylvania State University, 209 Chemistry Bldg., University Park, PA, 16802, USA.,Departments of Environmental and Occupational Health, Radiation Oncology, Critical Care Medicine, Center for Free Radical and Antioxidant Health and Safar Center for Resuscitation Research, University of Pittsburgh, USA.,Children's Neuroscience Institute, UPMC Children's Hospital, University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA, 15260, USA
| | - Valerian E Kagan
- Department of Chemistry, Pennsylvania State University, 209 Chemistry Bldg., University Park, PA, 16802, USA.,Departments of Environmental and Occupational Health, Chemistry, Radiation Oncology, Center for Free Radical and Antioxidant Health, University of Pittsburgh, USA.,Laboratory of Navigational Redox Lipidomics, IM Sechenov Moscow Medical State University, Russia
| | - Nicholas Winograd
- Department of Chemistry, Pennsylvania State University, 209 Chemistry Bldg., University Park, PA, 16802, USA
| |
Collapse
|