1
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Wu P, Zehnder J, Schröder N, Blümmel PEW, Salmon L, Damberger FF, Lipps G, Allain FHT, Wiegand T. Initial Primer Synthesis of a DNA Primase Monitored by Real-Time NMR Spectroscopy. J Am Chem Soc 2024; 146:9583-9596. [PMID: 38538061 PMCID: PMC11009956 DOI: 10.1021/jacs.3c11836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
Primases are crucial enzymes for DNA replication, as they synthesize a short primer required for initiating DNA replication. We herein present time-resolved nuclear magnetic resonance (NMR) spectroscopy in solution and in the solid state to study the initial dinucleotide formation reaction of archaeal pRN1 primase. Our findings show that the helix-bundle domain (HBD) of pRN1 primase prepares the two substrates and then hands them over to the catalytic domain to initiate the reaction. By using nucleotide triphosphate analogues, the reaction is substantially slowed down, allowing us to study the initial dinucleotide formation in real time. We show that the sedimented protein-DNA complex remains active in the solid-state NMR rotor and that time-resolved 31P-detected cross-polarization experiments allow monitoring the kinetics of dinucleotide formation. The kinetics in the sedimented protein sample are comparable to those determined by solution-state NMR. Protein conformational changes during primer synthesis are observed in time-resolved 1H-detected experiments at fast magic-angle spinning frequencies (100 kHz). A significant number of spectral changes cluster in the HBD pointing to the importance of the HBD for positioning the nucleotides and the dinucleotide.
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Affiliation(s)
- Pengzhi Wu
- Department
of Biology, Institute of Biochemistry, ETH
Zürich, 8093 Zurich, Switzerland
| | - Johannes Zehnder
- Laboratory
of Physical Chemistry, ETH Zürich, 8093 Zurich, Switzerland
| | - Nina Schröder
- Institute
of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
| | - Pascal E. W. Blümmel
- Department
of Biology, Institute of Biochemistry, ETH
Zürich, 8093 Zurich, Switzerland
| | - Loïc Salmon
- Department
of Biology, Institute of Biochemistry, ETH
Zürich, 8093 Zurich, Switzerland
| | - Fred. F. Damberger
- Department
of Biology, Institute of Biochemistry, ETH
Zürich, 8093 Zurich, Switzerland
| | - Georg Lipps
- Institute
of Chemistry and Bioanalytics, University
of Applied Sciences Northwestern Switzerland, Hofackerstrasses 30, 4132 Muttenz, Switzerland
| | - Frédéric H.-T. Allain
- Department
of Biology, Institute of Biochemistry, ETH
Zürich, 8093 Zurich, Switzerland
| | - Thomas Wiegand
- Laboratory
of Physical Chemistry, ETH Zürich, 8093 Zurich, Switzerland
- Institute
of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
- Max-Planck-Institute
for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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2
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de Vries T, Novakovic M, Ni Y, Smok I, Inghelram C, Bikaki M, Sarnowski CP, Han Y, Emmanouilidis L, Padroni G, Leitner A, Allain FHT. Specific protein-RNA interactions are mostly preserved in biomolecular condensates. Sci Adv 2024; 10:eadm7435. [PMID: 38446881 PMCID: PMC10917357 DOI: 10.1126/sciadv.adm7435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 01/30/2024] [Indexed: 03/08/2024]
Abstract
Many biomolecular condensates are enriched in and depend on RNAs and RNA binding proteins (RBPs). So far, only a few studies have addressed the characterization of the intermolecular interactions responsible for liquid-liquid phase separation (LLPS) and the impact of condensation on RBPs and RNAs. Here, we present an approach to study protein-RNA interactions inside biomolecular condensates by applying cross-linking of isotope labeled RNA and tandem mass spectrometry to phase-separating systems (LLPS-CLIR-MS). LLPS-CLIR-MS enables the characterization of intermolecular interactions present within biomolecular condensates at residue-specific resolution and allows a comparison with the same complexes in the dispersed phase. We observe that sequence-specific RBP-RNA interactions present in the dispersed phase are generally maintained inside condensates. In addition, LLPS-CLIR-MS identifies structural alterations at the protein-RNA interfaces, including additional unspecific contacts in the condensed phase. Our approach offers a procedure to derive structural information of protein-RNA complexes within biomolecular condensates that could be critical for integrative structural modeling of ribonucleoproteins (RNPs) in this form.
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Affiliation(s)
- Tebbe de Vries
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Mihajlo Novakovic
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Yinan Ni
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Izabela Smok
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Clara Inghelram
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Maria Bikaki
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Chris P. Sarnowski
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Yaning Han
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | | | - Giacomo Padroni
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
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3
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Blatter M, Meylan C, Cléry A, Giambruno R, Nikolaev Y, Heidecker M, Solanki JA, Diaz MO, Gabellini D, Allain FHT. RNA binding induces an allosteric switch in Cyp33 to repress MLL1-mediated transcription. Sci Adv 2023; 9:eadf5330. [PMID: 37075125 PMCID: PMC10115415 DOI: 10.1126/sciadv.adf5330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Mixed-lineage leukemia 1 (MLL1) is a transcription activator of the HOX family, which binds to specific epigenetic marks on histone H3 through its third plant homeodomain (PHD3) domain. Through an unknown mechanism, MLL1 activity is repressed by cyclophilin 33 (Cyp33), which binds to MLL1 PHD3. We determined solution structures of Cyp33 RNA recognition motif (RRM) free, bound to RNA, to MLL1 PHD3, and to both MLL1 and the histone H3 lysine N6-trimethylated. We found that a conserved α helix, amino-terminal to the RRM domain, adopts three different positions facilitating a cascade of binding events. These conformational changes are triggered by Cyp33 RNA binding and ultimately lead to MLL1 release from the histone mark. Together, our mechanistic findings rationalize how Cyp33 binding to MLL1 can switch chromatin to a transcriptional repressive state triggered by RNA binding as a negative feedback loop.
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Affiliation(s)
- Markus Blatter
- Department of Biology, Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
- Corresponding author. (F.H.-T.A.); (M.B.)
| | - Charlotte Meylan
- Department of Biology, Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Antoine Cléry
- Department of Biology, Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Roberto Giambruno
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Yaroslav Nikolaev
- Department of Biology, Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Michel Heidecker
- Department of Biology, Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Jessica Arvindbhai Solanki
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University of Chicago Medical Center, University of Chicago, Chicago, IL, USA
| | - Manuel O. Diaz
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University of Chicago Medical Center, University of Chicago, Chicago, IL, USA
| | - Davide Gabellini
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Frédéric H.-T. Allain
- Department of Biology, Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
- Corresponding author. (F.H.-T.A.); (M.B.)
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4
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Ritsch I, Esteban-Hofer L, Lehmann E, Emmanouilidis L, Yulikov M, Allain FHT, Jeschke G. Characterization of Weak Protein Domain Structure by Spin-Label Distance Distributions. Front Mol Biosci 2021; 8:636599. [PMID: 33912586 PMCID: PMC8072059 DOI: 10.3389/fmolb.2021.636599] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/19/2021] [Indexed: 01/04/2023] Open
Abstract
Function of intrinsically disordered proteins may depend on deviation of their conformational ensemble from that of a random coil. Such deviation may be hard to characterize and quantify, if it is weak. We explored the potential of distance distributions between spin labels, as they can be measured by electron paramagnetic resonance techniques, for aiding such characterization. On the example of the intrinsically disordered N-terminal domain 1-267 of fused in sarcoma (FUS) we examined what such distance distributions can and cannot reveal on the random-coil reference state. On the example of the glycine-rich domain 188-320 of heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) we studied whether deviation from a random-coil ensemble can be robustly detected with 19 distance distribution restraints. We discuss limitations imposed by ill-posedness of the conversion of primary data to distance distributions and propose overlap of distance distributions as a fit criterion that can tackle this problem. For testing consistency and size sufficiency of the restraint set, we propose jack-knife resampling. At current desktop computers, our approach is expected to be viable for domains up to 150 residues and for between 10 and 50 distance distribution restraints.
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Affiliation(s)
- Irina Ritsch
- Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Laura Esteban-Hofer
- Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | | | | | - Maxim Yulikov
- Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | | | - Gunnar Jeschke
- Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
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5
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Campagne S, Boigner S, Rüdisser S, Moursy A, Gillioz L, Knörlein A, Hall J, Ratni H, Cléry A, Allain FHT. Structural basis of a small molecule targeting RNA for a specific splicing correction. Nat Chem Biol 2019; 15:1191-1198. [DOI: 10.1038/s41589-019-0384-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 09/07/2019] [Indexed: 12/24/2022]
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6
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Loughlin FE, Lukavsky PJ, Kazeeva T, Reber S, Hock EM, Colombo M, Von Schroetter C, Pauli P, Cléry A, Mühlemann O, Polymenidou M, Ruepp MD, Allain FHT. The Solution Structure of FUS Bound to RNA Reveals a Bipartite Mode of RNA Recognition with Both Sequence and Shape Specificity. Mol Cell 2019; 73:490-504.e6. [DOI: 10.1016/j.molcel.2018.11.012] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 09/21/2018] [Accepted: 11/13/2018] [Indexed: 12/13/2022]
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7
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Boudet J, Devillier JC, Allain FHT, Lipps G. Structures to complement the archaeo-eukaryotic primases catalytic cycle description: What's next? Comput Struct Biotechnol J 2015; 13:339-51. [PMID: 25987967 PMCID: PMC4434180 DOI: 10.1016/j.csbj.2015.04.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/20/2015] [Accepted: 04/24/2015] [Indexed: 12/25/2022] Open
Abstract
DNA replication is a crucial stage in the transfer of genetic information from parent to daughter cells. This mechanism involves multiple proteins with one key player being the primase. Primases are single-stranded DNA dependent RNA polymerases. On the leading strand, they synthesize the primer once allowing DNA elongation while on the lagging strand primers are generated repeatedly (Okazaki fragments). Primases have the unique ability to create the first phosphodiester bond yielding a dinucleotide which is initially elongated by primases and then by DNA polymerases. Primase activity has been studied in the last decades but the detailed molecular steps explaining some unique features remain unclear. High-resolution structures of free and bound primases domains have brought significant insights in the understanding of the primase reaction cycle. Here, we give a short review of the structural work conducted in the field of archaeo-eukaryotic primases and we underline the missing “pictures” of the active forms of the enzyme which are of major interest. We organized our analysis with respect to the progression through the catalytic pathway.
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Affiliation(s)
- Julien Boudet
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
- Corresponding author. Tel.: + 41 446330723; fax: + 41 446331294.
| | - Jean-Christophe Devillier
- University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, 4132 Muttenz, Switzerland
| | - Frédéric H.-T. Allain
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Georg Lipps
- University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, 4132 Muttenz, Switzerland
- Corresponding author. Tel.: + 41 614674301; fax: + 41 614674701.
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8
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9
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Duss O, Michel E, Yulikov M, Schubert M, Jeschke G, Allain FHT. Structural basis of the non-coding RNA RsmZ acting as a protein sponge. Nature 2014; 509:588-92. [DOI: 10.1038/nature13271] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 03/24/2014] [Indexed: 01/01/2023]
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10
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Cléry A, Sinha R, Anczuków O, Corrionero A, Moursy A, Daubner GM, Valcárcel J, Krainer AR, Allain FHT. Isolated pseudo-RNA-recognition motifs of SR proteins can regulate splicing using a noncanonical mode of RNA recognition. Proc Natl Acad Sci U S A 2013; 110:E2802-11. [PMID: 23836656 PMCID: PMC3725064 DOI: 10.1073/pnas.1303445110] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Serine/arginine (SR) proteins, one of the major families of alternative-splicing regulators in Eukarya, have two types of RNA-recognition motifs (RRMs): a canonical RRM and a pseudo-RRM. Although pseudo-RRMs are crucial for activity of SR proteins, their mode of action was unknown. By solving the structure of the human SRSF1 pseudo-RRM bound to RNA, we discovered a very unusual and sequence-specific RNA-binding mode that is centered on one α-helix and does not involve the β-sheet surface, which typically mediates RNA binding by RRMs. Remarkably, this mode of binding is conserved in all pseudo-RRMs tested. Furthermore, the isolated pseudo-RRM is sufficient to regulate splicing of about half of the SRSF1 target genes tested, and the bound α-helix is a pivotal element for this function. Our results strongly suggest that SR proteins with a pseudo-RRM frequently regulate splicing by competing with, rather than recruiting, spliceosome components, using solely this unusual RRM.
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Affiliation(s)
- Antoine Cléry
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Rahul Sinha
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Olga Anczuków
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Anna Corrionero
- Institució Catalana de Recerca i Estudis Avançats, Universitat Pompeu Fabra 08003 Barcelona, Spain; and
- Centre de Regulació Genòmica, 08003 Barcelona, Spain
| | - Ahmed Moursy
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Gerrit M. Daubner
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Juan Valcárcel
- Institució Catalana de Recerca i Estudis Avançats, Universitat Pompeu Fabra 08003 Barcelona, Spain; and
- Centre de Regulació Genòmica, 08003 Barcelona, Spain
| | | | - Frédéric H.-T. Allain
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
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11
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Michel E, Skrisovska L, Wüthrich K, Allain FHT. Amino Acid-Selective Segmental Isotope Labeling of Multidomain Proteins for Structural Biology. Chembiochem 2013; 14:457-66. [DOI: 10.1002/cbic.201200732] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Indexed: 11/12/2022]
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12
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Schubert M, Bleuler-Martinez S, Butschi A, Wälti MA, Egloff P, Stutz K, Yan S, Wilson IBH, Hengartner MO, Aebi M, Allain FHT, Künzler M. Plasticity of the β-trefoil protein fold in the recognition and control of invertebrate predators and parasites by a fungal defence system. PLoS Pathog 2012; 8:e1002706. [PMID: 22615566 PMCID: PMC3355094 DOI: 10.1371/journal.ppat.1002706] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 04/02/2012] [Indexed: 11/29/2022] Open
Abstract
Discrimination between self and non-self is a prerequisite for any defence mechanism; in innate defence, this discrimination is often mediated by lectins recognizing non-self carbohydrate structures and so relies on an arsenal of host lectins with different specificities towards target organism carbohydrate structures. Recently, cytoplasmic lectins isolated from fungal fruiting bodies have been shown to play a role in the defence of multicellular fungi against predators and parasites. Here, we present a novel fruiting body lectin, CCL2, from the ink cap mushroom Coprinopsis cinerea. We demonstrate the toxicity of the lectin towards Caenorhabditis elegans and Drosophila melanogaster and present its NMR solution structure in complex with the trisaccharide, GlcNAcβ1,4[Fucα1,3]GlcNAc, to which it binds with high specificity and affinity in vitro. The structure reveals that the monomeric CCL2 adopts a β-trefoil fold and recognizes the trisaccharide by a single, topologically novel carbohydrate-binding site. Site-directed mutagenesis of CCL2 and identification of C. elegans mutants resistant to this lectin show that its nematotoxicity is mediated by binding to α1,3-fucosylated N-glycan core structures of nematode glycoproteins; feeding with fluorescently labeled CCL2 demonstrates that these target glycoproteins localize to the C. elegans intestine. Since the identified glycoepitope is characteristic for invertebrates but absent from fungi, our data show that the defence function of fruiting body lectins is based on the specific recognition of non-self carbohydrate structures. The trisaccharide specifically recognized by CCL2 is a key carbohydrate determinant of pollen and insect venom allergens implying this particular glycoepitope is targeted by both fungal defence and mammalian immune systems. In summary, our results demonstrate how the plasticity of a common protein fold can contribute to the recognition and control of antagonists by an innate defence mechanism, whereby the monovalency of the lectin for its ligand implies a novel mechanism of lectin-mediated toxicity.
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Affiliation(s)
- Mario Schubert
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
| | | | - Alex Butschi
- Institute of Molecular Life Sciences, University of Zürich, Switzerland
| | | | - Pascal Egloff
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Katrin Stutz
- Institute of Molecular Life Sciences, University of Zürich, Switzerland
| | - Shi Yan
- Department of Chemistry, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Iain B. H. Wilson
- Department of Chemistry, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | | | - Markus Aebi
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | | | - Markus Künzler
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
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Lamichhane R, Daubner GM, Thomas-Crusells J, Auweter S, Manatchal C, Austin KS, Valniuk O, Allain FHT, Rueda D. RNA Looping By PTB: Evidence Using Fret and NMR Spectroscopy and For a Role in Splicing Repression. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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14
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Slynko V, Schubert M, Numao S, Kowarik M, Aebi M, Allain FHT. NMR Structure Determination of a Segmentally Labeled Glycoprotein Using in Vitro Glycosylation. J Am Chem Soc 2009; 131:1274-81. [DOI: 10.1021/ja808682v] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Vadim Slynko
- Institute of Molecular Biology and Biophysics, and Institute of Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Mario Schubert
- Institute of Molecular Biology and Biophysics, and Institute of Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Shin Numao
- Institute of Molecular Biology and Biophysics, and Institute of Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Michael Kowarik
- Institute of Molecular Biology and Biophysics, and Institute of Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Markus Aebi
- Institute of Molecular Biology and Biophysics, and Institute of Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Frédéric H.-T. Allain
- Institute of Molecular Biology and Biophysics, and Institute of Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
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15
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Oberstrass FC, Allain FHT, Ravindranathan S. Changes in Dynamics of SRE-RNA on Binding to the VTS1p-SAM Domain Studied by 13C NMR Relaxation. J Am Chem Soc 2008; 130:12007-20. [DOI: 10.1021/ja8023115] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Florian C. Oberstrass
- Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zürich, Switzerland, and Central NMR Facility, National Chemical Laboratory, Pune 411008, India
| | - Frédéric H.-T. Allain
- Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zürich, Switzerland, and Central NMR Facility, National Chemical Laboratory, Pune 411008, India
| | - Sapna Ravindranathan
- Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zürich, Switzerland, and Central NMR Facility, National Chemical Laboratory, Pune 411008, India
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16
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Lapouge K, Schubert M, Allain FHT, Haas D. Gac/Rsm signal transduction pathway of γ-proteobacteria: from RNA recognition to regulation of social behaviour. Mol Microbiol 2007; 67:241-53. [DOI: 10.1111/j.1365-2958.2007.06042.x] [Citation(s) in RCA: 440] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Abstract
A code predicting the RNA sequence that will be bound by a certain protein based on its amino acid sequence or its structure would provide a useful tool for the design of RNA binders with desired sequence-specificity. Such de novo designed RNA binders could be of extraordinary use in both medical and basic research applications. Furthermore, a code could help to predict the cellular functions of RNA-binding proteins that have not yet been extensively studied. A comparative analysis of Pumilio homology domains, zinc-containing RNA binders, hnRNP K homology domains and RNA recognition motifs is performed in this review. Based on this, a set of binding rules is proposed that hints towards a code for RNA recognition by these domains. Furthermore, we discuss the intermolecular interactions that are important for RNA binding and summarize their importance in providing affinity and specificity.
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Affiliation(s)
- Sigrid D. Auweter
- Department of Biology, Institute for Molecular Biology and BiophysicsETH Zürich, CH-8093 Zürich, Switzerland
- Molecular Life Science PhD ProgramZürich, Switzerland
| | - Florian C. Oberstrass
- Department of Biology, Institute for Molecular Biology and BiophysicsETH Zürich, CH-8093 Zürich, Switzerland
- Molecular Life Science PhD ProgramZürich, Switzerland
| | - Frédéric H.-T. Allain
- Department of Biology, Institute for Molecular Biology and BiophysicsETH Zürich, CH-8093 Zürich, Switzerland
- To whom correspondence should be addressed. Tel: +41 44 633 3940; Fax: +41 44 63 31294;
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18
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Dominguez C, Allain FHT. NMR structure of the three quasi RNA recognition motifs (qRRMs) of human hnRNP F and interaction studies with Bcl-x G-tract RNA: a novel mode of RNA recognition. Nucleic Acids Res 2006; 34:3634-45. [PMID: 16885237 PMCID: PMC1540728 DOI: 10.1093/nar/gkl488] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2006] [Revised: 06/28/2006] [Accepted: 06/28/2006] [Indexed: 02/03/2023] Open
Abstract
The heterogeneous nuclear ribonucleoprotein (hnRNP) F belongs to the hnRNP H family involved in the regulation of alternative splicing and polyadenylation and specifically recognizes poly(G) sequences (G-tracts). In particular, hnRNP F binds a G-tract of the Bcl-x RNA and regulates its alternative splicing, leading to two isoforms, Bcl-x(S) and Bcl-x(L), with antagonist functions. In order to gain insight into G-tract recognition by hnRNP H members, we initiated an NMR study of human hnRNP F. We present the solution structure of the three quasi RNA recognition motifs (qRRMs) of hnRNP F and identify the residues that are important for the interaction with the Bcl-x RNA by NMR chemical shift perturbation and mutagenesis experiments. The three qRRMs exhibit the canonical betaalphabetabetaalphabeta RRM fold but additional secondary structure elements are present in the two N-terminal qRRMs of hnRNP F. We show that qRRM1 and qRRM2 but not qRRM3 are responsible for G-tract recognition and that the residues of qRRM1 and qRRM2 involved in G-tract interaction are not on the beta-sheet surface as observed for the classical RRM but are part of a short beta-hairpin and two adjacent loops. These regions define a novel interaction surface for RNA recognition by RRMs.
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Affiliation(s)
- Cyril Dominguez
- Institute of Molecular Biology and Biophysics, ETH ZürichCH-8093 Zürich, Switzerland
| | - Frédéric H.-T. Allain
- Institute of Molecular Biology and Biophysics, ETH ZürichCH-8093 Zürich, Switzerland
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Wenter P, Reymond L, Auweter SD, Allain FHT, Pitsch S. Short, synthetic and selectively 13C-labeled RNA sequences for the NMR structure determination of protein-RNA complexes. Nucleic Acids Res 2006; 34:e79. [PMID: 16807315 PMCID: PMC1904103 DOI: 10.1093/nar/gkl427] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Revised: 05/03/2006] [Accepted: 05/29/2006] [Indexed: 11/29/2022] Open
Abstract
We report an optimized synthesis of all canonical 2'-O-TOM protected ribonucleoside phosphoramidites and solid supports containing [13C5]-labeled ribose moieties, their sequence-specific introduction into very short RNA sequences and their use for the structure determination of two protein-RNA complexes. These specifically labeled sequences facilitate RNA resonance assignments and are essential to assign a high number of sugar-sugar and intermolecular NOEs, which ultimately improve the precision and accuracy of the resulting structures. This labeling strategy is particularly useful for the study of protein-RNA complexes with single-stranded RNA in solution, which is rapidly an increasingly relevant research area in biology.
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Affiliation(s)
- Philipp Wenter
- Institut des Science et Ingénierie Chimiques, Ecole Polytechnique Fédérale de LausanneEPFL-BCH, 1015 Lausanne, Switzerland
- Institute for Molecular Biology and Biophysics, Biology Department, Swiss Federal Institute of Technology ZürichETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Luc Reymond
- Institut des Science et Ingénierie Chimiques, Ecole Polytechnique Fédérale de LausanneEPFL-BCH, 1015 Lausanne, Switzerland
- Institute for Molecular Biology and Biophysics, Biology Department, Swiss Federal Institute of Technology ZürichETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Sigrid D. Auweter
- Institute for Molecular Biology and Biophysics, Biology Department, Swiss Federal Institute of Technology ZürichETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Frédéric H.-T. Allain
- Institute for Molecular Biology and Biophysics, Biology Department, Swiss Federal Institute of Technology ZürichETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Stefan Pitsch
- To whom correspondence should be addressed. Tel: 0041 21 6939380; Fax: 0041 21 6939380;
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Stefl R, Skrisovska L, Allain FHT. RNA sequence- and shape-dependent recognition by proteins in the ribonucleoprotein particle. EMBO Rep 2005; 6:33-8. [PMID: 15643449 PMCID: PMC1299235 DOI: 10.1038/sj.embor.7400325] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2004] [Accepted: 11/26/2004] [Indexed: 11/09/2022] Open
Abstract
At all stages of its life (from transcription to translation), an RNA transcript interacts with many different RNA-binding proteins. The composition of this supramolecular assembly, known as a ribonucleoprotein particle, is diverse and highly dynamic. RNA-binding proteins control the generation, maturation and lifespan of the RNA transcript and thus regulate and influence the cellular function of the encoded gene. Here, we review our current understanding of protein-RNA recognition mediated by the two most abundant RNA-binding domains (the RNA-recognition motif and the double-stranded RNA-binding motif) plus the zinc-finger motif, the most abundant nucleic-acid-binding domain. In addition, we discuss how not only the sequence but also the shape of the RNA are recognized by these three classes of RNA-binding protein.
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Affiliation(s)
- Richard Stefl
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology Zürich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Lenka Skrisovska
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology Zürich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Frédéric H.-T. Allain
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology Zürich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
- Tel: +41 (0)1 63 33940; Fax: +41 (0)1 63 31294;
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