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Thore S, Raoelijaona F, Talenton V, Fribourg S, Mackereth CD. Molecular details of the CPSF73-CPSF100 C-terminal heterodimer and interaction with Symplekin. Open Biol 2023; 13:230221. [PMID: 37989222 PMCID: PMC10688271 DOI: 10.1098/rsob.230221] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/27/2023] [Indexed: 11/23/2023] Open
Abstract
Eukaryotic pre-mRNA is processed by a large multiprotein complex to accurately cleave the 3' end, and to catalyse the addition of the poly(A) tail. Within this cleavage and polyadenylation specificity factor (CPSF) machinery, the CPSF73/CPSF3 endonuclease subunit directly contacts both CPSF100/CPSF2 and the scaffold protein Symplekin to form a subcomplex known as the core cleavage complex or mammalian cleavage factor. Here we have taken advantage of a stable CPSF73-CPSF100 minimal heterodimer from Encephalitozoon cuniculi to determine the solution structure formed by the first and second C-terminal domain (CTD1 and CTD2) of both proteins. We find a large number of contacts between both proteins in the complex, and notably in the region between CTD1 and CTD2. A similarity is also observed between CTD2 and the TATA-box binding protein (TBP) domains. Separately, we have determined the structure of the terminal CTD3 domain of CPSF73, which also belongs to the TBP domain family and is connected by a flexible linker to the rest of CPSF73. Biochemical assays demonstrate a key role for the CTD3 of CPSF73 in binding Symplekin, and structural models of the trimeric complex from other species allow for comparative analysis and support an overall conserved architecture.
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Affiliation(s)
- Stéphane Thore
- Inserm, CNRS, ARNA Laboratory, Univ. Bordeaux, U1212, UMR 5320, 33000 Bordeaux, France
| | - Finaritra Raoelijaona
- Inserm, CNRS, ARNA Laboratory, Univ. Bordeaux, U1212, UMR 5320, 33000 Bordeaux, France
| | - Vincent Talenton
- Inserm, CNRS, ARNA Laboratory, Univ. Bordeaux, Institut Européen de Chimie et Biologie, U1212, UMR 5320, 33600 Pessac, France
| | - Sébastien Fribourg
- Inserm, CNRS, ARNA Laboratory, Univ. Bordeaux, U1212, UMR 5320, 33000 Bordeaux, France
| | - Cameron D. Mackereth
- Inserm, CNRS, ARNA Laboratory, Univ. Bordeaux, Institut Européen de Chimie et Biologie, U1212, UMR 5320, 33600 Pessac, France
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Thore S, Fribourg S, Mackereth CD. 1H, 15N and 13C resonance assignments of a minimal CPSF73-CPSF100 C-terminal heterodimer. Biomol NMR Assign 2023; 17:43-48. [PMID: 36723825 DOI: 10.1007/s12104-023-10118-6] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 11/26/2022] [Indexed: 06/02/2023]
Abstract
The initial pre-mRNA transcript in eukaryotes is processed by a large multi-protein complex in order to correctly cleave the 3' end, and to subsequently add the polyadenosine tail. This cleavage and polyadenylation specificity factor (CPSF) is composed of separate subunits, with structural information available for both isolated subunits and also larger assembled complexes. Nevertheless, certain key components of CPSF still lack high-resolution atomic data. One such region is the heterodimer formed between the first and second C-terminal domains of the endonuclease CPSF73, with those from the catalytically inactive CPSF100. Here we report the backbone and sidechain resonance assignments of a minimal C-terminal heterodimer of CPSF73-CPSF100 derived from the parasite Encephalitozoon cuniculi. The assignment process used several amino-acid specific labeling strategies, and the chemical shift values allow for secondary structure prediction.
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Affiliation(s)
- Stéphane Thore
- Univ. Bordeaux, Inserm, CNRS, ARNA Laboratory, U1212, UMR 5320, F-33000, Bordeaux, France
| | - Sébastien Fribourg
- Univ. Bordeaux, Inserm, CNRS, ARNA Laboratory, U1212, UMR 5320, F-33000, Bordeaux, France
| | - Cameron D Mackereth
- Univ. Bordeaux, Inserm, CNRS, ARNA Laboratory, U1212, UMR 5320, Institut Européen de Chimie et Biologie, F-33600, Pessac, France.
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Thore S, Fribourg S. Structural insights into the 3′-end mRNA maturation machinery: Snapshot on polyadenylation signal recognition. Biochimie 2019; 164:105-110. [DOI: 10.1016/j.biochi.2019.03.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 03/26/2019] [Indexed: 12/22/2022]
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4
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Guédin A, Lin LY, Armane S, Lacroix L, Mergny JL, Thore S, Yatsunyk LA. Quadruplexes in 'Dicty': crystal structure of a four-quartet G-quadruplex formed by G-rich motif found in the Dictyostelium discoideum genome. Nucleic Acids Res 2019; 46:5297-5307. [PMID: 29718337 PMCID: PMC6007418 DOI: 10.1093/nar/gky290] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/06/2018] [Indexed: 11/25/2022] Open
Abstract
Guanine-rich DNA has the potential to fold into non-canonical G-quadruplex (G4) structures. Analysis of the genome of the social amoeba Dictyostelium discoideum indicates a low number of sequences with G4-forming potential (249–1055). Therefore, D. discoideum is a perfect model organism to investigate the relationship between the presence of G4s and their biological functions. As a first step in this investigation, we crystallized the dGGGGGAGGGGTACAGGGGTACAGGGG sequence from the putative promoter region of two divergent genes in D. discoideum. According to the crystal structure, this sequence folds into a four-quartet intramolecular antiparallel G4 with two lateral and one diagonal loops. The G-quadruplex core is further stabilized by a G-C Watson–Crick base pair and a A–T–A triad and displays high thermal stability (Tm > 90°C at 100 mM KCl). Biophysical characterization of the native sequence and loop mutants suggests that the DNA adopts the same structure in solution and in crystalline form, and that loop interactions are important for the G4 stability but not for its folding. Four-tetrad G4 structures are sparse. Thus, our work advances understanding of the structural diversity of G-quadruplexes and yields coordinates for in silico drug screening programs and G4 predictive tools.
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Affiliation(s)
- Aurore Guédin
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France
| | | | - Samir Armane
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France
| | | | - Jean-Louis Mergny
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France.,Institute of Biophysics of the CAS, v.v.i., Kraálovopolskaá 135, 612 65 Brno, Czech Republic
| | - Stéphane Thore
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France
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Abstract
RIO proteins form a conserved family of atypical protein kinases. RIO2 is a serine/threonine protein kinase/ATPase involved in pre-40S ribosomal maturation. Current crystal structures of archaeal and fungal Rio2 proteins report a monomeric form of the protein. Here, we describe three atomic structures of the human RIO2 kinase showing that it forms a homodimer in vitro. Upon self-association, each protomer ATP-binding pocket is partially remodelled and found in an apostate. The homodimerization is mediated by key residues previously shown to be responsible for ATP binding and catalysis. This unusual in vitro protein kinase dimer reveals an intricate mechanism where identical residues are involved in substrate binding and oligomeric state formation. We speculate that such an oligomeric state might be formed also in vivo and might function in maintaining the protein in an inactive state and could be employed during import.
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Affiliation(s)
| | | | - Stéphane Thore
- INSERM U1212, UMR CNRS 5320, Université de Bordeaux , Bordeaux , France
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Robinson GC, Kaufmann M, Roux C, Martinez-Font J, Hothorn M, Thore S, Fitzpatrick TB. Crystal structure of the pseudoenzyme PDX1.2 in complex with its cognate enzyme PDX1.3: a total eclipse. Acta Crystallogr D Struct Biol 2019; 75:400-415. [PMID: 30988257 DOI: 10.1107/s2059798319002912] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 02/25/2019] [Indexed: 11/10/2022]
Abstract
Pseudoenzymes have burst into the limelight recently as they provide another dimension to regulation of cellular protein activity. In the eudicot plant lineage, the pseudoenzyme PDX1.2 and its cognate enzyme PDX1.3 interact to regulate vitamin B6 biosynthesis. This partnership is important for plant fitness during environmental stress, in particular heat stress. PDX1.2 increases the catalytic activity of PDX1.3, with an overall increase in vitamin B6 biosynthesis. However, the mechanism by which this is achieved is not known. In this study, the Arabidopsis thaliana PDX1.2-PDX1.3 complex was crystallized in the absence and presence of ligands, and attempts were made to solve the X-ray structures. Three PDX1.2-PDX1.3 complex structures are presented: the PDX1.2-PDX1.3 complex as isolated, PDX1.2-PDX1.3-intermediate (in the presence of substrates) and a catalytically inactive complex, PDX1.2-PDX1.3-K97A. Data were also collected from a crystal of a selenomethionine-substituted complex, PDX1.2-PDX1.3-SeMet. In all cases the protein complexes assemble as dodecamers, similar to the recently reported individual PDX1.3 homomer. Intriguingly, the crystals of the protein complex are statistically disordered owing to the high degree of structural similarity of the individual PDX1 proteins, such that the resulting configuration is a composite of both proteins. Despite the differential methionine content, selenomethionine substitution of the PDX1.2-PDX1.3 complex did not resolve the problem. Furthermore, a comparison of the catalytically competent complex with a noncatalytic complex did not facilitate the resolution of the individual proteins. Interestingly, another catalytic lysine in PDX1.3 (Lys165) that pivots between the two active sites in PDX1 (P1 and P2), and the corresponding glutamine (Gln169) in PDX1.2, point towards P1, which is distinctive to the initial priming for catalytic action. This state was previously only observed upon trapping PDX1.3 in a catalytically operational state, as Lys165 points towards P2 in the resting state. Overall, the study shows that the integration of PDX1.2 into a heteromeric dodecamer assembly with PDX1.3 does not cause a major structural deviation from the overall architecture of the homomeric complex. Nonetheless, the structure of the PDX1.2-PDX1.3 complex highlights enhanced flexibility in key catalytic regions for the initial steps of vitamin B6 biosynthesis. This report highlights what may be an intrinsic limitation of X-ray crystallography in the structural investigation of pseudoenzymes.
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Affiliation(s)
- Graham C Robinson
- Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva, Switzerland
| | - Markus Kaufmann
- Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva, Switzerland
| | - Céline Roux
- Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva, Switzerland
| | - Jacobo Martinez-Font
- Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva, Switzerland
| | - Michael Hothorn
- Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva, Switzerland
| | - Stéphane Thore
- Department of Molecular Biology, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva, Switzerland
| | - Teresa B Fitzpatrick
- Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva, Switzerland
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Pérébaskine N, Thore S, Fribourg S. Structural and interaction analysis of the Rrp5 C-terminal region. FEBS Open Bio 2018; 8:1605-1614. [PMID: 30338212 PMCID: PMC6168700 DOI: 10.1002/2211-5463.12495] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/05/2018] [Accepted: 07/14/2018] [Indexed: 11/18/2022] Open
Abstract
Rrp5 is an essential factor during the ribosome biogenesis process. The protein contains a series of 12 S1 RNA-binding domains followed by a TetratricoPeptide Repeat (TPR) domain. In the past, several studies aiming at defining the function of the TPR domain have used nonequivalent Rrp5 constructs, as these protein fragments include not only the TPR module, but also three or four S1 domains. We solved the structure of the Rrp5 TPR module and demonstrated in vitro that the TPR region alone does not bind RNA, while the three S1 domains preceding the TPR module can associate with homopolymeric RNA. Finally, we tested the association of our Rrp5 constructs with several proposed interactors, in support of cryo-EM-based models. COORDINATES Atomic coordinates and structure factors have been deposited to the Protein Data Bank under the accession number 5NLG.
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Abstract
Ribosome biogenesis requires a variety of trans-acting factors in order to produce functional ribosomal subunits. In human cells, the complex formed by the proteins hNob1 and hPno1 is crucial to the site 3 cleavage occurring at the 3'-end of 18S pre-rRNA. However, the properties and activity of this complex are still poorly understood. We present here a detailed characterization of hNob1 organization and its interaction with hPno1. We redefine the boundaries of the endonuclease PIN domain present in hNob1 and we further delineate the precise interacting modules required for complex formation in hNob1 and hPno1. Altogether, our data contributes to a better understanding of the complex biology required during the site 3 cleavage step in ribosome biogenesis.
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Affiliation(s)
| | - Stéphane Thore
- a INSERM U1212, CNRS UMR5320 , Université de Bordeaux , Bordeaux , France
| | - Sébastien Fribourg
- a INSERM U1212, CNRS UMR5320 , Université de Bordeaux , Bordeaux , France
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Boehm E, Zaganelli S, Maundrell K, Jourdain AA, Thore S, Martinou JC. FASTKD1 and FASTKD4 have opposite effects on expression of specific mitochondrial RNAs, depending upon their endonuclease-like RAP domain. Nucleic Acids Res 2017; 45:6135-6146. [PMID: 28335001 PMCID: PMC5449608 DOI: 10.1093/nar/gkx164] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 02/28/2017] [Indexed: 11/14/2022] Open
Abstract
FASTK family proteins have been identified as regulators of mitochondrial RNA homeostasis linked to mitochondrial diseases, but much remains unknown about these proteins. We show that CRISPR-mediated disruption of FASTKD1 increases ND3 mRNA level, while disruption of FASTKD4 reduces the level of ND3 and of other mature mRNAs including ND5 and CYB, and causes accumulation of ND5-CYB precursor RNA. Disrupting both FASTKD1 and FASTKD4 in the same cell results in decreased ND3 mRNA similar to the effect of depleting FASTKD4 alone, indicating that FASTKD4 loss is epistatic. Interestingly, very low levels of FASTKD4 are sufficient to prevent ND3 loss and ND5-CYB precursor accumulation, suggesting that FASTKD4 may act catalytically. Furthermore, structural modeling predicts that each RAP domain of FASTK proteins contains a nuclease fold with a conserved aspartate residue at the putative active site. Accordingly, mutation of this residue in FASTKD4 abolishes its function. Experiments with FASTK chimeras indicate that the RAP domain is essential for the function of the FASTK proteins, while the region upstream determines RNA targeting and protein localization. In conclusion, this paper identifies new aspects of FASTK protein biology and suggests that the RAP domain function depends on an intrinsic nucleolytic activity.
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Affiliation(s)
- Erik Boehm
- Cell Biology Department, University of Geneva, 1211 Geneva 4, Switzerland
| | - Sofia Zaganelli
- Cell Biology Department, University of Geneva, 1211 Geneva 4, Switzerland
| | - Kinsey Maundrell
- Cell Biology Department, University of Geneva, 1211 Geneva 4, Switzerland
| | - Alexis A Jourdain
- Cell Biology Department, University of Geneva, 1211 Geneva 4, Switzerland
| | - Stéphane Thore
- INSERM U-1212, CNRS UMR 5320, Université de Bordeaux, ARNA Laboratory, Bordeaux 33000, France
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10
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Robinson GC, Vegunta Y, Gabus C, Gaubitz C, Thore S. Cloning, expression, purification, and characterisation of the HEAT-repeat domain of TOR from the thermophilic eukaryote Chaetomium thermophilum. Protein Expr Purif 2017; 133:90-95. [PMID: 28284995 DOI: 10.1016/j.pep.2017.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 03/02/2017] [Accepted: 03/06/2017] [Indexed: 11/29/2022]
Abstract
The Target of Rapamycin Complex is a central controller of cell growth and differentiation in eukaryotes. Its global architecture has been described by cryoelectron microscopy, and regions of its central TOR protein have been described by X-ray crystallography. However, the N-terminal region of this protein, which consists of a series of HEAT repeats, remains uncharacterised at high resolution, most likely due to the absence of a suitable purification procedure. Here, we present a robust method for the preparation of the HEAT-repeat domain, utilizing the thermophilic fungus Chaetomium thermophilum as a source organism. We describe construct design and stable expression in insect cells. An efficient two-step purification procedure is presented, and the purified product is characterised by SEC and MALDI-TOF MS. The methods described pave the way for a complete high-resolution characterisation of this elusive region of the TOR protein.
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Affiliation(s)
- Graham C Robinson
- Department of Molecular Biology, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Yogesh Vegunta
- Department of Molecular Biology, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Caroline Gabus
- Department of Molecular Biology, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Christl Gaubitz
- Department of Molecular Biology, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Stéphane Thore
- Department of Molecular Biology, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland; INSERM U-1212, CNRS UMR-5320, Université de Bordeaux, 146 rue Léo Saignat, 33000 Bordeaux, France.
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Rajappa-Titu L, Suematsu T, Munoz-Tello P, Long M, Demir Ö, Cheng KJ, Stagno JR, Luecke H, Amaro RE, Aphasizheva I, Aphasizhev R, Thore S. RNA Editing TUTase 1: structural foundation of substrate recognition, complex interactions and drug targeting. Nucleic Acids Res 2016; 44:10862-10878. [PMID: 27744351 PMCID: PMC5159558 DOI: 10.1093/nar/gkw917] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 09/27/2016] [Accepted: 10/04/2016] [Indexed: 11/13/2022] Open
Abstract
Terminal uridyltransferases (TUTases) execute 3′ RNA uridylation across protists, fungi, metazoan and plant species. Uridylation plays a particularly prominent role in RNA processing pathways of kinetoplastid protists typified by the causative agent of African sleeping sickness, Trypanosoma brucei. In mitochondria of this pathogen, most mRNAs are internally modified by U-insertion/deletion editing while guide RNAs and rRNAs are U-tailed. The founding member of TUTase family, RNA editing TUTase 1 (RET1), functions as a subunit of the 3′ processome in uridylation of gRNA precursors and mature guide RNAs. Along with KPAP1 poly(A) polymerase, RET1 also participates in mRNA translational activation. RET1 is divergent from human TUTases and is essential for parasite viability in the mammalian host and the insect vector. Given its robust in vitro activity, RET1 represents an attractive target for trypanocide development. Here, we report high-resolution crystal structures of the RET1 catalytic core alone and in complex with UTP analogs. These structures reveal a tight docking of the conserved nucleotidyl transferase bi-domain module with a RET1-specific C2H2 zinc finger and RNA recognition (RRM) domains. Furthermore, we define RET1 region required for incorporation into the 3′ processome, determinants for RNA binding, subunit oligomerization and processive UTP incorporation, and predict druggable pockets.
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Affiliation(s)
- Lional Rajappa-Titu
- Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Takuma Suematsu
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA 02118, USA
| | - Paola Munoz-Tello
- Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Marius Long
- Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Özlem Demir
- Department of Chemistry & Biochemistry and the National Biomedical Computation Resource, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kevin J Cheng
- Department of Chemistry & Biochemistry and the National Biomedical Computation Resource, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jason R Stagno
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Hartmut Luecke
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Rommie E Amaro
- Department of Chemistry & Biochemistry and the National Biomedical Computation Resource, University of California, San Diego, La Jolla, CA 92093, USA
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA 02118, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA 02118, USA .,Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Stéphane Thore
- Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland .,INSERM, U1212, ARNA Laboratory, Bordeaux 33000, France.,CNRS UMR5320, ARNA Laboratory, Bordeaux 33000, France.,University of Bordeaux, ARNA Laboratory, Bordeaux 33000, France
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12
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Guedich S, Puffer-Enders B, Baltzinger M, Hoffmann G, Da Veiga C, Jossinet F, Thore S, Bec G, Ennifar E, Burnouf D, Dumas P. Quantitative and predictive model of kinetic regulation by E. coli TPP riboswitches. RNA Biol 2016; 13:373-90. [PMID: 26932506 PMCID: PMC4841613 DOI: 10.1080/15476286.2016.1142040] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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] [Indexed: 12/25/2022] Open
Abstract
Riboswitches are non-coding elements upstream or downstream of mRNAs that, upon binding of a specific ligand, regulate transcription and/or translation initiation in bacteria, or alternative splicing in plants and fungi. We have studied thiamine pyrophosphate (TPP) riboswitches regulating translation of thiM operon and transcription and translation of thiC operon in E. coli, and that of THIC in the plant A. thaliana. For all, we ascertained an induced-fit mechanism involving initial binding of the TPP followed by a conformational change leading to a higher-affinity complex. The experimental values obtained for all kinetic and thermodynamic parameters of TPP binding imply that the regulation by A. thaliana riboswitch is governed by mass-action law, whereas it is of kinetic nature for the two bacterial riboswitches. Kinetic regulation requires that the RNA polymerase pauses after synthesis of each riboswitch aptamer to leave time for TPP binding, but only when its concentration is sufficient. A quantitative model of regulation highlighted how the pausing time has to be linked to the kinetic rates of initial TPP binding to obtain an ON/OFF switch in the correct concentration range of TPP. We verified the existence of these pauses and the model prediction on their duration. Our analysis also led to quantitative estimates of the respective efficiency of kinetic and thermodynamic regulations, which shows that kinetically regulated riboswitches react more sharply to concentration variation of their ligand than thermodynamically regulated riboswitches. This rationalizes the interest of kinetic regulation and confirms empirical observations that were obtained by numerical simulations.
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Affiliation(s)
- Sondés Guedich
- a IBMC-CNRS, Biophysique et Biologie Structurale, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France
| | - Barbara Puffer-Enders
- a IBMC-CNRS, Biophysique et Biologie Structurale, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France
| | - Mireille Baltzinger
- b IBMC-CNRS, Régulations post-transcriptionnelles et nutrition, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France
| | | | - Cyrielle Da Veiga
- a IBMC-CNRS, Biophysique et Biologie Structurale, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France
| | - Fabrice Jossinet
- d IBMC-CNRS, Evolution des ARN non codants chez la levure, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France
| | - Stéphane Thore
- e Université de Bordeaux, Institut Européen de Chimie et Biologie, ARNA laboratory; INSERM-U1212; CNRS-UMR5320 ; Bordeaux , France
| | - Guillaume Bec
- a IBMC-CNRS, Biophysique et Biologie Structurale, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France
| | - Eric Ennifar
- a IBMC-CNRS, Biophysique et Biologie Structurale, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France
| | - Dominique Burnouf
- a IBMC-CNRS, Biophysique et Biologie Structurale, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France
| | - Philippe Dumas
- a IBMC-CNRS, Biophysique et Biologie Structurale, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France
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Monfort A, Di Minin G, Postlmayr A, Freimann R, Arieti F, Thore S, Wutz A. Identification of Spen as a Crucial Factor for Xist Function through Forward Genetic Screening in Haploid Embryonic Stem Cells. Cell Rep 2015; 12:554-61. [PMID: 26190100 PMCID: PMC4530576 DOI: 10.1016/j.celrep.2015.06.067] [Citation(s) in RCA: 171] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/22/2015] [Accepted: 06/23/2015] [Indexed: 01/21/2023] Open
Abstract
In mammals, the noncoding Xist RNA triggers transcriptional silencing of one of the two X chromosomes in female cells. Here, we report a genetic screen for silencing factors in X chromosome inactivation using haploid mouse embryonic stem cells (ESCs) that carry an engineered selectable reporter system. This system was able to identify several candidate factors that are genetically required for chromosomal repression by Xist. Among the list of candidates, we identify the RNA-binding protein Spen, the homolog of split ends. Independent validation through gene deletion in ESCs confirms that Spen is required for gene repression by Xist. However, Spen is not required for Xist RNA localization and the recruitment of chromatin modifications, including Polycomb protein Ezh2. The identification of Spen opens avenues for further investigation into the gene-silencing pathway of Xist and shows the usefulness of haploid ESCs for genetic screening of epigenetic pathways. A haploid embryonic stem cell screen identifies factors required for Xist function The RNA-binding protein Spen is required for gene repression by Xist Recruitment of Polycomb group proteins by Xist is affected in the absence of Spen Spen binds Xist A-repeat RNA but cannot discriminate functional from mutant motifs
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Affiliation(s)
- Asun Monfort
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Giulio Di Minin
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Andreas Postlmayr
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Remo Freimann
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Fabiana Arieti
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno 62500, Czech Republic
| | - Stéphane Thore
- University of Bordeaux, European Institute for Chemistry and Biology (IECB), ARNA Laboratory, Bordeaux 33000, France; Institut National de la Sante et de la Recherche Medicale, INSERM, U869, ARNA Laboratory, Bordeaux 33000, France
| | - Anton Wutz
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, Otto-Stern-Weg 7, 8093 Zurich, Switzerland.
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14
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Gaubitz C, Oliveira TM, Prouteau M, Leitner A, Karuppasamy M, Konstantinidou G, Rispal D, Eltschinger S, Robinson GC, Thore S, Aebersold R, Schaffitzel C, Loewith R. Molecular Basis of the Rapamycin Insensitivity of Target Of Rapamycin Complex 2. Mol Cell 2015; 58:977-88. [PMID: 26028537 DOI: 10.1016/j.molcel.2015.04.031] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 03/31/2015] [Accepted: 04/22/2015] [Indexed: 10/23/2022]
Abstract
Target of Rapamycin (TOR) plays central roles in the regulation of eukaryote growth as the hub of two essential multiprotein complexes: TORC1, which is rapamycin-sensitive, and the lesser characterized TORC2, which is not. TORC2 is a key regulator of lipid biosynthesis and Akt-mediated survival signaling. In spite of its importance, its structure and the molecular basis of its rapamycin insensitivity are unknown. Using crosslinking-mass spectrometry and electron microscopy, we determined the architecture of TORC2. TORC2 displays a rhomboid shape with pseudo-2-fold symmetry and a prominent central cavity. Our data indicate that the C-terminal part of Avo3, a subunit unique to TORC2, is close to the FKBP12-rapamycin-binding domain of Tor2. Removal of this sequence generated a FKBP12-rapamycin-sensitive TORC2 variant, which provides a powerful tool for deciphering TORC2 function in vivo. Using this variant, we demonstrate a role for TORC2 in G2/M cell-cycle progression.
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Affiliation(s)
- Christl Gaubitz
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland
| | - Taiana M Oliveira
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France; Fondation ARC, 9 rue Guy Môquet, BP 90003, 04803 Villejuif Cedex, France
| | - Manoel Prouteau
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Manikandan Karuppasamy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Georgia Konstantinidou
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland
| | - Delphine Rispal
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland
| | - Sandra Eltschinger
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland
| | - Graham C Robinson
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland
| | - Stéphane Thore
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland; University of Bordeaux, European Institute for Chemistry and Biology, ARNA Laboratory, F-33607 Pessac, France; Institut National de la Santé Et de la Recherche Médicale, INSERM-U869, ARNA Laboratory, F-33000, Bordeaux, France
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland; Faculty of Science, University of Zürich, 8057 Zürich, Switzerland
| | - Christiane Schaffitzel
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France; School of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom.
| | - Robbie Loewith
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest Ansermet, CH1211 Geneva, Switzerland; National Centre of Competence in Research "Chemical Biology," University of Geneva, Geneva CH-1211, Switzerland.
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15
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Loyau J, Didelot G, Malinge P, Ravn U, Magistrelli G, Depoisier JF, Pontini G, Poitevin Y, Kosco-Vilbois M, Fischer N, Thore S, Rousseau F. Robust Antibody-Antigen Complexes Prediction Generated by Combining Sequence Analyses, Mutagenesis, In Vitro Evolution, X-ray Crystallography and In Silico Docking. J Mol Biol 2015; 427:2647-62. [PMID: 26013163 DOI: 10.1016/j.jmb.2015.05.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 05/18/2015] [Accepted: 05/19/2015] [Indexed: 11/15/2022]
Abstract
Hu 15C1 is a potent anti-human Toll-like receptor 4 (TLR4) neutralizing antibody. To better understand the molecular basis of its biological activity, we used a multidisciplinary approach to generate an accurate model of the Hu 15C1-TLR4 complex. By combining site-directed mutagenesis, in vitro antibody evolution, affinity measurements and X-ray crystallography of Fab fragments, we identified key interactions across the Hu 15C1-TLR4 interface. These contact points were used as restraints to predict the structure of the Fab region of Hu 15C1 bound to TLR4 using computational molecular docking. This model was further evaluated and validated by additional site-directed mutagenesis studies. The predicted structure of the Hu 15C1-TLR4 complex indicates that the antibody antagonizes the receptor dimerization necessary for its activation. This study exemplifies how iterative cycles of antibody engineering can facilitate the discovery of components of antibody-target interactions.
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Affiliation(s)
- Jérémy Loyau
- Novimmune SA, Chemin des Aulx 14, 1228 Plan-les-Ouates, Switzerland
| | - Gérard Didelot
- Novimmune SA, Chemin des Aulx 14, 1228 Plan-les-Ouates, Switzerland
| | - Pauline Malinge
- Novimmune SA, Chemin des Aulx 14, 1228 Plan-les-Ouates, Switzerland
| | - Ulla Ravn
- Novimmune SA, Chemin des Aulx 14, 1228 Plan-les-Ouates, Switzerland
| | | | | | | | - Yves Poitevin
- Novimmune SA, Chemin des Aulx 14, 1228 Plan-les-Ouates, Switzerland
| | | | - Nicolas Fischer
- Novimmune SA, Chemin des Aulx 14, 1228 Plan-les-Ouates, Switzerland
| | - Stéphane Thore
- Department of Molecular Biology, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva, Switzerland
| | - François Rousseau
- Novimmune SA, Chemin des Aulx 14, 1228 Plan-les-Ouates, Switzerland.
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16
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Coquille S, Filipovska A, Chia T, Rajappa L, Lingford JP, Razif MF, Thore S, Rackham O. An artificial PPR scaffold for programmable RNA recognition. Nat Commun 2014; 5:5729. [DOI: 10.1038/ncomms6729] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 10/31/2014] [Indexed: 01/01/2023] Open
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17
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Fitzpatrick TB, Thore S. Complex behavior: from cannibalism to suicide in the vitamin B1 biosynthesis world. Curr Opin Struct Biol 2014; 29:34-43. [DOI: 10.1016/j.sbi.2014.08.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/27/2014] [Accepted: 08/28/2014] [Indexed: 10/24/2022]
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18
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Arieti F, Gabus C, Tambalo M, Huet T, Round A, Thore S. The crystal structure of the Split End protein SHARP adds a new layer of complexity to proteins containing RNA recognition motifs. Nucleic Acids Res 2014; 42:6742-52. [PMID: 24748666 PMCID: PMC4041450 DOI: 10.1093/nar/gku277] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The Split Ends (SPEN) protein was originally discovered in Drosophila in the late 1990s. Since then, homologous proteins have been identified in eukaryotic species ranging from plants to humans. Every family member contains three predicted RNA recognition motifs (RRMs) in the N-terminal region of the protein. We have determined the crystal structure of the region of the human SPEN homolog that contains these RRMs—the SMRT/HDAC1 Associated Repressor Protein (SHARP), at 2.0 Å resolution. SHARP is a co-regulator of the nuclear receptors. We demonstrate that two of the three RRMs, namely RRM3 and RRM4, interact via a highly conserved interface. Furthermore, we show that the RRM3–RRM4 block is the main platform mediating the stable association with the H12–H13 substructure found in the steroid receptor RNA activator (SRA), a long, non-coding RNA previously shown to play a crucial role in nuclear receptor transcriptional regulation. We determine that SHARP association with SRA relies on both single- and double-stranded RNA sequences. The crystal structure of the SHARP–RRM fragment, together with the associated RNA-binding studies, extend the repertoire of nucleic acid binding properties of RRM domains suggesting a new hypothesis for a better understanding of SPEN protein functions.
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Affiliation(s)
- Fabiana Arieti
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
| | - Caroline Gabus
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
| | - Margherita Tambalo
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
| | - Tiphaine Huet
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
| | - Adam Round
- European Molecular Biology Laboratory, Grenoble Outstation and Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, Grenoble 38042, France
| | - Stéphane Thore
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
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19
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Huet T, Miannay FA, Patton JR, Thore S. Steroid receptor RNA activator (SRA) modification by the human pseudouridine synthase 1 (hPus1p): RNA binding, activity, and atomic model. PLoS One 2014; 9:e94610. [PMID: 24722331 PMCID: PMC3983220 DOI: 10.1371/journal.pone.0094610] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 03/18/2014] [Indexed: 11/23/2022] Open
Abstract
The most abundant of the modified nucleosides, and once considered as the “fifth” nucleotide in RNA, is pseudouridine, which results from the action of pseudouridine synthases. Recently, the mammalian pseudouridine synthase 1 (hPus1p) has been reported to modulate class I and class II nuclear receptor responses through its ability to modify the Steroid receptor RNA Activator (SRA). These findings highlight a new level of regulation in nuclear receptor (NR)-mediated transcriptional responses. We have characterised the RNA association and activity of the human Pus1p enzyme with its unusual SRA substrate. We validate that the minimal RNA fragment within SRA, named H7, is necessary for both the association and modification by hPus1p. Furthermore, we have determined the crystal structure of the catalytic domain of hPus1p at 2.0 Å resolution, alone and in a complex with several molecules present during crystallisation. This model shows an extended C-terminal helix specifically found in the eukaryotic protein, which may prevent the enzyme from forming a homodimer, both in the crystal lattice and in solution. Our biochemical and structural data help to understand the hPus1p active site architecture, and detail its particular requirements with regard to one of its nuclear substrates, the non-coding RNA SRA.
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Affiliation(s)
- Tiphaine Huet
- Department of Molecular Biology, University of Geneva, Sciences III, Geneva, Switzerland
| | | | - Jeffrey R. Patton
- Department of Pathology, Microbiology and Immunology, University of South Carolina, School of Medicine, Columbia, South Carolina, United States of America
| | - Stéphane Thore
- Department of Molecular Biology, University of Geneva, Sciences III, Geneva, Switzerland
- * E-mail:
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20
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Munoz-Tello P, Gabus C, Thore S. A critical switch in the enzymatic properties of the Cid1 protein deciphered from its product-bound crystal structure. Nucleic Acids Res 2013; 42:3372-80. [PMID: 24322298 PMCID: PMC3950679 DOI: 10.1093/nar/gkt1278] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The addition of uridine nucleotide by the poly(U) polymerase (PUP) enzymes has a demonstrated impact on various classes of RNAs such as microRNAs (miRNAs), histone-encoding RNAs and messenger RNAs. Cid1 protein is a member of the PUP family. We solved the crystal structure of Cid1 in complex with non-hydrolyzable UMPNPP and a short dinucleotide compound ApU. These structures revealed new residues involved in substrate/product stabilization. In particular, one of the three catalytic aspartate residues explains the RNA dependence of its PUP activity. Moreover, other residues such as residue N165 or the β-trapdoor are shown to be critical for Cid1 activity. We finally suggest that the length and sequence of Cid1 substrate RNA influence the balance between Cid1's processive and distributive activities. We propose that particular processes regulated by PUPs require the enzymes to switch between the two types of activity as shown for the miRNA biogenesis where PUPs can either promote DICER cleavage via short U-tail or trigger miRNA degradation by adding longer poly(U) tail. The enzymatic properties of these enzymes may be critical for determining their particular function in vivo.
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Affiliation(s)
- Paola Munoz-Tello
- Department of Molecular Biology, University of Geneva, Geneva, 1211, Switzerland
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21
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Coquille S, Roux C, Mehta A, Begley TP, Fitzpatrick TB, Thore S. High-resolution crystal structure of the eukaryotic HMP-P synthase (THIC) from Arabidopsis thaliana. J Struct Biol 2013; 184:438-44. [PMID: 24161603 DOI: 10.1016/j.jsb.2013.10.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 08/22/2013] [Accepted: 10/08/2013] [Indexed: 12/20/2022]
Abstract
Vitamin B₁ is an essential compound in all organisms acting as a cofactor in key metabolic reactions. It is formed by the condensation of two independently biosynthesized molecules referred to as the pyrimidine and thiazole moieties. In bacteria and plants, the biosynthesis of the pyrimidine moiety, 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P), requires a single enzyme, THIC (HMP-P synthase). The enzyme uses an iron-sulfur cluster as well as a 5'-deoxyadenosyl radical as cofactors to rearrange the 5-amino-imidazole ribonucleotide (AIR) substrate to the pyrimidine ring. So far, the only structure reported is the one from the bacteria Caulobacter crescentus. In an attempt to structurally characterize an eukaryotic HMP-P synthase, we have determined the high-resolution crystal structure of THIC from Arabidopsis thaliana at 1.6 Å. The structure is highly similar to its bacterial counterpart although several loop regions show significant differences with potential implications for the enzymatic properties. Furthermore, we have found a metal ion with octahedral coordination at the same location as a zinc ion in the bacterial enzyme. Our high-resolution atomic model shows a metal ion with multiple coordinated water molecules in the close vicinity of the substrate binding sites and is an important step toward the full characterization of the chemical rearrangement occurring during HMP-P biosynthesis.
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Affiliation(s)
- Sandrine Coquille
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland.
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22
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23
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Coquille S, Roux C, Fitzpatrick TB, Thore S. The last piece in the vitamin B1 biosynthesis puzzle: structural and functional insight into yeast 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P) synthase. J Biol Chem 2012; 287:42333-43. [PMID: 23048037 DOI: 10.1074/jbc.m112.397240] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Vitamin B(1) is essential for all organisms being well recognized as a necessary cofactor for key metabolic pathways such as glycolysis, and was more recently implicated in DNA damage responses. Little is known about the enzyme responsible for the formation of the pyrimidine moiety (4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P) synthase). We report a structure-function study of the HMP-P synthase from yeast, THI5p. Our crystallographic structure shows that THI5p is a mix between periplasmic binding proteins and pyridoxal 5'-phosphate-dependent enzymes. Mutational and yeast complementation studies identify the key residues for HMP-P biosynthesis as well as the use of pyridoxal 5'-phosphate as a substrate rather than as a cofactor. Furthermore, we could show that iron binding to HMP-P synthase is essential for the reaction.
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Affiliation(s)
- Sandrine Coquille
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
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24
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Munoz-Tello P, Gabus C, Thore S. Functional implications from the Cid1 poly(U) polymerase crystal structure. Structure 2012; 20:977-86. [PMID: 22608966 DOI: 10.1016/j.str.2012.04.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 04/17/2012] [Accepted: 04/17/2012] [Indexed: 01/08/2023]
Abstract
In eukaryotes, mRNA degradation begins with poly(A) tail removal, followed by decapping, and the mRNA body is degraded by exonucleases. In recent years, the major influence of 3'-end uridylation as a regulatory step within several RNA degradation pathways has generated significant attention toward the responsible enzymes, which are called poly(U) polymerases (PUPs). We determined the atomic structure of the Cid1 protein, the founding member of the PUP family, in its UTP-bound form, allowing unambiguous positioning of the UTP molecule. Our data also suggest that the RNA substrate accommodation and product translocation by the Cid1 protein rely on local and global movements of the enzyme. Supplemented by point mutations, the atomic model is used to propose a catalytic cycle. Our study underlines the Cid1 RNA binding properties, a feature with critical implications for miRNAs, histone mRNAs, and, more generally, cellular RNA degradation.
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Affiliation(s)
- Paola Munoz-Tello
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest Ansermet, Geneva 1211, Switzerland
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25
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Petty TJ, Nishimura T, Emamzadah S, Gabus C, Paszkowski J, Halazonetis TD, Thore S. Expression, crystallization and preliminary X-ray diffraction analysis of the CMM2 region of the Arabidopsis thaliana Morpheus' molecule 1 protein. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:916-8. [PMID: 20693667 DOI: 10.1107/s1744309110021068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Accepted: 06/02/2010] [Indexed: 11/10/2022]
Abstract
Of the known epigenetic control regulators found in plants, the Morpheus' molecule 1 (MOM1) protein is atypical in that the deletion of MOM1 does not affect the level of epigenetic marks controlling the transcriptional status of the genome. A short 197-amino-acid fragment of the MOM1 protein sequence can complement MOM1 deletion when coupled to a nuclear localization signal, suggesting that this region contains a functional domain that compensates for the loss of the full-length protein. Numerous constructs centred on the highly conserved MOM1 motif 2 (CMM2) present in these 197 residues have been generated and expressed in Escherichia coli. Following purification and crystallization screening, diamond-shaped single crystals were obtained that diffracted to approximately 3.2 A resolution. They belonged to the trigonal space group P3(1)21 (or P3(2)21), with unit-cell parameters a=85.64, c=292.74 A. Structure determination is ongoing.
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Affiliation(s)
- Tom J Petty
- Department of Molecular Biology, University of Geneva, Switzerland
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26
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Abstract
The thiamine pyrophosphate (TPP)-sensing riboswitch is the only riboswitch found in eukaryotes. In plants, TPP regulates its own production by binding to the 3' untranslated region of the mRNA encoding ThiC, a critical enzyme in thiamine biosynthesis, which promotes the formation of an unstable splicing variant. In order to better understand the molecular basis of TPP-analogue binding to the eukaryotic TPP-responsive riboswitch, we have determined the crystal structures of the Arabidopsis thaliana TPP-riboswitch in complex with oxythiamine pyrophosphate (OTPP) and with the antimicrobial compound pyrithiamine pyrophosphate (PTPP). The OTPP-riboswitch complex reveals that the pyrimidine ring of OTPP is stabilized in its enol form in order to retain key interactions with guanosine 28 of the riboswitch previously observed in the TPP complex. The structure of PTPP in complex with the riboswitch shows that the base moiety of guanosine 60 undergoes a conformational change to cradle the pyridine ring of the PTPP. Structural information from these complexes has implications for the design of novel antimicrobials targeting TPP-sensing riboswitches.
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Affiliation(s)
- Stéphane Thore
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
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27
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Wälti MA, Thore S, Aebi M, Künzler M. Crystal structure of the putative carbohydrate recognition domain of human galectin-related protein. Proteins 2008; 72:804-8. [DOI: 10.1002/prot.22078] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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28
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Abstract
Riboswitches are untranslated regions of messenger RNA, which adopt alternate structures depending on the binding of specific metabolites. Such conformational switching regulates the expression of proteins involved in the biosynthesis of riboswitch substrates. Here, we present the 2.9 angstrom-resolution crystal structure of the eukaryotic Arabidopsis thaliana thiamine pyrophosphate (TPP)-specific riboswitch in complex with its natural ligand. The riboswitch specifically recognizes the TPP via conserved residues located within two highly distorted parallel "sensor" helices. The structure provides the basis for understanding the reorganization of the riboswitch fold upon TPP binding and explains the mechanism of resistance to the antibiotic pyrithiamine.
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Affiliation(s)
- Stéphane Thore
- ETH Zurich, Institute of Molecular Biology and Biophysics, 8092 Zurich, Switzerland.
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29
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Affiliation(s)
- Turgay Kilic
- Structural and Computational Biology Programme, European Molecular Biology Laboratory, Heidelberg, Germany
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30
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Thore S, Mauxion F, Séraphin B, Suck D. X-ray structure and activity of the yeast Pop2 protein: a nuclease subunit of the mRNA deadenylase complex. EMBO Rep 2003; 4:1150-5. [PMID: 14618157 PMCID: PMC1326415 DOI: 10.1038/sj.embor.7400020] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2003] [Revised: 09/17/2003] [Accepted: 09/19/2003] [Indexed: 11/09/2022] Open
Abstract
In Saccharomyces cerevisiae, a large complex, known as the Ccr4-Not complex, containing two nucleases, is responsible for mRNA deadenylation. One of these nucleases is called Pop2 and has been identified by similarity with PARN, a human poly(A) nuclease. Here, we present the crystal structure of the nuclease domain of Pop2 at 2.3 A resolution. The domain has the fold of the DnaQ family and represents the first structure of an RNase from the DEDD superfamily. Despite the presence of two non-canonical residues in the active site, the domain displays RNase activity on a broad range of RNA substrates. Site-directed mutagenesis of active-site residues demonstrates the intrinsic ability of the Pop2 RNase D domain to digest RNA. This first structure of a nuclease involved in the 3'-5' deadenylation of mRNA in yeast provides information for the understanding of the mechanism by which the Ccr4-Not complex achieves its functions.
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Affiliation(s)
- Stéphane Thore
- European Molecular Biology Laboratory,
Heidelberg, Germany
- European Molecular Biology Laboratory,
Meyerhofstrasse 1, D-69117 Heidelberg,
Germany
| | - Fabienne Mauxion
- Equipe Labelisée La Ligue, Centre de
Génétique Moléculaire, Gif sur Yvette
Cedex, France
- Equipe Labelisée La Ligue, Centre de
Génétique Moléculaire, CNRS UPR2167, Avenue
de la Terrasse, 91198 Gif sur Yvette Cedex,
France
| | - Bertrand Séraphin
- Equipe Labelisée La Ligue, Centre de
Génétique Moléculaire, Gif sur Yvette
Cedex, France
- Equipe Labelisée La Ligue, Centre de
Génétique Moléculaire, CNRS UPR2167, Avenue
de la Terrasse, 91198 Gif sur Yvette Cedex,
France
| | - Dietrich Suck
- European Molecular Biology Laboratory,
Heidelberg, Germany
- European Molecular Biology Laboratory,
Meyerhofstrasse 1, D-69117 Heidelberg,
Germany
- Tel: +49 6221 387 307; Fax: +49 6221 387 306;
E-mail:
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Thore S, Mayer C, Sauter C, Weeks S, Suck D. Crystal structures of the Pyrococcus abyssi Sm core and its complex with RNA. Common features of RNA binding in archaea and eukarya. J Biol Chem 2003; 278:1239-47. [PMID: 12409299 DOI: 10.1074/jbc.m207685200] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. Their proposed function is to mediate RNA-RNA interactions. We present here the crystal structures of Pyrococcus abyssi Sm protein (PA-Sm1) and its complex with a uridine heptamer. The overall structure of the protein complex, a heptameric ring with a central cavity, is similar to that proposed for the eukaryotic Sm core complex and found for other archaeal Sm proteins. RNA molecules bind to the protein at two different sites. They interact specifically inside the ring with three highly conserved residues, defining the uridine-binding pocket. In addition, nucleotides also interact on the surface formed by the N-terminal alpha-helix as well as a conserved aromatic residue in beta-strand 2 of the PA-Sm1 protein. The mutation of this conserved aromatic residue shows the importance of this second site for the discrimination between RNA sequences. Given the high structural homology between archaeal and eukaryotic Sm proteins, the PA-Sm1.RNA complex provides a model for how the small nuclear RNA contacts the Sm proteins in the Sm core. In addition, it suggests how Sm proteins might exert their function as modulators of RNA-RNA interactions.
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Affiliation(s)
- Stéphane Thore
- Structural Biology Program, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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Thore S, Mayer C, Sauter C, Suck D. Structure of Pyrococcus abyssiSm protein in complex with RNA, suggestions for eukaryotic Sm proteins. Acta Crystallogr A 2002. [DOI: 10.1107/s0108767302096022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Törö I, Thore S, Mayer C, Basquin J, Séraphin B, Suck D. RNA binding in an Sm core domain: X-ray structure and functional analysis of an archaeal Sm protein complex. EMBO J 2001; 20:2293-303. [PMID: 11331594 PMCID: PMC125243 DOI: 10.1093/emboj/20.9.2293] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic Sm and Sm-like proteins associate with RNA to form the core domain of ribonucleoprotein particles involved in pre-mRNA splicing and other processes. Recently, putative Sm proteins of unknown function have been identified in Archaea. We show by immunoprecipitation experiments that the two Sm proteins present in Archaeoglobus fulgidus (AF-Sm1 and AF-Sm2) associate with RNase P RNA in vivo, suggesting a role in tRNA processing. The AF-Sm1 protein also interacts specifically with oligouridylate in vitro. We have solved the crystal structures of this protein and a complex with RNA. AF-Sm1 forms a seven-membered ring, with the RNA interacting inside the central cavity on one face of the doughnut-shaped complex. The bases are bound via stacking and specific hydrogen bonding contacts in pockets lined by residues highly conserved in archaeal and eukaryotic Sm proteins, while the phosphates remain solvent accessible. A comparison with the structures of human Sm protein dimers reveals closely related monomer folds and intersubunit contacts, indicating that the architecture of the Sm core domain and RNA binding have been conserved during evolution.
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Affiliation(s)
| | | | - Claudine Mayer
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Postfach 102209, 69012 Heidelberg, Germany and
Centre de Génétique Moleculaire, CNRS, Avenue De la Terrasse, 91198 Gif sur Yvette Cedex, France Present address: Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris, France Corresponding author e-mail:
S.Thore and C.Mayer contributed equally to this work
| | | | - Bertrand Séraphin
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Postfach 102209, 69012 Heidelberg, Germany and
Centre de Génétique Moleculaire, CNRS, Avenue De la Terrasse, 91198 Gif sur Yvette Cedex, France Present address: Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris, France Corresponding author e-mail:
S.Thore and C.Mayer contributed equally to this work
| | - Dietrich Suck
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Postfach 102209, 69012 Heidelberg, Germany and
Centre de Génétique Moleculaire, CNRS, Avenue De la Terrasse, 91198 Gif sur Yvette Cedex, France Present address: Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris, France Corresponding author e-mail:
S.Thore and C.Mayer contributed equally to this work
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Törõ I, Mayer C, Thore S, Basquin J, Dreher H, Dreher M, Séraphin B, Suck D. Structural studies of Sm-related proteins from archaea. Acta Crystallogr A 2000. [DOI: 10.1107/s0108767300022522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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