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Klenk C, Scrivens M, Niederer A, Shi S, Mueller L, Gersz E, Zauderer M, Smith ES, Strohner R, Plückthun A. A Vaccinia-based system for directed evolution of GPCRs in mammalian cells. Nat Commun 2023; 14:1770. [PMID: 36997531 PMCID: PMC10063554 DOI: 10.1038/s41467-023-37191-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/06/2023] [Indexed: 04/03/2023] Open
Abstract
Directed evolution in bacterial or yeast display systems has been successfully used to improve stability and expression of G protein-coupled receptors for structural and biophysical studies. Yet, several receptors cannot be tackled in microbial systems due to their complex molecular composition or unfavorable ligand properties. Here, we report an approach to evolve G protein-coupled receptors in mammalian cells. To achieve clonality and uniform expression, we develop a viral transduction system based on Vaccinia virus. By rational design of synthetic DNA libraries, we first evolve neurotensin receptor 1 for high stability and expression. Second, we demonstrate that receptors with complex molecular architectures and large ligands, such as the parathyroid hormone 1 receptor, can be readily evolved. Importantly, functional receptor properties can now be evolved in the presence of the mammalian signaling environment, resulting in receptor variants exhibiting increased allosteric coupling between the ligand binding site and the G protein interface. Our approach thus provides insights into the intricate molecular interplay required for GPCR activation.
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Affiliation(s)
- Christoph Klenk
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
| | - Maria Scrivens
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Anina Niederer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Shuying Shi
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Loretta Mueller
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Elaine Gersz
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Maurice Zauderer
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Ernest S Smith
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Ralf Strohner
- MorphoSys AG, Semmelweisstr. 7, 82152, Planegg, Germany
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
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2
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Qiu C, Erinne OC, Dave JM, Cui P, Jin H, Muthukrishnan N, Tang LK, Ganesh Babu S, Lam KC, Vandeventer PJ, Strohner R, Van den Brulle J, Sze SH, Kaplan CD. Correction: High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop. PLoS Genet 2018; 14:e1007158. [PMID: 29298339 PMCID: PMC5751974 DOI: 10.1371/journal.pgen.1007158] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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3
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Eylenstein R, Weinfurtner D, Härtle S, Strohner R, Böttcher J, Augustin M, Ostendorp R, Steidl S. Molecular basis of in vitro affinity maturation and functional evolution of a neutralizing anti-human GM-CSF antibody. MAbs 2015; 8:176-86. [PMID: 26406987 DOI: 10.1080/19420862.2015.1099774] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
X-ray structure analysis of 4 antibody Fab fragments, each in complex with human granulocyte macrophage colony stimulating factor (GM-CSF), was performed to investigate the changes at the protein-protein binding interface during the course of in vitro affinity maturation by phage display selection. The parental antibody MOR03929 was compared to its derivatives MOR04252 (CDR-H2 optimized), MOR04302 (CDR-L3 optimized) and MOR04357 (CDR-H2 and CDR-L3 optimized). All antibodies bind to a conformational epitope that can be divided into 3 sub-epitopes. Specifically, MOR04357 binds to a region close to the GM-CSF N-terminus (residues 11-24), a short second sub-epitope (residues 83-89) and a third at the C-terminus (residues 112-123). Modifications introduced during affinity maturation in CDR-H2 and CDR-L3 led to the establishment of additional hydrogen bonds and van der Waals contacts, respectively, providing a rationale for the observed improvement in binding affinity and neutralization potency. Once GM-CSF is complexed to the antibodies, modeling predicts a sterical clash with GM-CSF binding to GM-CSF receptor α and β chain. This predicted mutually exclusive binding was confirmed by a GM-CSF receptor α chain ligand binding inhibition assay. Finally, high throughput sequencing of clones obtained after affinity maturation phage display pannings revealed highly selected consensus sequences for CDR-H2 as well for CDR-L3, which are in accordance with the sequence of the highest affinity antibody MOR04357. The resolved crystal structures highlight the criticality of these strongly selected residues for high affinity interaction with GM-CSF.
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Affiliation(s)
- Roy Eylenstein
- a MorphoSys AG ; Lena-Christ-Str. 48; 82152 Martinsried ; Germany.,d These authors contributed equally to this work
| | - Daniel Weinfurtner
- a MorphoSys AG ; Lena-Christ-Str. 48; 82152 Martinsried ; Germany.,d These authors contributed equally to this work
| | - Stefan Härtle
- a MorphoSys AG ; Lena-Christ-Str. 48; 82152 Martinsried ; Germany
| | - Ralf Strohner
- a MorphoSys AG ; Lena-Christ-Str. 48; 82152 Martinsried ; Germany
| | - Jark Böttcher
- b Proteros Biostructures GmbH ; Bunsenstr. 7a; 82152 Martinsried ; Germany.,c Current affiliation: Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11,1121 Vienna , Austria
| | - Martin Augustin
- b Proteros Biostructures GmbH ; Bunsenstr. 7a; 82152 Martinsried ; Germany
| | - Ralf Ostendorp
- a MorphoSys AG ; Lena-Christ-Str. 48; 82152 Martinsried ; Germany
| | - Stefan Steidl
- a MorphoSys AG ; Lena-Christ-Str. 48; 82152 Martinsried ; Germany
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Manelyte L, Strohner R, Gross T, Längst G. Chromatin targeting signals, nucleosome positioning mechanism and non-coding RNA-mediated regulation of the chromatin remodeling complex NoRC. PLoS Genet 2014; 10:e1004157. [PMID: 24651573 PMCID: PMC3961174 DOI: 10.1371/journal.pgen.1004157] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [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: 10/05/2013] [Accepted: 12/17/2013] [Indexed: 11/21/2022] Open
Abstract
Active and repressed ribosomal RNA (rRNA) genes are characterised by specific epigenetic marks and differentially positioned nucleosomes at their promoters. Repression of the rRNA genes requires a non-coding RNA (pRNA) and the presence of the nucleolar remodeling complex (NoRC). ATP-dependent chromatin remodeling enzymes are essential regulators of DNA-dependent processes, and this regulation occurs via the modulation of DNA accessibility in chromatin. We have studied the targeting of NoRC to the rRNA gene promoter; its mechanism of nucleosome positioning, in which a nucleosome is placed over the transcription initiation site; and the functional role of the pRNA. We demonstrate that NoRC is capable of recognising and binding to the nucleosomal rRNA gene promoter on its own and binds with higher affinity the nucleosomes positioned at non-repressive positions. NoRC recognises the promoter nucleosome within a chromatin array and positions the nucleosomes, as observed in vivo. NoRC uses the release mechanism of positioning, which is characterised by a reduced affinity for the remodeled substrate. The pRNA specifically binds to NoRC and regulates the enzyme by switching off its ATPase activity. Given the known role of pRNA in tethering NoRC to the rDNA, we propose that pRNA is a key factor that links the chromatin modification activity and scaffolding function of NoRC. Tumour cells overexpress ribosomal RNA (rRNA), which is required for ribosome assembly and cell growth. rRNA gene repression is mediated by the chromatin remodeling complex (NoRC) and a non-coding RNA that binds to this enzyme. This study addresses the mechanism of nucleosome positioning by NoRC and the functional role of the non-coding RNA, which is termed pRNA because it corresponds to the promoter sequence. NoRC recognises the promoter nucleosome in a chromatin array with high affinity and uses a release mechanism to position the nucleosome over the transcription initiation site. The pRNA binds specifically to NoRC and inhibits its ATPase activity. We suggest that the RNA retains NoRC at the gene promoter after remodeling, linking its chromatin modification and scaffolding activity to inactive rDNA copies.
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Affiliation(s)
- Laura Manelyte
- Biochemistry Centre Regensburg (BCR), University of Regensburg, Regensburg, Germany
| | - Ralf Strohner
- Biochemistry Centre Regensburg (BCR), University of Regensburg, Regensburg, Germany
| | - Thomas Gross
- Biochemistry Centre Regensburg (BCR), University of Regensburg, Regensburg, Germany
| | - Gernot Längst
- Biochemistry Centre Regensburg (BCR), University of Regensburg, Regensburg, Germany
- * E-mail:
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5
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Tiller T, Schuster I, Deppe D, Siegers K, Strohner R, Herrmann T, Berenguer M, Poujol D, Stehle J, Stark Y, Heßling M, Daubert D, Felderer K, Kaden S, Kölln J, Enzelberger M, Urlinger S. A fully synthetic human Fab antibody library based on fixed VH/VL framework pairings with favorable biophysical properties. MAbs 2013; 5:445-70. [PMID: 23571156 DOI: 10.4161/mabs.24218] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
This report describes the design, generation and testing of Ylanthia, a fully synthetic human Fab antibody library with 1.3E+11 clones. Ylanthia comprises 36 fixed immunoglobulin (Ig) variable heavy (VH)/variable light (VL) chain pairs, which cover a broad range of canonical complementarity-determining region (CDR) structures. The variable Ig heavy and Ig light (VH/VL) chain pairs were selected for biophysical characteristics favorable to manufacturing and development. The selection process included multiple parameters, e.g., assessment of protein expression yield, thermal stability and aggregation propensity in fragment antigen binding (Fab) and IgG1 formats, and relative Fab display rate on phage. The framework regions are fixed and the diversified CDRs were designed based on a systematic analysis of a large set of rearranged human antibody sequences. Care was taken to minimize the occurrence of potential posttranslational modification sites within the CDRs. Phage selection was performed against various antigens and unique antibodies with excellent biophysical properties were isolated. Our results confirm that quality can be built into an antibody library by prudent selection of unmodified, fully human VH/VL pairs as scaffolds.
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Schlinkmann KM, Hillenbrand M, Rittner A, Künz M, Strohner R, Plückthun A. Maximizing detergent stability and functional expression of a GPCR by exhaustive recombination and evolution. J Mol Biol 2012; 422:414-28. [PMID: 22683350 DOI: 10.1016/j.jmb.2012.05.039] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 05/27/2012] [Accepted: 05/30/2012] [Indexed: 10/28/2022]
Abstract
To identify structural features in a G-protein-coupled receptor (GPCR) crucial for biosynthesis, stability in the membrane and stability in detergent micelles, we developed an evolutionary approach using expression in the inner membrane of Escherichia coli. From the analysis of 800,000 sequences of the rat neurotensin receptor 1, in which every amino acid had been varied to all 64 codons, we uncovered several "shift" positions, where the selected population focuses on a residue different from wild type. Here, we employed in vitro DNA recombination and a comprehensive synthetic binary library made by the Slonomics® technology, allowing us to uncover additive and synergistic effects in the structure that maximize both detergent stability and functional expression. We identified variants with >25,000 functional molecules per E. coli cell, a 50-fold increase over wild type, and observed strong coevolution of detergent stability. We arrived at receptor variants highly stable in short-chain detergents, much more so than those found by alanine scanning on the same receptor. These evolved GPCRs continue to be able to signal through the G-protein. We discuss the structural reasons for these improvements achieved through directed evolution.
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Affiliation(s)
- Karola M Schlinkmann
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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7
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Zhai W, Glanville J, Fuhrmann M, Mei L, Ni I, Sundar PD, Van Blarcom T, Abdiche Y, Lindquist K, Strohner R, Telman D, Cappuccilli G, Finlay WJJ, Van den Brulle J, Cox DR, Pons J, Rajpal A. Synthetic antibodies designed on natural sequence landscapes. J Mol Biol 2011; 412:55-71. [PMID: 21787786 DOI: 10.1016/j.jmb.2011.07.018] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 06/27/2011] [Accepted: 07/11/2011] [Indexed: 12/16/2022]
Abstract
We present a method for synthetic antibody library generation that combines the use of high-throughput immune repertoire analysis and a novel synthetic technology. The library design recapitulates positional amino acid frequencies observed in natural antibody repertoires. V-segment diversity in four heavy (V(H)) and two kappa (V(κ)) germlines was introduced based on the analysis of somatically hypermutated donor-derived repertoires. Complementarity-determining region 3 length and amino acid designs were based on aggregate frequencies of all V(H) and V(κ) sequences in the data set. The designed libraries were constructed through an adaptation of a novel gene synthesis technology that enables precise positional control of amino acid composition and incorporation frequencies. High-throughput pyrosequencing was used to monitor the fidelity of construction and characterize genetic diversity in the final 3.6×10(10) transformants. The library exhibited Fab expression superior to currently reported synthetic approaches of equivalent diversity, with greater than 93% of clones observed to successfully display both a correctly folded heavy chain and a correctly folded light chain. Genetic diversity in the library was high, with 95% of 7.0×10(5) clones sequenced observed only once. The obtained library diversity explores a comparable sequence space as the donor-derived natural repertoire and, at the same time, is able to access novel recombined diversity due to lack of segmental linkage. The successful isolation of low- and subnanomolar-affinity antibodies against a diverse panel of receptors, growth factors, enzymes, antigens from infectious reagents, and peptides confirms the functional viability of the design strategy.
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Affiliation(s)
- Wenwu Zhai
- Rinat, Pfizer Inc., 230 East Grand Avenue, South San Francisco, CA 94080, USA
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Rippe K, Schrader A, Riede P, Strohner R, Lehmann E, Längst G. DNA sequence- and conformation-directed positioning of nucleosomes by chromatin-remodeling complexes. Proc Natl Acad Sci U S A 2007; 104:15635-40. [PMID: 17893337 PMCID: PMC2000439 DOI: 10.1073/pnas.0702430104] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chromatin-remodeling complexes can translocate nucleosomes along the DNA in an ATP-coupled reaction. This process is an important regulator of all DNA-dependent processes because it determines whether certain DNA sequences are found in regions between nucleosomes with increased accessibility for other factors or wrapped around the histone octamer complex. In a comparison of seven different chromatin-remodeling machines (ACF, ISWI, Snf2H, Chd1, Mi-2, Brg1, and NURF), it is demonstrated that these complexes can read out DNA sequence features to establish specific nucleosome-positioning patterns. For one of the remodelers, ACF, we identified a 40-bp DNA sequence element that directs nucleosome positioning. Furthermore, we show that nucleosome positioning by the remodelers ACF and Chd1 is determined by a reduced affinity to the end product of the translocation reaction. The results suggest that the linkage of differential remodeling activities with the intrinsic binding preferences of nucleosomes can result in establishing distinct chromatin structures that depend on the DNA sequence and define the DNA accessibility for other protein factors.
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Affiliation(s)
- Karsten Rippe
- *Division of Genome Organization and Function, Deutsches Krebsforschungszentrum and Bioquant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Anna Schrader
- Biochemie III, Universität Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Philipp Riede
- Biochemie III, Universität Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Ralf Strohner
- Biochemie III, Universität Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Elisabeth Lehmann
- Gene Center Munich, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany; and
| | - Gernot Längst
- Biochemie III, Universität Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
- To whom correspondence should be addressed. E-mail:
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Strohner R, Wachsmuth M, Dachauer K, Mazurkiewicz J, Hochstatter J, Rippe K, Längst G. A 'loop recapture' mechanism for ACF-dependent nucleosome remodeling. Nat Struct Mol Biol 2005; 12:683-90. [PMID: 16025127 DOI: 10.1038/nsmb966] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [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: 03/22/2005] [Accepted: 06/23/2005] [Indexed: 11/10/2022]
Abstract
The ATPase ISWI is the molecular motor of several nucleosome remodeling complexes including ACF. We analyzed the ACF-nucleosome interactions and determined the characteristics of ACF-dependent nucleosome remodeling. In contrast to ISWI, ACF interacts symmetrically with DNA entry sites of the nucleosome. Two-color fluorescence cross-correlation spectroscopy measurements show that ACF can bind four DNA duplexes simultaneously in a complex that contains two Acf1 and ISWI molecules. Using bead-bound nucleosomal substrates, nucleosome movement by mechanisms involving DNA twisting was excluded. Furthermore, an ACF-dependent local detachment of DNA from the nucleosome was demonstrated in a novel assay based on the preferred intercalation of ethidium bromide to free DNA. The findings suggest a loop recapture mechanism in which ACF introduces a DNA loop at the nucleosomal entry site that propagates over the histone octamer surface and leads to nucleosome repositioning.
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Affiliation(s)
- Ralf Strohner
- Adolf-Butenandt-Institut, Molekularbiologie, Schillerstrasse 44, 80336 München, Germany
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Németh A, Strohner R, Grummt I, Längst G. The chromatin remodeling complex NoRC and TTF-I cooperate in the regulation of the mammalian rRNA genes in vivo. Nucleic Acids Res 2004; 32:4091-9. [PMID: 15292447 PMCID: PMC514363 DOI: 10.1093/nar/gkh732] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The transcription termination factor (TTF)-I is a multifunctional nucleolar protein that terminates ribosomal gene transcription, mediates replication fork arrest and regulates RNA polymerase I transcription on chromatin. TTF-I plays a dual role in rDNA regulation, being involved in both activation and silencing of rDNA transcription. The N-terminal part of TTF-I contains a negative regulatory domain (NRD) that inhibits DNA binding. Here we show that interactions between the NRD and the C-terminal part of TTF-I mask the DNA-binding domain of TTF-I. However, interaction with TIP5, a subunit of the nucleolar chromatin remodeling complex, NoRC, recovers DNA-binding activity. We have mapped the protein domains that mediate the interaction between TTF-I and TIP5. The association of TIP5 with the NRD facilitates DNA binding of TTF-I and leads to the recruitment of NoRC to the rDNA promoter. Thus, TTF-I and NoRC act in concert to silence rDNA transcription.
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Affiliation(s)
- Attila Németh
- Adolf Butenandt Institut, Molekularbiologie, Ludwig-Maximilians-Universität München, Schillerstrasse 44, D-80336 München, Germany
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Strohner R, Németh A, Nightingale KP, Grummt I, Becker PB, Längst G. Recruitment of the nucleolar remodeling complex NoRC establishes ribosomal DNA silencing in chromatin. Mol Cell Biol 2004; 24:1791-8. [PMID: 14749393 PMCID: PMC344174 DOI: 10.1128/mcb.24.4.1791-1798.2004] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The rRNA gene cluster consists of multiple transcription units. Half of these are active, while the other half are transcriptionally inactive. Previously, in vivo studies have demonstrated that silencing of ribosomal DNA (rDNA) is mediated by the chromatin remodeling NoRC (nucleolar remodeling complex). To explore the mechanisms underlying NoRC-directed silencing of rDNA transcription, we investigated the effect of recombinant NoRC on RNA polymerase I transcription on reconstituted chromatin templates. We show that NoRC interacts with the transcription terminator factor (TTF-I), and this interaction is required both for the binding of TTF-I to its promoter-proximal target site and for the recruitment of NoRC to the promoter. After association with the rDNA promoter, NoRC alters the position of the promoter-bound nucleosome, thereby repressing RNA polymerase I transcription. This NoRC-directed rDNA repression requires the N terminus of histone H4. Repression is effective before preinitiation complex formation and as such is unable to exert an effect upon activated rDNA genes. Furthermore, the early steps of rDNA repression do not depend on DNA and histone modifications. These results reveal an important role for TTF-I in recruiting NoRC to rDNA and an active role for NoRC in the establishment of rDNA silencing.
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MESH Headings
- Acetylation
- Adenosine Triphosphatases/genetics
- Adenosine Triphosphatases/metabolism
- Animals
- Cell Line
- Chromatin/genetics
- Chromatin/metabolism
- Chromatin Assembly and Disassembly
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- DNA Methylation
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal/metabolism
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- DNA, Superhelical/metabolism
- DNA-Binding Proteins/metabolism
- Gene Silencing
- Histones/chemistry
- Histones/metabolism
- Kinetics
- Macromolecular Substances
- Promoter Regions, Genetic/genetics
- Protein Binding
- RNA Polymerase I/metabolism
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Templates, Genetic
- Transcription Factors
- Transcription, Genetic/genetics
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Affiliation(s)
- Ralf Strohner
- Adolf-Butenandt-Institut, Molekularbiologie, Ludwig Maximilians Universität, 80336 Munich. German
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Bonaldi T, Längst G, Strohner R, Becker PB, Bianchi ME. The DNA chaperone HMGB1 facilitates ACF/CHRAC-dependent nucleosome sliding. EMBO J 2004. [PMID: 12486007 DOI: 10.1093/embo/cdf692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Nucleosome remodelling complexes CHRAC and ACF contribute to chromatin dynamics by converting chemical energy into sliding of histone octamers on DNA. Their shared ATPase subunit ISWI binds DNA at the sites of entry into the nucleosome. A prevalent model assumes that DNA distortions catalysed by ISWI are converted into relocation of DNA relative to a histone octamer. HMGB1, one of the most abundant nuclear non-histone proteins, binds with preference to distorted DNA. We have now found that transient interaction of HMGB1 with nucleosomal linker DNA overlapping ISWI-binding sites enhances the ability of ACF to bind nucleosomal DNA and accelerates the sliding activity of limiting concentrations of remodelling factor. By contrast, an HMGB1 mutant with increased binding affinity was inhibitory. These observations are consistent with a role for HMGB1 as a DNA chaperone facilitating the rate-limiting DNA distortion during nucleosome remodelling.
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Affiliation(s)
- Tiziana Bonaldi
- Adolf-Butenandt Institut, Molekularbiologie, Schillerstrasse 44, D-80336 München, Germany
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Bonaldi T, Längst G, Strohner R, Becker PB, Bianchi ME. The DNA chaperone HMGB1 facilitates ACF/CHRAC-dependent nucleosome sliding. EMBO J 2002; 21:6865-73. [PMID: 12486007 PMCID: PMC139112 DOI: 10.1093/emboj/cdf692] [Citation(s) in RCA: 204] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2002] [Revised: 10/11/2002] [Accepted: 11/05/2002] [Indexed: 11/14/2022] Open
Abstract
Nucleosome remodelling complexes CHRAC and ACF contribute to chromatin dynamics by converting chemical energy into sliding of histone octamers on DNA. Their shared ATPase subunit ISWI binds DNA at the sites of entry into the nucleosome. A prevalent model assumes that DNA distortions catalysed by ISWI are converted into relocation of DNA relative to a histone octamer. HMGB1, one of the most abundant nuclear non-histone proteins, binds with preference to distorted DNA. We have now found that transient interaction of HMGB1 with nucleosomal linker DNA overlapping ISWI-binding sites enhances the ability of ACF to bind nucleosomal DNA and accelerates the sliding activity of limiting concentrations of remodelling factor. By contrast, an HMGB1 mutant with increased binding affinity was inhibitory. These observations are consistent with a role for HMGB1 as a DNA chaperone facilitating the rate-limiting DNA distortion during nucleosome remodelling.
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Affiliation(s)
- Tiziana Bonaldi
- Adolf-Butenandt Institut, Molekularbiologie, Schillerstrasse 44, D-80336 München, Germany,
DIBIT, San Raffaele Scientific Institute and Università Vita Salute San Raffaele, Via Olgettina 58, 4, I-20132 Milano, Italy Corresponding author e-mail: T.Bonaldi and G.Längst contributed equally to this work
| | | | | | - Peter B. Becker
- Adolf-Butenandt Institut, Molekularbiologie, Schillerstrasse 44, D-80336 München, Germany,
DIBIT, San Raffaele Scientific Institute and Università Vita Salute San Raffaele, Via Olgettina 58, 4, I-20132 Milano, Italy Corresponding author e-mail: T.Bonaldi and G.Längst contributed equally to this work
| | - Marco E. Bianchi
- Adolf-Butenandt Institut, Molekularbiologie, Schillerstrasse 44, D-80336 München, Germany,
DIBIT, San Raffaele Scientific Institute and Università Vita Salute San Raffaele, Via Olgettina 58, 4, I-20132 Milano, Italy Corresponding author e-mail: T.Bonaldi and G.Längst contributed equally to this work
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Strohner R, Nemeth A, Jansa P, Hofmann-Rohrer U, Santoro R, Längst G, Grummt I. NoRC--a novel member of mammalian ISWI-containing chromatin remodeling machines. EMBO J 2001; 20:4892-900. [PMID: 11532953 PMCID: PMC125270 DOI: 10.1093/emboj/20.17.4892] [Citation(s) in RCA: 256] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Transcription by RNA polymerase I on nucleosomal templates requires binding of the transcription termination factor TTF-I to a cognate site 160 bp upstream of the transcription start site. Binding of TTF-I is accompanied by changes in the chromatin architecture which suggests that TTF-I recruits a remodeling activity to the rDNA promoter. We have cloned a cDNA that encodes TIP5 (TTF-I-interacting protein 5), a 205 kDa protein that shares a number of important protein domains with WSTF (Williams syndrome transcription factor) and hAcf1/WCRF180, the largest subunits of human chromatin remodeling complexes hCHRAC and WCRF. TIP5 co-localizes with the basal RNA polymerase I transcription factor UBF in the nucleolus and is associated with SNF2h. The cellular TIP5-SNF2h complex, termed NoRC (nucleolar remodeling complex), induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. The results suggest that NoRC is a novel nucleolar chromatin remodeling machine that may serve a role in the regulation of the rDNA locus.
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Affiliation(s)
- Ralf Strohner
- Division of Molecular Biology of the Cell II, Deutsches Krebsforschungszentrum, D-69120 Heidelberg and
Adolf-Butenandt-Institut, Schillerstraße 44, D-80336 München, Germany Present address: Academy of Sciences of the Czech Republic, Institute of Molecular Genetics, Videnska 1083, 142 20 Praha 4, Czech Republic Corresponding author e-mail:
Ralf Strohner and Attila Nemeth contributed equally to this work
| | | | - Petr Jansa
- Division of Molecular Biology of the Cell II, Deutsches Krebsforschungszentrum, D-69120 Heidelberg and
Adolf-Butenandt-Institut, Schillerstraße 44, D-80336 München, Germany Present address: Academy of Sciences of the Czech Republic, Institute of Molecular Genetics, Videnska 1083, 142 20 Praha 4, Czech Republic Corresponding author e-mail:
Ralf Strohner and Attila Nemeth contributed equally to this work
| | | | | | - Gernot Längst
- Division of Molecular Biology of the Cell II, Deutsches Krebsforschungszentrum, D-69120 Heidelberg and
Adolf-Butenandt-Institut, Schillerstraße 44, D-80336 München, Germany Present address: Academy of Sciences of the Czech Republic, Institute of Molecular Genetics, Videnska 1083, 142 20 Praha 4, Czech Republic Corresponding author e-mail:
Ralf Strohner and Attila Nemeth contributed equally to this work
| | - Ingrid Grummt
- Division of Molecular Biology of the Cell II, Deutsches Krebsforschungszentrum, D-69120 Heidelberg and
Adolf-Butenandt-Institut, Schillerstraße 44, D-80336 München, Germany Present address: Academy of Sciences of the Czech Republic, Institute of Molecular Genetics, Videnska 1083, 142 20 Praha 4, Czech Republic Corresponding author e-mail:
Ralf Strohner and Attila Nemeth contributed equally to this work
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Strohner R, Strohner H. [Long-term effects of speech training with a mentally handicapped girl (author's transl)]. Rehabilitation (Stuttg) 1980; 19:44-8. [PMID: 7423002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
After an intensive training in regular verbs used in different contexts of fifteen-year-old mentally and speech retarded girl was able to produce creative sentences such as "Yesterday I made the bed". Before the training she only used sentences without conjugating the verbs, e.g., "Yesterday make bed". Upon re-examination three years after completion of the training the effects of the treatment were still evident. Also, when describing pictures, re-telling something or freely relating the girl used regular verb forms as often correctly as she did in the training sentences, both immediately after the training and three years later. The same appplies to irregular verbs despite the fact they were not included in the training programme.
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Strohner R, Strohner H. [Producing generative sentence usage in a retarded girl (author's transl)]. Rehabilitation (Stuttg) 1978; 17:102-7. [PMID: 653092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The purpose of the study was to teach a 15-years old mentally and speech retarded girl the use of simple generative sentences by means of question-answer procedures (cf. Clark & Sherman 1975). Whereas at the beginning the girl rarely produced correct new sentences, there was a marked improvement towards the end of the training programme. The generalisation effect--probably a result of the training--was such that also irregular verbs were formed with regular endings.
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