1
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Feng H, Lu XJ, Maji S, Liu L, Ustianenko D, Rudnick ND, Zhang C. Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes. Nat Commun 2024; 15:2279. [PMID: 38480694 PMCID: PMC10937933 DOI: 10.1038/s41467-024-46429-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: 08/06/2023] [Accepted: 02/26/2024] [Indexed: 03/17/2024] Open
Abstract
UV-crosslinking of protein and RNA in direct contacts has been widely used to study protein-RNA complexes while our understanding of the photo-crosslinking mechanisms remains poor. This knowledge gap is due to the challenge of precisely mapping the crosslink sites in protein and RNA simultaneously in their native sequence and structural contexts. Here we systematically analyze protein-RNA interactions and photo-crosslinking by bridging crosslinked nucleotides and amino acids mapped using different assays with protein-RNA complex structures. We developed a computational method PxR3D-map which reliably predicts crosslink sites using structural information characterizing protein-RNA interaction interfaces. Analysis of the informative features revealed that photo-crosslinking is facilitated by base stacking with not only aromatic residues, but also dipeptide bonds that involve glycine, and distinct mechanisms are utilized by different RNA-binding domains. Our work suggests protein-RNA photo-crosslinking is highly selective in the cellular environment, which can guide data interpretation and further technology development for UV-crosslinking-based assays.
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Affiliation(s)
- Huijuan Feng
- Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Xiang-Jun Lu
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Suvrajit Maji
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Linxi Liu
- Department of Statistics, Columbia University, New York, NY, 10027, USA
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Dmytro Ustianenko
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Noam D Rudnick
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA.
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2
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Knörlein A, Sarnowski CP, de Vries T, Stoltz M, Götze M, Aebersold R, Allain FHT, Leitner A, Hall J. Nucleotide-amino acid π-stacking interactions initiate photo cross-linking in RNA-protein complexes. Nat Commun 2022; 13:2719. [PMID: 35581222 PMCID: PMC9114321 DOI: 10.1038/s41467-022-30284-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 04/20/2022] [Indexed: 12/26/2022] Open
Abstract
Photo-induced cross-linking is a mainstay technique to characterize RNA-protein interactions. However, UV-induced cross-linking between RNA and proteins at “zero-distance” is poorly understood. Here, we investigate cross-linking of the RBFOX alternative splicing factor with its hepta-ribonucleotide binding element as a model system. We examine the influence of nucleobase, nucleotide position and amino acid composition using CLIR-MS technology (crosslinking-of-isotope-labelled-RNA-and-tandem-mass-spectrometry), that locates cross-links on RNA and protein with site-specific resolution. Surprisingly, cross-linking occurs only at nucleotides that are π-stacked to phenylalanines. Notably, this π-stacking interaction is also necessary for the amino-acids flanking phenylalanines to partake in UV-cross-linking. We confirmed these observations in several published datasets where cross-linking sites could be mapped to a high resolution structure. We hypothesize that π-stacking to aromatic amino acids activates cross-linking in RNA-protein complexes, whereafter nucleotide and peptide radicals recombine. These findings will facilitate interpretation of cross-linking data from structural studies and from genome-wide datasets generated using CLIP (cross-linking-and-immunoprecipitation) methods. Although UV-induced cross-linking is a widely used method to study RNA-protein complexes, the cross-linking reactions are poorly understood. Here, the authors show that π-stacking interactions between nucleobases and aromatic amino acids play a key role in the cross-linking process.
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Affiliation(s)
- Anna Knörlein
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Chris P Sarnowski
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Tebbe de Vries
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Moritz Stoltz
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Michael Götze
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Free University Berlin, Berlin, Germany
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Frédéric H-T Allain
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland.
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3
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Sarnowski CP, Bikaki M, Leitner A. Cross-linking and mass spectrometry as a tool for studying the structural biology of ribonucleoproteins. Structure 2022; 30:441-461. [PMID: 35366400 DOI: 10.1016/j.str.2022.03.003] [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: 07/29/2021] [Revised: 02/03/2022] [Accepted: 03/01/2022] [Indexed: 11/17/2022]
Abstract
Cross-linking and mass spectrometry (XL-MS) workflows represent an increasingly popular technique for low-resolution structural studies of macromolecular complexes. Cross-linking reactions take place in the solution state, capturing contact sites between components of a complex that represent the native, functionally relevant structure. Protein-protein XL-MS protocols are widely adopted, providing precise localization of cross-linking sites to single amino acid positions within a pair of cross-linked peptides. In contrast, protein-RNA XL-MS workflows are evolving rapidly and differ in their ability to localize interaction regions within the RNA sequence. Here, we review protein-protein and protein-RNA XL-MS workflows, and discuss their applications in studies of protein-RNA complexes. The examples highlight the complementary value of XL-MS in structural studies of protein-RNA complexes, where more established high-resolution techniques might be unable to produce conclusive data.
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Affiliation(s)
- Chris P Sarnowski
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zurich, Switzerland; Systems Biology PhD Program, University of Zürich and ETH Zürich, Zurich, Switzerland
| | - Maria Bikaki
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zurich, Switzerland
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zurich, Switzerland.
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4
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Götze M, Sarnowski CP, de Vries T, Knörlein A, Allain FHT, Hall J, Aebersold R, Leitner A. Single Nucleotide Resolution RNA-Protein Cross-Linking Mass Spectrometry: A Simple Extension of the CLIR-MS Workflow. Anal Chem 2021; 93:14626-14634. [PMID: 34714631 PMCID: PMC8581962 DOI: 10.1021/acs.analchem.1c02384] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
RNA–protein
interactions mediate many intracellular processes.
CLIR-MS (cross-linking of isotope-labeled RNA and tandem mass spectrometry)
allows the identification of RNA–protein interaction sites
at single nucleotide/amino acid resolution in a single experiment.
Using isotopically labeled RNA segments for UV-light-induced cross-linking
generates characteristic isotope patterns that constrain the sequence
database searches, increasing spatial resolution. Whereas the use
of segmentally isotopically labeled RNA is effective, it is technically
involved and not applicable in some settings, e.g., in cell or tissue
samples. Here we introduce an extension of the CLIR-MS workflow that
uses unlabeled RNA during cross-linking and subsequently adds an isotopic
label during sample preparation for MS analysis. After RNase and protease
digests of a cross-linked complex, the nucleic acid part of a peptide–RNA
conjugate is labeled using the enzyme T4 polynucleotide kinase and
a 1:1 mixture of heavy 18O4-γ-ATP and
light ATP. In this simple, one-step reaction, three heavy oxygen atoms
are transferred from the γ-phosphate to the 5′-end of
the RNA, introducing an isotopic shift of 6.01 Da that is detectable
by mass spectrometry. We applied this approach to the RNA recognition
motif (RRM) of the protein FOX1 in complex with its cognate binding
substrate, FOX-binding element (FBE) RNA. We also labeled a single
phosphate within an RNA and unambiguously determined the cross-linking
site of the FOX1-RRM binding to FBE at single residue resolution on
the RNA and protein level and used differential ATP labeling for relative
quantification based on isotope dilution. Data are available via ProteomeXchange
with the identifier PXD024010.
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Affiliation(s)
- Michael Götze
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich 8093, Switzerland
| | - Chris P Sarnowski
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich 8093, Switzerland
| | - Tebbe de Vries
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich 8093, Switzerland
| | - Anna Knörlein
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, Zürich 8093, Switzerland
| | - Frédéric H-T Allain
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich 8093, Switzerland
| | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, Zürich 8093, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich 8093, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich 8093, Switzerland
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5
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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6
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Leitner A, Dorn G, Allain FHT. Combining Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) Spectroscopy for Integrative Structural Biology of Protein-RNA Complexes. Cold Spring Harb Perspect Biol 2019; 11:a032359. [PMID: 31262947 PMCID: PMC6601463 DOI: 10.1101/cshperspect.a032359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Deciphering complex RNA-protein interactions on a (near-)atomic level is a hurdle that hinders advancing our understanding of fundamental processes in RNA metabolism and RNA-based gene regulation. To overcome challenges associated with individual structure determination methods, structural information derived from complementary biophysical methods can be combined in integrative structural biology approaches. Here, we review recent advances in such hybrid structural approaches with a focus on combining mass spectrometric analysis of cross-linked protein-RNA complexes and nuclear magnetic resonance (NMR) spectroscopy.
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Affiliation(s)
- Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Georg Dorn
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
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7
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Weng G, Sun B, Liu Z, Wang F, Pan Y. Analysis of oligonucleotides by ion-pair reversed-phase liquid chromatography coupled with positive mode electrospray ionization mass spectrometry. Anal Bioanal Chem 2019; 411:4167-4173. [PMID: 30989264 DOI: 10.1007/s00216-019-01819-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/12/2019] [Accepted: 03/28/2019] [Indexed: 11/28/2022]
Abstract
Oligonucleotides are usually analyzed by ion-pair reversed-phase liquid chromatography (IP-RPLC) coupled with negative mode electrospray ionization mass spectrometry (ESI-MS) due to their highly negative charged phosphodiester backbones. Herein, the signal suppression effect of triethylamine (TEA) adducts caused the ion-pair reagent TEA/hexafluoroisopropanol (HFIP) is greatly alleviated after improving the in-source energy in positive mode ESI-MS. This strategy is applied for different RNA sequencing through analyzing their formic acid hydrolysates via IP-RPLC MS. Comparing with negative ion mode, we demonstrate that IP-RPLC MS analysis in positive ion mode is more suitable for RNA sequencing with fewer contaminant interferences. Finally, simultaneous online separation and detection of oligonucleotides and protein digests are achieved in positive ion mode IP-RPLC MS analysis with little interference to each other.
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Affiliation(s)
- Guofeng Weng
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, China.,CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, Liaoning, China
| | - Binwen Sun
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, Liaoning, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, Liaoning, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, Liaoning, China.
| | - Yuanjiang Pan
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang, China.
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8
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Stulz R, Meuller J, Baždarević D, Wennberg Huldt C, Strömberg R, Andersson S, Dahlén A. A Versatile and Convenient Synthesis of 34 S-Labeled Phosphorothioate Oligonucleotides. Chembiochem 2018; 19:2114-2119. [PMID: 30062829 PMCID: PMC6585993 DOI: 10.1002/cbic.201800417] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/20/2022]
Abstract
A synthetic protocol for 34 S-labeled phosphorothioate oligonucleotides (PS ONs) was developed to facilitate MS-based assay analysis. This was enabled by a highly efficient, two-step, one-pot synthesis of 34 S-labeled phenylacetyl disulfide (34 S-PADS), starting from 34 S-enriched elemental sulfur (34 S8 ). 34 S-PADS was subsequently used for stable isotope labeling (SIL) of oligonucleotides containing a phosphorothioate backbone. The 34 S-SIL PS ONs are shown to retain the same melting temperature, antisense activity, and secondary structure as those of the corresponding unlabeled 32 S PS ONs.
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Affiliation(s)
- Rouven Stulz
- Cardiovascular, Renal and Metabolism IMED Biotech Unit, AstraZeneca, Pepparedsleden 1, 43150, Mölndal, Sweden.,Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Hälsovägen 9, 14157, Huddinge, Sweden
| | - Johan Meuller
- Discovery Sciences IMED Biotech Unit, AstraZeneca, Pepparedsleden 1, 43150, Mölndal, Sweden
| | - Dženita Baždarević
- Cardiovascular, Renal and Metabolism IMED Biotech Unit, AstraZeneca, Pepparedsleden 1, 43150, Mölndal, Sweden
| | - Charlotte Wennberg Huldt
- Cardiovascular, Renal and Metabolism IMED Biotech Unit, AstraZeneca, Pepparedsleden 1, 43150, Mölndal, Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Hälsovägen 9, 14157, Huddinge, Sweden
| | - Shalini Andersson
- Cardiovascular, Renal and Metabolism IMED Biotech Unit, AstraZeneca, Pepparedsleden 1, 43150, Mölndal, Sweden
| | - Anders Dahlén
- Cardiovascular, Renal and Metabolism IMED Biotech Unit, AstraZeneca, Pepparedsleden 1, 43150, Mölndal, Sweden
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9
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Flett FJ, Sachsenberg T, Kohlbacher O, Mackay CL, Interthal H. Differential Enzymatic 16O/ 18O Labeling for the Detection of Cross-Linked Nucleic Acid-Protein Heteroconjugates. Anal Chem 2017; 89:11208-11213. [PMID: 28885003 DOI: 10.1021/acs.analchem.7b01625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cross-linking of nucleic acids to proteins in combination with mass spectrometry permits the precise identification of interacting residues between nucleic acid-protein complexes. However, the mass spectrometric identification and characterization of cross-linked nucleic acid-protein heteroconjugates within a complex sample is challenging. Here we establish a novel enzymatic differential 16O/18O-labeling approach, which uniquely labels heteroconjugates. We have developed an automated data analysis workflow based on OpenMS for the identification of differentially isotopically labeled heteroconjugates against a complex background. We validated our method using synthetic model DNA oligonucleotide-peptide heteroconjugates, which were subjected to the labeling reaction and analyzed by high-resolution FTICR mass spectrometry.
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Affiliation(s)
- Fiona J Flett
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3FF, Scotland, U.K
| | - Timo Sachsenberg
- Center for Bioinformatics, Quantitative Biology Center and Department of Computer Science, University of Tübingen , Sand 14, 72076 Tübingen, Germany
| | - Oliver Kohlbacher
- Center for Bioinformatics, Quantitative Biology Center and Department of Computer Science, University of Tübingen , Sand 14, 72076 Tübingen, Germany.,Max Planck Institute for Developmental Biology , Spemannstr. 35, 72076 Tübingen, Germany
| | - C Logan Mackay
- School of Chemistry, University of Edinburgh , Edinburgh EH9 3FJ, Scotland, U.K
| | - Heidrun Interthal
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3FF, Scotland, U.K
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10
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Lian L, Yan S, Yao B, Chan SA, Song W. Photochemical Transformation of Nicotine in Wastewater Effluent. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:11718-11730. [PMID: 28942634 DOI: 10.1021/acs.est.7b03223] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Nicotine is a highly toxic tobacco alkaloid that is ubiquitous in wastewater effluent. For the first time, we report the identification of the products and the pathways for the photodegradation of nicotine in an effluent matrix under simulated solar irradiation. Nicotine was found to be degraded by triplet-state organic matter (3OM*), thus indicating that electron transfer is a preferred reaction mechanism. Using the multivariate statistical strategies orthogonal projection to latent structures discriminant analysis (OPLS-DA) and hierarchical clustering, 49 potential transformation products (TPs) of nicotine were successfully extracted from the water matrix via high-resolution ultrahigh-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS). Overall, 30 TPs, including 4 groups of nonseparated isomeric photo TPs, were identified with various levels of confidence based on the tandem mass spectrometry information on standard compounds and the isotope-labeling method (using rac-nicotine-2',3',3'-D3, rac-nicotine-13CD3, and rac-nicotine-D4) under air-saturated conditions. The pyrrolidine ring of nicotine was found to be the reactive site under sunlight irradiation. Pseudooxynicotine was the main primary TP from nicotine, with a maximum transformation ratio of 64%. Nicotinic acid, cotinine, 3'-hydroxycotinine, and myosmine were the final stable TPs after 72 h of solar irradiation, with yields of 13%, 3%, 5%, and 5%, respectively.
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Affiliation(s)
- Lushi Lian
- Department of Environmental Science and Engineering, Fudan University , Shanghai 200433, China
| | - Shuwen Yan
- Department of Environmental Science and Engineering, Fudan University , Shanghai 200433, China
| | - Bo Yao
- Department of Environmental Science and Engineering, Fudan University , Shanghai 200433, China
| | - Shen-An Chan
- Agilent Technology, Inc. , 1350 North Sichuan Road, Shanghai 200080, PR China
| | - Weihua Song
- Department of Environmental Science and Engineering, Fudan University , Shanghai 200433, China
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11
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Ransey E, Björkbom A, Lelyveld VS, Biecek P, Pantano L, Szostak JW, Sliz P. Comparative analysis of LIN28-RNA binding sites identified at single nucleotide resolution. RNA Biol 2017; 14:1756-1765. [PMID: 28945502 PMCID: PMC5731800 DOI: 10.1080/15476286.2017.1356566] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
It remains a formidable challenge to characterize the diverse complexes of RNA binding proteins and their targets. While crosslink and immunoprecipitation (CLIP) methods are powerful techniques that identify RNA targets on a global scale, the resolution and consistency of these methods is a matter of debate. Here we present a comparative analysis of LIN28-pre-let-7 UV-induced crosslinking using a tandem mass spectrometry (MS/MS) and deep sequencing interrogation of in vitro crosslinked complexes. Interestingly, analyses by the two methods diverge in their identification of crosslinked nucleotide identity – whereas bioinformatics and sequencing analyses suggest guanine in mammalian cells, MS/MS identifies uridine. This work suggests the need for comprehensive analysis and validation of crosslinking methodologies.
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Affiliation(s)
- Elizabeth Ransey
- a Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , MA
| | - Anders Björkbom
- c Department of Molecular Biology and Center for Computational and Integrative Biology , Howard Hughes Medical Institute, Massachusetts General Hospital , Boston , MA , USA.,d Åbo Akademi University , Department of Biosciences , Artillerigatan 6, FI-20520 Åbo , Finland
| | - Victor S Lelyveld
- c Department of Molecular Biology and Center for Computational and Integrative Biology , Howard Hughes Medical Institute, Massachusetts General Hospital , Boston , MA , USA
| | - Przemyslaw Biecek
- e Faculty of Mathematics Informatics and Mechanics, University of Warsaw , Banacha 2, Warsaw , Poland
| | - Lorena Pantano
- f Department of Biostatistics , Harvard T.H. Chan School of Public Health , Boston , MA , USA
| | - Jack W Szostak
- c Department of Molecular Biology and Center for Computational and Integrative Biology , Howard Hughes Medical Institute, Massachusetts General Hospital , Boston , MA , USA
| | - Piotr Sliz
- a Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , MA.,b Division of Molecular Medicine , Boston Children's Hospital , Boston , MA , USA
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12
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Dorn G, Leitner A, Boudet J, Campagne S, von Schroetter C, Moursy A, Aebersold R, Allain FHT. Structural modeling of protein-RNA complexes using crosslinking of segmentally isotope-labeled RNA and MS/MS. Nat Methods 2017; 14:487-490. [PMID: 28346450 PMCID: PMC5505470 DOI: 10.1038/nmeth.4235] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 02/22/2017] [Indexed: 11/09/2022]
Abstract
Ribonucleoproteins (RNPs) are key regulators of cellular function. We established an efficient approach that combines segmental isotope labeling of RNA with photo-crosslinking and tandem mass spectrometry to localize protein-RNA interactions simultaneously at amino acid and nucleotide resolution. The approach was tested on Polypyrimidine Tract Binding Protein 1 and U1 small nuclear RNP and the results support integrative atomic-scale structural modeling thus providing mechanistic insights into RNP regulated processes.
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Affiliation(s)
- G Dorn
- Department of Biology, Institute for Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - A Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - J Boudet
- Department of Biology, Institute for Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - S Campagne
- Department of Biology, Institute for Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - C von Schroetter
- Department of Biology, Institute for Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - A Moursy
- Department of Biology, Institute for Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - R Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland.,Faculty of Science, University of Zurich, Zürich, Switzerland
| | - F H-T Allain
- Department of Biology, Institute for Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
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Sugihara Y, Tatsumi S, Kobori A. Development of Novel Photoresponsive Oligodeoxyribonucleotides with a 2′-O-Diazirine-conjugated Adenosine for DNA Interstrand Crosslinking. CHEM LETT 2017. [DOI: 10.1246/cl.160998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Wright TH, Bower BJ, Chalker JM, Bernardes GJL, Wiewiora R, Ng WL, Raj R, Faulkner S, Vallée MRJ, Phanumartwiwath A, Coleman OD, Thézénas ML, Khan M, Galan SRG, Lercher L, Schombs MW, Gerstberger S, Palm-Espling ME, Baldwin AJ, Kessler BM, Claridge TDW, Mohammed S, Davis BG. Posttranslational mutagenesis: A chemical strategy for exploring protein side-chain diversity. Science 2016; 354:science.aag1465. [PMID: 27708059 DOI: 10.1126/science.aag1465] [Citation(s) in RCA: 220] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/12/2016] [Indexed: 12/26/2022]
Abstract
Posttranslational modification of proteins expands their structural and functional capabilities beyond those directly specified by the genetic code. However, the vast diversity of chemically plausible (including unnatural but functionally relevant) side chains is not readily accessible. We describe C (sp3)-C (sp3) bond-forming reactions on proteins under biocompatible conditions, which exploit unusual carbon free-radical chemistry, and use them to form Cβ-Cγ bonds with altered side chains. We demonstrate how these transformations enable a wide diversity of natural, unnatural, posttranslationally modified (methylated, glycosylated, phosphorylated, hydroxylated), and labeled (fluorinated, isotopically labeled) side chains to be added to a common, readily accessible dehydroalanine precursor in a range of representative protein types and scaffolds. This approach, outside of the rigid constraints of the ribosome and enzymatic processing, may be modified more generally for access to diverse proteins.
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Affiliation(s)
- Tom H Wright
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Ben J Bower
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Justin M Chalker
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | | | - Rafal Wiewiora
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Wai-Lung Ng
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Ritu Raj
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Sarah Faulkner
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | | | | | - Oliver D Coleman
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Marie-Laëtitia Thézénas
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Headington, Oxford OX3 7FZ, UK
| | - Maola Khan
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | | | - Lukas Lercher
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | | | | | | | - Andrew J Baldwin
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Headington, Oxford OX3 7FZ, UK
| | | | - Shabaz Mohammed
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Benjamin G Davis
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.
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