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Shepherdson JL, Granas DM, Li J, Shariff Z, Plassmeyer SP, Holehouse AS, White MA, Cohen BA. Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain. bioRxiv 2024:2024.03.21.585809. [PMID: 38585983 PMCID: PMC10996540 DOI: 10.1101/2024.03.21.585809] [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] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Cone-Rod Homeobox, encoded by CRX, is a transcription factor (TF) essential for the terminal differentiation and maintenance of mammalian photoreceptors. Structurally, CRX comprises an ordered DNA-binding homeodomain and an intrinsically disordered transcriptional effector domain. Although a handful of human variants in CRX have been shown to cause several different degenerative retinopathies with varying cone and rod predominance, as with most human disease genes the vast majority of observed CRX genetic variants are uncharacterized variants of uncertain significance (VUS). We performed a deep mutational scan (DMS) of nearly all possible single amino acid substitution variants in CRX, using an engineered cell-based transcriptional reporter assay. We measured the ability of each CRX missense variant to transactivate a synthetic fluorescent reporter construct in a pooled fluorescence-activated cell sorting assay and compared the activation strength of each variant to that of wild-type CRX to compute an activity score, identifying thousands of variants with altered transcriptional activity. We calculated a statistical confidence for each activity score derived from multiple independent measurements of each variant marked by unique sequence barcodes, curating a high-confidence list of nearly 2,000 variants with significantly altered transcriptional activity compared to wild-type CRX. We evaluated the performance of the DMS assay as a clinical variant classification tool using gold-standard classified human variants from ClinVar, and determined that activity scores could be used to identify pathogenic variants with high specificity. That this performance could be achieved using a synthetic reporter assay in a foreign cell type, even for a highly cell type-specific TF like CRX, suggests that this approach shows promise for DMS of other TFs that function in cell types that are not easily accessible. Per-position average activity scores closely aligned to a predicted structure of the ordered homeodomain and demonstrated position-specific residue requirements. The intrinsically disordered transcriptional effector domain, by contrast, displayed a qualitatively different pattern of substitution effects, following compositional constraints without specific residue position requirements in the peptide chain. The observed compositional constraints of the effector domain were consistent with the acidic exposure model of transcriptional activation. Together, the results of the CRX DMS identify molecular features of the CRX effector domain and demonstrate clinical utility for variant classification.
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Affiliation(s)
- James L. Shepherdson
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - David M. Granas
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Jie Li
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Zara Shariff
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Stephen P. Plassmeyer
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Center for Biomolecular Condensates, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Center for Biomolecular Condensates, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Michael A. White
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Barak A. Cohen
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
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Raicu AM, Suresh M, Arnosti DN. A regulatory role for the unstructured C-terminal domain of the CtBP transcriptional corepressor. J Biol Chem 2024; 300:105490. [PMID: 38000659 PMCID: PMC10788531 DOI: 10.1016/j.jbc.2023.105490] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/31/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
The C-terminal binding protein (CtBP) is a transcriptional corepressor that plays critical roles in development, tumorigenesis, and cell fate. CtBP proteins are structurally similar to alpha hydroxyacid dehydrogenases and feature a prominent intrinsically disordered region in the C terminus. In the mammalian system, CtBP proteins lacking the C-terminal domain (CTD) are able to function as transcriptional regulators and oligomerize, putting into question the significance of this unstructured domain for gene regulation. Yet, the presence of an unstructured CTD of ∼100 residues, including some short motifs, is conserved across Bilateria, indicating the importance of maintaining this domain over evolutionary time. To uncover the significance of the CtBP CTD, we functionally tested naturally occurring Drosophila isoforms of CtBP that possess or lack the CTD, namely CtBP(L) and CtBP(S). We used the CRISPRi system to recruit dCas9-CtBP(L) and dCas9-CtBP(S) to endogenous promoters to directly compare their transcriptional impacts in vivo. Interestingly, CtBP(S) was able to significantly repress transcription of the Mpp6 promoter, while CtBP(L) was much weaker, suggesting that the long CTD may modulate CtBP's repression activity. In contrast, in cell culture, the isoforms behaved similarly on a transfected Mpp6 reporter gene. The context-specific differences in activity of these two developmentally regulated isoforms suggests that the CTD may help provide a spectrum of repression activity suitable for developmental programs.
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Affiliation(s)
- Ana-Maria Raicu
- Cell and Molecular Biology Program, Michigan State University, East Lansing, Michigan, USA
| | - Megha Suresh
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - David N Arnosti
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA.
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Pérez-Jover I, Rochon K, Hu D, Mohan PM, Santos-Perez I, Gisasola JO, Galvez JMM, Agirre J, Qi X, Mears JA, Shnyrova AV, Ramachandran R. Allosteric control of dynamin-related protein 1-catalyzed mitochondrial fission through a conserved disordered C-terminal Short Linear Motif. Res Sq 2023:rs.3.rs-3161608. [PMID: 37503116 PMCID: PMC10371074 DOI: 10.21203/rs.3.rs-3161608/v1] [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] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The mechanochemical GTPase dynamin-related protein 1 (Drp1) catalyzes mitochondrial fission, but the regulatory mechanisms remain ambiguous. Here we found that a conserved, intrinsically disordered, six-residue Short Linear Motif at the extreme Drp1 C-terminus, named CT-SLiM, constitutes a critical allosteric site that controls Drp1 structure and function in vitro and in vivo. Extension of the CT-SLiM by non-native residues, or its interaction with the protein partner GIPC-1, constrains Drp1 subunit conformational dynamics, alters self-assembly properties, and limits cooperative GTP hydrolysis, leading to the fission of model membranes in vitro. In vivo, the availability of the native CT-SLiM is a requirement for productive mitochondrial fission, as both non-native extension and deletion of the CT-SLiM severely impair its progression. Thus, contrary to prevailing models, Drp1-catalyzed mitochondrial fission relies on allosteric communication mediated by the CT-SLiM, deceleration of GTPase activity, and coupled changes in subunit architecture and assembly-disassembly dynamics.
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Affiliation(s)
- Isabel Pérez-Jover
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
- Instituto Biofisika, University of the Basque Country, 48940 Leioa, Spain
| | - Kristy Rochon
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Di Hu
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Pooja Madan Mohan
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Isaac Santos-Perez
- Electron Microscopy and Crystallography Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Science and Technology Park Bld 800, 48160-Derio, Bizkaia, Spain
| | - Julene Ormaetxea Gisasola
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
- Instituto Biofisika, University of the Basque Country, 48940 Leioa, Spain
| | - Juan Manuel Martinez Galvez
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
- Instituto Biofisika, University of the Basque Country, 48940 Leioa, Spain
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK
| | - Xin Qi
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Jason A. Mears
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Anna V. Shnyrova
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
- Instituto Biofisika, University of the Basque Country, 48940 Leioa, Spain
| | - Rajesh Ramachandran
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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Jarrin M, Kalligeraki AA, Uwineza A, Cawood CS, Brown AP, Ward EN, Le K, Freitag-Pohl S, Pohl E, Kiss B, Tapodi A, Quinlan RA. Independent Membrane Binding Properties of the Caspase Generated Fragments of the Beaded Filament Structural Protein 1 (BFSP1) Involves an Amphipathic Helix. Cells 2023; 12:1580. [PMID: 37371051 DOI: 10.3390/cells12121580] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND BFSP1 (beaded filament structural protein 1) is a plasma membrane, Aquaporin 0 (AQP0/MIP)-associated intermediate filament protein expressed in the eye lens. BFSP1 is myristoylated, a post-translation modification that requires caspase cleavage at D433. Bioinformatic analyses suggested that the sequences 434-452 were α-helical and amphipathic. METHODS AND RESULTS By CD spectroscopy, we show that the addition of trifluoroethanol induced a switch from an intrinsically disordered to a more α-helical conformation for the residues 434-467. Recombinantly produced BFSP1 fragments containing this amphipathic helix bind to lens lipid bilayers as determined by surface plasmon resonance (SPR). Lastly, we demonstrate by transient transfection of non-lens MCF7 cells that these same BFSP1 C-terminal sequences localise to plasma membranes and to cytoplasmic vesicles. These can be co-labelled with the vital dye, lysotracker, but other cell compartments, such as the nuclear and mitochondrial membranes, were negative. The N-terminal myristoylation of the amphipathic helix appeared not to change either the lipid affinity or membrane localisation of the BFSP1 polypeptides or fragments we assessed by SPR and transient transfection, but it did appear to enhance its helical content. CONCLUSIONS These data support the conclusion that C-terminal sequences of human BFSP1 distal to the caspase site at G433 have independent membrane binding properties via an adjacent amphipathic helix.
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Affiliation(s)
- Miguel Jarrin
- Department of Biosciences, Upper Mountjoy Science Site, The University of Durham, South Road, Durham DH1 3LE, UK
- Biophysical Sciences Institute, Durham University, Upper Mountjoy, South Road, Durham DH1 3LE, UK
| | - Alexia A Kalligeraki
- Department of Biosciences, Upper Mountjoy Science Site, The University of Durham, South Road, Durham DH1 3LE, UK
- Biophysical Sciences Institute, Durham University, Upper Mountjoy, South Road, Durham DH1 3LE, UK
| | - Alice Uwineza
- Department of Biosciences, Upper Mountjoy Science Site, The University of Durham, South Road, Durham DH1 3LE, UK
- Biophysical Sciences Institute, Durham University, Upper Mountjoy, South Road, Durham DH1 3LE, UK
| | - Chris S Cawood
- Department of Biosciences, Upper Mountjoy Science Site, The University of Durham, South Road, Durham DH1 3LE, UK
- Biophysical Sciences Institute, Durham University, Upper Mountjoy, South Road, Durham DH1 3LE, UK
| | - Adrian P Brown
- Department of Biosciences, Upper Mountjoy Science Site, The University of Durham, South Road, Durham DH1 3LE, UK
| | - Edward N Ward
- Department of Biosciences, Upper Mountjoy Science Site, The University of Durham, South Road, Durham DH1 3LE, UK
- Biophysical Sciences Institute, Durham University, Upper Mountjoy, South Road, Durham DH1 3LE, UK
| | - Khoa Le
- Biophysical Sciences Institute, Durham University, Upper Mountjoy, South Road, Durham DH1 3LE, UK
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Stefanie Freitag-Pohl
- Department of Chemistry, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, UK
| | - Ehmke Pohl
- Biophysical Sciences Institute, Durham University, Upper Mountjoy, South Road, Durham DH1 3LE, UK
- Department of Chemistry, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, UK
| | - Bence Kiss
- Department of Biochemistry and Medical Chemistry, Medical School, University of Pécs, 7624 Pécs, Hungary
| | - Antal Tapodi
- Department of Biosciences, Upper Mountjoy Science Site, The University of Durham, South Road, Durham DH1 3LE, UK
- Biophysical Sciences Institute, Durham University, Upper Mountjoy, South Road, Durham DH1 3LE, UK
- Department of Biochemistry and Medical Chemistry, Medical School, University of Pécs, 7624 Pécs, Hungary
| | - Roy A Quinlan
- Department of Biosciences, Upper Mountjoy Science Site, The University of Durham, South Road, Durham DH1 3LE, UK
- Biophysical Sciences Institute, Durham University, Upper Mountjoy, South Road, Durham DH1 3LE, UK
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
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5
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Ritsch I, Lehmann E, Emmanouilidis L, Yulikov M, Allain F, Jeschke G. Phase Separation of Heterogeneous Nuclear Ribonucleoprotein A1 upon Specific RNA-Binding Observed by Magnetic Resonance. Angew Chem Int Ed Engl 2022; 61:e202204311. [PMID: 35866309 PMCID: PMC9804974 DOI: 10.1002/anie.202204311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Indexed: 01/09/2023]
Abstract
Interaction of heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) with specific single-stranded RNA and its relation to liquid-liquid phase separation (LLPS) were studied in vitro by magnetic resonance based on site-directed spin labelling. An ensemble model of dispersed hnRNP A1 in the absence of RNA was derived from distance distributions between spin labelled sites and small angle X-ray scattering. This model revealed a compact state of the low-complexity domain and its interaction with the RNA recognition motifs. Paramagnetic relaxation enhancement NMR spectroscopy confirmed this interaction. Addition of RNA to dispersed hnRNP A1 induced liquid-droplet formation. Such LLPS depended on RNA concentration and sequence, with continuous wave EPR spectroscopy showing an influence of RNA point mutations on local protein dynamics. We propose that an interplay of sequence-specific RNA binding and LLPS contributes to regulation of specific RNA segregation during stress response.
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Affiliation(s)
- Irina Ritsch
- Laboratory of Physical ChemistryDepartment of Chemistry and Applied BioscienceETH ZurichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Elisabeth Lehmann
- Institute of BiochemistryDepartment of BiologyETH ZurichHönggerbergring 648093ZürichSwitzerland
| | - Leonidas Emmanouilidis
- Institute of BiochemistryDepartment of BiologyETH ZurichHönggerbergring 648093ZürichSwitzerland
| | - Maxim Yulikov
- Laboratory of Physical ChemistryDepartment of Chemistry and Applied BioscienceETH ZurichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Frédéric Allain
- Institute of BiochemistryDepartment of BiologyETH ZurichHönggerbergring 648093ZürichSwitzerland
| | - Gunnar Jeschke
- Laboratory of Physical ChemistryDepartment of Chemistry and Applied BioscienceETH ZurichVladimir-Prelog-Weg 28093ZürichSwitzerland
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Lin J, Bao X, Li XD. A tri-functional amino acid enables mapping of binding sites for posttranslational-modification-mediated protein-protein interactions. Mol Cell 2021; 81:2669-2681.e9. [PMID: 33894155 DOI: 10.1016/j.molcel.2021.04.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 03/01/2021] [Accepted: 03/31/2021] [Indexed: 12/16/2022]
Abstract
Posttranslational modification (PTM), through the recruitment of effector proteins (i.e., "readers") that signal downstream events, plays key roles in regulating a variety of cellular processes. To understand how a PTM is recognized, it is necessary to find its readers and, importantly, the location of the binding pockets responsible for PTM recognition. Although various methods have been developed to identify PTM readers, it remains a challenge to directly map the PTM-binding regions, especially for intrinsically disordered domains. Here, we demonstrate a photo-crosslinkable, clickable, and cleavable tri-functional amino acid, ADdis-Cys, that when coupled with mass spectrometry (ADdis-Cys-MS) can not only identify PTM readers from complex proteomes but also simultaneously map their PTM-recognition modules. Using ADdis-Cys-MS, we successfully identify the binding sites of several reader-PTM interactions, among which we discover human C1QBP as a histone chaperone. This robust method should find wide applications in examining other histone or non-histone PTM-mediated protein-protein interactions.
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Manica G, Ghenea S, Munteanu CVA, Martin EC, Butnaru C, Surleac M, Chiritoiu GN, Alexandru PR, Petrescu AJ, Petrescu SM. EDEM3 Domains Cooperate to Perform Its Overall Cell Functioning. Int J Mol Sci 2021; 22:2172. [PMID: 33671632 PMCID: PMC7926307 DOI: 10.3390/ijms22042172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/15/2021] [Accepted: 02/19/2021] [Indexed: 01/20/2023] Open
Abstract
EDEM3 recognizes and directs misfolded proteins to the ER-associated protein degradation (ERAD) process. EDEM3 was predicted to act as lectin or as a mannosidase because of its homology with the GH47 catalytic domain of the Man1B1, but the contribution of the other regions remained unresolved. Here, we dissect the molecular determinants governing EDEM3 function and its cellular interactions. LC/MS analysis indicates very few stable ER interactors, suggesting EDEM3 availability for transient substrate interactions. Sequence analysis reveals that EDEM3 consists of four consecutive modules defined as GH47, intermediate (IMD), protease-associated (PA), and intrinsically disordered (IDD) domain. Using an EDEM3 knock-out cell line, we expressed EDEM3 and domain deletion mutants to address EDEM3 function. We find that the mannosidase domain provides substrate binding even in the absence of mannose trimming and requires the IMD domain for folding. The PA and IDD domains deletions do not impair the trimming, but specifically modulate the turnover of two misfolded proteins, NHK and the soluble tyrosinase mutant. Hence, we demonstrate that EDEM3 provides a unique ERAD timing to misfolded glycoproteins, not only by its mannose trimming activity, but also by the positive and negative feedback modulated by the protease-associated and intrinsically disordered domain, respectively.
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Affiliation(s)
- Georgiana Manica
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (G.M.); (S.G.); (G.N.C.); (P.R.A.)
| | - Simona Ghenea
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (G.M.); (S.G.); (G.N.C.); (P.R.A.)
| | - Cristian V. A. Munteanu
- Department of Bioinformatics and Structural Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (C.V.A.M.); (E.C.M.); (C.B.); (M.S.); (A.-J.P.)
| | - Eliza C. Martin
- Department of Bioinformatics and Structural Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (C.V.A.M.); (E.C.M.); (C.B.); (M.S.); (A.-J.P.)
| | - Cristian Butnaru
- Department of Bioinformatics and Structural Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (C.V.A.M.); (E.C.M.); (C.B.); (M.S.); (A.-J.P.)
| | - Marius Surleac
- Department of Bioinformatics and Structural Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (C.V.A.M.); (E.C.M.); (C.B.); (M.S.); (A.-J.P.)
- Research Institute of the University of Bucharest, 030018 Bucharest 17, Romania
| | - Gabriela N. Chiritoiu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (G.M.); (S.G.); (G.N.C.); (P.R.A.)
| | - Petruta R. Alexandru
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (G.M.); (S.G.); (G.N.C.); (P.R.A.)
| | - Andrei-Jose Petrescu
- Department of Bioinformatics and Structural Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (C.V.A.M.); (E.C.M.); (C.B.); (M.S.); (A.-J.P.)
| | - Stefana M. Petrescu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (G.M.); (S.G.); (G.N.C.); (P.R.A.)
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Rempel IL, Popken P, Ghavami A, Mishra A, Hapsari RA, Wolters AHG, Veldsink AC, Klaassens M, Meinema AC, Poolman B, Giepmans BNG, Onck PR, Steen A, Veenhoff LM. Flexible and Extended Linker Domains Support Efficient Targeting of Heh2 to the Inner Nuclear Membrane. Structure 2020; 28:185-195.e5. [PMID: 31806352 DOI: 10.1016/j.str.2019.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 08/09/2019] [Accepted: 11/08/2019] [Indexed: 10/25/2022]
Abstract
The nuclear pore complex (NPC) is embedded in the nuclear envelope and forms the main gateway to the nuclear interior including the inner nuclear membrane (INM). Two INM proteins in yeast are selectively imported. Their sorting signals consist of a nuclear localization signal, separated from the transmembrane domain by a long intrinsically disordered (ID) linker. We used computational models to predict the dynamic conformations of ID linkers and analyzed the INM targeting efficiency of proteins with linker regions with altered Stokes radii and decreased flexibilities. We find that flexibility, Stokes radius, and the frequency at which the linkers are at an extended end-to-end distance larger than 25 nm are good predictors for the targeting of the proteins. The data are consistent with a transport mechanism in which INM targeting of Heh2 is dependent on an ID linker that facilitates the crossing of the approximately 25-nm thick NPC scaffold.
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Affiliation(s)
- Irina L Rempel
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, Netherlands
| | - Petra Popken
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, Netherlands; Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands; Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
| | - Ali Ghavami
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
| | - Ankur Mishra
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
| | - Rizqiya A Hapsari
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, Netherlands
| | - Anouk H G Wolters
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, Netherlands
| | - Annemiek C Veldsink
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, Netherlands
| | - Marindy Klaassens
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, Netherlands
| | - Anne C Meinema
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
| | - Bert Poolman
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands; Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
| | - Ben N G Giepmans
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, Netherlands
| | - Patrick R Onck
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands.
| | - Anton Steen
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, Netherlands.
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, Netherlands.
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Duan TL, He GJ, Hu LD, Yan YB. The Intrinsically Disordered C-Terminal Domain Triggers Nucleolar Localization and Function Switch of PARN in Response to DNA Damage. Cells 2019; 8:cells8080836. [PMID: 31387300 PMCID: PMC6721724 DOI: 10.3390/cells8080836] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 07/23/2019] [Accepted: 07/29/2019] [Indexed: 12/11/2022] Open
Abstract
Poly(A)-specific ribonuclease (PARN), a multifunctional multi-domain deadenylase, is crucial to the regulation of mRNA turnover and the maturation of various non-coding RNAs. Despite extensive studies of the well-folding domains responsible for PARN catalysis, the structure and function of the C-terminal domain (CTD) remains elusive. PARN is a cytoplasm-nucleus shuttle protein with concentrated nucleolar distribution. Here, we identify the nuclear and nucleolar localization signals in the CTD of PARN. Spectroscopic studies indicated that PARN-CTD is intrinsically disordered with loosely packed local structures/tertiary structure. Phosphorylation-mimic mutation S557D disrupted the local structure and facilitated the binding of the CTD with the well-folded domains, with no impact on PARN deadenylase activity. Under normal conditions, the nucleolus-residing PARN recruited CBP80 into the nucleoli to repress its deadenylase activity, while DNA damage-induced phosphorylation of PARN-S557 expelled CBP80 from the nucleoli to discharge activity inhibition and attracted nucleoplasm-located CstF-50 into the nucleoli to activate deadenylation. The structure switch-induced function switch of PARN reshaped the profile of small nuclear non-coding RNAs to respond to DNA damage. Our findings highlight that the structure switch of the CTD induced by posttranslational modifications redefines the subset of binding partners, and thereby the RNA targets in the nucleoli.
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Affiliation(s)
- Tian-Li Duan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guang-Jun He
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Li-Dan Hu
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yong-Bin Yan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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Kwong PN, Chambers M, Vashisht AA, Turki-Judeh W, Yau TY, Wohlschlegel JA, Courey AJ. The Central Region of the Drosophila Co-repressor Groucho as a Regulatory Hub. J Biol Chem 2015; 290:30119-30. [PMID: 26483546 DOI: 10.1074/jbc.m115.681171] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Indexed: 12/23/2022] Open
Abstract
Groucho (Gro) is a Drosophila co-repressor that regulates the expression of a large number of genes, many of which are involved in developmental control. Previous studies have shown that its central region is essential for function even though its three domains are poorly conserved and intrinsically disordered. Using these disordered domains as affinity reagents, we have now identified multiple embryonic Gro-interacting proteins. The interactors include protein complexes involved in chromosome organization, mRNA processing, and signaling. Further investigation of the interacting proteins using a reporter assay showed that many of them modulate Gro-mediated repression either positively or negatively. The positive regulators include components of the spliceosomal subcomplex U1 small nuclear ribonucleoprotein (U1 snRNP). A co-immunoprecipitation experiment confirms this finding and suggests that a sizable fraction of nuclear U1 snRNP is associated with Gro. The use of RNA-seq to analyze the gene expression profile of cells subjected to knockdown of Gro or snRNP-U1-C (a component of U1 snRNP) showed a significant overlap between genes regulated by these two factors. Furthermore, comparison of our RNA-seq data with Gro and RNA polymerase II ChIP data led to a number of insights, including the finding that Gro-repressed genes are enriched for promoter-proximal RNA polymerase II. We conclude that the Gro central domains mediate multiple interactions required for repression, thus functioning as a regulatory hub. Furthermore, interactions with the spliceosome may contribute to repression by Gro.
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Affiliation(s)
- Pak N Kwong
- From the Departments of Chemistry and Biochemistry and
| | | | | | - Wiam Turki-Judeh
- From the Departments of Chemistry and Biochemistry and Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Tak Yu Yau
- From the Departments of Chemistry and Biochemistry and
| | - James A Wohlschlegel
- Biological Chemistry and Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Albert J Courey
- From the Departments of Chemistry and Biochemistry and Molecular Biology Institute, UCLA, Los Angeles, California 90095
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11
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Sahoo N, Goradia N, Ohlenschläger O, Schönherr R, Friedrich M, Plass W, Kappl R, Hoshi T, Heinemann SH. Heme impairs the ball-and-chain inactivation of potassium channels. Proc Natl Acad Sci U S A 2013; 110:E4036-44. [PMID: 24082096 DOI: 10.1073/pnas.1313247110] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Fine-tuned regulation of K(+) channel inactivation enables excitable cells to adjust action potential firing. Fast inactivation present in some K(+) channels is mediated by the distal N-terminal structure (ball) occluding the ion permeation pathway. Here we show that Kv1.4 K(+) channels are potently regulated by intracellular free heme; heme binds to the N-terminal inactivation domain and thereby impairs the inactivation process, thus enhancing the K(+) current with an apparent EC50 value of ∼20 nM. Functional studies on channel mutants and structural investigations on recombinant inactivation ball domain peptides encompassing the first 61 residues of Kv1.4 revealed a heme-responsive binding motif involving Cys13:His16 and a secondary histidine at position 35. Heme binding to the N-terminal inactivation domain induces a conformational constraint that prevents it from reaching its receptor site at the vestibule of the channel pore.
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