51
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Core-Level Spectroscopy of 2-Thiouracil at the Sulfur L 1- and L 2,3-Edges Utilizing a SASE Free-Electron Laser. Molecules 2021; 26:molecules26216469. [PMID: 34770877 PMCID: PMC8586990 DOI: 10.3390/molecules26216469] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/17/2022] Open
Abstract
In this paper, we report X-ray absorption and core-level electron spectra of the nucleobase derivative 2-thiouracil at the sulfur L1- and L2,3-edges. We used soft X-rays from the free-electron laser FLASH2 for the excitation of isolated molecules and dispersed the outgoing electrons with a magnetic bottle spectrometer. We identified photoelectrons from the 2p core orbital, accompanied by an electron correlation satellite, as well as resonant and non-resonant Coster–Kronig and Auger–Meitner emission at the L1- and L2,3-edges, respectively. We used the electron yield to construct X-ray absorption spectra at the two edges. The experimental data obtained are put in the context of the literature currently available on sulfur core-level and 2-thiouracil spectroscopy.
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52
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Bae JW, Kim S, Kim VN, Kim JS. Photoactivatable ribonucleosides mark base-specific RNA-binding sites. Nat Commun 2021; 12:6026. [PMID: 34654832 PMCID: PMC8519950 DOI: 10.1038/s41467-021-26317-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/28/2021] [Indexed: 12/13/2022] Open
Abstract
RNA-protein interaction can be captured by crosslinking and enrichment followed by tandem mass spectrometry, but it remains challenging to pinpoint RNA-binding sites (RBSs) or provide direct evidence for RNA-binding. To overcome these limitations, we here developed pRBS-ID, by incorporating the benefits of UVA-based photoactivatable ribonucleoside (PAR; 4-thiouridine and 6-thioguanosine) crosslinking and chemical RNA cleavage. pRBS-ID robustly detects peptides crosslinked to PAR adducts, offering direct RNA-binding evidence and identifying RBSs at single amino acid-resolution with base-specificity (U or G). Using pRBS-ID, we could profile uridine-contacting RBSs globally and discover guanosine-contacting RBSs, which allowed us to characterize the base-specific interactions. We also applied the search pipeline to analyze the datasets from UVC-based RBS-ID experiments, altogether offering a comprehensive list of human RBSs with high coverage (3,077 RBSs in 532 proteins in total). pRBS-ID is a widely applicable platform to investigate the molecular basis of posttranscriptional regulation.
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Affiliation(s)
- Jong Woo Bae
- Center for RNA Research, Institute for Basic Science, Seoul, 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | | | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul, 08826, Korea.
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea.
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science, Seoul, 08826, Korea.
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea.
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53
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Tang J, Zhao W, Hendricks NG, Zhao L. High-Resolution Mapping of Amino Acid Residues in DNA-Protein Cross-Links Enabled by Ribonucleotide-Containing DNA. Anal Chem 2021; 93:13398-13406. [PMID: 34559515 DOI: 10.1021/acs.analchem.1c03481] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA-protein cross-links have broad applications in mapping DNA-protein interactions and provide structural insights into macromolecular structures. However, high-resolution mapping of DNA-interacting amino acid residues with tandem mass spectrometry remains challenging due to difficulties in sample preparation and data analysis. Herein, we developed a method for identifying cross-linking amino residues in DNA-protein cross-links at single amino acid resolution. We leveraged the alkaline lability of ribonucleotides and designed ribonucleotide-containing DNA to produce structurally defined nucleic acid-peptide cross-links under our optimized ribonucleotide cleavage conditions. The structurally defined oligonucleotide-peptide heteroconjugates improved ionization, reduced the database search space, and facilitated the identification of cross-linking residues in peptides. We applied the workflow to identifying abasic (AP) site-interacting residues in human mitochondrial transcription factor A (TFAM)-DNA cross-links. With sub-nmol sample input, we obtained high-quality fragmentation spectra for nucleic acid-peptide cross-links and identified 14 cross-linked lysine residues with the home-built AP_CrosslinkFinder program. Semi-quantification based on integrated peak areas revealed that K186 of TFAM is the major cross-linking residue, consistent with K186 being the closest (to the AP modification) lysine residue in solved TFAM:DNA crystal structures. Additional cross-linking lysine residues (K69, K76, K136, K154) support the dynamic characteristics of TFAM:DNA complexes. Overall, our combined workflow using ribonucleotide as a chemically cleavable DNA modification together with optimized sample preparation and data analysis offers a simple yet powerful approach for mapping cross-linking sites in DNA-protein cross-links. The method is amendable to other chemical or photo-cross-linking systems and can be extended to complex biological samples.
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Affiliation(s)
- Jin Tang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Wenxin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Nathan G Hendricks
- Proteomics Core, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California 92521, United States
| | - Linlin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States.,Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521, United States
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54
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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: 39] [Impact Index Per Article: 13.0] [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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55
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Boczek EE, Fürsch J, Niedermeier ML, Jawerth L, Jahnel M, Ruer-Gruß M, Kammer KM, Heid P, Mediani L, Wang J, Yan X, Pozniakovski A, Poser I, Mateju D, Hubatsch L, Carra S, Alberti S, Hyman AA, Stengel F. HspB8 prevents aberrant phase transitions of FUS by chaperoning its folded RNA-binding domain. eLife 2021; 10:69377. [PMID: 34487489 PMCID: PMC8510580 DOI: 10.7554/elife.69377] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
Aberrant liquid-to-solid phase transitions of biomolecular condensates have been linked to various neurodegenerative diseases. However, the underlying molecular interactions that drive aging remain enigmatic. Here, we develop quantitative time-resolved crosslinking mass spectrometry to monitor protein interactions and dynamics inside condensates formed by the protein fused in sarcoma (FUS). We identify misfolding of the RNA recognition motif of FUS as a key driver of condensate aging. We demonstrate that the small heat shock protein HspB8 partitions into FUS condensates via its intrinsically disordered domain and prevents condensate hardening via condensate-specific interactions that are mediated by its α-crystallin domain (αCD). These αCD-mediated interactions are altered in a disease-associated mutant of HspB8, which abrogates the ability of HspB8 to prevent condensate hardening. We propose that stabilizing aggregation-prone folded RNA-binding domains inside condensates by molecular chaperones may be a general mechanism to prevent aberrant phase transitions.
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Affiliation(s)
- Edgar E Boczek
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Dewpoint Therapeutics GmbH, Dresden, Germany
| | - Julius Fürsch
- University of Konstanz, Department of Biology, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Marie Laura Niedermeier
- University of Konstanz, Department of Biology, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Louise Jawerth
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Marcus Jahnel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Martine Ruer-Gruß
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Kai-Michael Kammer
- University of Konstanz, Department of Biology, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Peter Heid
- University of Konstanz, Department of Biology, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Laura Mediani
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Jie Wang
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Xiao Yan
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Andrej Pozniakovski
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Dewpoint Therapeutics GmbH, Dresden, Germany
| | - Daniel Mateju
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Lars Hubatsch
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Serena Carra
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden (CSBD), Dresden, Germany
| | - Florian Stengel
- University of Konstanz, Department of Biology, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
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56
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Qin W, Myers SA, Carey DK, Carr SA, Ting AY. Spatiotemporally-resolved mapping of RNA binding proteins via functional proximity labeling reveals a mitochondrial mRNA anchor promoting stress recovery. Nat Commun 2021; 12:4980. [PMID: 34404792 PMCID: PMC8370977 DOI: 10.1038/s41467-021-25259-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
Proximity labeling (PL) with genetically-targeted promiscuous enzymes has emerged as a powerful tool for unbiased proteome discovery. By combining the spatiotemporal specificity of PL with methods for functional protein enrichment, we show that it is possible to map specific protein subclasses within distinct compartments of living cells. In particular, we develop a method to enrich subcompartment-specific RNA binding proteins (RBPs) by combining peroxidase-catalyzed PL with organic-aqueous phase separation of crosslinked protein-RNA complexes (“APEX-PS”). We use APEX-PS to generate datasets of nuclear, nucleolar, and outer mitochondrial membrane (OMM) RBPs, which can be mined for novel functions. For example, we find that the OMM RBP SYNJ2BP retains specific nuclear-encoded mitochondrial mRNAs at the OMM during translation stress, facilitating their local translation and import of protein products into the mitochondrion during stress recovery. Functional PL in general, and APEX-PS in particular, represent versatile approaches for the discovery of proteins with novel function in specific subcellular compartments. Proximity labeling is used to map and discover proteins in specific subcellular compartments. Here the authors combine APEX-mediated proximity labeling with organic-aqueous phase separation to identify nuclear, nucleolar, and outer mitochondrial membrane RNA binding proteins.
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Affiliation(s)
- Wei Qin
- Departments of Biology, Genetics, and Chemistry, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Samuel A Myers
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Steven A Carr
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alice Y Ting
- Departments of Biology, Genetics, and Chemistry, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
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57
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Wippel HH, Fioramonte M, Chavez JD, Bruce JE. Deciphering the architecture and interactome of hnRNP proteins and enigmRBPs. Mol Omics 2021; 17:503-516. [PMID: 34017973 PMCID: PMC8355073 DOI: 10.1039/d1mo00024a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
RNA-binding proteins (RBPs) have conserved domains and consensus sequences that interact with RNAs and other proteins forming ribonucleoprotein (RNP) complexes. RNPs are involved in the regulation of several cellular processes, including transcription, pre-mRNA splicing, mRNA transport, localization, degradation and storage, and ultimately control of translation. Heterogeneous nuclear ribonucleoproteins (hnRNPs) comprise a family of RBPs that mediate transcription control and nuclear processing of transcripts. Some hnRNPs are part of the spliceosome complex, a dynamic machinery formed by RNPs that regulate alternative splicing of pre-mRNAs. Here, chemical crosslinking of proteins was applied to identify specific interacting regions and protein structural features of hnRNPs: hnRNPA1, hnRNPA2/B1, hnRNPC, and RALY. The results reveal interaction of these proteins within RNA-binding domains and conserved motifs, providing evidence of a coordinated action of known regulatory sequences of RBPs. Moreover, these crosslinking data enable structural model generation for RBPs, illustrating how crosslinking mass spectrometry can complement other structural methods.
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Affiliation(s)
- Helisa H Wippel
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Mariana Fioramonte
- Department of Genome Sciences, University of Washington, Seattle, WA, USA. and University of Campinas, Campinas, SP, Brazil
| | - Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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58
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Sievers K, Welp L, Urlaub H, Ficner R. Structural and functional insights into human tRNA guanine transgylcosylase. RNA Biol 2021; 18:382-396. [PMID: 34241577 DOI: 10.1080/15476286.2021.1950980] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The eukaryotic tRNA guanine transglycosylase (TGT) is an RNA modifying enzyme incorporating queuine, a hypermodified guanine derivative, into the tRNAsAsp,Asn,His,Tyr. While both subunits of the functional heterodimer have been crystallized individually, much of our understanding of its dimer interface or recognition of a target RNA has been inferred from its more thoroughly studied bacterial homolog. However, since bacterial TGT, by incorporating queuine precursor preQ1, deviates not only in function, but as a homodimer, also in its subunit architecture, any inferences regarding the subunit association of the eukaryotic heterodimer or the significance of its unique catalytically inactive subunit are based on unstable footing. Here, we report the crystal structure of human TGT in its heterodimeric form and in complex with a 25-mer stem loop RNA, enabling detailed analysis of its dimer interface and interaction with a minimal substrate RNA. Based on a model of bound tRNA, we addressed a potential functional role of the catalytically inactive subunit QTRT2 by UV-crosslinking and mutagenesis experiments, identifying the two-stranded βEβF-sheet of the QTRT2 subunit as an additional RNA-binding motif.
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Affiliation(s)
- Katharina Sievers
- Department of Molecular Structural Biology, University of Göttingen, Göttingen, Germany
| | - Luisa Welp
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, University of Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (Mbexc), University of Göttingen, Göttingen, Germany
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59
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The expanding world of metabolic enzymes moonlighting as RNA binding proteins. Biochem Soc Trans 2021; 49:1099-1108. [PMID: 34110361 DOI: 10.1042/bst20200664] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 12/15/2022]
Abstract
RNA binding proteins play key roles in many aspects of RNA metabolism and function, including splicing, transport, translation, localization, stability and degradation. Within the past few years, proteomics studies have identified dozens of enzymes in intermediary metabolism that bind to RNA. The wide occurrence and conservation of RNA binding ability across distant branches of the evolutionary tree suggest that these moonlighting enzymes are involved in connections between intermediary metabolism and gene expression that comprise far more extensive regulatory networks than previously thought. There are many outstanding questions about the molecular structures and mechanisms involved, the effects of these interactions on enzyme and RNA functions, and the factors that regulate the interactions. The effects on RNA function are likely to be wider than regulation of translation, and some enzyme-RNA interactions have been found to regulate the enzyme's catalytic activity. Several enzyme-RNA interactions have been shown to be affected by cellular factors that change under different intracellular and environmental conditions, including concentrations of substrates and cofactors. Understanding the molecular mechanisms involved in the interactions between the enzymes and RNA, the factors involved in regulation, and the effects of the enzyme-RNA interactions on both the enzyme and RNA functions will lead to a better understanding of the role of the many newly identified enzyme-RNA interactions in connecting intermediary metabolism and gene expression.
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60
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Blersch KF, Burchert JP, August SC, Welp L, Neumann P, Köster S, Urlaub H, Ficner R. Structural model of the M7G46 Methyltransferase TrmB in complex with tRNA. RNA Biol 2021; 18:2466-2479. [PMID: 34006170 DOI: 10.1080/15476286.2021.1925477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
TrmB belongs to the class I S-adenosylmethionine (SAM)-dependent methyltransferases (MTases) and introduces a methyl group to guanine at position 7 (m7G) in tRNA. In tRNAs m7G is most frequently found at position 46 in the variable loop and forms a tertiary base pair with C13 and U22, introducing a positive charge at G46. The TrmB/Trm8 enzyme family is structurally diverse, as TrmB proteins exist in a monomeric, homodimeric, and heterodimeric form. So far, the exact enzymatic mechanism, as well as the tRNA-TrmB crystal structure is not known. Here we present the first crystal structures of B. subtilis TrmB in complex with SAM and SAH. The crystal structures of TrmB apo and in complex with SAM and SAH have been determined by X-ray crystallography to 1.9 Å (apo), 2.5 Å (SAM), and 3.1 Å (SAH). The obtained crystal structures revealed Tyr193 to be important during SAM binding and MTase activity. Applying fluorescence polarization, the dissociation constant Kd of TrmB and tRNAPhe was determined to be 0.12 µM ± 0.002 µM. Luminescence-based methyltransferase activity assays revealed cooperative effects during TrmB catalysis with half-of-the-site reactivity at physiological SAM concentrations. Structural data retrieved from small-angle x-ray scattering (SAXS), mass-spectrometry of cross-linked complexes, and molecular docking experiments led to the determination of the TrmB-tRNAPhe complex structure.
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Affiliation(s)
- Katharina F Blersch
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg August University Göttingen, Göttingen, Germany
| | - Jan-Philipp Burchert
- Institute for X-Ray Physics, Georg August University Göttingen, Göttingen, Germany
| | | | - Luisa Welp
- Bioanalytical Mass Spectrometry Research Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg August University Göttingen, Göttingen, Germany
| | - Sarah Köster
- Institute for X-Ray Physics, Georg August University Göttingen, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Research Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg August University Göttingen, Göttingen, Germany
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61
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Rapidly Growing Protein-Centric Technologies to Extensively Identify Protein-RNA Interactions: Application to the Analysis of Co-Transcriptional RNA Processing. Int J Mol Sci 2021; 22:ijms22105312. [PMID: 34070162 PMCID: PMC8158511 DOI: 10.3390/ijms22105312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 12/11/2022] Open
Abstract
During mRNA transcription, diverse RNA-binding proteins (RBPs) are recruited to RNA polymerase II (RNAP II) transcription machinery. These RBPs bind to distinct sites of nascent RNA to co-transcriptionally operate mRNA processing. Recent studies have revealed a close relationship between transcription and co-transcriptional RNA processing, where one affects the other’s activity, indicating an essential role of protein–RNA interactions for the fine-tuning of mRNA production. Owing to their limited amount in cells, the detection of protein–RNA interactions specifically assembled on the transcribing RNAP II machinery still remains challenging. Currently, cross-linking and immunoprecipitation (CLIP) has become a standard method to detect in vivo protein–RNA interactions, although it requires a large amount of input materials. Several improved methods, such as infrared-CLIP (irCLIP), enhanced CLIP (eCLIP), and target RNA immunoprecipitation (tRIP), have shown remarkable enhancements in the detection efficiency. Furthermore, the utilization of an RNA editing mechanism or proximity labeling strategy has achieved the detection of faint protein–RNA interactions in cells without depending on crosslinking. This review aims to explore various methods being developed to detect endogenous protein–RNA interaction sites and discusses how they may be applied to the analysis of co-transcriptional RNA processing.
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62
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Vieira-Vieira CH, Selbach M. Opportunities and Challenges in Global Quantification of RNA-Protein Interaction via UV Cross-Linking. Front Mol Biosci 2021; 8:669939. [PMID: 34055886 PMCID: PMC8155585 DOI: 10.3389/fmolb.2021.669939] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/12/2021] [Indexed: 12/15/2022] Open
Abstract
RNA-binding proteins (RBPs) are key mediators of posttranscriptional gene expression control. However, the links between cell signaling on the one hand and RBP function on the other are understudied. While thousands of posttranslational modification (PTM) sites on RBPs have been identified, their functional roles are only poorly characterized. RNA-interactome capture (RIC) and cross-linking and immunoprecipitation (CLIP) are attractive methods that provide information about RBP-RNA interactions on a genome-wide scale. Both approaches rely on the in situ UV cross-linking of RBPs and RNAs, biochemical enrichment and analysis by RNA-sequencing (CLIP) or mass spectrometry (RIC). In principle, RIC- and CLIP-like methods could be used to globally quantify RBP-RNA interactions in response to perturbations. However, several biases have to be taken into account to avoid misinterpretation of the results obtained. Here, we focus on RIC-like methods and discuss four key aspects relevant for quantitative interpretation: (1) the RNA isolation efficiency, (2) the inefficient and highly variable UV cross-linking, (3) the baseline RNA occupancy of RBPs, and (4) indirect factors affecting RBP-RNA interaction. We highlight these points by presenting selected examples of PTMs that might induce differential quantification in RIC-like experiments without necessarily affecting RNA-binding. We conclude that quantifying RBP-RNA interactions via RIC or CLIP-like methods should not be regarded as an end in itself but rather as starting points for deeper analysis.
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Affiliation(s)
- Carlos H Vieira-Vieira
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Faculty of Life Sciences, Humboldt Universität zu Berlin, Berlin, Germany
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
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63
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Abstract
Proteomics studies rely on the accurate assignment of peptides to the acquired tandem mass spectra-a task where machine learning algorithms have proven invaluable. We describe mokapot, which provides a flexible semisupervised learning algorithm that allows for highly customized analyses. We demonstrate some of the unique features of mokapot by improving the detection of RNA-cross-linked peptides from an analysis of RNA-binding proteins and increasing the consistency of peptide detection in a single-cell proteomics study.
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Affiliation(s)
- William
E. Fondrie
- Department
of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - William S. Noble
- Department
of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
- Paul
G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
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64
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Kalathiya U, Padariya M, Faktor J, Coyaud E, Alfaro JA, Fahraeus R, Hupp TR, Goodlett DR. Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS). Biomolecules 2021; 11:382. [PMID: 33806612 PMCID: PMC8001575 DOI: 10.3390/biom11030382] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 12/28/2022] Open
Abstract
The fundamentals of how protein-protein/RNA/DNA interactions influence the structures and functions of the workhorses from the cells have been well documented in the 20th century. A diverse set of methods exist to determine such interactions between different components, particularly, the mass spectrometry (MS) methods, with its advanced instrumentation, has become a significant approach to analyze a diverse range of biomolecules, as well as bring insights to their biomolecular processes. This review highlights the principal role of chemistry in MS-based structural proteomics approaches, with a particular focus on the chemical cross-linking of protein-protein/DNA/RNA complexes. In addition, we discuss different methods to prepare the cross-linked samples for MS analysis and tools to identify cross-linked peptides. Cross-linking mass spectrometry (CLMS) holds promise to identify interaction sites in larger and more complex biological systems. The typical CLMS workflow allows for the measurement of the proximity in three-dimensional space of amino acids, identifying proteins in direct contact with DNA or RNA, and it provides information on the folds of proteins as well as their topology in the complexes. Principal CLMS applications, its notable successes, as well as common pipelines that bridge proteomics, molecular biology, structural systems biology, and interactomics are outlined.
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Affiliation(s)
- Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
| | - Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
| | - Jakub Faktor
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
| | - Etienne Coyaud
- Protéomique Réponse Inflammatoire Spectrométrie de Mass—PRISM, Inserm U1192, University Lille, CHU Lille, F-59000 Lille, France;
| | - Javier A. Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, UK
| | - Robin Fahraeus
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
| | - Ted R. Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, UK
| | - David R. Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, BC V8Z 7X8, Canada
- Genome BC Proteome Centre, University of Victoria, Victoria, BC V8Z 5N3, Canada
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65
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Hafner M, Katsantoni M, Köster T, Marks J, Mukherjee J, Staiger D, Ule J, Zavolan M. CLIP and complementary methods. ACTA ACUST UNITED AC 2021. [DOI: 10.1038/s43586-021-00018-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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66
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The search for RNA-binding proteins: a technical and interdisciplinary challenge. Biochem Soc Trans 2021; 49:393-403. [PMID: 33492363 PMCID: PMC7925008 DOI: 10.1042/bst20200688] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/21/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022]
Abstract
RNA-binding proteins are customarily regarded as important facilitators of gene expression. In recent years, RNA–protein interactions have also emerged as a pervasive force in the regulation of homeostasis. The compendium of proteins with provable RNA-binding function has swelled from the hundreds to the thousands astride the partnership of mass spectrometry-based proteomics and RNA sequencing. At the foundation of these advances is the adaptation of RNA-centric capture methods that can extract bound protein that has been cross-linked in its native environment. These methods reveal snapshots in time displaying an extensive network of regulation and a wealth of data that can be used for both the discovery of RNA-binding function and the molecular interfaces at which these interactions occur. This review will focus on the impact of these developments on our broader perception of post-transcriptional regulation, and how the technical features of current capture methods, as applied in mammalian systems, create a challenging medium for interpretation by systems biologists and target validation by experimental researchers.
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67
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Glycation of glyceraldehyde-3-phosphate dehydrogenase inhibits the binding with α-synuclein and RNA. Arch Biochem Biophys 2020; 698:108744. [PMID: 33385367 DOI: 10.1016/j.abb.2020.108744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 01/18/2023]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) shows great diversity of functions, interaction partners and post-translational modifications. GAPDH undergoes glycation of positively charged residues in diabetic patient's tissues and therefore may change interaction with partners. The influence of GAPDH glycation on interaction with two important partners, α-synuclein and RNA, has been investigated in silico using molecular dynamics simulations and in vitro using surface plasmon resonance measurements. Since positively charged groove including substrate- and NAD+-binding sites is proposed as potential binding site for α-synuclein and RNA, GAPDH was glycated on residues in grooves and randomly distributed over the whole surface. Lysine residues were replaced with negatively charged carboxymethyl lysine as a widespread advanced glycation end product. As results, GAPDH glycation suppressed the interaction with α-synuclein and RNA. Although the modified GAPDH residues participated in binding with α-synuclein, no stable binding site with both glycated forms was observed. Glycation along the whole GAPDH surface completely suppressed interaction with RNA, whereas the alternative possible RNA binding site was identified in case of groove glycation. The findings were supported by direct measurement of the binding affinity. The obtained results clarify effect of glycation on GAPDH interaction with α-synuclein and RNA and elucidate a possible mechanism of interplay between glycation occurred in diabetes and neurodegenerative diseases, which GAPDH and α-synuclein are involved in.
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68
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An emerging role of chromatin-interacting RNA-binding proteins in transcription regulation. Essays Biochem 2020; 64:907-918. [PMID: 33034346 DOI: 10.1042/ebc20200004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/08/2020] [Accepted: 09/15/2020] [Indexed: 01/01/2023]
Abstract
Transcription factors (TFs) are well-established key factors orchestrating gene transcription, and RNA-binding proteins (RBPs) are mainly thought to participate in post-transcriptional control of gene. In fact, these two steps are functionally coupled, offering a possibility for reciprocal communications between transcription and regulatory RNAs and RBPs. Recently, a series of exploratory studies, utilizing functional genomic strategies, have revealed that RBPs are prevalently involved in transcription control genome-wide through their interactions with chromatin. Here, we present a refined census of RBPs to grope for such an emerging role and discuss the global view of RBP-chromatin interactions and their functional diversities in transcription regulation.
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69
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Gebauer F, Schwarzl T, Valcárcel J, Hentze MW. RNA-binding proteins in human genetic disease. Nat Rev Genet 2020; 22:185-198. [PMID: 33235359 DOI: 10.1038/s41576-020-00302-y] [Citation(s) in RCA: 310] [Impact Index Per Article: 77.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2020] [Indexed: 12/27/2022]
Abstract
RNA-binding proteins (RBPs) are critical effectors of gene expression, and as such their malfunction underlies the origin of many diseases. RBPs can recognize hundreds of transcripts and form extensive regulatory networks that help to maintain cell homeostasis. System-wide unbiased identification of RBPs has increased the number of recognized RBPs into the four-digit range and revealed new paradigms: from the prevalence of structurally disordered RNA-binding regions with roles in the formation of membraneless organelles to unsuspected and potentially pervasive connections between intermediary metabolism and RNA regulation. Together with an increasingly detailed understanding of molecular mechanisms of RBP function, these insights are facilitating the development of new therapies to treat malignancies. Here, we provide an overview of RBPs involved in human genetic disorders, both Mendelian and somatic, and discuss emerging aspects in the field with emphasis on molecular mechanisms of disease and therapeutic interventions.
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Affiliation(s)
- Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain. .,University Pompeu Fabra (UPF), Barcelona, Spain.
| | - Thomas Schwarzl
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Juan Valcárcel
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,University Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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70
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Stützer A, Welp LM, Raabe M, Sachsenberg T, Kappert C, Wulf A, Lau AM, David SS, Chernev A, Kramer K, Politis A, Kohlbacher O, Fischle W, Urlaub H. Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry. Nat Commun 2020; 11:5250. [PMID: 33067435 PMCID: PMC7567871 DOI: 10.1038/s41467-020-19047-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 09/24/2020] [Indexed: 02/08/2023] Open
Abstract
Protein–DNA interactions are key to the functionality and stability of the genome. Identification and mapping of protein–DNA interaction interfaces and sites is crucial for understanding DNA-dependent processes. Here, we present a workflow that allows mass spectrometric (MS) identification of proteins in direct contact with DNA in reconstituted and native chromatin after cross-linking by ultraviolet (UV) light. Our approach enables the determination of contact interfaces at amino-acid level. With the example of chromatin-associated protein SCML2 we show that our technique allows differentiation of nucleosome-binding interfaces in distinct states. By UV cross-linking of isolated nuclei we determined the cross-linking sites of several factors including chromatin-modifying enzymes, demonstrating that our workflow is not restricted to reconstituted materials. As our approach can distinguish between protein–RNA and DNA interactions in one single experiment, we project that it will be possible to obtain insights into chromatin and its regulation in the future. Cross-linking mass spectrometry (XLMS) allows mapping of protein-protein and protein-RNA interactions, but the analysis of protein-DNA complexes remains challenging. Here, the authors develop a UV light-based XLMS workflow to determine protein-DNA interfaces in reconstituted chromatin and isolated nuclei.
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Affiliation(s)
- Alexandra Stützer
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Luisa M Welp
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Monika Raabe
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Timo Sachsenberg
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076, Tübingen, Germany.,Applied Bioinformatics, Department for Computer Science, University of Tübingen, 72076, Tübingen, Germany
| | - Christin Kappert
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.,Somatosensory Signaling and Systems Biology Group, Max Planck Institute of Experimental Medicine, 37075, Göttingen, Germany
| | - Alexander Wulf
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Andy M Lau
- Department of Chemistry, King's College London, London, SE1 1DB, UK
| | - Stefan-Sebastian David
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.,King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, 23955, Thuwal, Saudi Arabia
| | - Aleksandar Chernev
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | | | - Argyris Politis
- Department of Chemistry, King's College London, London, SE1 1DB, UK
| | - Oliver Kohlbacher
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076, Tübingen, Germany.,Applied Bioinformatics, Department for Computer Science, University of Tübingen, 72076, Tübingen, Germany.,Institute for Translational Bioinformatics, University Hospital Tübingen, 72076, Tübingen, Germany.,Biomolecular Interactions, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.,King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, 23955, Thuwal, Saudi Arabia
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany. .,Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, 37075, Göttingen, Germany.
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71
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Müller M, Schauer T, Krause S, Villa R, Thomae AW, Becker PB. Two-step mechanism for selective incorporation of lncRNA into a chromatin modifier. Nucleic Acids Res 2020; 48:7483-7501. [PMID: 32510132 PMCID: PMC7528653 DOI: 10.1093/nar/gkaa492] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/25/2020] [Accepted: 05/29/2020] [Indexed: 02/04/2023] Open
Abstract
The MLE DExH helicase and the roX lncRNAs are essential components of the chromatin modifying Dosage Compensation Complex (DCC) in Drosophila. To explore the mechanism of ribonucleoprotein complex assembly, we developed vitRIP, an unbiased, transcriptome-wide in vitro assay that reveals RNA binding specificity. We found that MLE has intrinsic specificity for U-/A-rich sequences and tandem stem-loop structures and binds many RNAs beyond roX in vitro. The selectivity of the helicase for physiological substrates is further enhanced by the core DCC. Unwinding of roX2 by MLE induces a highly selective RNA binding surface in the unstructured C-terminus of the MSL2 subunit and triggers-specific association of MLE and roX2 with the core DCC. The exquisite selectivity of roX2 incorporation into the DCC thus originates from intimate cooperation between the helicase and the core DCC involving two distinct RNA selection principles and their mutual refinement.
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Affiliation(s)
- Marisa Müller
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Tamas Schauer
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.,Bioinformatics Unit, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Silke Krause
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Raffaella Villa
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Andreas W Thomae
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.,Core Facility Bioimaging at the Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Peter B Becker
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
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72
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Backlund M, Stein F, Rettel M, Schwarzl T, Perez-Perri JI, Brosig A, Zhou Y, Neu-Yilik G, Hentze MW, Kulozik AE. Plasticity of nuclear and cytoplasmic stress responses of RNA-binding proteins. Nucleic Acids Res 2020; 48:4725-4740. [PMID: 32313943 PMCID: PMC7229827 DOI: 10.1093/nar/gkaa256] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/01/2020] [Accepted: 04/04/2020] [Indexed: 02/07/2023] Open
Abstract
Cellular stress causes multifaceted reactions to trigger adaptive responses to environmental cues at all levels of the gene expression pathway. RNA-binding proteins (RBP) are key contributors to stress-induced regulation of RNA fate and function. Here, we uncover the plasticity of the RNA interactome in stressed cells, differentiating between responses in the nucleus and in the cytoplasm. We applied enhanced RNA interactome capture (eRIC) analysis preceded by nucleo-cytoplasmic fractionation following arsenite-induced oxidative stress. The data reveal unexpectedly compartmentalized RNA interactomes and their responses to stress, including differential responses of RBPs in the nucleus versus the cytoplasm, which would have been missed by whole cell analyses.
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Affiliation(s)
- Michael Backlund
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- To whom correspondence should be addressed. Tel: +49 6221 564555;
| | - Frank Stein
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Mandy Rettel
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Thomas Schwarzl
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Joel I Perez-Perri
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Annika Brosig
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Yang Zhou
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Gabriele Neu-Yilik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Matthias W Hentze
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Correspondence may also be addressed to Matthias W. Hentze.
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany & European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany & Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
- Correspondence may also be addressed to Andreas E. Kulozik.
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73
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Sarni S, Biswas B, Liu S, Olson ED, Kitzrow JP, Rein A, Wysocki VH, Musier-Forsyth K. HIV-1 Gag protein with or without p6 specifically dimerizes on the viral RNA packaging signal. J Biol Chem 2020; 295:14391-14401. [PMID: 32817318 DOI: 10.1074/jbc.ra120.014835] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/10/2020] [Indexed: 02/04/2023] Open
Abstract
The HIV-1 Gag protein is responsible for genomic RNA (gRNA) packaging and immature viral particle assembly. Although the presence of gRNA in virions is required for viral infectivity, in its absence, Gag can assemble around cellular RNAs and form particles resembling gRNA-containing particles. When gRNA is expressed, it is selectively packaged despite the presence of excess host RNA, but how it is selectively packaged is not understood. Specific recognition of a gRNA packaging signal (Psi) has been proposed to stimulate the efficient nucleation of viral assembly. However, the heterogeneity of Gag-RNA interactions renders capturing this transient nucleation complex using traditional structural biology approaches challenging. Here, we used native MS to investigate RNA binding of wild-type (WT) Gag and Gag lacking the p6 domain (GagΔp6). Both proteins bind to Psi RNA primarily as dimers, but to a control RNA primarily as monomers. The dimeric complexes on Psi RNA require an intact dimer interface within Gag. GagΔp6 binds to Psi RNA with high specificity in vitro and also selectively packages gRNA in particles produced in mammalian cells. These studies provide direct support for the idea that Gag binding to Psi specifically promotes nucleation of Gag-Gag interactions at the early stages of immature viral particle assembly in a p6-independent manner.
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Affiliation(s)
- Samantha Sarni
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA.,Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA.,Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Banhi Biswas
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Shuohui Liu
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA.,Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
| | - Erik D Olson
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA.,Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA.,Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
| | - Jonathan P Kitzrow
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA.,Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA.,Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
| | - Alan Rein
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Vicki H Wysocki
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA .,Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA.,Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Karin Musier-Forsyth
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA .,Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA.,Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
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74
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Single and Combined Methods to Specifically or Bulk-Purify RNA-Protein Complexes. Biomolecules 2020; 10:biom10081160. [PMID: 32784769 PMCID: PMC7464009 DOI: 10.3390/biom10081160] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/31/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022] Open
Abstract
The ribonome interconnects the proteome and the transcriptome. Specific biology is situated at this interface, which can be studied in bulk using omics approaches or specifically by targeting an individual protein or RNA species. In this review, we focus on both RNA- and ribonucleoprotein-(RNP) centric methods. These methods can be used to study the dynamics of the ribonome in response to a stimulus or to identify the proteins that interact with a specific RNA species. The purpose of this review is to provide and discuss an overview of strategies to cross-link RNA to proteins and the currently available RNA- and RNP-centric approaches to study RNPs. We elaborate on some major challenges common to most methods, involving RNP yield, purity and experimental cost. We identify the origin of these difficulties and propose to combine existing approaches to overcome these challenges. The solutions provided build on the recently developed organic phase separation protocols, such as Cross-Linked RNA eXtraction (XRNAX), orthogonal organic phase separation (OOPS) and Phenol-Toluol extraction (PTex).
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75
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Reim A, Ackermann R, Font-Mateu J, Kammel R, Beato M, Nolte S, Mann M, Russmann C, Wierer M. Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry. Nat Commun 2020; 11:3019. [PMID: 32541649 PMCID: PMC7295792 DOI: 10.1038/s41467-020-16837-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 05/27/2020] [Indexed: 11/09/2022] Open
Abstract
Transcription factors (TFs) regulate target genes by specific interactions with DNA sequences. Detecting and understanding these interactions at the molecular level is of fundamental importance in biological and clinical contexts. Crosslinking mass spectrometry is a powerful tool to assist the structure prediction of protein complexes but has been limited to the study of protein-protein and protein-RNA interactions. Here, we present a femtosecond laser-induced crosslinking mass spectrometry (fliX-MS) workflow, which allows the mapping of protein-DNA contacts at single nucleotide and up to single amino acid resolution. Applied to recombinant histone octamers, NF1, and TBP in complex with DNA, our method is highly specific for the mapping of DNA binding domains. Identified crosslinks are in close agreement with previous biochemical data on DNA binding and mostly fit known complex structures. Applying fliX-MS to cells identifies several bona fide crosslinks on DNA binding domains, paving the way for future large scale ex vivo experiments.
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Affiliation(s)
- Alexander Reim
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Roland Ackermann
- Institute of Applied Physics, Abbe Center of Photonics, Friedrich-Schiller-Universität Jena, Albert-Einstein-Straße 15, 07745, Jena, Germany
| | - Jofre Font-Mateu
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Robert Kammel
- Institute of Applied Physics, Abbe Center of Photonics, Friedrich-Schiller-Universität Jena, Albert-Einstein-Straße 15, 07745, Jena, Germany
| | - Miguel Beato
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
- University Pompeu Fabra (UPF), 08002, Barcelona, Spain
| | - Stefan Nolte
- Institute of Applied Physics, Abbe Center of Photonics, Friedrich-Schiller-Universität Jena, Albert-Einstein-Straße 15, 07745, Jena, Germany
- Fraunhofer Institute for Applied Optics and Engineering (IOF), Albert-Einstein-Straße 7, 07745, Jena, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Christoph Russmann
- University of Applied Sciences and Arts Hildesheim/Holzminden/Goettingen (HAWK), Von-Ossietzky-Straße 99, 37085, Göttingen, Germany.
- Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA.
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
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76
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Bae JW, Kwon SC, Na Y, Kim VN, Kim JS. Chemical RNA digestion enables robust RNA-binding site mapping at single amino acid resolution. Nat Struct Mol Biol 2020; 27:678-682. [PMID: 32514175 DOI: 10.1038/s41594-020-0436-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/15/2020] [Indexed: 12/21/2022]
Abstract
RNA-binding sites (RBSs) can be identified by liquid chromatography and tandem mass spectrometry analyses of the protein-RNA conjugates created by crosslinking, but RBS mapping remains highly challenging due to the complexity of the formed RNA adducts. Here, we introduce RBS-ID, a method that uses hydrofluoride to fully cleave RNA into mono-nucleosides, thereby minimizing the search space to drastically enhance coverage and to reach single amino acid resolution. Moreover, the simple mono-nucleoside adducts offer a confident and quantitative measure of direct RNA-protein interaction. Using RBS-ID, we profiled ~2,000 human RBSs and probed Streptococcus pyogenes Cas9 to discover residues important for genome editing.
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Affiliation(s)
- Jong Woo Bae
- Center for RNA Research, Institute for Basic Science, Seoul, Korea.,School of Biological Sciences, Seoul National University, Seoul, Korea
| | - S Chul Kwon
- Center for RNA Research, Institute for Basic Science, Seoul, Korea.,School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Yongwoo Na
- Center for RNA Research, Institute for Basic Science, Seoul, Korea.,School of Biological Sciences, Seoul National University, Seoul, Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul, Korea. .,School of Biological Sciences, Seoul National University, Seoul, Korea.
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science, Seoul, Korea. .,School of Biological Sciences, Seoul National University, Seoul, Korea.
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77
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Lang B, Armaos A, Tartaglia GG. RNAct: Protein-RNA interaction predictions for model organisms with supporting experimental data. Nucleic Acids Res 2020; 47:D601-D606. [PMID: 30445601 PMCID: PMC6324028 DOI: 10.1093/nar/gky967] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/11/2018] [Indexed: 01/15/2023] Open
Abstract
Protein-RNA interactions are implicated in a number of physiological roles as well as diseases, with molecular mechanisms ranging from defects in RNA splicing, localization and translation to the formation of aggregates. Currently, ∼1400 human proteins have experimental evidence of RNA-binding activity. However, only ∼250 of these proteins currently have experimental data on their target RNAs from various sequencing-based methods such as eCLIP. To bridge this gap, we used an established, computationally expensive protein-RNA interaction prediction method, catRAPID, to populate a large database, RNAct. RNAct allows easy lookup of known and predicted interactions and enables global views of the human, mouse and yeast protein-RNA interactomes, expanding them in a genome-wide manner far beyond experimental data (http://rnact.crg.eu).
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Affiliation(s)
- Benjamin Lang
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Alexandros Armaos
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Gian G Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 23 Passeig Lluís Companys, Barcelona 08010, Spain.,Universitat Pompeu Fabra (UPF), Department of Experimental and Health Sciences, Barcelona 08003, Spain.,Department of Biology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
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78
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Bach-Pages M, Homma F, Kourelis J, Kaschani F, Mohammed S, Kaiser M, van der Hoorn RAL, Castello A, Preston GM. Discovering the RNA-Binding Proteome of Plant Leaves with an Improved RNA Interactome Capture Method. Biomolecules 2020; 10:E661. [PMID: 32344669 PMCID: PMC7226388 DOI: 10.3390/biom10040661] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 12/12/2022] Open
Abstract
RNA-binding proteins (RBPs) play a crucial role in regulating RNA function and fate. However, the full complement of RBPs has only recently begun to be uncovered through proteome-wide approaches such as RNA interactome capture (RIC). RIC has been applied to various cell lines and organisms, including plants, greatly expanding the repertoire of RBPs. However, several technical challenges have limited the efficacy of RIC when applied to plant tissues. Here, we report an improved version of RIC that overcomes the difficulties imposed by leaf tissue. Using this improved RIC method in Arabidopsis leaves, we identified 717 RBPs, generating a deep RNA-binding proteome for leaf tissues. While 75% of these RBPs can be linked to RNA biology, the remaining 25% were previously not known to interact with RNA. Interestingly, we observed that a large number of proteins related to photosynthesis associate with RNA in vivo, including proteins from the four major photosynthetic supercomplexes. As has previously been reported for mammals, a large proportion of leaf RBPs lack known RNA-binding domains, suggesting unconventional modes of RNA binding. We anticipate that this improved RIC method will provide critical insights into RNA metabolism in plants, including how cellular RBPs respond to environmental, physiological and pathological cues.
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Affiliation(s)
- Marcel Bach-Pages
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; (M.B.-P.); (F.H.); (J.K.); (R.A.L.v.d.H.)
| | - Felix Homma
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; (M.B.-P.); (F.H.); (J.K.); (R.A.L.v.d.H.)
| | - Jiorgos Kourelis
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; (M.B.-P.); (F.H.); (J.K.); (R.A.L.v.d.H.)
| | - Farnusch Kaschani
- Fakultät für Biologie, Universität Duisburg-Essen, North Rhine-Westphalia, 45117 Essen, Germany; (F.K.); (M.K.)
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK;
| | - Markus Kaiser
- Fakultät für Biologie, Universität Duisburg-Essen, North Rhine-Westphalia, 45117 Essen, Germany; (F.K.); (M.K.)
| | - Renier A. L. van der Hoorn
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; (M.B.-P.); (F.H.); (J.K.); (R.A.L.v.d.H.)
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK;
| | - Gail M. Preston
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; (M.B.-P.); (F.H.); (J.K.); (R.A.L.v.d.H.)
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79
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Y-Box Binding Proteins in mRNP Assembly, Translation, and Stability Control. Biomolecules 2020; 10:biom10040591. [PMID: 32290447 PMCID: PMC7226217 DOI: 10.3390/biom10040591] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/06/2020] [Accepted: 04/10/2020] [Indexed: 12/12/2022] Open
Abstract
Y-box binding proteins (YB proteins) are DNA/RNA-binding proteins belonging to a large family of proteins with the cold shock domain. Functionally, these proteins are known to be the most diverse, although the literature hardly offers any molecular mechanisms governing their activities in the cell, tissue, or the whole organism. This review describes the involvement of YB proteins in RNA-dependent processes, such as mRNA packaging into mRNPs, mRNA translation, and mRNA stabilization. In addition, recent data on the structural peculiarities of YB proteins underlying their interactions with nucleic acids are discussed.
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80
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Saha A, Duchambon P, Masson V, Loew D, Bombard S, Teulade-Fichou MP. Nucleolin Discriminates Drastically between Long-Loop and Short-Loop Quadruplexes. Biochemistry 2020; 59:1261-1272. [PMID: 32191439 DOI: 10.1021/acs.biochem.9b01094] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We investigate herein the interaction between nucleolin (NCL) and a set of G4 sequences derived from the CEB25 human minisatellite that adopt a parallel topology while differing in the length of the central loop (from nine nucleotides to one nucleotide). It is revealed that NCL strongly binds to long-loop (five to nine nucleotides) G4 while interacting weakly with the shorter variants (loop with fewer than three nucleotides). Photo-cross-linking experiments using 5-bromo-2'-deoxyuridine (BrU)-modified sequences further confirmed the loop-length dependency, thereby indicating that the WT-CEB25-L191 (nine-nucleotide loop) is the best G4 substrate. Quantitative proteomic analysis (LC-MS/MS) of the product(s) obtained by photo-cross-linking NCL to this sequence enabled the identification of one contact site corresponding to a 15-amino acid fragment located in helix α2 of RNA binding domain 2 (RBD2), which sheds light on the role of this structural element in G4-loop recognition. Then, the ability of a panel of benchmark G4 ligands to prevent the NCL-G4 interaction was explored. It was found that only the most potent ligand PhenDC3 can inhibit NCL binding, thereby suggesting that the terminal guanine quartet is also a strong determinant of G4 recognition, putatively through interaction with the RGG domain. This study describes the molecular mechanism by which NCL recognizes G4-containing long loops and leads to the proposal of a model implying a concerted action of RBD2 and RGG domains to achieve specific G4 recognition via a dual loop-quartet interaction.
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Affiliation(s)
- Abhijit Saha
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405 Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405 Orsay, France
| | - Patricia Duchambon
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405 Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405 Orsay, France
| | - Vanessa Masson
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, Paris 75248 Cedex 05, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, Paris 75248 Cedex 05, France
| | - Sophie Bombard
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405 Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405 Orsay, France
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405 Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405 Orsay, France
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81
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Integrative Structural Biology of Protein-RNA Complexes. Structure 2020; 28:6-28. [DOI: 10.1016/j.str.2019.11.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 11/17/2019] [Accepted: 11/27/2019] [Indexed: 12/16/2022]
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82
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Kilchert C, Sträßer K, Kunetsky V, Änkö ML. From parts lists to functional significance-RNA-protein interactions in gene regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1582. [PMID: 31883228 DOI: 10.1002/wrna.1582] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/03/2019] [Accepted: 12/07/2019] [Indexed: 12/17/2022]
Abstract
Hundreds of canonical RNA binding proteins facilitate diverse and essential RNA processing steps in cells forming a central regulatory point in gene expression. However, recent discoveries including the identification of a large number of noncanonical proteins bound to RNA have changed our view on RNA-protein interactions merely as necessary steps in RNA biogenesis. As the list of proteins interacting with RNA has expanded, so has the scope of regulation through RNA-protein interactions. In addition to facilitating RNA metabolism, RNA binding proteins help to form subcellular structures and membraneless organelles, and provide means to recruit components of macromolecular complexes to their sites of action. Moreover, RNA-protein interactions are not static in cells but the ribonucleoprotein (RNP) complexes are highly dynamic in response to cellular cues. The identification of novel proteins in complex with RNA and ways cells use these interactions to control cellular functions continues to broaden the scope of RNA regulation in cells and the current challenge is to move from cataloguing the components of RNPs into assigning them functions. This will not only facilitate our understanding of cellular homeostasis but may bring in key insights into human disease conditions where RNP components play a central role. This review brings together the classical view of regulation accomplished through RNA-protein interactions with the novel insights gained from the identification of RNA binding interactomes. We discuss the challenges in combining molecular mechanism with cellular functions on the journey towards a comprehensive understanding of the regulatory functions of RNA-protein interactions in cells. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications aRNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition.
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Affiliation(s)
- Cornelia Kilchert
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Katja Sträßer
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Vladislav Kunetsky
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Minna-Liisa Änkö
- Centre for Reproductive Health and Centre for Cancer Research, Hudson Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Molecular and Translational Science, School of Clinical Sciences, Monash University, Melbourne, Victoria, Australia
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83
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Ayoubi LE, Dumay-Odelot H, Chernev A, Boissier F, Minvielle-Sébastia L, Urlaub H, Fribourg S, Teichmann M. The hRPC62 subunit of human RNA polymerase III displays helicase activity. Nucleic Acids Res 2019; 47:10313-10326. [PMID: 31529052 PMCID: PMC6821166 DOI: 10.1093/nar/gkz788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 08/30/2019] [Accepted: 09/12/2019] [Indexed: 11/20/2022] Open
Abstract
In Eukaryotes, tRNAs, 5S RNA and U6 RNA are transcribed by RNA polymerase (Pol) III. Human Pol III is composed of 17 subunits. Three specific Pol III subunits form a stable ternary subcomplex (RPC62-RPC39-RPC32α/β) being involved in pre-initiation complex formation. No paralogues for subunits of this subcomplex subunits have been found in Pols I or II, but hRPC62 was shown to be structurally related to the general Pol II transcription factor hTFIIEα. Here we show that these structural homologies extend to functional similarities. hRPC62 as well as hTFIIEα possess intrinsic ATP-dependent 3′-5′ DNA unwinding activity. The ATPase activities of both proteins are stimulated by single-stranded DNA. Moreover, the eWH domain of hTFIIEα can replace the first eWH (eWH1) domain of hRPC62 in ATPase and DNA unwinding assays. Our results identify intrinsic enzymatic activities in hRPC62 and hTFIIEα.
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Affiliation(s)
- Leyla El Ayoubi
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, 33000 Bordeaux, France
| | - Hélène Dumay-Odelot
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, 33000 Bordeaux, France
- Correspondence may also be addressed to Hélène Dumay-Odelot.
| | - Aleksandar Chernev
- Max Planck Institute for Biophysical Chemistry, Research group Mass Spectrometry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Fanny Boissier
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, 33000 Bordeaux, France
| | | | - Henning Urlaub
- Max Planck Institute for Biophysical Chemistry, Research group Mass Spectrometry, Am Faßberg 11, 37077 Göttingen, Germany
- Bioanalytics, Institute for Clinical Chemistry, University Medical Center, Robert-Koch-Strasse 420, 37075 Göttingen, Germany
| | - Sébastien Fribourg
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, 33000 Bordeaux, France
| | - Martin Teichmann
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, 33000 Bordeaux, France
- To whom correspondence should be addressed. Tel: +33 5 5757 4647;
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84
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Nechay M, Kleiner RE. High-throughput approaches to profile RNA-protein interactions. Curr Opin Chem Biol 2019; 54:37-44. [PMID: 31812895 DOI: 10.1016/j.cbpa.2019.11.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/22/2019] [Accepted: 11/03/2019] [Indexed: 12/17/2022]
Abstract
RNA-protein interactions play a critical role in post-transcriptional gene regulation. Characterizing these interactions in their native context has been challenging; however, advances in RNA sequencing and mass spectrometrybased proteomics combined with innovative chemical biological tools have heralded the development of robust strategies for performing biochemistry on a cellular scale. Herein, we review recent advances in the development and application of proteomic and transcriptomic approaches to profile cellular RNA-protein interactions, focusing on sequencing-based strategies and proteomic analysis of RNA-binding proteins, as well as approaches to address the role of RNA modifications in protein-RNA binding events.
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Affiliation(s)
- Misha Nechay
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Ralph E Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
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85
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Manchalu S, Mittal N, Spang A, Jansen RP. Local translation of yeast ERG4 mRNA at the endoplasmic reticulum requires the brefeldin A resistance protein Bfr1. RNA (NEW YORK, N.Y.) 2019; 25:1661-1672. [PMID: 31455610 PMCID: PMC6859859 DOI: 10.1261/rna.072017.119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/20/2019] [Indexed: 05/13/2023]
Abstract
Brefeldin A resistance factor 1 (Bfr1p) is a nonessential RNA-binding protein and multicopy suppressor of brefeldin A sensitivity in Saccharomyces cerevisiae Deletion of BFR1 leads to multiple defects, including altered cell shape and size, change in ploidy, induction of P-bodies and chromosomal missegregation. Bfr1p has been shown to associate with polysomes, binds to several hundred mRNAs, and can target some of them to P-bodies. Although this implies a role of Bfr1p in translational control of mRNAs, its molecular function remains elusive. In the present study, we show that mutations in RNA-binding residues of Bfr1p impede its RNA-dependent colocalization with ER, yet do not mimic the known cellular defects seen upon BFR1 deletion. However, a Bfr1 RNA-binding mutant is impaired in binding to ERG4 mRNA, which encodes an enzyme required for the final step of ergosterol biosynthesis. Consistently, bfr1Δ strains show a strong reduction in Erg4p protein levels, most likely because of degradation of misfolded Erg4p. Polysome profiling of bfr1Δ or bfr1 mutant strains reveals a strong shift of ERG4 mRNA to polysomes, consistent with a function of Bfr1p in elongation or increased ribosome loading. Collectively, our data reveal that Bfr1 has at least two separable functions: one in RNA binding and cotranslational protein translocation into the ER and one in ploidy control or chromosome segregation.
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Affiliation(s)
- Srinivas Manchalu
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen 72076, Germany
| | - Nitish Mittal
- Biozentrum, University of Basel, Basel 4056, Switzerland
| | - Anne Spang
- Biozentrum, University of Basel, Basel 4056, Switzerland
| | - Ralf-Peter Jansen
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen 72076, Germany
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86
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Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Wallingford JB, Finkelstein IJ, Marcotte EM, Drew K. Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes. Cell Rep 2019; 29:1351-1368.e5. [PMID: 31665645 PMCID: PMC6873818 DOI: 10.1016/j.celrep.2019.09.060] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 08/30/2019] [Accepted: 09/18/2019] [Indexed: 12/16/2022] Open
Abstract
RNA-binding proteins (RBPs) play essential roles in biology and are frequently associated with human disease. Although recent studies have systematically identified individual RNA-binding proteins, their higher-order assembly into ribonucleoprotein (RNP) complexes has not been systematically investigated. Here, we describe a proteomics method for systematic identification of RNP complexes in human cells. We identify 1,428 protein complexes that associate with RNA, indicating that more than 20% of known human protein complexes contain RNA. To explore the role of RNA in the assembly of each complex, we identify complexes that dissociate, change composition, or form stable protein-only complexes in the absence of RNA. We use our method to systematically identify cell-type-specific RNA-associated proteins in mouse embryonic stem cells and finally, distribute our resource, rna.MAP, in an easy-to-use online interface (rna.proteincomplexes.org). Our system thus provides a methodology for explorations across human tissues, disease states, and throughout all domains of life.
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Affiliation(s)
- Anna L Mallam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Wisath Sae-Lee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Jeffrey M Schaub
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Fan Tu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Anna Battenhouse
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Yu Jin Jang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - John B Wallingford
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Kevin Drew
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
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87
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Fast and unbiased purification of RNA-protein complexes after UV cross-linking. Methods 2019; 178:72-82. [PMID: 31586594 DOI: 10.1016/j.ymeth.2019.09.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 09/04/2019] [Accepted: 09/16/2019] [Indexed: 12/13/2022] Open
Abstract
Post-transcriptional regulation of gene expression in cells is facilitated by formation of RNA-protein complexes (RNPs). While many methods to study eukaryotic (m)RNPs rely on purification of polyadenylated RNA, other important regulatory RNA classes or bacterial mRNA could not be investigated at the same depth. To overcome this limitation, we developed Phenol Toluol extraction (PTex), a novel and unbiased method for the purification of UV cross-linked RNPs in living cells. PTex is a fast (2-3 h) and simple protocol. The purification principle is solely based on physicochemical properties of cross-linked RNPs, enabling us to interrogate RNA-protein interactions system-wide and beyond poly(A) RNA from a variety of species and source material. Here, we are presenting an introduction of the underlying separation principles and give a detailed discussion of the individual steps as well as incorporation of PTex in high-throughput pipelines.
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88
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Youn JY, Dyakov BJ, Zhang J, Knight JD, Vernon RM, Forman-Kay JD, Gingras AC. Properties of Stress Granule and P-Body Proteomes. Mol Cell 2019; 76:286-294. [DOI: 10.1016/j.molcel.2019.09.014] [Citation(s) in RCA: 159] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 01/01/2023]
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89
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Köster T, Reichel M, Staiger D. CLIP and RNA interactome studies to unravel genome-wide RNA-protein interactions in vivo in Arabidopsis thaliana. Methods 2019; 178:63-71. [PMID: 31494244 DOI: 10.1016/j.ymeth.2019.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/14/2019] [Accepted: 09/01/2019] [Indexed: 12/11/2022] Open
Abstract
Post-transcriptional regulation makes an important contribution to adjusting the transcriptome to environmental changes in plants. RNA-binding proteins are key players that interact specifically with mRNAs to co-ordinate their fate. While the regulatory interactions between proteins and RNA are well understood in animals, until recently little information was available on the global binding landscape of RNA-binding proteins in higher plants. This is not least due to technical challenges in plants. In turn, while numerous RNA-binding proteins have been identified through mutant analysis and homology-based searches in plants, only recently a full compendium of proteins with RNA-binding activity has been experimentally determined for the reference plant Arabidopsis thaliana. State-of-the-art techniques to determine RNA-protein interactions genome-wide in animals are based on the covalent fixation of RNA and protein in vivo by UV light. This has only recently been successfully applied to plants. Here, we present practical considerations on the application of UV irradiation based methods to comprehensively determine in vivo RNA-protein interactions in Arabidopsis thaliana, focussing on individual nucleotide resolution crosslinking immunoprecipitation (iCLIP) and mRNA interactome capture.
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Affiliation(s)
- Tino Köster
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Marlene Reichel
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany.
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90
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Sonnleitner E, Wulf A, Campagne S, Pei XY, Wolfinger MT, Forlani G, Prindl K, Abdou L, Resch A, Allain FHT, Luisi BF, Urlaub H, Bläsi U. Interplay between the catabolite repression control protein Crc, Hfq and RNA in Hfq-dependent translational regulation in Pseudomonas aeruginosa. Nucleic Acids Res 2019; 46:1470-1485. [PMID: 29244160 PMCID: PMC5815094 DOI: 10.1093/nar/gkx1245] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/01/2017] [Indexed: 12/23/2022] Open
Abstract
In Pseudomonas aeruginosa the RNA chaperone Hfq and the catabolite repression control protein (Crc) act as post-transcriptional regulators during carbon catabolite repression (CCR). In this regard Crc is required for full-fledged Hfq-mediated translational repression of catabolic genes. RNAseq based transcriptome analyses revealed a significant overlap between the Crc and Hfq regulons, which in conjunction with genetic data supported a concerted action of both proteins. Biochemical and biophysical approaches further suggest that Crc and Hfq form an assembly in the presence of RNAs containing A-rich motifs, and that Crc interacts with both, Hfq and RNA. Through these interactions, Crc enhances the stability of Hfq/Crc/RNA complexes, which can explain its facilitating role in Hfq-mediated translational repression. Hence, these studies revealed for the first time insights into how an interacting protein can modulate Hfq function. Moreover, Crc is shown to interfere with binding of a regulatory RNA to Hfq, which bears implications for riboregulation. These results are discussed in terms of a working model, wherein Crc prioritizes the function of Hfq toward utilization of favored carbon sources.
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Affiliation(s)
- Elisabeth Sonnleitner
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Alexander Wulf
- Biophysical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Sébastien Campagne
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Xue-Yuan Pei
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Michael T Wolfinger
- Institute of Theoretical Chemistry, University of Vienna, 1090 Vienna, Austria.,Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Giada Forlani
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Konstantin Prindl
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Laetitia Abdou
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Armin Resch
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Frederic H-T Allain
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Henning Urlaub
- Biophysical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
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91
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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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92
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CAPRI enables comparison of evolutionarily conserved RNA interacting regions. Nat Commun 2019; 10:2682. [PMID: 31213602 PMCID: PMC6581911 DOI: 10.1038/s41467-019-10585-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 05/21/2019] [Indexed: 12/21/2022] Open
Abstract
RNA-protein complexes play essential regulatory roles at nearly all levels of gene expression. Using in vivo crosslinking and RNA capture, we report a comprehensive RNA-protein interactome in a metazoan at four levels of resolution: single amino acids, domains, proteins and multisubunit complexes. We devise CAPRI, a method to map RNA-binding domains (RBDs) by simultaneous identification of RNA interacting crosslinked peptides and peptides adjacent to such crosslinked sites. CAPRI identifies more than 3000 RNA proximal peptides in Drosophila and human proteins with more than 45% of them forming new interaction interfaces. The comparison of orthologous proteins enables the identification of evolutionary conserved RBDs in globular domains and intrinsically disordered regions (IDRs). By comparing the sequences of IDRs through evolution, we classify them based on the type of motif, accumulation of tandem repeats, conservation of amino acid composition and high sequence divergence. Comprehensive characterisation of RNA-protein interactions requires different levels of resolution. Here, the authors present an integrated mass spectrometry-based approach that allows them to define the Drosophila RNA-protein interactome from the level of multisubunit complexes down to the RNA-binding amino acid.
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93
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Bechtella L, Kirschbaum C, Cosset M, Clodic G, Matheron L, Bolbach G, Sagan S, Walrant A, Sachon E. Benzophenone Photoreactivity in a Lipid Bilayer To Probe Peptide/Membrane Interactions: Simple System, Complex Information. Anal Chem 2019; 91:9102-9110. [DOI: 10.1021/acs.analchem.9b01584] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Leïla Bechtella
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
| | - Carla Kirschbaum
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
- Sorbonne Université, Institut de Biologie Paris Seine, Plateforme de spectrométrie de masse et protéomique, 75005 Paris, France
| | - Marine Cosset
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
| | - Gilles Clodic
- Sorbonne Université, Institut de Biologie Paris Seine, Plateforme de spectrométrie de masse et protéomique, 75005 Paris, France
| | - Lucrèce Matheron
- Sorbonne Université, Institut de Biologie Paris Seine, Plateforme de spectrométrie de masse et protéomique, 75005 Paris, France
| | - Gérard Bolbach
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
- Sorbonne Université, Institut de Biologie Paris Seine, Plateforme de spectrométrie de masse et protéomique, 75005 Paris, France
| | - Sandrine Sagan
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
| | - Astrid Walrant
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
| | - Emmanuelle Sachon
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
- Sorbonne Université, Institut de Biologie Paris Seine, Plateforme de spectrométrie de masse et protéomique, 75005 Paris, France
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94
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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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95
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Shchepachev V, Bresson S, Spanos C, Petfalski E, Fischer L, Rappsilber J, Tollervey D. Defining the RNA interactome by total RNA-associated protein purification. Mol Syst Biol 2019; 15:e8689. [PMID: 30962360 PMCID: PMC6452921 DOI: 10.15252/msb.20188689] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/05/2019] [Accepted: 03/13/2019] [Indexed: 12/13/2022] Open
Abstract
The RNA binding proteome (RBPome) was previously investigated using UV crosslinking and purification of poly(A)-associated proteins. However, most cellular transcripts are not polyadenylated. We therefore developed total RNA-associated protein purification (TRAPP) based on 254 nm UV crosslinking and purification of all RNA-protein complexes using silica beads. In a variant approach (PAR-TRAPP), RNAs were labelled with 4-thiouracil prior to 350 nm crosslinking. PAR-TRAPP in yeast identified hundreds of RNA binding proteins, strongly enriched for canonical RBPs. In comparison, TRAPP identified many more proteins not expected to bind RNA, and this correlated strongly with protein abundance. Comparing TRAPP in yeast and E. coli showed apparent conservation of RNA binding by metabolic enzymes. Illustrating the value of total RBP purification, we discovered that the glycolytic enzyme enolase interacts with tRNAs. Exploiting PAR-TRAPP to determine the effects of brief exposure to weak acid stress revealed specific changes in late 60S ribosome biogenesis. Furthermore, we identified the precise sites of crosslinking for hundreds of RNA-peptide conjugates, using iTRAPP, providing insights into potential regulation. We conclude that TRAPP is a widely applicable tool for RBPome characterization.
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Affiliation(s)
- Vadim Shchepachev
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Stefan Bresson
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Christos Spanos
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | | | - Lutz Fischer
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - David Tollervey
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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96
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Webster MW, Chen YH, Stowell JAW, Alhusaini N, Sweet T, Graveley BR, Coller J, Passmore LA. mRNA Deadenylation Is Coupled to Translation Rates by the Differential Activities of Ccr4-Not Nucleases. Mol Cell 2019; 70:1089-1100.e8. [PMID: 29932902 PMCID: PMC6024076 DOI: 10.1016/j.molcel.2018.05.033] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/17/2018] [Accepted: 05/24/2018] [Indexed: 01/01/2023]
Abstract
Translation and decay of eukaryotic mRNAs is controlled by shortening of the poly(A) tail and release of the poly(A)-binding protein Pab1/PABP. The Ccr4-Not complex contains two exonucleases—Ccr4 and Caf1/Pop2—that mediate mRNA deadenylation. Here, using a fully reconstituted biochemical system with proteins from the fission yeast Schizosaccharomyces pombe, we show that Pab1 interacts with Ccr4-Not, stimulates deadenylation, and differentiates the roles of the nuclease enzymes. Surprisingly, Pab1 release relies on Ccr4 activity. In agreement with this, in vivo experiments in budding yeast show that Ccr4 is a general deadenylase that acts on all mRNAs. In contrast, Caf1 only trims poly(A) not bound by Pab1. As a consequence, Caf1 is a specialized deadenylase required for the selective deadenylation of transcripts with lower rates of translation elongation and reduced Pab1 occupancy. These findings reveal a coupling between the rates of translation and deadenylation that is dependent on Pab1 and Ccr4-Not. Poly(A)-binding protein is efficiently released by Ccr4-Not nuclease activity Ccr4, but not Caf1, removes poly(A) tails bound to Pab1 Ccr4 acts on all transcripts and Caf1 acts on transcripts with low codon optimality Deadenylation by Ccr4-Not connects translation with mRNA stability
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Affiliation(s)
| | - Ying-Hsin Chen
- The Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106-4960, USA
| | | | - Najwa Alhusaini
- The Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106-4960, USA
| | - Thomas Sweet
- The Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106-4960, USA
| | - Brenton R Graveley
- Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Jeff Coller
- The Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106-4960, USA.
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97
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Urdaneta EC, Vieira-Vieira CH, Hick T, Wessels HH, Figini D, Moschall R, Medenbach J, Ohler U, Granneman S, Selbach M, Beckmann BM. Purification of cross-linked RNA-protein complexes by phenol-toluol extraction. Nat Commun 2019; 10:990. [PMID: 30824702 PMCID: PMC6397201 DOI: 10.1038/s41467-019-08942-3] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/11/2019] [Indexed: 12/30/2022] Open
Abstract
Recent methodological advances allowed the identification of an increasing number of RNA-binding proteins (RBPs) and their RNA-binding sites. Most of those methods rely, however, on capturing proteins associated to polyadenylated RNAs which neglects RBPs bound to non-adenylate RNA classes (tRNA, rRNA, pre-mRNA) as well as the vast majority of species that lack poly-A tails in their mRNAs (including all archea and bacteria). We have developed the Phenol Toluol extraction (PTex) protocol that does not rely on a specific RNA sequence or motif for isolation of cross-linked ribonucleoproteins (RNPs), but rather purifies them based entirely on their physicochemical properties. PTex captures RBPs that bind to RNA as short as 30 nt, RNPs directly from animal tissue and can be used to simplify complex workflows such as PAR-CLIP. Finally, we provide a global RNA-bound proteome of human HEK293 cells and the bacterium Salmonella Typhimurium.
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Affiliation(s)
- Erika C Urdaneta
- IRI Life Sciences, Humboldt University, Philippstr. 13, 10115, Berlin, Germany
| | - Carlos H Vieira-Vieira
- Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Timon Hick
- IRI Life Sciences, Humboldt University, Philippstr. 13, 10115, Berlin, Germany
| | - Hans-Herrmann Wessels
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Department of Biology, Humboldt University, Philippstr. 13, 10115, Berlin, Germany
| | - Davide Figini
- IRI Life Sciences, Humboldt University, Philippstr. 13, 10115, Berlin, Germany
| | - Rebecca Moschall
- Biochemistry I, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Jan Medenbach
- Biochemistry I, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Uwe Ohler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Department of Biology, Humboldt University, Philippstr. 13, 10115, Berlin, Germany
| | - Sander Granneman
- Centre for Systems and Synthetic Biology (SynthSys), University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Matthias Selbach
- Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Benedikt M Beckmann
- IRI Life Sciences, Humboldt University, Philippstr. 13, 10115, Berlin, Germany.
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98
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Ramanathan M, Porter DF, Khavari PA. Methods to study RNA-protein interactions. Nat Methods 2019; 16:225-234. [PMID: 30804549 PMCID: PMC6692137 DOI: 10.1038/s41592-019-0330-1] [Citation(s) in RCA: 208] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/28/2019] [Indexed: 12/26/2022]
Abstract
Noncoding RNA sequences, including long noncoding RNAs, small nucleolar RNAs, and untranslated mRNA regions, accomplish many of their diverse functions through direct interactions with RNA-binding proteins (RBPs). Recent efforts have identified hundreds of new RBPs that lack known RNA-binding domains, thus underscoring the complexity and diversity of RNA-protein complexes. Recent progress has expanded the number of methods for studying RNA-protein interactions in two general categories: approaches that characterize proteins bound to an RNA of interest (RNA-centric), and those that examine RNAs bound to a protein of interest (protein-centric). Each method has unique strengths and limitations, which makes it important to select optimal approaches for the biological question being addressed. Here we review methods for the study of RNA-protein interactions, with a focus on their suitability for specific applications.
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Affiliation(s)
- Muthukumar Ramanathan
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Douglas F Porter
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA.
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99
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Ponce-Salvatierra A, Astha, Merdas K, Nithin C, Ghosh P, Mukherjee S, Bujnicki JM. Computational modeling of RNA 3D structure based on experimental data. Biosci Rep 2019; 39:BSR20180430. [PMID: 30670629 PMCID: PMC6367127 DOI: 10.1042/bsr20180430] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 01/02/2023] Open
Abstract
RNA molecules are master regulators of cells. They are involved in a variety of molecular processes: they transmit genetic information, sense cellular signals and communicate responses, and even catalyze chemical reactions. As in the case of proteins, RNA function is dictated by its structure and by its ability to adopt different conformations, which in turn is encoded in the sequence. Experimental determination of high-resolution RNA structures is both laborious and difficult, and therefore the majority of known RNAs remain structurally uncharacterized. To address this problem, predictive computational methods were developed based on the accumulated knowledge of RNA structures determined so far, the physical basis of the RNA folding, and taking into account evolutionary considerations, such as conservation of functionally important motifs. However, all theoretical methods suffer from various limitations, and they are generally unable to accurately predict structures for RNA sequences longer than 100-nt residues unless aided by additional experimental data. In this article, we review experimental methods that can generate data usable by computational methods, as well as computational approaches for RNA structure prediction that can utilize data from experimental analyses. We outline methods and data types that can be potentially useful for RNA 3D structure modeling but are not commonly used by the existing software, suggesting directions for future development.
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Affiliation(s)
- Almudena Ponce-Salvatierra
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw PL-02-109, Poland
| | - Astha
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw PL-02-109, Poland
| | - Katarzyna Merdas
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw PL-02-109, Poland
| | - Chandran Nithin
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw PL-02-109, Poland
| | - Pritha Ghosh
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw PL-02-109, Poland
| | - Sunandan Mukherjee
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw PL-02-109, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw PL-02-109, Poland
- Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, Poznan PL-61-614, Poland
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100
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Winz ML, Peil L, Turowski TW, Rappsilber J, Tollervey D. Molecular interactions between Hel2 and RNA supporting ribosome-associated quality control. Nat Commun 2019; 10:563. [PMID: 30718516 PMCID: PMC6362110 DOI: 10.1038/s41467-019-08382-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 12/21/2018] [Indexed: 01/28/2023] Open
Abstract
Ribosome-associated quality control (RQC) pathways monitor and respond to ribosome stalling. Using in vivo UV-crosslinking and mass spectrometry, we identified a C-terminal region in Hel2/Rqt1 as an RNA binding domain. Complementary crosslinking and sequencing data for Hel2 revealed binding to 18S rRNA and translated mRNAs. Hel2 preferentially bound mRNAs upstream and downstream of the stop codon. C-terminal truncation of Hel2 abolished the major 18S crosslink and polysome association, and altered mRNA binding. HEL2 deletion caused loss of RQC and, we report here, no-go decay (NGD), with comparable effects for Hel2 truncation including the RNA-binding site. Asc1 acts upstream of Hel2 in RQC and asc1∆ impaired Hel2 binding to 18S and mRNA. In conclusion: Hel2 is recruited or stabilized on translating 40S ribosomal subunits by interactions with 18S rRNA and Asc1. This 18S interaction is required for Hel2 function in RQC and NGD. Hel2 probably interacts with mRNA during translation termination. Ribosome-associated quality control (RQC) pathways monitor and respond to stalling of the translating ribosome. Here the authors show that the ribosome associated RQC factor Hel2/ZNF598, an E3 ubiquitin ligase, generally interacts with mRNAs in the vicinity of stop codons.
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Affiliation(s)
- Marie-Luise Winz
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh, EH9 3BF, Scotland
| | - Lauri Peil
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh, EH9 3BF, Scotland.,Institute of Technology, University of Tartu, Nooruse 150411, Tartu, Estonia
| | - Tomasz W Turowski
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh, EH9 3BF, Scotland
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh, EH9 3BF, Scotland.,Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355, Berlin, Germany
| | - David Tollervey
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh, EH9 3BF, Scotland.
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