32 results on '"Stefanie Jonas"'
Search Results
2. USP16 counteracts mono-ubiquitination of RPS27a and promotes maturation of the 40S ribosomal subunit
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Christian Montellese, Jasmin van den Heuvel, Caroline Ashiono, Kerstin Dörner, André Melnik, Stefanie Jonas, Ivo Zemp, Paola Picotti, Ludovic C Gillet, and Ulrike Kutay
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ribosome biogenesis ,translation ,deubiquitinase ,USP16 ,quality control ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Establishment of translational competence represents a decisive cytoplasmic step in the biogenesis of 40S ribosomal subunits. This involves final 18S rRNA processing and release of residual biogenesis factors, including the protein kinase RIOK1. To identify novel proteins promoting the final maturation of human 40S subunits, we characterized pre-ribosomal subunits trapped on RIOK1 by mass spectrometry, and identified the deubiquitinase USP16 among the captured factors. We demonstrate that USP16 constitutes a component of late cytoplasmic pre-40S subunits that promotes the removal of ubiquitin from an internal lysine of ribosomal protein RPS27a/eS31. USP16 deletion leads to late 40S subunit maturation defects, manifesting in incomplete processing of 18S rRNA and retarded recycling of late-acting ribosome biogenesis factors, revealing an unexpected contribution of USP16 to the ultimate step of 40S synthesis. Finally, ubiquitination of RPS27a appears to depend on active translation, pointing at a potential connection between 40S maturation and protein synthesis.
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- 2020
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3. Targeted high throughput mutagenesis of the human spliceosome reveals itsin vivooperating principles
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Irene Beusch, Beiduo Rao, Michael Studer, Tetiana Luhovska, Viktorija Šukytė, Susan Lei, Juan Oses-Prieto, Em SeGraves, Alma Burlingame, Stefanie Jonas, and Hiten D. Madhani
- Abstract
SUMMARYThe spliceosome is a staggeringly complex machine comprising, in humans, 5 snRNAs and >150 proteins. We scaled haploid CRISPR-Cas9 base editing to target the entire human spliceosome and interrogated the mutants using the U2 snRNP/SF3b inhibitor, pladienolide B. Hypersensitive substitutions define functional sites in the U1/U2-containing A-complex but also in components that act as late as the second chemical step after SF3b is dissociated. Viable resistance substitutions map not only to the pladienolide B binding site but also to the G-patch (ATPase activator) domain of SUGP1, which lacks orthologs in yeast. We used these mutants and biochemical approaches to identify the spliceosomal disassemblase DHX15/hPrp43 as the ATPase ligand for SUGP1. These and other data support a model in which SUGP1 promotes splicing fidelity by triggering early spliceosome disassembly in response to kinetic blocks. Our approach provides a template for the analysis of essential cellular machines in humans.
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- 2022
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4. Structural basis for DEAH-helicase activation by G-patch proteins
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Lazar Ivanović, Michael K. Studer, Sabrina Marti, Stefanie Jonas, and Marco E. Weber
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G-patch proteins ,DEAH/RHA helicase ,ribosome biogenesis ,splicing ,Protein Conformation ,Ribosome biogenesis ,Biochemistry ,RNA Helicases ,Ribosome assembly ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Protein Domains ,Humans ,030304 developmental biology ,Adenosine Triphosphatases ,0303 health sciences ,Multidisciplinary ,biology ,Helicase ,RNA ,Biological Sciences ,Cell biology ,Repressor Proteins ,Adenosine diphosphate ,HEK293 Cells ,chemistry ,RNA splicing ,Spliceosomes ,biology.protein ,Adenosine triphosphate ,030217 neurology & neurosurgery - Abstract
RNA helicases of the DEAH/RHA family are involved in many essential cellular processes, such as splicing or ribosome biogenesis, where they remodel large RNA–protein complexes to facilitate transitions to the next intermediate. DEAH helicases couple adenosine triphosphate (ATP) hydrolysis to conformational changes of their catalytic core. This movement results in translocation along RNA, which is held in place by auxiliary C-terminal domains. The activity of DEAH proteins is strongly enhanced by the large and diverse class of G-patch activators. Despite their central roles in RNA metabolism, insight into the molecular basis of G-patch–mediated helicase activation is missing. Here, we have solved the structure of human helicase DHX15/Prp43, which has a dual role in splicing and ribosome assembly, in complex with the G-patch motif of the ribosome biogenesis factor NKRF. The G-patch motif binds in an extended conformation across the helicase surface. It tethers the catalytic core to the flexibly attached C-terminal domains, thereby fixing a conformation that is compatible with RNA binding. Structures in the presence or absence of adenosine diphosphate (ADP) suggest that motions of the catalytic core, which are required for ATP binding, are still permitted. Concomitantly, RNA affinity, helicase, and ATPase activity of DHX15 are increased when G-patch is bound. Mutations that detach one end of the tether but maintain overall binding severely impair this enhancement. Collectively, our data suggest that the G-patch motif acts like a flexible brace between dynamic portions of DHX15 that restricts excessive domain motions but maintains sufficient flexibility for catalysis., Proceedings of the National Academy of Sciences of the United States of America, 117 (13), ISSN:0027-8424, ISSN:1091-6490
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- 2020
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5. Sequence-specific RNA recognition by an RGG motif connects U1 and U2 snRNP for spliceosome assembly
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Tebbe de Vries, William Martelly, Sébastien Campagne, Kevin Sabath, Chris P. Sarnowski, Jason Wong, Alexander Leitner, Stefanie Jonas, Shalini Sharma, and Frédéric H.-T. Allain
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splicing ,Multidisciplinary ,RGG motif ,spliceosome assembly ,ubiquitin-like domain ,Humans ,RNA Splicing Factors ,Nucleotide Motifs ,Ribonucleoprotein, U2 Small Nuclear ,Crystallography, X-Ray ,Nuclear Magnetic Resonance, Biomolecular ,Ribonucleoprotein, U1 Small Nuclear - Abstract
In mammals, the structural basis for the interaction between U1 and U2 small nuclear ribonucleoproteins (snRNPs) during the early steps of splicing is still elusive. The binding of the ubiquitin-like (UBL) domain of SF3A1 to the stem-loop 4 of U1 snRNP (U1-SL4) contributes to this interaction. Here, we determined the 3D structure of the complex between the UBL of SF3A1 and U1-SL4 RNA. Our crystallography, NMR spectroscopy, and cross-linking mass spectrometry data show that SF3A1-UBL recognizes, sequence specifically, the GCG/CGC RNA stem and the apical UUCG tetraloop of U1-SL4. In vitro and in vivo mutational analyses support the observed intermolecular contacts and demonstrate that the carboxyl-terminal arginine-glycine-glycine-arginine (RGGR) motif of SF3A1-UBL binds sequence specifically by inserting into the RNA major groove. Thus, the characterization of the SF3A1-UBL/U1-SL4 complex expands the repertoire of RNA binding domains and reveals the capacity of RGG/RG motifs to bind RNA in a sequencespecific manner., Proceedings of the National Academy of Sciences of the United States of America, 119 (6), ISSN:0027-8424, ISSN:1091-6490
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- 2022
6. Biomolecular solid-state NMR spectroscopy at highest field: the gain in resolution at 1200 MHz
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Marie-Laure Fogeron, Stefanie Jonas, Rajdeep Deb, Anja Böckmann, Dawid Zyla, Václav Rímal, Beat H. Meier, Matías Chávez, Rudolf Glockshuber, Marco E. Weber, Matthias Ernst, Johannes Zehnder, Andreas Hunkeler, Anahit Torosyan, Lauriane Lecoq, Michael Nassal, Alexander Däpp, Thomas Wiegand, Sara Pfister, Alexander A. Malär, Morgane Callon, and Riccardo Cadalbert
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NMR spectra database ,Materials science ,Solid-state nuclear magnetic resonance ,Field (physics) ,Resolution (electron density) ,Superconducting magnet ,Spectroscopy ,Molecular physics ,Spectral line ,Magnetic field - Abstract
Progress in NMR in general and in biomolecular applications in particular is driven by increasing magnetic-field strengths leading to improved resolution and sensitivity of the NMR spectra. Recently, persistent superconducting magnets at a magnetic field strength (magnetic induction) of 28.2 T corresponding to 1200 MHz proton resonance frequency became commercially available. We present here a collection of high-field NMR spectra of a variety of proteins, including molecular machines, membrane proteins and viral capsids and others. We show this large panel in order to provide an overview over a range of representative systems under study, rather than a single best performing model system. We discuss both carbon-13 and proton-detected experiments, and show that in13C spectra substantially higher numbers of peaks can be resolved compared to 850 MHz while for1H spectra the most impressive increase in resolution is observed for aliphatic side-chain resonances.
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- 2021
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7. Biomolecular solid-state NMR spectroscopy at 1200 MHz : the gain in resolution
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Anja Böckmann, Lauriane Lecoq, Riccardo Cadalbert, Andreas Hunkeler, Morgane Callon, Matías Chávez, Matthias Ernst, Beat H. Meier, Marco E. Weber, Thomas Wiegand, Alexander A. Malär, Marie-Laure Fogeron, Dawid Zyla, Michael Nassal, Alexander Däpp, Rajdeep Deb, Stefanie Jonas, Rudolf Glockshuber, Johannes Zehnder, Anahit Torosyan, Sara Pfister, Václav Římal, Microbiologie moléculaire et biochimie structurale / Molecular Microbiology and Structural Biochemistry (MMSB), Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)
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Superconducting magnet ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Solid-state NMR ,Article ,Magic-angle spinning ,Biomolecular NMR ,High field ,Helicases ,Viruses ,03 medical and health sciences ,Capsid ,[CHIM.ANAL]Chemical Sciences/Analytical chemistry ,Magic angle spinning ,Spectroscopy ,Nuclear Magnetic Resonance, Biomolecular ,030304 developmental biology ,0303 health sciences ,Carbon Isotopes ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,Chemistry ,Resolution (electron density) ,Membrane Proteins ,equipment and supplies ,Molecular machine ,0104 chemical sciences ,3. Good health ,Magnetic field ,NMR spectra database ,Solid-state nuclear magnetic resonance ,Chemical physics ,Protons - Abstract
Journal of biomolecular NMR 75(6/7), 255-272 (2021). doi:10.1007/s10858-021-00373-x, Published by Springer Science + Business Media B.V, Dordrecht [u.a.]
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- 2021
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8. Regulation of DEAH-box RNA helicases by G-patch proteins
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Katherine E. Bohnsack, Markus T. Bohnsack, Stefanie Jonas, and Ralf Ficner
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0301 basic medicine ,RNA helicase ,G-patch protein ,Clinical Biochemistry ,Glycine ,Ribosome biogenesis ,ribosome biogenesis ,Biochemistry ,DEAD-box RNA Helicases ,03 medical and health sciences ,0302 clinical medicine ,Humans ,Small nucleolar RNA ,Molecular Biology ,Messenger RNA ,biology ,Chemistry ,RNA ,Helicase ,Signal transducing adaptor protein ,RNA-Binding Proteins ,cofactor ,RNA Helicase A ,Cell biology ,DEAH/RHA family ,pre-mRNA splicing ,030104 developmental biology ,RNA splicing ,biology.protein ,030217 neurology & neurosurgery - Abstract
RNA helicases of the DEAH/RHA family form a large and conserved class of enzymes that remodel RNA protein complexes (RNPs) by translocating along the RNA. Driven by ATP hydrolysis, they exert force to dissociate hybridized RNAs, dislocate bound proteins or unwind secondary structure elements in RNAs. The sub-cellular localization of DEAH-helicases and their concomitant association with different pathways in RNA metabolism, such as pre-mRNA splicing or ribosome biogenesis, can be guided by cofactor proteins that specifically recruit and simultaneously activate them. Here we review the mode of action of a large class of DEAH-specific adaptor proteins of the G-patch family. Defined only by their eponymous short glycine-rich motif, which is sufficient for helicase binding and stimulation, this family encompasses an immensely varied array of domain compositions and is linked to an equally diverse set of functions. G-patch proteins are conserved throughout eukaryotes and are even encoded within retroviruses. They are involved in mRNA, rRNA and snoRNA maturation, telomere maintenance and the innate immune response. Only recently was the structural and mechanistic basis for their helicase enhancing activity determined. We summarize the molecular and functional details of G-patch-mediated helicase regulation in their associated pathways and their involvement in human diseases., Biological Chemistry, 402 (5), ISSN:1431-6730, ISSN:1437-4315
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- 2021
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9. Mille viae in eukaryotic mRNA decapping
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Oliver Weichenrieder, Eugene Valkov, and Stefanie Jonas
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Models, Molecular ,RNA Caps ,0301 basic medicine ,RNA Stability ,Molecular Conformation ,Biology ,Catalysis ,Structure-Activity Relationship ,03 medical and health sciences ,Structural Biology ,Transcription (biology) ,Endoribonucleases ,RNA, Messenger ,Enhancer ,Molecular Biology ,Decapping enzyme ,Decapping ,Messenger RNA ,Effector ,Hydrolysis ,Eukaryota ,Cell biology ,Decapping complex ,030104 developmental biology ,Biochemistry ,Mrna level - Abstract
Cellular mRNA levels are regulated via rates of transcription and decay. Since the removal of the mRNA 5'-cap by the decapping enzyme DCP2 is generally an irreversible step towards decay, it requires regulation. Control of DCP2 activity is likely effected by two interdependent means: by conformational control of the DCP2-DCP1 complex, and by assembly control of the decapping network, an array of mutually interacting effector proteins. Here, we compare three recent and conformationally distinct crystal structures of the DCP2-DCP1 decapping complex in the presence of substrate analogs and decapping enhancers and we discuss alternative substrate recognition modes for the catalytic domain of DCP2. Together with structure-based insight into decapping network assembly, we propose that DCP2-mediated decapping follows more than one path.
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- 2017
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10. Author response: USP16 counteracts mono-ubiquitination of RPS27a and promotes maturation of the 40S ribosomal subunit
- Author
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Stefanie Jonas, Ludovic C Gillet, Ulrike Kutay, Kerstin Dörner, Ivo Zemp, Jasmin van den Heuvel, Caroline Ashiono, Andre Melnik, Paola Picotti, and Christian Montellese
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Ubiquitin ,biology ,Chemistry ,Protein subunit ,biology.protein ,Eukaryotic Small Ribosomal Subunit ,Ribosomal RNA ,RPS27A ,Cell biology - Published
- 2020
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11. USP16 counteracts mono-ubiquitination of RPS27a and promotes maturation of the 40S ribosomal subunit
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Caroline Ashiono, Christian Montellese, Ivo Zemp, Stefanie Jonas, Kerstin Dörner, Paola Picotti, Jasmin van den Heuvel, Andre Melnik, Ludovic C Gillet, and Ulrike Kutay
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Ribosomal Proteins ,QH301-705.5 ,Protein subunit ,Science ,Ribosome biogenesis ,ribosome biogenesis ,translation ,RPS27A ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,0302 clinical medicine ,Ribosomal protein ,Humans ,Eukaryotic Small Ribosomal Subunit ,Cloning, Molecular ,quality control ,Biology (General) ,Ubiquitins ,030304 developmental biology ,Ribosome Subunits, Small, Eukaryotic ,0303 health sciences ,General Immunology and Microbiology ,Chemistry ,General Neuroscience ,Ubiquitination ,Translation (biology) ,General Medicine ,Cell Biology ,Ribosomal RNA ,USP16 ,3. Good health ,Cell biology ,deubiquitinase ,HEK293 Cells ,Gene Expression Regulation ,Protein Biosynthesis ,Medicine ,Ubiquitin Thiolesterase ,030217 neurology & neurosurgery ,Biogenesis ,Gene Deletion ,Research Article ,Human - Abstract
Establishment of translational competence represents a decisive cytoplasmic step in the biogenesis of 40S ribosomal subunits. This involves final 18S rRNA processing and release of residual biogenesis factors, including the protein kinase RIOK1. To identify novel proteins promoting the final maturation of human 40S subunits, we characterized pre-ribosomal subunits trapped on RIOK1 by mass spectrometry, and identified the deubiquitinase USP16 among the captured factors. We demonstrate that USP16 constitutes a component of late cytoplasmic pre-40S subunits that promotes the removal of ubiquitin from an internal lysine of ribosomal protein RPS27a/eS31. USP16 deletion leads to late 40S subunit maturation defects, manifesting in incomplete processing of 18S rRNA and retarded recycling of late-acting ribosome biogenesis factors, revealing an unexpected contribution of USP16 to the ultimate step of 40S synthesis. Finally, ubiquitination of RPS27a appears to depend on active translation, pointing at a potential connection between 40S maturation and protein synthesis.
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- 2020
12. Evolutionary repurposing of a sulfatase: A new Michaelis complex leads to efficient transition state charge offset
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Bálint Kintses, Fernanda Duarte, Gerhard Fischer, Bert van Loo, Stefanie Jonas, Marko Hyvönen, Florian Hollfelder, Shina Caroline Lynn Kamerlin, Nobuhiko Tokuriki, Mark F. Mohamed, and Charlotte M. Miton
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0301 basic medicine ,Stereochemistry ,Protein Conformation ,In silico ,010402 general chemistry ,01 natural sciences ,Catalysis ,03 medical and health sciences ,chemistry.chemical_compound ,Molecular recognition ,Organophosphorus Compounds ,Catalytic Domain ,Hydrolase ,Arylsulfatases ,Multidisciplinary ,biology ,Chemistry ,Hydrolysis ,Leaving group ,Substrate (chemistry) ,Active site ,Directed evolution ,Phosphonate ,0104 chemical sciences ,030104 developmental biology ,PNAS Plus ,biology.protein ,Directed Molecular Evolution - Abstract
The recruitment and evolutionary optimization of promiscuous enzymes is key to the rapid adaptation of organisms to changing environments. Our understanding of the precise mechanisms underlying enzyme repurposing is, however, limited: What are the active-site features that enable the molecular recognition of multiple substrates with contrasting catalytic requirements? To gain insights into the molecular determinants of adaptation in promiscuous enzymes, we performed the laboratory evolution of an arylsulfatase to improve its initially weak phenylphosphonate hydrolase activity. The evolutionary trajectory led to a 100,000-fold enhancement of phenylphosphonate hydrolysis, while the native sulfate and promiscuous phosphate mono- and diester hydrolyses were only marginally affected (≤50-fold). Structural, kinetic, and in silico characterizations of the evolutionary intermediates revealed that two key mutations, T50A and M72V, locally reshaped the active site, improving access to the catalytic machinery for the phosphonate. Measured transition state (TS) charge changes along the trajectory suggest the creation of a new Michaelis complex (E•S, enzyme–substrate), with enhanced leaving group stabilization in the TS for the promiscuous phosphonate (βleavinggroupfrom −1.08 to −0.42). Rather than altering the catalytic machinery, evolutionary repurposing was achieved by fine-tuning the molecular recognition of the phosphonate in the Michaelis complex, and by extension, also in the TS. This molecular scenario constitutes a mechanistic alternative to adaptation solely based on enzyme flexibility and conformational selection. Instead, rapid functional transitions between distinct chemical reactions rely on the high reactivity of permissive active-site architectures that allow multiple substrate binding modes.
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- 2019
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13. Balancing Specificity and Promiscuity in Enzyme Evolution: Multidimensional Activity Transitions in the Alkaline Phosphatase Superfamily
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Celine Dutruel, Mark F. Mohamed, Marko Hyvönen, Gerhard Fischer, Bert van Loo, Christopher D. Bayer, Anastassia A. Vorobieva, Florian Hollfelder, Eugene Valkov, Stefanie Jonas, Hollfelder, Florian [0000-0002-1367-6312], Hyvonen, Marko [0000-0001-8683-4070], Apollo - University of Cambridge Repository, and Department of Bio-engineering Sciences
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Models, Molecular ,Chemistry(all) ,Sequence alignment ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Catalysis ,Substrate Specificity ,Evolution, Molecular ,Colloid and Surface Chemistry ,Phylogenetics ,Catalytic Domain ,Hydrolase ,Loss function ,Phylogeny ,chemistry.chemical_classification ,Phylogenetic tree ,Bacteria ,Chemistry ,General Chemistry ,Arylsulfatases ,Alkaline Phosphatase ,0104 chemical sciences ,Kinetics ,Enzyme ,Alkaline phosphatase ,Sequence Alignment - Abstract
Highly proficient, promiscuous enzymes can be springboards for functional evolution, able to avoid loss of function during adaptation by their capacity to promote multiple reactions. We employ a systematic comparative study of structure, sequence, and substrate specificity to track the evolution of specificity and reactivity between promiscuous members of clades of the alkaline phosphatase (AP) superfamily. Construction of a phylogenetic tree of protein sequences maps out the likely transition zone between arylsulfatases (ASs) and phosphonate monoester hydrolases (PMHs). Kinetic analysis shows that all enzymes characterized have four chemically distinct phospho- and sulfoesterase activities, with rate accelerations ranging from 10 11 - to 10 17 -fold for their primary and 10 9 - to 10 12 -fold for their promiscuous reactions, suggesting that catalytic promiscuity is widespread in the AP-superfamily. This functional characterization and crystallography reveal a novel class of ASs that is so similar in sequence to known PMHs that it had not been recognized as having diverged in function. Based on analysis of snapshots of catalytic promiscuity "in transition", we develop possible models that would allow functional evolution and determine scenarios for trade-off between multiple activities. For the new ASs, we observe largely invariant substrate specificity that would facilitate the transition from ASs to PMHs via trade-off-free molecular exaptation, that is, evolution without initial loss of primary activity and specificity toward the original substrate. This ability to bypass low activity generalists provides a molecular solution to avoid adaptive conflict.
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- 2019
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14. Structure of the Dcp2–Dcp1 mRNA-decapping complex in the activated conformation
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Oliver Weichenrieder, Elisa Izaurralde, Chung Te Chang, Sowndarya Muthukumar, Stefanie Jonas, and Eugene Valkov
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0301 basic medicine ,chemistry.chemical_classification ,RNA metabolism ,Protein Conformation ,MRNA decapping complex ,Peptide ,Crystal structure ,Biology ,Crystallography, X-Ray ,Cell biology ,03 medical and health sciences ,030104 developmental biology ,chemistry ,Structural Biology ,Catalytic Domain ,Schizosaccharomyces ,Hydrolase ,Schizosaccharomyces pombe Proteins ,Protein Multimerization ,Peptides ,Molecular Biology ,Decapping enzyme - Abstract
The removal of the mRNA 5' cap (decapping) by Dcp2 shuts down translation and commits mRNA to full degradation. Dcp2 activity is enhanced by activator proteins such as Dcp1 and Edc1. However, owing to conformational flexibility, the active conformation of Dcp2 and the mechanism of decapping activation have remained unknown. Here, we report a 1.6-Å-resolution crystal structure of the Schizosaccharomyces pombe Dcp2-Dcp1 heterodimer in an unprecedented conformation that is tied together by an intrinsically disordered peptide from Edc1. In this ternary complex, an unforeseen rotation of the Dcp2 catalytic domain allows residues from both Dcp2 and Dcp1 to cooperate in RNA binding, thus explaining decapping activation by increased substrate affinity. The architecture of the Dcp2-Dcp1-Edc1 complex provides a rationale for the conservation of a sequence motif in Edc1 that is also present in unrelated decapping activators, thus indicating that the presently described mechanism of decapping activation is evolutionarily conserved.
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- 2016
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15. Towards a molecular understanding of microRNA-mediated gene silencing
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Elisa Izaurralde and Stefanie Jonas
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Genetics ,RNA-induced silencing complex ,MRNA destabilization ,RNA Stability ,Trans-acting siRNA ,Argonaute ,Biology ,Cell biology ,MicroRNAs ,RNA silencing ,Protein Biosynthesis ,P-bodies ,microRNA ,Animals ,Humans ,Gene silencing ,Gene Silencing ,Molecular Biology ,Genetics (clinical) - Abstract
MicroRNAs (miRNAs) are a conserved class of small non-coding RNAs that assemble with Argonaute proteins into miRNA-induced silencing complexes (miRISCs) to direct post-transcriptional silencing of complementary mRNA targets. Silencing is accomplished through a combination of translational repression and mRNA destabilization, with the latter contributing to most of the steady-state repression in animal cell cultures. Degradation of the mRNA target is initiated by deadenylation, which is followed by decapping and 5'-to-3' exonucleolytic decay. Recent work has enhanced our understanding of the mechanisms of silencing, making it possible to describe in molecular terms a continuum of direct interactions from miRNA target recognition to mRNA deadenylation, decapping and 5'-to-3' degradation. Furthermore, an intricate interplay between translational repression and mRNA degradation is emerging.
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- 2015
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16. Mehrwert von ergänzenden qualitativen Methoden in Survey-Feedback-Prozessen
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Cathrin Eireiner and Stefanie Jonas-Klemm
- Abstract
Das Prinzip „You can’t change, what you don’t measure“ hat in den letzten beiden Jahrzehnten – gerade im Bereich der Mitarbeiterbefragung als Survey-Feedback-Prozess – zu einer quantitativen Methodenauswahl gefuhrt. Der Wunsch vor allem der Managementebenen nach effizienten Mittelwertvergleichen und das scheinbar notwendige Benchmarking der Ergebnisse nach ausen und innen stellten die Quantifizierung von weichen Faktoren wie Zufriedenheit, Commitment und/oder Engagement sowie von Mitarbeitermeinungen zur Arbeitssituation in den Fokus. Diese Ausrichtung ist nachvollziehbar in unserer zahlenorientierten Welt – kann jedoch von der Verbindung mit qualitativen Methoden profitieren. Um das Potenzial qualitativer Methoden in Erganzung zu quantitativ ausgerichteten Befragungsinstrumenten geht es in diesem Beitrag, der drei elementare Methoden der qualitativen Datenerhebung und deren wertbringenden Einsatz bei Mitarbeiterbefragungen vorstellt.
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- 2018
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17. Structural basis for the Nanos-mediated recruitment of the CCR4–NOT complex and translational repression
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Stefanie Jonas, Dipankar Bhandari, Tobias Raisch, Oliver Weichenrieder, and Elisa Izaurralde
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Models, Molecular ,Receptors, CCR4 ,RNA Stability ,Amino Acid Motifs ,RNA-binding protein ,Plasma protein binding ,Biology ,Conserved sequence ,Molecular recognition ,Nuclear Receptor Subfamily 4, Group A, Member 2 ,Genetics ,CCR4-NOT complex ,Humans ,natural sciences ,RNA, Messenger ,Protein Structure, Quaternary ,Conserved Sequence ,Regulation of gene expression ,Effector ,HEK 293 cells ,technology, industry, and agriculture ,RNA-Binding Proteins ,Reproducibility of Results ,Cell biology ,HEK293 Cells ,Gene Expression Regulation ,Multiprotein Complexes ,Peptides ,Research Paper ,Protein Binding ,Developmental Biology - Abstract
The RNA-binding proteins of the Nanos family play an essential role in germ cell development and survival in a wide range of metazoan species. They function by suppressing the expression of target mRNAs through the recruitment of effector complexes, which include the CCR4–NOT deadenylase complex. Here, we show that the three human Nanos paralogs (Nanos1–3) interact with the CNOT1 C-terminal domain and determine the structural basis for the specific molecular recognition. Nanos1–3 bind CNOT1 through a short CNOT1-interacting motif (NIM) that is conserved in all vertebrates and some invertebrate species. The crystal structure of the human Nanos1 NIM peptide bound to CNOT1 reveals that the peptide opens a conserved hydrophobic pocket on the CNOT1 surface by inserting conserved aromatic residues. The substitutions of these aromatic residues in the Nanos1–3 NIMs abolish binding to CNOT1 and abrogate the ability of the proteins to repress translation. Our findings provide the structural basis for the recruitment of the CCR4–NOT complex by vertebrate Nanos, indicate that the NIMs are the major determinants of the translational repression mediated by Nanos, and identify the CCR4–NOT complex as the main effector complex for Nanos function.
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- 2014
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18. The activation of the decapping enzyme DCP2 by DCP1 occurs on the EDC4 scaffold and involves a conserved loop in DCP1
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Natalia Bercovich, Belinda Loh, Chung Te Chang, Stefanie Jonas, and Elisa Izaurralde
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Microtubule-associated protein ,Phenylalanine ,Biology ,Conserved sequence ,03 medical and health sciences ,0302 clinical medicine ,EVH1 domain ,Endoribonucleases ,Coactivator ,Genetics ,Humans ,Protein Interaction Domains and Motifs ,Short linear motif ,Amino Acid Sequence ,Binding site ,Conserved Sequence ,030304 developmental biology ,0303 health sciences ,Messenger RNA ,Proteins ,Cell biology ,Decapping complex ,Biochemistry ,Exoribonucleases ,Trans-Activators ,RNA ,Microtubule-Associated Proteins ,030217 neurology & neurosurgery - Abstract
The removal of the 5′-cap structure by the decapping enzyme DCP2 and its coactivator DCP1 shuts down translation and exposes the mRNA to 5′-to-3′ exonucleolytic degradation by XRN1. Although yeast DCP1 and DCP2 directly interact, an additional factor, EDC4, promotes DCP1–DCP2 association in metazoan. Here, we elucidate how the human proteins interact to assemble an active decapping complex and how decapped mRNAs are handed over to XRN1. We show that EDC4 serves as a scaffold for complex assembly, providing binding sites for DCP1, DCP2 and XRN1. DCP2 and XRN1 bind simultaneously to the EDC4 C-terminal domain through short linear motifs (SLiMs). Additionally, DCP1 and DCP2 form direct but weak interactions that are facilitated by EDC4. Mutational and functional studies indicate that the docking of DCP1 and DCP2 on the EDC4 scaffold is a critical step for mRNA decapping in vivo. They also revealed a crucial role for a conserved asparagine–arginine containing loop (the NR-loop) in the DCP1 EVH1 domain in DCP2 activation. Our data indicate that DCP2 activation by DCP1 occurs preferentially on the EDC4 scaffold, which may serve to couple DCP2 activation by DCP1 with 5′-to-3′ mRNA degradation by XRN1 in human cells.
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- 2014
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19. Structure and properties of the esterase from non-LTR retrotransposons suggest a role for lipids in retrotransposition
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Steffen Schmidt, Anna Milena Schneider, Stefanie Jonas, Elena Khazina, Oliver Weichenrieder, and Benjamin Vollmer
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Coiled coil ,Models, Molecular ,Retroelements ,Fatty Acids ,Molecular Sequence Data ,Esterases ,RNA ,Retrotransposon ,Acetylesterase ,Biology ,Zebrafish Proteins ,Esterase ,Reverse transcriptase ,Protein Structure, Tertiary ,Open reading frame ,Biochemistry ,Structural Biology ,Liposomes ,Genetics ,Animals ,Amino Acid Sequence ,Protein Multimerization ,Phospholipids ,Zebrafish ,Ribonucleoprotein - Abstract
Non-LTR retrotransposons are mobile genetic elements and play a major role in eukaryotic genome evolution and disease. Similar to retroviruses they encode a reverse transcriptase, but their genomic integration mechanism is fundamentally different, and they lack homologs of the retroviral nucleocapsid-forming protein Gag. Instead, their first open reading frames encode distinct multi-domain proteins (ORF1ps) presumed to package the retrotransposon-encoded RNA into ribonucleoprotein particles (RNPs). The mechanistic roles of ORF1ps are poorly understood, particularly of ORF1ps that appear to harbor an enzymatic function in the form of an SGNH-type lipolytic acetylesterase. We determined the crystal structures of the coiled coil and esterase domains of the ORF1p from the Danio rerio ZfL2-1 element. We demonstrate a dimerization of the coiled coil and a hydrolytic activity of the esterase. Furthermore, the esterase binds negatively charged phospholipids and liposomes, but not oligo-(A) RNA. Unexpectedly, the esterase can split into two dynamic half-domains, suited to engulf long fatty acid substrates extending from the active site. These properties indicate a role for lipids and membranes in non-LTR retrotransposition. We speculate that Gag-like membrane targeting properties of ORF1ps could play a role in RNP assembly and in membrane-dependent transport or localization processes.
- Published
- 2013
20. Human AATF/Che-1 forms a nucleolar protein complex with NGDN and NOL10 required for 40S ribosomal subunit synthesis
- Author
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Lukas Bammert, Ulrike Kutay, Stefanie Jonas, and Rosemarie Ungricht
- Subjects
0301 basic medicine ,Nucleolus ,Protein subunit ,Ribosome biogenesis ,Biology ,Ribosome ,Cell Line ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Genetics ,Animals ,Humans ,Protein Interaction Domains and Motifs ,Eukaryotic Small Ribosomal Subunit ,Molecular Biology ,Ribosome Subunits, Small, Eukaryotic ,Eukaryotic Large Ribosomal Subunit ,Nuclear Proteins ,RNA-Binding Proteins ,Ribosomal RNA ,Cell biology ,Repressor Proteins ,Protein Transport ,030104 developmental biology ,Ribosome Subunits ,Multiprotein Complexes ,Protein Biosynthesis ,030220 oncology & carcinogenesis ,Apoptosis Regulatory Proteins ,Ribosomes ,Cell Nucleolus ,Protein Binding - Abstract
Mammalian AATF/Che-1 is essential for embryonic development, however, the underlying molecular mechanism is unclear. By immunoprecipitation of human AATF we discovered that AATF forms a salt-stable protein complex together with neuroguidin (NGDN) and NOL10, and demonstrate that the AATF-NGDN-NOL10 (ANN) complex functions in ribosome biogenesis. All three ANN complex members localize to nucleoli and display a mutual dependence with respect to protein stability. Mapping of protein-protein interaction domains revealed the importance of both the evolutionary conserved WD40 repeats in NOL10 and the UTP3/SAS10 domain in NGDN for complex formation. Functional analysis showed that the ANN complex supports nucleolar steps of 40S ribosomal subunit biosynthesis. All complex members were required for 18S rRNA maturation and their individual depletion affected the same nucleolar cleavage steps in the 5΄ETS and ITS1 regions of the ribosomal RNA precursor. Collectively, we identified the ANN complex as a novel functional module supporting the nucleolar maturation of 40S ribosomal subunits. Our data help to explain the described role of AATF in cell proliferation during mouse development as well as its requirement for malignant tumor growth., Nucleic Acids Research, 44 (20), ISSN:1362-4962, ISSN:0301-5610
- Published
- 2016
21. SMG6 interacts with the exon junction complex via two conserved EJC-binding motifs (EBMs) required for nonsense-mediated mRNA decay
- Author
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Isao Kashima, Gretel Buchwald, Elisa Izaurralde, Elena Conti, Uma Jayachandran, Stefanie Jonas, and Andrei N. Lupas
- Subjects
Immunoprecipitation ,RNA Stability ,Amino Acid Motifs ,Blotting, Western ,Green Fluorescent Proteins ,Molecular Sequence Data ,Nonsense-mediated decay ,RNA-binding protein ,Plasma protein binding ,Biology ,Exon ,RNA interference ,Genetics ,Humans ,Amino Acid Sequence ,RNA, Messenger ,Telomerase ,Binding Sites ,Sequence Homology, Amino Acid ,RNA-Binding Proteins ,Exons ,Stop codon ,Cell biology ,HEK293 Cells ,Codon, Nonsense ,Exon junction complex ,RNA Interference ,HeLa Cells ,Protein Binding ,Research Paper ,Developmental Biology - Abstract
Nonsense-mediated mRNA decay (NMD) is a quality control mechanism that detects and degrades mRNAs containing premature stop codons (PTCs). In vertebrates, PTCs trigger efficient NMD when located upstream of an exon junction complex (EJC). Degradation of PTC-containing mRNAs requires the endonucleolytic activity of SMG6, a conserved NMD factor; nevertheless, the precise role for the EJC in NMD and how the SMG6 endonuclease is recruited to NMD targets have been unclear. Here we show that SMG6 interacts directly with the EJC via two conserved EJC-binding motifs (EBMs). We further show that the SMG6–EJC interaction is required for NMD. Our results reveal an unprecedented role for the EJC in recruiting the SMG6 endonuclease to NMD targets. More generally, our findings identify the EBM as a protein motif present in a handful of proteins, and suggest that EJCs establish multiple and mutually exclusive interactions with various protein partners, providing a plausible explanation for the myriad functions performed by this complex in post-transcriptional mRNA regulation.
- Published
- 2010
- Full Text
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22. A New Member of the Alkaline Phosphatase Superfamily with a Formylglycine Nucleophile: Structural and Kinetic Characterisation of a Phosphonate Monoester Hydrolase/Phosphodiesterase from Rhizobium leguminosarum
- Author
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Stefanie Jonas, Marko Hyvönen, Florian Hollfelder, and Bert van Loo
- Subjects
Models, Molecular ,Protein Folding ,Stereochemistry ,Static Electricity ,Phosphatase ,Glycine ,Crystallography, X-Ray ,010402 general chemistry ,medicine.disease_cause ,01 natural sciences ,Catalysis ,Protein Structure, Secondary ,Rhizobium leguminosarum ,Substrate Specificity ,Evolution, Molecular ,03 medical and health sciences ,chemistry.chemical_compound ,Structural Biology ,Hydrolase ,medicine ,Protein Structure, Quaternary ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,Binding Sites ,biology ,Phosphoric Diester Hydrolases ,Hydrolysis ,Active site ,Alkaline Phosphatase ,Phosphonate ,0104 chemical sciences ,Kinetics ,Burst kinetics ,Biochemistry ,chemistry ,Metals ,Mutagenesis ,Structural Homology, Protein ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,biology.protein ,Alkaline phosphatase ,Mutant Proteins ,Cysteine - Abstract
The alkaline phosphatase superfamily comprises a large number of hydrolytic metalloenzymes such as phosphatases and sulfatases. We have characterised a new member of this superfamily, a phosphonate monoester hydrolase/phosphodiesterase from Rhizobium leguminosarum (RlPMH) both structurally and kinetically. The 1.42 A crystal structure shows structural homology to arylsulfatases with conservation of the core α/β-fold, the mononuclear active site and most of the active-site residues. Sulfatases use a unique formylglycine nucleophile, formed by posttranslational modification of a cysteine/serine embedded in a signature sequence (C/S)XPXR. We provide mass spectrometric and mutational evidence that RlPMH is the first non-sulfatase enzyme shown to use a formylglycine as the catalytic nucleophile. RlPMH hydrolyses phosphonate monoesters and phosphate diesters with similar efficiency. Burst kinetics suggest that substrate hydrolysis proceeds via a double-displacement mechanism. Kinetic characterisation of active-site mutations establishes the catalytic contributions of individual residues. A mechanism for substrate hydrolysis is proposed on the basis of the kinetic data and structural comparisons with E. coli alkaline phosphatase and Pseudomonas aeruginosa arylsulfatase. RlPMH represents a further example of conservation of the overall structure and mechanism within the alkaline phosphatase superfamily.
- Published
- 2008
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23. Mechanism and Catalytic Promiscuity: Emerging Mechanistic Principles for Identification and Manipulation of Catalytically Promiscuous Enzymes
- Author
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Florian Hollfelder and Stefanie Jonas
- Subjects
chemistry.chemical_classification ,Promiscuity ,Enzyme ,chemistry ,Biochemistry ,Mechanism (philosophy) ,Identification (biology) ,Computational biology ,Protein superfamily ,Biology ,Catalysis - Published
- 2008
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24. An Essential GTPase Promotes Assembly of Preribosomal RNA Processing Complexes
- Author
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Stefanie Jonas, Jennifer A. Doudna, and Katrin Karbstein
- Subjects
Saccharomyces cerevisiae Proteins ,Preribosome ,Ribosome biogenesis ,RNA-binding protein ,Saccharomyces cerevisiae ,GTPase ,Biology ,Guanosine Diphosphate ,Ribosome ,GTP Phosphohydrolases ,GTP-Binding Proteins ,Sequence Analysis, Protein ,Preribosomal RNA ,Escherichia coli ,RNA, Small Nucleolar ,RNA Processing, Post-Transcriptional ,Small nucleolar RNA ,Molecular Biology ,Genetics ,Sequence Analysis, RNA ,Nuclear Proteins ,RNA-Binding Proteins ,RNA ,Cell Biology ,Protein Structure, Tertiary ,Cell biology ,Kinetics ,RNA, Ribosomal ,Mutation ,Guanosine Triphosphate ,Ribosomes - Abstract
Ribosome biogenesis in eukaryotes is a highly regulated process involving hundreds of transiently associated proteins and RNAs. Although most of these assembly factors have been genetically linked to specific step(s) in the biogenesis pathway, their biochemical functions are generally unknown. Bms1, an essential protein in yeast, is the only known GTPase required for biosynthesis of the 40S ribosomal subunit and interacts with Rcl1, an essential protein suggested to be an endonuclease. Here, we show thermodynamic coupling in the binding of Bms1 to GTP, Rcl1, and U3 small nucleolar RNA (snoRNA), an essential RNA that base pairs to pre-rRNA. Rcl1 binding to preribosomes is severely limited in yeast cells expressing a Bms1 mutant defective for Rcl1 binding. Additionally, we provide evidence that the C-terminal domain of Bms1 acts as an intramolecular GTPase-activating protein. Together, these data suggest that Bms1 functions as a GTP-regulated switch to deliver Rcl1 to preribosomes, providing molecular insight into preribosome assembly.
- Published
- 2005
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25. An asymmetric PAN3 dimer recruits a single PAN2 exonuclease to mediate mRNA deadenylation and decay
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Mary Christie, Daniel Peter, Dipankar Bhandari, Stefanie Jonas, Belinda Loh, Elisa Izaurralde, Eric Huntzinger, and Oliver Weichenrieder
- Subjects
Exonuclease ,Dimer ,RNA Stability ,MRNA Decay ,Crystallography, X-Ray ,MRNA deadenylation ,Neurospora crassa ,Fungal Proteins ,chemistry.chemical_compound ,Structural Biology ,Protein Interaction Mapping ,Molecule ,RNA, Messenger ,Molecular Biology ,Regulation of gene expression ,Binding Sites ,biology ,biology.organism_classification ,Protein Structure, Tertiary ,Biochemistry ,chemistry ,Exoribonucleases ,Biophysics ,biology.protein ,Linker ,Dimerization - Abstract
Structural analyses reveal the asymmetric assembly of Neurospora crassa PAN2–PAN3 complex and, along with functional work on the proteins from different species, indicate an essential role for PAN3 in coordinating PAN2-mediated deadenylation with subsequent steps in mRNA decay. The PAN2–PAN3 complex functions in general and microRNA-mediated mRNA deadenylation. However, mechanistic insight into PAN2 and its complex with the asymmetric PAN3 dimer is lacking. Here, we describe crystal structures that show that Neurospora crassa PAN2 comprises two independent structural units: a C-terminal catalytic unit and an N-terminal assembly unit that engages in a bipartite interaction with PAN3 dimers. The catalytic unit contains the exonuclease domain in an intimate complex with a potentially modulatory ubiquitin-protease–like domain. The assembly unit contains a WD40 propeller connected to an adaptable linker. The propeller contacts the PAN3 C-terminal domain, whereas the linker reinforces the asymmetry of the PAN3 dimer and prevents the recruitment of a second PAN2 molecule. Functional data indicate an essential role for PAN3 in coordinating PAN2-mediated deadenylation with subsequent steps in mRNA decay, which lead to complete mRNA degradation.
- Published
- 2014
26. The role of disordered protein regions in the assembly of decapping complexes and RNP granules
- Author
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Stefanie Jonas and Elisa Izaurralde
- Subjects
Review ,Biology ,03 medical and health sciences ,0302 clinical medicine ,Endoribonucleases ,Genetics ,Animals ,Humans ,Short linear motif ,Enhancer ,030304 developmental biology ,Ribonucleoprotein ,0303 health sciences ,Messenger RNA ,Cap binding complex ,Molecular Structure ,Translation (biology) ,RNA Helicase A ,Cell biology ,Protein Structure, Tertiary ,Decapping complex ,Ribonucleoproteins ,Protein Multimerization ,030217 neurology & neurosurgery ,Developmental Biology ,Protein Binding - Abstract
The removal of the 5′ cap structure by the decapping enzyme DCP2 inhibits translation and generally commits the mRNA to irreversible 5′-to-3′ exonucleolytic degradation by XRN1. DCP2 catalytic activity is stimulated by DCP1, and these proteins form the conserved core of the decapping complex. Additional decapping factors orchestrate the recruitment and activity of this complex in vivo. These factors include enhancer of decapping 3 (EDC3), EDC4, like Sm14A (LSm14A), Pat, the LSm1–7 complex, and the RNA helicase DDX6. Decapping factors are often modular and feature folded domains flanked or connected by low-complexity disordered regions. Recent studies have made important advances in understanding how these disordered regions contribute to the assembly of decapping complexes and promote phase transitions that drive RNP granule formation. These studies have also revealed that the decapping network is governed by interactions mediated by short linear motifs (SLiMs) in these disordered regions. Consequently, the network has rapidly evolved, and although decapping factors are conserved, individual interactions between orthologs have been rewired during evolution. The plasticity of the network facilitates the acquisition of additional subunits or domains in pre-existing subunits, enhances opportunities for regulating mRNA degradation, and eventually leads to the emergence of novel functions.
- Published
- 2013
27. The SMG5-SMG7 heterodimer directly recruits the CCR4-NOT deadenylase complex to mRNAs containing nonsense codons via interaction with POP2
- Author
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Elisa Izaurralde, Belinda Loh, and Stefanie Jonas
- Subjects
Receptors, CCR4 ,Protein subunit ,RNA Stability ,Mutant ,Plasma protein binding ,medicine.disease_cause ,03 medical and health sciences ,Endonuclease ,0302 clinical medicine ,Catalytic Domain ,Nuclear Receptor Subfamily 4, Group A, Member 2 ,Genetics ,medicine ,Humans ,RNA, Messenger ,Transcription factor ,030304 developmental biology ,0303 health sciences ,Mutation ,biology ,HEK 293 cells ,Genetic Complementation Test ,RNA ,Cell biology ,Protein Subunits ,HEK293 Cells ,Codon, Nonsense ,biology.protein ,Carrier Proteins ,Dimerization ,030217 neurology & neurosurgery ,Developmental Biology ,HeLa Cells ,Protein Binding ,Transcription Factors ,Research Paper - Abstract
Nonsense-mediated mRNA decay (NMD) is a eukaryotic quality control mechanism that detects aberrant mRNAs containing nonsense codons and induces their rapid degradation. This degradation is mediated by SMG6, an NMD-specific endonuclease, as well as the SMG5 and SMG7 proteins, which recruit general mRNA decay enzymes. However, it remains unknown which specific decay factors are recruited and whether this recruitment is direct. Here, we show that SMG7 binds directly to POP2, a catalytic subunit of the CCR4–NOT deadenylase complex, and elicits deadenylation-dependent decapping and 5′-to-3′ decay of NMD targets. Accordingly, a catalytically inactive POP2 mutant partially suppresses NMD in human cells. The SMG7–POP2 interaction is critical for NMD in cells depleted of SMG6, indicating that SMG7 and SMG6 act redundantly to promote the degradation of NMD targets. We further show that UPF1 provides multiple binding sites for decapping factors. These data unveil a missing direct physical link between NMD and the general mRNA decay machinery and indicate that NMD employs diverse and partially redundant mechanisms to ensure robust degradation of aberrant mRNAs.
- Published
- 2013
28. Structure and assembly of the NOT module of the human CCR4-NOT complex
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Lara Wohlbold, Tobias Raisch, Duygu Kuzuoğlu-Öztürk, Ying Chen, Oliver Weichenrieder, Stefanie Jonas, Elisa Izaurralde, and Andreas Boland
- Subjects
Models, Molecular ,Receptors, CCR4 ,Protein Conformation ,DNA Mutational Analysis ,Crystallography, X-Ray ,Models, Biological ,03 medical and health sciences ,0302 clinical medicine ,Structural Biology ,MRNA degradation ,CCR4-NOT complex ,Humans ,RNA, Messenger ,Molecular Biology ,030304 developmental biology ,Regulation of gene expression ,0303 health sciences ,Messenger RNA ,Chemistry ,Translation (biology) ,Structural framework ,Cell biology ,Repressor Proteins ,Mrna regulation ,030220 oncology & carcinogenesis ,Protein Multimerization ,Protein Binding ,Transcription Factors - Abstract
The CCR4-NOT deadenylase complex is a master regulator of translation and mRNA stability. Its NOT module orchestrates recruitment of the catalytic subunits to target mRNAs. We report the crystal structure of the human NOT module formed by the CNOT1, CNOT2 and CNOT3 C-terminal (-C) regions. CNOT1-C provides a rigid scaffold consisting of two perpendicular stacks of HEAT-like repeats. CNOT2-C and CNOT3-C heterodimerize through their SH3-like NOT-box domains. The heterodimer is stabilized and tightly anchored to the surface of CNOT1 through an unexpected intertwined arrangement of peptide regions lacking defined secondary structure. These assembly peptides mold onto their respective binding surfaces and form extensive interfaces. Mutagenesis of individual interfaces and perturbation of endogenous protein ratios cause defects in complex assembly and mRNA decay. Our studies provide a structural framework for understanding the recruitment of the CCR4-NOT complex to mRNA targets.
- Published
- 2013
29. An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily
- Author
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Marko Hyvönen, Bert van Loo, Florian Hollfelder, Stefanie Jonas, Olivier Berteau, Ann C. Babtie, Alhosna Benjdia, Department of Biochemistry, University of Cambridge [UK] (CAM), Unité de recherche d'Écologie et Physiologie du Système Digestif (UEPSD), Institut National de la Recherche Agronomique (INRA), Biotechnology and Biological Sciences Research Council (BBSRC), Medical Research Council (MRC), EU, ProSA, and German National Academic Foundation BBSRC CASE/GlaxoSmithKline
- Subjects
Models, Molecular ,catalytic promiscuity ,Stereochemistry ,Burkholderia ,Hydrolases ,Protein Conformation ,[SDV]Life Sciences [q-bio] ,mechanism ,010402 general chemistry ,sulfatase ,01 natural sciences ,Catalysis ,Substrate Specificity ,Evolution, Molecular ,03 medical and health sciences ,chemistry.chemical_compound ,Protein structure ,Catalytic Domain ,Hydrolase ,evolution ,Enzyme kinetics ,030304 developmental biology ,superfamily ,chemistry.chemical_classification ,0303 health sciences ,Multidisciplinary ,Molecular Structure ,Chemistry ,Sulfatase ,Substrate (chemistry) ,Hydrogen-Ion Concentration ,Alkaline Phosphatase ,Phosphonate ,0104 chemical sciences ,Enzyme ,Mutation ,Physical Sciences ,Chromatography, Gel ,Alkaline phosphatase - Abstract
We report a catalytically promiscuous enzyme able to efficiently promote the hydrolysis of six different substrate classes. Originally assigned as a phosphonate monoester hydrolase (PMH) this enzyme exhibits substantial second-order rate accelerations (( k cat / K M )/ k w ), ranging from 10 7 to as high as 10 19 , for the hydrolyses of phosphate mono-, di-, and triesters, phosphonate monoesters, sulfate monoesters, and sulfonate monoesters. This substrate collection encompasses a range of substrate charges between 0 and -2, transition states of a different nature, and involves attack at two different reaction centers (P and S). Intrinsic reactivities (half-lives) range from 200 days to 10 5 years under near neutrality. The substantial rate accelerations for a set of relatively difficult reactions suggest that efficient catalysis is not necessarily limited to efficient stabilization of just one transition state. The crystal structure of PMH identifies it as a member of the alkaline phosphatase superfamily. PMH encompasses four of the native activities previously observed in this superfamily and extends its repertoire by two further activities, one of which, sulfonate monoesterase, has not been observed previously for a natural enzyme. PMH is thus one of the most promiscuous hydrolases described to date. The functional links between superfamily activities can be presumed to have played a role in functional evolution by gene duplication.
- Published
- 2010
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30. Follow-up-Prozesse konkret gestalten: Follow-up-Instrumente
- Author
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Stefanie Jonas-Klemm, Tammo Straatmann, Beate Bladowski, Stefanie Winter, Virginia Madukanya, Markus Hodapp, Sabine Racky, and Karsten Müller
- Abstract
Das MAB-Marketing ist ein umfassender Ansatz, um die Akzeptanz der Befragung zu sichern und die Nutzlichkeit des Instruments zu steigern. Im Sinne des Marketings stellt die MAB eine „Dienstleistung« dar, bei der die Mitarbeiter als “Kunden« der MAB auftreten, deren Erfolg auch von der internen »Vermarktung« abhangt. Der Begriff Marketing bezieht sich hierbei nicht nur auf die Ausarbeitung eines umfassenden Informationskonzeptes, sondern auch auf die Gestaltung des Befragungsinstruments, die Kosten und den Nutzen fur die Mitarbeiter und auf die Leichtigkeit der Teilnahme. Zunachst wird hier das Konzept des MAB-Marketings naher erlautert, bevor in den folgenden Abschnitten die verschiedenen Punkte des MAB-Marketings ausfuhrlich betrachtet werden.
- Published
- 2007
- Full Text
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31. Integration der Mitarbeiter- und Patientenperspektive in das Qualitätsmanagement im Krankenhaus
- Author
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Stefanie Jonas-Klemm and Cathrin Niethammer
- Published
- 2005
- Full Text
- View/download PDF
32. Erratum: An asymmetric PAN3 dimer recruits a single PAN2 exonuclease to mediate mRNA deadenylation and decay
- Author
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Stefanie Jonas, Mary Christie, Daniel Peter, Dipankar Bhandari, Belinda Loh, Eric Huntzinger, Oliver Weichenrieder, and Elisa Izaurralde
- Subjects
Structural Biology ,Molecular Biology - Published
- 2014
- Full Text
- View/download PDF
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