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Talbi N, Blekemolen MC, Janevska S, Zendler D, van Tilbeurgh H, Fudal I, Takken FLW. Facilitation of Symplastic Effector Protein Mobility by Paired Effectors Is Conserved in Different Classes of Fungal Pathogens. Mol Plant Microbe Interact 2024; 37:304-314. [PMID: 37782126 DOI: 10.1094/mpmi-07-23-0103-fi] [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] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
It has been discovered that plant pathogens produce effectors that spread via plasmodesmata (PD) to allow modulation of host processes in distal uninfected cells. Fusarium oxysporum f. sp. lycopersici (Fol) facilitates effector translocation by expansion of the size-exclusion limit of PD using the Six5/Avr2 effector pair. How other fungal pathogens manipulate PD is unknown. We recently reported that many fungal pathogens belonging to different families carry effector pairs that resemble the SIX5/AVR2 gene pair from Fol. Here, we performed structural predictions of three of these effector pairs from Leptosphaeria maculans (Lm) and tested their ability to manipulate PD and to complement the virulence defect of a Fol SIX5 knockout mutant. We show that the AvrLm10A homologs are structurally related to FolSix5 and localize at PD when they are expressed with their paired effectors. Furthermore, these effectors were found to complement FolSix5 function in cell-to-cell mobility assays and in fungal virulence. We conclude that distantly related fungal species rely on structurally related paired effector proteins to manipulate PD and facilitate effector mobility. The wide distribution of these effector pairs implies Six5-mediated effector translocation to be a conserved propensity among fungal plant pathogens. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Nacera Talbi
- Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Mila C Blekemolen
- Molecular Plant Pathology, Swammerdam Institute of Life Science (SILS), University of Amsterdam, Amsterdam, the Netherlands
| | - Slavica Janevska
- Molecular Plant Pathology, Swammerdam Institute of Life Science (SILS), University of Amsterdam, Amsterdam, the Netherlands
| | - Daniel Zendler
- Molecular Plant Pathology, Swammerdam Institute of Life Science (SILS), University of Amsterdam, Amsterdam, the Netherlands
| | - Herman van Tilbeurgh
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Frank L W Takken
- Molecular Plant Pathology, Swammerdam Institute of Life Science (SILS), University of Amsterdam, Amsterdam, the Netherlands
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Lazar N, Mesarich CH, Petit-Houdenot Y, Talbi N, Li de la Sierra-Gallay I, Zélie E, Blondeau K, Gracy J, Ollivier B, Blaise F, Rouxel T, Balesdent MH, Idnurm A, van Tilbeurgh H, Fudal I. A new family of structurally conserved fungal effectors displays epistatic interactions with plant resistance proteins. PLoS Pathog 2022; 18:e1010664. [PMID: 35793393 PMCID: PMC9292093 DOI: 10.1371/journal.ppat.1010664] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 03/30/2022] [Revised: 07/18/2022] [Accepted: 06/10/2022] [Indexed: 12/31/2022] Open
Abstract
Recognition of a pathogen avirulence (AVR) effector protein by a cognate plant resistance (R) protein triggers a set of immune responses that render the plant resistant. Pathogens can escape this so-called Effector-Triggered Immunity (ETI) by different mechanisms including the deletion or loss-of-function mutation of the AVR gene, the incorporation of point mutations that allow recognition to be evaded while maintaining virulence function, and the acquisition of new effectors that suppress AVR recognition. The Dothideomycete Leptosphaeria maculans, causal agent of oilseed rape stem canker, is one of the few fungal pathogens where suppression of ETI by an AVR effector has been demonstrated. Indeed, AvrLm4-7 suppresses Rlm3- and Rlm9-mediated resistance triggered by AvrLm3 and AvrLm5-9, respectively. The presence of AvrLm4-7 does not impede AvrLm3 and AvrLm5-9 expression, and the three AVR proteins do not appear to physically interact. To decipher the epistatic interaction between these L. maculans AVR effectors, we determined the crystal structure of AvrLm5-9 and obtained a 3D model of AvrLm3, based on the crystal structure of Ecp11-1, a homologous AVR effector candidate from Fulvia fulva. Despite a lack of sequence similarity, AvrLm5-9 and AvrLm3 are structural analogues of AvrLm4-7 (structure previously characterized). Structure-informed sequence database searches identified a larger number of putative structural analogues among L. maculans effector candidates, including the AVR effector AvrLmS-Lep2, all produced during the early stages of oilseed rape infection, as well as among effector candidates from other phytopathogenic fungi. These structural analogues are named LARS (for Leptosphaeria AviRulence and Suppressing) effectors. Remarkably, transformants of L. maculans expressing one of these structural analogues, Ecp11-1, triggered oilseed rape immunity in several genotypes carrying Rlm3. Furthermore, this resistance could be suppressed by AvrLm4-7. These results suggest that Ecp11-1 shares a common activity with AvrLm3 within the host plant which is detected by Rlm3, or that the Ecp11-1 structure is sufficiently close to that of AvrLm3 to be recognized by Rlm3. An efficient strategy to control fungal diseases in the field is genetic control using resistant crop cultivars. Crop resistance mainly relies on gene-for-gene relationships between plant resistance (R) genes and pathogen avirulence (AVR) genes, as defined by Flor in the 1940s. However, such gene-for-gene relationships can increase in complexity over the course of plant-pathogen co-evolution. Resistance against the plant-pathogenic fungus Leptosphaeria maculans by Brassica napus and other Brassica species relies on the recognition of effector (AVR) proteins by R proteins; however, L. maculans produces an effector that suppresses a subset of these specific resistances. Using a protein structure approach, we revealed structural analogy between several of the resistance-triggering effectors, the resistance-suppressing effector, and effectors from other plant-pathogenic species in the Dothideomycetes and Sordariomycetes classes, defining a new family of effectors called LARS. Notably, cross-species expression of one LARS effector from Fulvia fulva, a pathogen of tomato, in L. maculans resulted in recognition by resistant cultivars of oilseed rape. These results highlight the need to integrate knowledge on effector structures to improve resistance management and to develop broad-spectrum resistances for multi-pathogen control of diseases.
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Affiliation(s)
- Noureddine Lazar
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Carl H. Mesarich
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | | | - Nacera Talbi
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
| | - Ines Li de la Sierra-Gallay
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Emilie Zélie
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Karine Blondeau
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Jérôme Gracy
- CNRS UMR 5048, INSERM U1054, Centre de Biochimie Structurale, Université Montpellier, Montpellier, France
| | | | - Françoise Blaise
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
| | | | - Alexander Idnurm
- School of BioSciences, The University of Melbourne, Melbourne, Australia
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
- * E-mail: (HVT); (IF)
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
- * E-mail: (HVT); (IF)
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Lazar N, Mesarich CH, Petit-Houdenot Y, Talbi N, Li de la Sierra-Gallay I, Zélie E, Blondeau K, Gracy J, Ollivier B, Blaise F, Rouxel T, Balesdent MH, Idnurm A, van Tilbeurgh H, Fudal I. A new family of structurally conserved fungal effectors displays epistatic interactions with plant resistance proteins. PLoS Pathog 2022. [PMID: 35793393 DOI: 10.1101/2020.12.17.423041v1.full] [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] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Recognition of a pathogen avirulence (AVR) effector protein by a cognate plant resistance (R) protein triggers a set of immune responses that render the plant resistant. Pathogens can escape this so-called Effector-Triggered Immunity (ETI) by different mechanisms including the deletion or loss-of-function mutation of the AVR gene, the incorporation of point mutations that allow recognition to be evaded while maintaining virulence function, and the acquisition of new effectors that suppress AVR recognition. The Dothideomycete Leptosphaeria maculans, causal agent of oilseed rape stem canker, is one of the few fungal pathogens where suppression of ETI by an AVR effector has been demonstrated. Indeed, AvrLm4-7 suppresses Rlm3- and Rlm9-mediated resistance triggered by AvrLm3 and AvrLm5-9, respectively. The presence of AvrLm4-7 does not impede AvrLm3 and AvrLm5-9 expression, and the three AVR proteins do not appear to physically interact. To decipher the epistatic interaction between these L. maculans AVR effectors, we determined the crystal structure of AvrLm5-9 and obtained a 3D model of AvrLm3, based on the crystal structure of Ecp11-1, a homologous AVR effector candidate from Fulvia fulva. Despite a lack of sequence similarity, AvrLm5-9 and AvrLm3 are structural analogues of AvrLm4-7 (structure previously characterized). Structure-informed sequence database searches identified a larger number of putative structural analogues among L. maculans effector candidates, including the AVR effector AvrLmS-Lep2, all produced during the early stages of oilseed rape infection, as well as among effector candidates from other phytopathogenic fungi. These structural analogues are named LARS (for Leptosphaeria AviRulence and Suppressing) effectors. Remarkably, transformants of L. maculans expressing one of these structural analogues, Ecp11-1, triggered oilseed rape immunity in several genotypes carrying Rlm3. Furthermore, this resistance could be suppressed by AvrLm4-7. These results suggest that Ecp11-1 shares a common activity with AvrLm3 within the host plant which is detected by Rlm3, or that the Ecp11-1 structure is sufficiently close to that of AvrLm3 to be recognized by Rlm3.
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Affiliation(s)
- Noureddine Lazar
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Carl H Mesarich
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | | | - Nacera Talbi
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
| | - Ines Li de la Sierra-Gallay
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Emilie Zélie
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Karine Blondeau
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Jérôme Gracy
- CNRS UMR 5048, INSERM U1054, Centre de Biochimie Structurale, Université Montpellier, Montpellier, France
| | | | - Françoise Blaise
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
| | | | - Alexander Idnurm
- School of BioSciences, The University of Melbourne, Melbourne, Australia
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
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Mao W, Lazar N, van Tilbeurgh H, Loiseau PM, Pomel S. Minor Impact of A258D Mutation on Biochemical and Enzymatic Properties of Leishmania infantum GDP-Mannose Pyrophosphorylase. Microorganisms 2022; 10:microorganisms10020231. [PMID: 35208687 PMCID: PMC8877407 DOI: 10.3390/microorganisms10020231] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 12/31/2021] [Accepted: 01/17/2022] [Indexed: 02/01/2023] Open
Abstract
Background: Leishmaniasis, a vector-borne disease caused by the protozoan parasite from the genus Leishmania, is endemic to tropical and subtropical areas. Few treatments are available against leishmaniasis, with all presenting issues of toxicity, resistance, and/or cost. In this context, the development of new antileishmanial drugs is urgently needed. GDP-mannose pyrophosphorylase (GDP-MP), an enzyme involved in the mannosylation pathway, has been described to constitute an attractive therapeutic target for the development of specific antileishmanial agents. Methods: In this work, we produced, purified, and analyzed the enzymatic properties of the recombinant L. infantum GDP-MP (LiGDP-MP), a single leishmanial GDP-MP that presents mutation of an aspartate instead of an alanine at position 258, which is also the single residue difference with the homolog in L. donovani: LdGDP-MP. Results: The purified LiGDP-MP displayed high substrate and cofactor specificities, a sequential random mechanism of reaction, and the following kinetic constants: Vm at 0.6 µM·min−1, Km from 15–18 µM, kcat from 12.5–13 min−1, and kcat/Km at around 0.8 min−1µM−1. Conclusions: These results show that LiGDP-MP has similar biochemical and enzymatic properties to LdGDP-MP. Further studies are needed to determine the advantage for L. infantum of the A258D residue change in GDP-MP.
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Affiliation(s)
- Wei Mao
- Université Paris-Saclay, CNRS, BioCIS, 92290 Châtenay-Malabry, France; (W.M.); (P.M.L.)
| | - Noureddine Lazar
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France; (N.L.); (H.v.T.)
| | - Herman van Tilbeurgh
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France; (N.L.); (H.v.T.)
| | - Philippe M. Loiseau
- Université Paris-Saclay, CNRS, BioCIS, 92290 Châtenay-Malabry, France; (W.M.); (P.M.L.)
| | - Sébastien Pomel
- Université Paris-Saclay, CNRS, BioCIS, 92290 Châtenay-Malabry, France; (W.M.); (P.M.L.)
- Correspondence:
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5
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Kopina BJ, Missoury S, Collinet B, Fulton MG, Cirio C, van Tilbeurgh H, Lauhon CT. Structure of a reaction intermediate mimic in t6A biosynthesis bound in the active site of the TsaBD heterodimer from Escherichia coli. Nucleic Acids Res 2021; 49:2141-2160. [PMID: 33524148 PMCID: PMC7913687 DOI: 10.1093/nar/gkab026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/21/2020] [Accepted: 01/15/2021] [Indexed: 11/14/2022] Open
Abstract
The tRNA modification N6-threonylcarbamoyladenosine (t6A) is universally conserved in all organisms. In bacteria, the biosynthesis of t6A requires four proteins (TsaBCDE) that catalyze the formation of t6A via the unstable intermediate l-threonylcarbamoyl-adenylate (TC-AMP). While the formation and stability of this intermediate has been studied in detail, the mechanism of its transfer to A37 in tRNA is poorly understood. To investigate this step, the structure of the TsaBD heterodimer from Escherichia coli has been solved bound to a stable phosphonate isosteric mimic of TC-AMP. The phosphonate inhibits t6A synthesis in vitro with an IC50 value of 1.3 μM in the presence of millimolar ATP and L-threonine. The inhibitor binds to TsaBD by coordination to the active site Zn atom via an oxygen atom from both the phosphonate and the carboxylate moieties. The bound conformation of the inhibitor suggests that the catalysis exploits a putative oxyanion hole created by a conserved active site loop of TsaD and that the metal essentially serves as a binding scaffold for the intermediate. The phosphonate bound crystal structure should be useful for the rational design of potent, drug-like small molecule inhibitors as mechanistic probes or potentially novel antibiotics.
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Affiliation(s)
- Brett J Kopina
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Sophia Missoury
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Bruno Collinet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.,Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne-Université, UMR7590 CNRS, MNHN, Paris, France
| | - Mark G Fulton
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Charles Cirio
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Herman van Tilbeurgh
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Charles T Lauhon
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
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de la Sierra-Gallay IL, Belnou M, Chambraud B, Genet M, van Tilbeurgh H, Aumont-Nicaise M, Desmadril M, Baulieu EE, Jacquot Y, Byrne C. Bioinspired Hybrid Fluorescent Ligands for the FK1 Domain of FKBP52. J Med Chem 2020; 63:10330-10338. [PMID: 32866001 DOI: 10.1021/acs.jmedchem.0c00825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The protein FKBP52 is a steroid hormone receptor coactivator likely involved in neurodegenerative disease. A series of small, water-soluble, bioinspired, pseudopeptidic fluorescent ligands for the FK1 domain of this protein are described. The design is such that engulfing of the ligand in the pocket of this domain is accompanied by hydrogen-bonding of the dansyl chromophore which functions as both an integral part of the ligand and a fluorescent reporter. Binding is concomitant with a significant wavelength shift and an enhancement of the ligand fluorescence signal. Excitation of FK1 domain native tryptophan residues in the presence of bound ligand results in Förster resonance energy transfer. Variation of key ligand residues within the short sequence was undertaken, and the interaction of the resulting library with the protein was measured by techniques including isothermal calorimetry analysis, fluorescence, and FRET quenching, and a range of Kd values were determined. Cocrystallization of a protein ligand complex at 2.30 Å resolution provided detailed information at the atomic scale, while also providing insight into native substrate binding.
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Affiliation(s)
- Inès Li de la Sierra-Gallay
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS UMR9198, Université Paris-Saclay, Université Paris-Sud, 91405 Orsay, France
| | - Mathilde Belnou
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France
| | | | - Melanie Genet
- Institut Baulieu, INSERM UMR 1195, Neuroprotection et Neurorégénération, Université Paris-Saclay, 94270Le Kremlin Bicêtre, France
| | - Herman van Tilbeurgh
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS UMR9198, Université Paris-Saclay, Université Paris-Sud, 91405 Orsay, France
| | - Magali Aumont-Nicaise
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS UMR9198, Université Paris-Saclay, Université Paris-Sud, 91405 Orsay, France
| | - Michel Desmadril
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS UMR9198, Université Paris-Saclay, Université Paris-Sud, 91405 Orsay, France
| | - Etienne-Emile Baulieu
- Institut Baulieu, INSERM UMR 1195, Neuroprotection et Neurorégénération, Université Paris-Saclay, 94270Le Kremlin Bicêtre, France
| | - Yves Jacquot
- Cibles Thérapeutiques et Conception de Médicaments (CiTCoM), CNRS UMR 8038, INSERM U1268, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, 75270 Paris Cedex 06, France
| | - Cillian Byrne
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France.,Institut Baulieu, INSERM UMR 1195, Neuroprotection et Neurorégénération, Université Paris-Saclay, 94270Le Kremlin Bicêtre, France
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Ahmad L, Plancqueel S, Lazar N, Korri-Youssoufi H, Li de la Sierra-Gallay I, van Tilbeurgh H, Salmon L. Novel N-substituted 5-phosphate-d-arabinonamide derivatives as strong inhibitors of phosphoglucose isomerases: Synthesis, structure-activity relationship and crystallographic studies. Bioorg Chem 2020; 102:104048. [PMID: 32682158 DOI: 10.1016/j.bioorg.2020.104048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 01/27/2020] [Revised: 05/26/2020] [Accepted: 06/24/2020] [Indexed: 10/24/2022]
Abstract
Phosphoglucose isomerase (PGI) is a cytosolic enzyme that catalyzes the reversible interconversion of d-glucose 6-phosphate and d-fructose 6-phosphate in glycolysis. Outside the cell, PGI is also known as autocrine motility factor (AMF), a cytokine secreted by a large variety of tumor cells that stimulates motility of cancer cells in vitro and metastases development in vivo. Human PGI and AMF are strictly identical proteins both in terms of sequence and 3D structure, and AMF activity is known to involve, at least in part, the enzymatic active site. Hence, with the purpose of finding new strong AMF-PGI inhibitors that could be potentially used as anticancer agents and/or as bioreceptors for carbohydrate-based electrochemical biosensors, we report in this study the synthesis and kinetic evaluation of several new human PGI inhibitors derived from the synthon 5-phospho-d-arabinono-1,4-lactone. Although not designed as high-energy intermediate analogue inhibitors of the enzyme catalyzed isomerization reaction, several of these N-substituted 5-phosphate-d-arabinonamide derivatives appears as new strong PGI inhibitors. For one of them, we report its crystal structure in complex with human PGI at 2.38 Å. Detailed analysis of its interactions at the active site reveals a new binding mode and shows that human PGI is relatively tolerant for modified inhibitors at the "head" C-1 part, offering promising perspectives for the future design of carbohydrate-based biosensors.
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Affiliation(s)
- Lama Ahmad
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Equipe de Chimie Bioorganique et Bioinorganique, CNRS UMR8182, LabEx LERMIT, Université Paris-Saclay, Rue du Doyen Georges Poitou, bât. 420, 91405 Orsay Cedex, France
| | - Stéphane Plancqueel
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS UMR9198, Université Paris-Saclay, Rue du Doyen Georges Poitou, bât. 430, 91405 Orsay Cedex, France
| | - Noureddine Lazar
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS UMR9198, Université Paris-Saclay, Rue du Doyen Georges Poitou, bât. 430, 91405 Orsay Cedex, France
| | - Hafsa Korri-Youssoufi
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Equipe de Chimie Bioorganique et Bioinorganique, CNRS UMR8182, LabEx LERMIT, Université Paris-Saclay, Rue du Doyen Georges Poitou, bât. 420, 91405 Orsay Cedex, France
| | - Inès Li de la Sierra-Gallay
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS UMR9198, Université Paris-Saclay, Rue du Doyen Georges Poitou, bât. 430, 91405 Orsay Cedex, France
| | - Herman van Tilbeurgh
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS UMR9198, Université Paris-Saclay, Rue du Doyen Georges Poitou, bât. 430, 91405 Orsay Cedex, France
| | - Laurent Salmon
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Equipe de Chimie Bioorganique et Bioinorganique, CNRS UMR8182, LabEx LERMIT, Université Paris-Saclay, Rue du Doyen Georges Poitou, bât. 420, 91405 Orsay Cedex, France.
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Dietrich C, Li de la Sierra-Gallay I, Masi M, Girard E, Dautin N, Constantinesco-Becker F, Tropis M, Daffé M, van Tilbeurgh H, Bayan N. The C-terminal domain of Corynebacterium glutamicum mycoloyltransferase A is composed of five repeated motifs involved in cell wall binding and stability. Mol Microbiol 2020; 114:1-16. [PMID: 32073722 DOI: 10.1111/mmi.14492] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/07/2020] [Indexed: 12/29/2022]
Abstract
The genomes of Corynebacteriales contain several genes encoding mycoloyltransferases (Myt) that are specific cell envelope enzymes essential for the biogenesis of the outer membrane. MytA is a major mycoloyltransferase of Corynebacterium glutamicum, displaying an N-terminal domain with esterase activity and a C-terminal extension containing a conserved repeated Leu-Gly-Phe-Pro (LGFP) sequence motif of unknown function. This motif is highly conserved in Corynebacteriales and found associated with cell wall hydrolases and with proteins of unknown function. In this study, we determined the crystal structure of MytA and found that its C-terminal domain is composed of five LGFP motifs and forms a long stalk perpendicular to the N-terminal catalytic α/β-hydrolase domain. The LGFP motifs are composed of a 4-stranded β-fold and occupy alternating orientations along the axis of the stalk. Multiple acetate binding pockets were identified in the stalk, which could correspond to putative ligand-binding sites. By using various MytA mutants and complementary in vitro and in vivo approaches, we provide evidence that the C-terminal LGFP domain interacts with the cell wall peptidoglycan-arabinogalactan polymer. We also show that the C-terminal LGFP domain is not required for the activity of MytA but rather contributes to the overall integrity of the cell envelope.
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Affiliation(s)
- Christiane Dietrich
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Ines Li de la Sierra-Gallay
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Muriel Masi
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Eric Girard
- University of Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Nathalie Dautin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | | | - Maryelle Tropis
- Institut de Pharmacologie et de Biologie Structurale, CNRS UMR 5089, Toulouse Cedex, France
| | - Mamadou Daffé
- Institut de Pharmacologie et de Biologie Structurale, CNRS UMR 5089, Toulouse Cedex, France
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Nicolas Bayan
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
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9
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Missoury S, Plancqueel S, Li de la Sierra-Gallay I, Zhang W, Liger D, Durand D, Dammak R, Collinet B, van Tilbeurgh H. The structure of the TsaB/TsaD/TsaE complex reveals an unexpected mechanism for the bacterial t6A tRNA-modification. Nucleic Acids Res 2019; 47:9464-9465. [PMID: 31428791 PMCID: PMC6755083 DOI: 10.1093/nar/gkz719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Sophia Missoury
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Stéphane Plancqueel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Ines Li de la Sierra-Gallay
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Wenhua Zhang
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Dominique Liger
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Raoudha Dammak
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Bruno Collinet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France.,Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR7590 CNRS/Sorbonne-Université, UPMC, Paris, France
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
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10
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Pichard-Kostuch A, Zhang W, Liger D, Daugeron MC, Létoquart J, Li de la Sierra-Gallay I, Forterre P, Collinet B, van Tilbeurgh H, Basta T. Structure-function analysis of Sua5 protein reveals novel functional motifs required for the biosynthesis of the universal t 6A tRNA modification. RNA 2018; 24:926-938. [PMID: 29650678 PMCID: PMC6004061 DOI: 10.1261/rna.066092.118] [Citation(s) in RCA: 6] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 04/10/2018] [Indexed: 06/08/2023]
Abstract
N6-threonyl-carbamoyl adenosine (t6A) is a universal tRNA modification found at position 37, next to the anticodon, in almost all tRNAs decoding ANN codons (where N = A, U, G, or C). t6A stabilizes the codon-anticodon interaction and hence promotes translation fidelity. The first step of the biosynthesis of t6A, the production of threonyl-carbamoyl adenylate (TC-AMP), is catalyzed by the Sua5/TsaC family of enzymes. While TsaC is a single domain protein, Sua5 enzymes are composed of the TsaC-like domain, a linker and an extra domain called SUA5 of unknown function. In the present study, we report structure-function analysis of Pyrococcus abyssi Sua5 (Pa-Sua5). Crystallographic data revealed binding sites for bicarbonate substrate and pyrophosphate product. The linker of Pa-Sua5 forms a loop structure that folds into the active site gorge and closes it. Using structure-guided mutational analysis, we established that the conserved sequence motifs in the linker and the domain-domain interface are essential for the function of Pa-Sua5. We propose that the linker participates actively in the biosynthesis of TC-AMP by binding to ATP/PPi and by stabilizing the N-carboxy-l-threonine intermediate. Hence, TsaC orthologs which lack such a linker and SUA5 domain use a different mechanism for TC-AMP synthesis.
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Affiliation(s)
- Adeline Pichard-Kostuch
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Wenhua Zhang
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Dominique Liger
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Marie-Claire Daugeron
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Juliette Létoquart
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Ines Li de la Sierra-Gallay
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Patrick Forterre
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, 75014 Paris, France
| | - Bruno Collinet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Tamara Basta
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
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11
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Missoury S, Plancqueel S, Li de la Sierra-Gallay I, Zhang W, Liger D, Durand D, Dammak R, Collinet B, van Tilbeurgh H. The structure of the TsaB/TsaD/TsaE complex reveals an unexpected mechanism for the bacterial t6A tRNA-modification. Nucleic Acids Res 2018; 46:5850-5860. [PMID: 29741707 PMCID: PMC6009658 DOI: 10.1093/nar/gky323] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/09/2018] [Accepted: 04/17/2018] [Indexed: 12/25/2022] Open
Abstract
The universal N6-threonylcarbamoyladenosine (t6A) modification at position A37 of ANN-decoding tRNAs is essential for translational fidelity. In bacteria the TsaC enzyme first synthesizes an l-threonylcarbamoyladenylate (TC-AMP) intermediate. In cooperation with TsaB and TsaE, TsaD then transfers the l-threonylcarbamoyl-moiety from TC-AMP onto tRNA. We determined the crystal structure of the TsaB-TsaE-TsaD (TsaBDE) complex of Thermotoga maritima in presence of a non-hydrolysable AMPCPP. TsaE is positioned at the entrance of the active site pocket of TsaD, contacting both the TsaB and TsaD subunits and prohibiting simultaneous tRNA binding. AMPCPP occupies the ATP binding site of TsaE and is sandwiched between TsaE and TsaD. Unexpectedly, the binding of TsaE partially denatures the active site of TsaD causing loss of its essential metal binding sites. TsaE interferes in a pre- or post-catalytic step and its binding to TsaBD is regulated by ATP hydrolysis. This novel binding mode and activation mechanism of TsaE offers good opportunities for antimicrobial drug development.
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Affiliation(s)
- Sophia Missoury
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Stéphane Plancqueel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Ines Li de la Sierra-Gallay
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Wenhua Zhang
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Dominique Liger
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Raoudha Dammak
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Bruno Collinet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR7590 CNRS/Sorbonne-Université, UPMC, Paris, France
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
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12
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Chevrel A, Mesneau A, Sanchez D, Celma L, Quevillon-Cheruel S, Cavagnino A, Nessler S, Li de la Sierra-Gallay I, van Tilbeurgh H, Minard P, Valerio-Lepiniec M, Urvoas A. Alpha repeat proteins (αRep) as expression and crystallization helpers. J Struct Biol 2018; 201:88-99. [DOI: 10.1016/j.jsb.2017.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 07/28/2017] [Accepted: 08/14/2017] [Indexed: 12/30/2022]
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13
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Ma M, Li de la Sierra-Gallay I, Lazar N, Pellegrini O, Durand D, Marchfelder A, Condon C, van Tilbeurgh H. The crystal structure of Trz1, the long form RNase Z from yeast. Nucleic Acids Res 2017; 45:6209-6216. [PMID: 28379452 PMCID: PMC5449637 DOI: 10.1093/nar/gkx216] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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] [Received: 01/16/2017] [Accepted: 04/03/2017] [Indexed: 01/25/2023] Open
Abstract
tRNAs are synthesized as precursor RNAs that have to undergo processing steps to become functional. Yeast Trz1 is a key endoribonuclease involved in the 3΄ maturation of tRNAs in all domains of life. It is a member of the β-lactamase family of RNases, characterized by an HxHxDH sequence motif involved in coordination of catalytic Zn-ions. The RNase Z family consists of two subfamilies: the short (250-400 residues) and the long forms (about double in size). Short form RNase Z enzymes act as homodimers: one subunit embraces tRNA with a protruding arm, while the other provides the catalytic site. The long form is thought to contain two fused β-lactamase domains within a single polypeptide. Only structures of short form RNase Z enzymes are known. Here we present the 3.1 Å crystal structure of the long-form Trz1 from Saccharomyces cerevisiae. Trz1 is organized into two β-lactamase domains connected by a long linker. The N-terminal domain has lost its catalytic residues, but retains the long flexible arm that is important for tRNA binding, while it is the other way around in the C-terminal domain. Trz1 likely evolved from a duplication and fusion of the gene encoding the monomeric short form RNase Z.
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Affiliation(s)
- Miao Ma
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, University of Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Ines Li de la Sierra-Gallay
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, University of Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Noureddine Lazar
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, University of Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Olivier Pellegrini
- UMR8261 (CNRS-University of Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, University of Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | | | - Ciarán Condon
- UMR8261 (CNRS-University of Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, University of Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
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14
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Braun DA, Rao J, Mollet G, Schapiro D, Daugeron MC, Tan W, Gribouval O, Boyer O, Revy P, Jobst-Schwan T, Schmidt JM, Lawson JA, Schanze D, Ashraf S, Ullmann JFP, Hoogstraten CA, Boddaert N, Collinet B, Martin G, Liger D, Lovric S, Furlano M, Guerrera IC, Sanchez-Ferras O, Hu JF, Boschat AC, Sanquer S, Menten B, Vergult S, De Rocker N, Airik M, Hermle T, Shril S, Widmeier E, Gee HY, Choi WI, Sadowski CE, Pabst WL, Warejko JK, Daga A, Basta T, Matejas V, Scharmann K, Kienast SD, Behnam B, Beeson B, Begtrup A, Bruce M, Ch'ng GS, Lin SP, Chang JH, Chen CH, Cho MT, Gaffney PM, Gipson PE, Hsu CH, Kari JA, Ke YY, Kiraly-Borri C, Lai WM, Lemyre E, Littlejohn RO, Masri A, Moghtaderi M, Nakamura K, Ozaltin F, Praet M, Prasad C, Prytula A, Roeder ER, Rump P, Schnur RE, Shiihara T, Sinha MD, Soliman NA, Soulami K, Sweetser DA, Tsai WH, Tsai JD, Topaloglu R, Vester U, Viskochil DH, Vatanavicharn N, Waxler JL, Wierenga KJ, Wolf MTF, Wong SN, Leidel SA, Truglio G, Dedon PC, Poduri A, Mane S, Lifton RP, Bouchard M, Kannu P, Chitayat D, Magen D, Callewaert B, van Tilbeurgh H, Zenker M, Antignac C, Hildebrandt F. Mutations in KEOPS-complex genes cause nephrotic syndrome with primary microcephaly. Nat Genet 2017; 49:1529-1538. [PMID: 28805828 DOI: 10.1038/ng.3933] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 07/20/2017] [Indexed: 12/19/2022]
Abstract
Galloway-Mowat syndrome (GAMOS) is an autosomal-recessive disease characterized by the combination of early-onset nephrotic syndrome (SRNS) and microcephaly with brain anomalies. Here we identified recessive mutations in OSGEP, TP53RK, TPRKB, and LAGE3, genes encoding the four subunits of the KEOPS complex, in 37 individuals from 32 families with GAMOS. CRISPR-Cas9 knockout in zebrafish and mice recapitulated the human phenotype of primary microcephaly and resulted in early lethality. Knockdown of OSGEP, TP53RK, or TPRKB inhibited cell proliferation, which human mutations did not rescue. Furthermore, knockdown of these genes impaired protein translation, caused endoplasmic reticulum stress, activated DNA-damage-response signaling, and ultimately induced apoptosis. Knockdown of OSGEP or TP53RK induced defects in the actin cytoskeleton and decreased the migration rate of human podocytes, an established intermediate phenotype of SRNS. We thus identified four new monogenic causes of GAMOS, describe a link between KEOPS function and human disease, and delineate potential pathogenic mechanisms.
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Affiliation(s)
- Daniela A Braun
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jia Rao
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Geraldine Mollet
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - David Schapiro
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Marie-Claire Daugeron
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Weizhen Tan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Olivier Gribouval
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Olivia Boyer
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France.,Department of Pediatric Nephrology, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Patrick Revy
- Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France.,INSERM, U1163, Imagine Institute, Laboratory of Genome Dynamics in the Immune system, Paris, France
| | - Tilman Jobst-Schwan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Johanna Magdalena Schmidt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jennifer A Lawson
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Denny Schanze
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Shazia Ashraf
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeremy F P Ullmann
- Epilepsy Genetics Program and F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA
| | - Charlotte A Hoogstraten
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Nathalie Boddaert
- Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France.,INSERM, U1163, Imagine Institute, Laboratory of Molecular and Pathophysiological Bases of Cognitive Disorders, and INSERM U1000, Paris, France.,Department of Pediatric Radiology, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Bruno Collinet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.,Sorbonne Universités UPMC, UFR 927, Sciences de la Vie, Paris, France.,Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie UMR 7590, Sorbonne Universités, UPMC, Université Paris 06, Paris, France
| | - Gaëlle Martin
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Dominique Liger
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Svjetlana Lovric
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Monica Furlano
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France.,Nephrology Department, Fundació Puigvert, IIB Sant Pau, Universitat Autònoma de Barcelona and REDINREN, Barcelona, Spain
| | - I Chiara Guerrera
- Proteomics platform 3P5-Necker, Université Paris Descartes-Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Oraly Sanchez-Ferras
- Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jennifer F Hu
- Departments of Chemistry and Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Sylvia Sanquer
- Department of Metabolomic and Proteomic Biochemistry, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France.,INSERM UMR-S1124, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Björn Menten
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Nina De Rocker
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Merlin Airik
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tobias Hermle
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Eugen Widmeier
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medicine, Renal Division, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Heon Yung Gee
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Won-Il Choi
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Carolin E Sadowski
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Werner L Pabst
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jillian K Warejko
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ankana Daga
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tamara Basta
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Verena Matejas
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Karin Scharmann
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany.,Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, Germany
| | - Sandra D Kienast
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany.,Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, Germany
| | - Babak Behnam
- Department of Medical Genetics and Molecular Biology, Iran University of Medical Sciences (IUMS), Tehran, Iran.,Medical Genetics Branch, National Human Genome Research Institute (NHGRI), Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Brendan Beeson
- Department of Diagnostic Imaging, Princess Margaret and King Edward Memorial Hospitals, Perth, Western Australia, Australia
| | | | - Malcolm Bruce
- Department of Diagnostic Imaging, Princess Margaret and King Edward Memorial Hospitals, Perth, Western Australia, Australia
| | - Gaik-Siew Ch'ng
- Department of Genetics, Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
| | - Shuan-Pei Lin
- Department of Pediatric Genetics, MacKay Children's Hospital, Taipei, Taiwan.,Department of Medicine, MacKay Medical College, New Taipei City, Taiwan
| | - Jui-Hsing Chang
- Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan
| | - Chao-Huei Chen
- Department of Pediatrics, Taichung Veterans General Hospital, Taichung, Taiwan
| | | | - Patrick M Gaffney
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Patrick E Gipson
- Internal Medicine and Pediatrics Divisions of Adult and Pediatric Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Chyong-Hsin Hsu
- Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan
| | - Jameela A Kari
- Pediatric Nephrology Center of Excellence and Pediatric Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Yu-Yuan Ke
- Department of Pediatrics, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Cathy Kiraly-Borri
- Genetic Services of Western Australia, Princess Margaret Hospital for Children and King Edward Memorial Hospital for Women, Subiaco, Western Australia, Australia
| | - Wai-Ming Lai
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, China
| | - Emmanuelle Lemyre
- Service de Génétique Médicale, Département de Pédiatrie, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Rebecca Okashah Littlejohn
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Amira Masri
- Department of Pediatrics, Division of Child Neurology, Faculty of Medicine, University of Jordan, Amman, Jordan
| | - Mastaneh Moghtaderi
- Chronic Kidney Disease Research Center, Tehran University of Medical Science, Tehran, Iran
| | - Kazuyuki Nakamura
- Department of Pediatrics, Yamagata University School of Medicine, Yamagata, Japan
| | - Fatih Ozaltin
- Department of Pediatric Nephrology, Hacettepe University Faculty of Medicine, Hacettepe University, Ankara, Turkey.,Nephrogenetics Laboratory, Hacettepe University Faculty of Medicine, Hacettepe University, Ankara, Turkey.,Hacettepe University Center for Biobanking and Genomics, Hacettepe University, Ankara, Turkey
| | - Marleen Praet
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Chitra Prasad
- Department of Genetics, Metabolism and Pediatrics, Western University, London Health Sciences Centre, London, Ontario, Canada
| | | | - Elizabeth R Roeder
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Patrick Rump
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Takashi Shiihara
- Department of Pediatrics, Yamagata University School of Medicine, Yamagata, Japan
| | - Manish D Sinha
- Department of Paediatric Nephrology, Kings College London, Evelina London Children's Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Neveen A Soliman
- Department of Pediatrics, Center of Pediatric Nephrology &Transplantation, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt.,Egyptian Group for Orphan Renal Diseases, Cairo, Egypt
| | - Kenza Soulami
- Department of Nephrology, Ibn Rochd University Hospital, Casablanca, Morocco
| | - David A Sweetser
- Division of Medical Genetics, Massachusetts General Hospital for Children, Boston, Massachusetts, USA
| | - Wen-Hui Tsai
- Division of Genetics and Metabolism, Department of Pediatrics, Chi Mei Medical Center, Tainan, Taiwan
| | - Jeng-Daw Tsai
- Department of Medicine, MacKay Medical College, New Taipei City, Taiwan.,Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan.,Department of Pediatrics, Taipei Medical University Hospital, Taipei, Taiwan.,Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Rezan Topaloglu
- Department of Pediatric Nephrology, Hacettepe University Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Udo Vester
- Department of Pediatrics II, University Hospital Essen, Essen, Germany
| | - David H Viskochil
- Department of Pediatrics, Division of Medical Genetics, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Nithiwat Vatanavicharn
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jessica L Waxler
- Division of Medical Genetics, Massachusetts General Hospital for Children, Boston, Massachusetts, USA
| | - Klaas J Wierenga
- Department of Pediatrics, Oklahoma University Health Sciences Center (OUHSC), Oklahoma City, Oklahoma, USA
| | - Matthias T F Wolf
- Division of Pediatric Nephrology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Sik-Nin Wong
- Department of Pediatrics and Adolescent Medicine, Tuen Mun Hospital, Tuen Mun, Hong Kong, China
| | - Sebastian A Leidel
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany.,Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, Germany.,Medical Faculty, University of Muenster, Muenster, Germany
| | - Gessica Truglio
- Epilepsy Genetics Program and F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Singapore-MIT Alliance for Research and Technology, Infectious Disease IRG, Singapore
| | - Annapurna Poduri
- Epilepsy Genetics Program and F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York, USA
| | - Maxime Bouchard
- Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Peter Kannu
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - David Chitayat
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Daniella Magen
- Pediatric Nephrology Institute, Rambam Health Care Campus, Haifa, Israel
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Corinne Antignac
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France.,Department of Genetics, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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15
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Urbonavičius J, Rutkienė R, Lopato A, Tauraitė D, Stankevičiūtė J, Aučynaitė A, Kaliniene L, van Tilbeurgh H, Meškys R. Evolution of tRNAPhe:imG2 methyltransferases involved in the biosynthesis of wyosine derivatives in Archaea. RNA 2016; 22:1871-1883. [PMID: 27852927 PMCID: PMC5113207 DOI: 10.1261/rna.057059.116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/19/2016] [Indexed: 06/06/2023]
Abstract
Tricyclic wyosine derivatives are found at position 37 of eukaryotic and archaeal tRNAPhe In Archaea, the intermediate imG-14 is targeted by three different enzymes that catalyze the formation of yW-86, imG, and imG2. We have suggested previously that a peculiar methyltransferase (aTrm5a/Taw22) likely catalyzes two distinct reactions: N1-methylation of guanosine to yield m1G; and C7-methylation of imG-14 to yield imG2. Here we show that the recombinant aTrm5a/Taw22-like enzymes from both Pyrococcus abyssi and Nanoarchaeum equitans indeed possess such dual specificity. We also show that substitutions of individual conservative amino acids of P. abyssi Taw22 (P260N, E173A, and R174A) have a differential effect on the formation of m1G/imG2, while replacement of R134, F165, E213, and P262 with alanine abolishes the formation of both derivatives of G37. We further demonstrate that aTrm5a-type enzyme SSO2439 from Sulfolobus solfataricus, which has no N1-methyltransferase activity, exhibits C7-methyltransferase activity, thereby producing imG2 from imG-14. We thus suggest renaming such aTrm5a methyltransferases as Taw21 to distinguish between monofunctional and bifunctional aTrm5a enzymes.
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Affiliation(s)
- Jaunius Urbonavičius
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, Vilnius 10223, Lithuania
| | - Rasa Rutkienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
| | - Anželika Lopato
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, Vilnius 10223, Lithuania
| | - Daiva Tauraitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
| | - Jonita Stankevičiūtė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
| | - Agota Aučynaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
| | - Laura Kaliniene
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
| | - Herman van Tilbeurgh
- Institut de Biologie Intégrative de la Cellule, I2BC, CNRS Université Paris-Sud UMR9198, Orsay, France
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania
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16
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Liger D, Mora L, Lazar N, Figaro S, Henri J, Scrima N, Buckingham RH, van Tilbeurgh H, Heurgué-Hamard V, Graille M. Mechanism of activation of methyltransferases involved in translation by the Trm112 'hub' protein. Nucleic Acids Res 2015; 44:1482. [PMID: 26503247 PMCID: PMC4756814 DOI: 10.1093/nar/gkv1172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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17
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Létoquart J, van Tran N, Caroline V, Aleksandrov A, Lazar N, van Tilbeurgh H, Liger D, Graille M. Insights into molecular plasticity in protein complexes from Trm9-Trm112 tRNA modifying enzyme crystal structure. Nucleic Acids Res 2015; 43:10989-1002. [PMID: 26438534 PMCID: PMC4678810 DOI: 10.1093/nar/gkv1009] [Citation(s) in RCA: 30] [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] [Received: 03/02/2015] [Accepted: 09/24/2015] [Indexed: 11/15/2022] Open
Abstract
Most of the factors involved in translation (tRNA, rRNA and proteins) are subject to post-transcriptional and post-translational modifications, which participate in the fine-tuning and tight control of ribosome and protein synthesis processes. In eukaryotes, Trm112 acts as an obligate activating platform for at least four methyltransferases (MTase) involved in the modification of 18S rRNA (Bud23), tRNA (Trm9 and Trm11) and translation termination factor eRF1 (Mtq2). Trm112 is then at a nexus between ribosome synthesis and function. Here, we present a structure-function analysis of the Trm9-Trm112 complex, which is involved in the 5-methoxycarbonylmethyluridine (mcm5U) modification of the tRNA anticodon wobble position and hence promotes translational fidelity. We also compare the known crystal structures of various Trm112-MTase complexes, highlighting the structural plasticity allowing Trm112 to interact through a very similar mode with its MTase partners, although those share less than 20% sequence identity.
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Affiliation(s)
- Juliette Létoquart
- Laboratoire de Biochimie, CNRS, UMR 7654, Ecole Polytechnique, F-91128 Palaiseau Cedex, France Fonction et Architecture des Assemblages Macromoléculaires, Département B3S, Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, UMR 9198, CEA, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Nhan van Tran
- Laboratoire de Biochimie, CNRS, UMR 7654, Ecole Polytechnique, F-91128 Palaiseau Cedex, France
| | - Vonny Caroline
- Laboratoire de Biochimie, CNRS, UMR 7654, Ecole Polytechnique, F-91128 Palaiseau Cedex, France
| | - Alexey Aleksandrov
- Laboratoire de Biochimie, CNRS, UMR 7654, Ecole Polytechnique, F-91128 Palaiseau Cedex, France
| | - Noureddine Lazar
- Fonction et Architecture des Assemblages Macromoléculaires, Département B3S, Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, UMR 9198, CEA, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Herman van Tilbeurgh
- Fonction et Architecture des Assemblages Macromoléculaires, Département B3S, Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, UMR 9198, CEA, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Dominique Liger
- Fonction et Architecture des Assemblages Macromoléculaires, Département B3S, Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, UMR 9198, CEA, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Marc Graille
- Laboratoire de Biochimie, CNRS, UMR 7654, Ecole Polytechnique, F-91128 Palaiseau Cedex, France Fonction et Architecture des Assemblages Macromoléculaires, Département B3S, Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, UMR 9198, CEA, Université Paris Sud, F-91405 Orsay Cedex, France
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18
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Julien S, Tondl P, Durand F, Dagkessamanskaia A, van Tilbeurgh H, François JM, Mourey L, Zerbib D, Martin-Yken H, Maveyraud L. Crystallographic studies of the structured core domain of Knr4 from Saccharomyces cerevisiae. Acta Crystallogr F Struct Biol Commun 2015; 71:1120-4. [PMID: 26323295 PMCID: PMC4555916 DOI: 10.1107/s2053230x15012522] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 06/30/2015] [Indexed: 11/10/2022] Open
Abstract
The potentially structured core domain of the intrinsically disordered protein Knr4 from Saccharomyces cerevisiae, comprising residues 80-340, was expressed in Escherichia coli and crystallized using the hanging-drop vapour-diffusion method. Selenomethionine-containing (SeMet) protein was also purified and crystallized. Crystals of both proteins belonged to space group P6522, with unit-cell parameters a = b = 112.44, c = 265.21 Å for the native protein and a = b = 112.49, c = 262.21 Å for the SeMet protein, and diffracted to 3.50 and 3.60 Å resolution, respectively. There are two molecules in the asymmetric unit related by a twofold axis. The anomalous signal of selenium was recorded and yielded an electron-density map of sufficient quality to allow the identification of secondary-structure elements.
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Affiliation(s)
- Sylviane Julien
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Centre National de la Recherche Scientifique (CNRS), 205 Route de Narbonne, BP 64182, 31077 Toulouse, France
- Université de Toulouse, Université Paul Sabatier, IPBS, 31077 Toulouse, France
| | - Patrick Tondl
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Centre National de la Recherche Scientifique (CNRS), 205 Route de Narbonne, BP 64182, 31077 Toulouse, France
- Université de Toulouse, Université Paul Sabatier, IPBS, 31077 Toulouse, France
| | - Fabien Durand
- Université de Toulouse, INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, 31077 Toulouse, France
- INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, 31400 Toulouse, France
- CNRS, UMR5504, 31400 Toulouse, France
| | - Adilia Dagkessamanskaia
- Université de Toulouse, INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, 31077 Toulouse, France
- INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, 31400 Toulouse, France
- CNRS, UMR5504, 31400 Toulouse, France
| | - Herman van Tilbeurgh
- Institut de Biologie Intégrative de la Cellule, UMR9198, CNRS–Université Paris Sud, Bâtiment 430, 91400 Orsay, France
| | - Jean Marie François
- Université de Toulouse, INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, 31077 Toulouse, France
- INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, 31400 Toulouse, France
- CNRS, UMR5504, 31400 Toulouse, France
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Centre National de la Recherche Scientifique (CNRS), 205 Route de Narbonne, BP 64182, 31077 Toulouse, France
- Université de Toulouse, Université Paul Sabatier, IPBS, 31077 Toulouse, France
| | - Didier Zerbib
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Centre National de la Recherche Scientifique (CNRS), 205 Route de Narbonne, BP 64182, 31077 Toulouse, France
- Université de Toulouse, Université Paul Sabatier, IPBS, 31077 Toulouse, France
- Université de Toulouse, INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, 31077 Toulouse, France
- INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, 31400 Toulouse, France
- CNRS, UMR5504, 31400 Toulouse, France
| | - Hélène Martin-Yken
- Université de Toulouse, INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, 31077 Toulouse, France
- INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, 31400 Toulouse, France
- CNRS, UMR5504, 31400 Toulouse, France
| | - Laurent Maveyraud
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Centre National de la Recherche Scientifique (CNRS), 205 Route de Narbonne, BP 64182, 31077 Toulouse, France
- Université de Toulouse, Université Paul Sabatier, IPBS, 31077 Toulouse, France
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19
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Blondeau K, Blaise F, Graille M, Kale SD, Linglin J, Ollivier B, Labarde A, Lazar N, Daverdin G, Balesdent MH, Choi DHY, Tyler BM, Rouxel T, van Tilbeurgh H, Fudal I. Crystal structure of the effector AvrLm4-7 of Leptosphaeria maculans reveals insights into its translocation into plant cells and recognition by resistance proteins. Plant J 2015; 83:610-24. [PMID: 26082394 DOI: 10.1111/tpj.12913] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 06/02/2015] [Accepted: 06/08/2015] [Indexed: 05/13/2023]
Abstract
The avirulence gene AvrLm4-7 of Leptosphaeria maculans, the causal agent of stem canker in Brassica napus (oilseed rape), confers a dual specificity of recognition by two resistance genes (Rlm4 and Rlm7) and is strongly involved in fungal fitness. In order to elucidate the biological function of AvrLm4-7 and understand the specificity of recognition by Rlm4 and Rlm7, the AvrLm4-7 protein was produced in Pichia pastoris and its crystal structure was determined. It revealed the presence of four disulfide bridges, but no close structural analogs could be identified. A short stretch of amino acids in the C terminus of the protein, (R/N)(Y/F)(R/S)E(F/W), was well-conserved among AvrLm4-7 homologs. Loss of recognition of AvrLm4-7 by Rlm4 is caused by the mutation of a single glycine to an arginine residue located in a loop of the protein. Loss of recognition by Rlm7 is governed by more complex mutational patterns, including gene loss or drastic modifications of the protein structure. Three point mutations altered residues in the well-conserved C-terminal motif or close to the glycine involved in Rlm4-mediated recognition, resulting in the loss of Rlm7-mediated recognition. Transient expression in Nicotiana benthamiana (tobacco) and particle bombardment experiments on leaves from oilseed rape suggested that AvrLm4-7 interacts with its cognate R proteins inside the plant cell, and can be translocated into plant cells in the absence of the pathogen. Translocation of AvrLm4-7 into oilseed rape leaves is likely to require the (R/N)(Y/F)(R/S)E(F/W) motif as well as an RAWG motif located in a nearby loop that together form a positively charged region.
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Affiliation(s)
- Karine Blondeau
- I2BC, Université Paris-Saclay, CEA, CNRS, Université Paris Sud, UMR9198, Bât 430, F-91405, Orsay, France
| | - Françoise Blaise
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Marc Graille
- I2BC, Université Paris-Saclay, CEA, CNRS, Université Paris Sud, UMR9198, Bât 430, F-91405, Orsay, France
| | - Shiv D Kale
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Juliette Linglin
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Bénédicte Ollivier
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Audrey Labarde
- I2BC, Université Paris-Saclay, CEA, CNRS, Université Paris Sud, UMR9198, Bât 430, F-91405, Orsay, France
| | - Noureddine Lazar
- I2BC, Université Paris-Saclay, CEA, CNRS, Université Paris Sud, UMR9198, Bât 430, F-91405, Orsay, France
| | - Guillaume Daverdin
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Marie-Hélène Balesdent
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Danielle H Y Choi
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, 24061, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | - Brett M Tyler
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, 24061, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | - Thierry Rouxel
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Herman van Tilbeurgh
- I2BC, Université Paris-Saclay, CEA, CNRS, Université Paris Sud, UMR9198, Bât 430, F-91405, Orsay, France
| | - Isabelle Fudal
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
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20
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Sanchez D, Boudes M, van Tilbeurgh H, Durand D, Quevillon-Cheruel S. Modeling the ComD/ComE/comcdeinteraction network using small angle X-ray scattering. FEBS J 2015; 282:1538-53. [DOI: 10.1111/febs.13240] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 01/12/2015] [Accepted: 02/16/2015] [Indexed: 01/20/2023]
Affiliation(s)
- Dyana Sanchez
- Institute for Integrative Biology of the Cell; Université Paris-Sud; Orsay France
| | - Marion Boudes
- Institute for Integrative Biology of the Cell; Université Paris-Sud; Orsay France
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell; Université Paris-Sud; Orsay France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell; Université Paris-Sud; Orsay France
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21
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Zhang W, Collinet B, Perrochia L, Durand D, van Tilbeurgh H. The ATP-mediated formation of the YgjD-YeaZ-YjeE complex is required for the biosynthesis of tRNA t6A in Escherichia coli. Nucleic Acids Res 2015; 43:1804-17. [PMID: 25578970 PMCID: PMC4330362 DOI: 10.1093/nar/gku1397] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The essential and universal N6-threonylcarbamoyladenosine (t6A) modification at position 37 of ANN-decoding tRNAs plays a pivotal role in translational fidelity through enhancement of the cognate codon recognition and stabilization of the codon–anticodon interaction. In Escherichia coli, the YgjD (TsaD), YeaZ (TsaB), YjeE (TsaE) and YrdC (TsaC) proteins are necessary and sufficient for the in vitro biosynthesis of t6A, using tRNA, ATP, L-threonine and bicarbonate as substrates. YrdC synthesizes the short-lived L-threonylcarbamoyladenylate (TCA), and YgjD, YeaZ and YjeE cooperate to transfer the L-threonylcarbamoyl-moiety from TCA onto adenosine at position 37 of substrate tRNA. We determined the crystal structure of the heterodimer YgjD–YeaZ at 2.3 Å, revealing the presence of an unexpected molecule of ADP bound at an atypical site situated at the YgjD–YeaZ interface. We further showed that the ATPase activity of YjeE is strongly activated by the YgjD–YeaZ heterodimer. We established by binding experiments and SAXS data analysis that YgjD–YeaZ and YjeE form a compact ternary complex only in presence of ATP. The formation of the ternary YgjD–YeaZ–YjeE complex is required for the in vitro biosynthesis of t6A but not its ATPase activity.
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Affiliation(s)
- Wenhua Zhang
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, UMR 8619, CNRS, Bâtiment 430, Université de Paris-Sud, 91405 Orsay Cedex, France
| | - Bruno Collinet
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, UMR 8619, CNRS, Bâtiment 430, Université de Paris-Sud, 91405 Orsay Cedex, France Sorbonne Universités, UPMC Univ Paris 06, UFR 927, Sciences de la vie, F-75005 Paris, France
| | - Ludovic Perrochia
- Institut de Génétique et de Microbiologie, Université Paris-Sud, UMR8621-CNRS, 91405 Orsay, France
| | - Dominique Durand
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, UMR 8619, CNRS, Bâtiment 430, Université de Paris-Sud, 91405 Orsay Cedex, France
| | - Herman van Tilbeurgh
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, UMR 8619, CNRS, Bâtiment 430, Université de Paris-Sud, 91405 Orsay Cedex, France
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Tiouajni M, Durand D, Blondeau K, Graille M, Urvoas A, Valerio-Lepiniec M, Guellouz A, Aumont-Nicaise M, Minard P, van Tilbeurgh H. Structural and functional analysis of the fibronectin-binding protein FNE from Streptococcus equi spp. equi. FEBS J 2014; 281:5513-31. [PMID: 25290767 DOI: 10.1111/febs.13092] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [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: 07/30/2014] [Revised: 09/24/2014] [Accepted: 09/30/2014] [Indexed: 12/17/2022]
Abstract
Streptococcus equi is a horse pathogen belonging to Lancefield group C. Infection by S. equi ssp. equi causes strangles, a serious and highly contagious disease of the upper respiratory tract. S. equi ssp. equi secretes a fibronectin (Fn)-binding protein, FNE, that does not contain cell wall-anchoring motifs. FNE binds to the gelatin-binding domain (GBD) of Fn, composed of the motifs (6) FI (12) FII (789) FI . FNE lacks the canonical Fn-binding peptide repeats observed in many microbial surface components recognizing adhesive matrix molecules. We found that the interaction between FNE and the human GBD is mediated by the binding of the disordered C-terminal region (residues 208-262) of FNE to the (789) FI GBD subfragment. The crystal structure of FNE showed that it is similar to the minor pilus protein Spy0125 of Streptococcus pyogenes, found at the end of pilus polymers and responsible for adhesion. FNE and Spy0125 both have a superimposable internal thioester bond between highly conserved Cys and Gln residues. Small-angle X-ray scattering of the FNE-(789) FI complex provided a model that aligns the C-terminal peptide of FNE with the E-strands of the FI domains, adopting the β-zipper extension model observed in previous structures of microbial surface components recognizing adhesive matrix molecule adhesion peptides bound to FI domains.
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Affiliation(s)
- Mounira Tiouajni
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR 8619 CNRS, Université Paris Sud, Orsay, France
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Tripsianes K, Friberg A, Barrandon C, Brooks M, van Tilbeurgh H, Seraphin B, Sattler M. A novel protein-protein interaction in the RES (REtention and Splicing) complex. J Biol Chem 2014; 289:28640-50. [PMID: 25160624 PMCID: PMC4192513 DOI: 10.1074/jbc.m114.592311] [Citation(s) in RCA: 18] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The retention and splicing (RES) complex is a conserved spliceosome-associated module that was shown to enhance splicing of a subset of transcripts and promote the nuclear retention of unspliced pre-mRNAs in yeast. The heterotrimeric RES complex is organized around the Snu17p protein that binds to both the Bud13p and Pml1p subunits. Snu17p exhibits an RRM domain that resembles a U2AF homology motif (UHM) and Bud13p harbors a Trp residue reminiscent of an UHM-ligand motif (ULM). It has therefore been proposed that the interaction between Snu17p and Bud13p resembles canonical UHM-ULM complexes. Here, we have used biochemical and NMR structural analysis to characterize the structure of the yeast Snu17p-Bud13p complex. Unlike known UHMs that sequester the Trp residue of the ULM ligand in a hydrophobic pocket, Snu17p and Bud13p utilize a large interaction surface formed around the two helices of the Snu17p domain. In total 18 residues of the Bud13p ligand wrap around the Snu17p helical surface in an U-turn-like arrangement. The invariant Trp232 in Bud13p is located in the center of the turn, and contacts surface residues of Snu17p. The structural data are supported by mutational analysis and indicate that Snu17p provides an extended binding surface with Bud13p that is notably distinct from canonical UHM-ULM interactions. Our data highlight structural diversity in RRM-protein interactions, analogous to the one seen for nucleic acid interactions.
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Affiliation(s)
- Konstantinos Tripsianes
- From the Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 62500 Brno, Czech Republic,
| | - Anders Friberg
- the Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, the Center for Integrated Protein Science Munich and Chair of Biomolecular NMR, TU München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Charlotte Barrandon
- the Centre de Génétique Moléculaire, CNRS, Avenue de la Terrasse, 91198 Gif sur Yvette, France
| | - Mark Brooks
- the University Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR8619, F-91405 Orsay, France, and
| | - Herman van Tilbeurgh
- the University Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR8619, F-91405 Orsay, France, and
| | - Bertrand Seraphin
- the Centre de Génétique Moléculaire, CNRS, Avenue de la Terrasse, 91198 Gif sur Yvette, France, the Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de Recherche Scientifique (CNRS) UMR 7104, Institut National de Santé et de Recherche Médicale (INSERM) U964, Université de Strasbourg, 67404 Illkirch, France
| | - Michael Sattler
- the Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, the Center for Integrated Protein Science Munich and Chair of Biomolecular NMR, TU München, Lichtenbergstr. 4, 85747 Garching, Germany,
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Lisboa J, Andreani J, Sanchez D, Boudes M, Collinet B, Liger D, van Tilbeurgh H, Guérois R, Quevillon-Cheruel S. Molecular determinants of the DprA-RecA interaction for nucleation on ssDNA. Nucleic Acids Res 2014; 42:7395-408. [PMID: 24782530 PMCID: PMC4066776 DOI: 10.1093/nar/gku349] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [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: 11/23/2022] Open
Abstract
Natural transformation is a major mechanism of horizontal gene transfer in bacteria that depends on DNA recombination. RecA is central to the homologous recombination pathway, catalyzing DNA strand invasion and homology search. DprA was shown to be a key binding partner of RecA acting as a specific mediator for its loading on the incoming exogenous ssDNA. Although the 3D structures of both RecA and DprA have been solved, the mechanisms underlying their cross-talk remained elusive. By combining molecular docking simulations and experimental validation, we identified a region on RecA, buried at its self-assembly interface and involving three basic residues that contact an acidic triad of DprA previously shown to be crucial for the interaction. At the core of these patches, DprAM238 and RecAF230 are involved in the interaction. The other DprA binding regions of RecA could involve the N-terminal α-helix and a DNA-binding region. Our data favor a model of DprA acting as a cap of the RecA filament, involving a DprA−RecA interplay at two levels: their own oligomeric states and their respective interaction with DNA. Our model forms the basis for a mechanistic explanation of how DprA can act as a mediator for the loading of RecA on ssDNA.
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Affiliation(s)
- Johnny Lisboa
- Université Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR 8619, F-91405 Orsay, France
| | - Jessica Andreani
- CEA, iBiTecS, F-91191 Gif sur Yvette, France Université Paris-Sud & CNRS, UMR 8221, F-91191 Gif sur Yvette, France
| | - Dyana Sanchez
- Université Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR 8619, F-91405 Orsay, France
| | - Marion Boudes
- Université Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR 8619, F-91405 Orsay, France
| | - Bruno Collinet
- Université Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR 8619, F-91405 Orsay, France UFR sciences de la vie, Université Pierre et Marie Curie UPMC, Sorbonne Universités, F-75005 Paris, France
| | - Dominique Liger
- Université Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR 8619, F-91405 Orsay, France
| | - Herman van Tilbeurgh
- Université Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR 8619, F-91405 Orsay, France
| | - Raphael Guérois
- CEA, iBiTecS, F-91191 Gif sur Yvette, France Université Paris-Sud & CNRS, UMR 8221, F-91191 Gif sur Yvette, France
| | - Sophie Quevillon-Cheruel
- Université Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR 8619, F-91405 Orsay, France
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Boudes M, Sanchez D, Graille M, van Tilbeurgh H, Durand D, Quevillon-Cheruel S. Structural insights into the dimerization of the response regulator ComE from Streptococcus pneumoniae. Nucleic Acids Res 2014; 42:5302-13. [PMID: 24500202 PMCID: PMC4005675 DOI: 10.1093/nar/gku110] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 01/09/2014] [Accepted: 01/13/2014] [Indexed: 12/18/2022] Open
Abstract
Natural transformation contributes to the maintenance and to the evolution of the bacterial genomes. In Streptococcus pneumoniae, this function is reached by achieving the competence state, which is under the control of the ComD-ComE two-component system. We present the crystal and solution structures of ComE. We mimicked the active and non-active states by using the phosphorylated mimetic ComE(D58E) and the unphosphorylatable ComE(D58A) mutants. In the crystal, full-length ComE(D58A) dimerizes through its canonical REC receiver domain but with an atypical mode, which is also adopted by the isolated REC(D58A) and REC(D58E). The LytTR domain adopts a tandem arrangement consistent with the two direct repeats of its promoters. However ComE(D58A) is monomeric in solution, as seen by SAXS, by contrast to ComE(D58E) that dimerizes. For both, a relative mobility between the two domains is assumed. Based on these results we propose two possible ways for activation of ComE by phosphorylation.
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Affiliation(s)
- Marion Boudes
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université de Paris-Sud XI, UMR8619, Bât 430, 91405 Orsay, France and Centre National de la Recherche Scientifique, Orsay, 91405, France
| | - Dyana Sanchez
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université de Paris-Sud XI, UMR8619, Bât 430, 91405 Orsay, France and Centre National de la Recherche Scientifique, Orsay, 91405, France
| | - Marc Graille
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université de Paris-Sud XI, UMR8619, Bât 430, 91405 Orsay, France and Centre National de la Recherche Scientifique, Orsay, 91405, France
| | - Herman van Tilbeurgh
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université de Paris-Sud XI, UMR8619, Bât 430, 91405 Orsay, France and Centre National de la Recherche Scientifique, Orsay, 91405, France
| | - Dominique Durand
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université de Paris-Sud XI, UMR8619, Bât 430, 91405 Orsay, France and Centre National de la Recherche Scientifique, Orsay, 91405, France
| | - Sophie Quevillon-Cheruel
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université de Paris-Sud XI, UMR8619, Bât 430, 91405 Orsay, France and Centre National de la Recherche Scientifique, Orsay, 91405, France
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Guellouz A, Valerio-Lepiniec M, Urvoas A, Chevrel A, Graille M, Fourati-Kammoun Z, Desmadril M, van Tilbeurgh H, Minard P. Selection of specific protein binders for pre-defined targets from an optimized library of artificial helicoidal repeat proteins (alphaRep). PLoS One 2013; 8:e71512. [PMID: 24014183 PMCID: PMC3754942 DOI: 10.1371/journal.pone.0071512] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 07/01/2013] [Indexed: 12/16/2022] Open
Abstract
We previously designed a new family of artificial proteins named αRep based on a subgroup of thermostable helicoidal HEAT-like repeats. We have now assembled a large optimized αRep library. In this library, the side chains at each variable position are not fully randomized but instead encoded by a distribution of codons based on the natural frequency of side chains of the natural repeats family. The library construction is based on a polymerization of micro-genes and therefore results in a distribution of proteins with a variable number of repeats. We improved the library construction process using a “filtration” procedure to retain only fully coding modules that were recombined to recreate sequence diversity. The final library named Lib2.1 contains 1.7×109 independent clones. Here, we used phage display to select, from the previously described library or from the new library, new specific αRep proteins binding to four different non-related predefined protein targets. Specific binders were selected in each case. The results show that binders with various sizes are selected including relatively long sequences, with up to 7 repeats. ITC-measured affinities vary with Kd values ranging from micromolar to nanomolar ranges. The formation of complexes is associated with a significant thermal stabilization of the bound target protein. The crystal structures of two complexes between αRep and their cognate targets were solved and show that the new interfaces are established by the variable surfaces of the repeated modules, as well by the variable N-cap residues. These results suggest that αRep library is a new and versatile source of tight and specific binding proteins with favorable biophysical properties.
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Affiliation(s)
- Asma Guellouz
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris-Sud, Orsay, France
- Unité Mixte de Recherche 8619, Centre National de Recherche Scientifique, Orsay, France
| | - Marie Valerio-Lepiniec
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris-Sud, Orsay, France
- Unité Mixte de Recherche 8619, Centre National de Recherche Scientifique, Orsay, France
| | - Agathe Urvoas
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris-Sud, Orsay, France
- Unité Mixte de Recherche 8619, Centre National de Recherche Scientifique, Orsay, France
| | - Anne Chevrel
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris-Sud, Orsay, France
- Unité Mixte de Recherche 8619, Centre National de Recherche Scientifique, Orsay, France
| | - Marc Graille
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris-Sud, Orsay, France
- Unité Mixte de Recherche 8619, Centre National de Recherche Scientifique, Orsay, France
| | - Zaineb Fourati-Kammoun
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris-Sud, Orsay, France
- Unité Mixte de Recherche 8619, Centre National de Recherche Scientifique, Orsay, France
| | - Michel Desmadril
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris-Sud, Orsay, France
- Unité Mixte de Recherche 8619, Centre National de Recherche Scientifique, Orsay, France
| | - Herman van Tilbeurgh
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris-Sud, Orsay, France
- Unité Mixte de Recherche 8619, Centre National de Recherche Scientifique, Orsay, France
| | - Philippe Minard
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris-Sud, Orsay, France
- Unité Mixte de Recherche 8619, Centre National de Recherche Scientifique, Orsay, France
- * E-mail:
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Ait Benkhali J, Coppin E, Brun S, Peraza-Reyes L, Martin T, Dixelius C, Lazar N, van Tilbeurgh H, Debuchy R. A network of HMG-box transcription factors regulates sexual cycle in the fungus Podospora anserina. PLoS Genet 2013; 9:e1003642. [PMID: 23935511 PMCID: PMC3730723 DOI: 10.1371/journal.pgen.1003642] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 06/03/2013] [Indexed: 12/14/2022] Open
Abstract
High-mobility group (HMG) B proteins are eukaryotic DNA-binding proteins characterized by the HMG-box functional motif. These transcription factors play a pivotal role in global genomic functions and in the control of genes involved in specific developmental or metabolic pathways. The filamentous ascomycete Podospora anserina contains 12 HMG-box genes. Of these, four have been previously characterized; three are mating-type genes that control fertilization and development of the fruit-body, whereas the last one encodes a factor involved in mitochondrial DNA stability. Systematic deletion analysis of the eight remaining uncharacterized HMG-box genes indicated that none were essential for viability, but that seven were involved in the sexual cycle. Two HMG-box genes display striking features. PaHMG5, an ortholog of SpSte11 from Schizosaccharomyces pombe, is a pivotal activator of mating-type genes in P. anserina, whereas PaHMG9 is a repressor of several phenomena specific to the stationary phase, most notably hyphal anastomoses. Transcriptional analyses of HMG-box genes in HMG-box deletion strains indicated that PaHMG5 is at the hub of a network of several HMG-box factors that regulate mating-type genes and mating-type target genes. Genetic analyses revealed that this network also controls fertility genes that are not regulated by mating-type transcription factors. This study points to the critical role of HMG-box members in sexual reproduction in fungi, as 11 out of 12 members were involved in the sexual cycle in P. anserina. PaHMG5 and SpSte11 are conserved transcriptional regulators of mating-type genes, although P. anserina and S. pombe diverged 550 million years ago. Two HMG-box genes, SOX9 and its upstream regulator SRY, also play an important role in sex determination in mammals. The P. anserina and S. pombe mating-type genes and their upstream regulatory factor form a module of HMG-box genes analogous to the SRY/SOX9 module, revealing a commonality of sex regulation in animals and fungi. Podospora anserina, a coprophilous fungus, is used extensively as a model organism to address questions of sexual development and mating-type functions. Its mating-type locus contains three HMGB genes that encode transcription factors involved in fertilization and fruit-body development. We present the functional characterization of the remaining HMGB genes, which revealed that 11 of 12 HMGB genes were involved in sexual development. An analysis of the relationships between these genes uncovered a regulatory network governing the expression of mating-type genes. PaHMG5 is a key transcription factor that operates upstream of mating-type genes in this network. A homolog of PaHMG5 performs a similar function in the fission yeast Schizosaccharomyces pombe, which diverged from P. anserina 550 million years ago. The conservation of a regulatory circuit over such a prolonged timeframe is a striking exception to the general observation that sex developmental pathways are highly variable, even across closely related lineages. A module consisting of two HMGB transcription factors (Sry and Sox9) is a key regulator of sex determination in mammals. We propose that the module containing PaHMG5 and mating-type HMGB genes is the fungal counterpart of the mammalian module, revealing a commonality of sex regulation in animals and fungi.
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Affiliation(s)
- Jinane Ait Benkhali
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
| | - Evelyne Coppin
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
| | - Sylvain Brun
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- Université Paris Diderot, Sorbonne Paris Cité, Institut des Energies de Demain (IED), Paris, France
| | - Leonardo Peraza-Reyes
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
| | - Tom Martin
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Christina Dixelius
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Noureddine Lazar
- Université Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR8619, Orsay, France
| | - Herman van Tilbeurgh
- Université Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR8619, Orsay, France
| | - Robert Debuchy
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- * E-mail:
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Basta T, Boum Y, Briffotaux J, Becker HF, Lamarre-Jouenne I, Lambry JC, Skouloubris S, Liebl U, Graille M, van Tilbeurgh H, Myllykallio H. Mechanistic and structural basis for inhibition of thymidylate synthase ThyX. Open Biol 2013; 2:120120. [PMID: 23155486 PMCID: PMC3498832 DOI: 10.1098/rsob.120120] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [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: 08/16/2012] [Accepted: 09/11/2012] [Indexed: 11/12/2022] Open
Abstract
Nature has established two mechanistically and structurally unrelated families of thymidylate synthases that produce de novo thymidylate or dTMP, an essential DNA precursor. Representatives of the alternative flavin-dependent thymidylate synthase family, ThyX, are found in a large number of microbial genomes, but are absent in humans. We have exploited the nucleotide binding pocket of ThyX proteins to identify non-substrate-based tight-binding ThyX inhibitors that inhibited growth of genetically modified Escherichia coli cells dependent on thyX in a manner mimicking a genetic knockout of thymidylate synthase. We also solved the crystal structure of a viral ThyX bound to 2-hydroxy-3-(4-methoxybenzyl)-1,4-naphthoquinone at a resolution of 2.6 Å. This inhibitor was found to bind within the conserved active site of the tetrameric ThyX enzyme, at the interface of two monomers, partially overlapping with the dUMP binding pocket. Our studies provide new chemical tools for investigating the ThyX reaction mechanism and establish a novel mechanistic and structural basis for inhibition of thymidylate synthesis. As essential ThyX proteins are found e.g. in Mycobacterium tuberculosis and Helicobacter pylori, our studies have also potential to pave the way towards the development of new anti-microbial compounds.
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Affiliation(s)
- Tamara Basta
- Laboratoire d'Optique et Biosciences, INSERM U696, CNRS UMR 7645, Ecole Polytechnique, Palaiseau Cedex, Palaiseau 91228, France
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Fonvielle M, Li de La Sierra-Gallay I, El-Sagheer AH, Lecerf M, Patin D, Mellal D, Mayer C, Blanot D, Gale N, Brown T, van Tilbeurgh H, Ethève-Quelquejeu M, Arthur M. The structure of FemX(Wv) in complex with a peptidyl-RNA conjugate: mechanism of aminoacyl transfer from Ala-tRNA(Ala) to peptidoglycan precursors. Angew Chem Int Ed Engl 2013; 52:7278-81. [PMID: 23744707 DOI: 10.1002/anie.201301411] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Matthieu Fonvielle
- Laboratoire de Recherche Moléculaire sur les Antibiotiques, Centre de Recherche des Cordeliers, Equipe 12, INSERM, U872, 75006 Paris, France
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Perrochia L, Crozat E, Hecker A, Zhang W, Bareille J, Collinet B, van Tilbeurgh H, Forterre P, Basta T. In vitro biosynthesis of a universal t6A tRNA modification in Archaea and Eukarya. Nucleic Acids Res 2012; 41:1953-64. [PMID: 23258706 PMCID: PMC3561968 DOI: 10.1093/nar/gks1287] [Citation(s) in RCA: 60] [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] [Indexed: 11/21/2022] Open
Abstract
N6-threonylcarbamoyladenosine (t6A) is a modified nucleotide found in all transfer RNAs (tRNAs) decoding codons starting with adenosine. Its role is to facilitate codon–anticodon pairing and to prevent frameshifting during protein synthesis. Genetic studies demonstrated that two universal proteins, Kae1/YgjD and Sua5/YrdC, are necessary for t6A synthesis in Saccharomyces cerevisiae and Escherichia coli. In Archaea and Eukarya, Kae1 is part of a conserved protein complex named kinase, endopeptidase and other proteins of small size (KEOPS), together with three proteins that have no bacterial homologues. Here, we reconstituted for the first time an in vitro system for t6A modification in Archaea and Eukarya, using purified KEOPS and Sua5. We demonstrated binding of tRNAs to archaeal KEOPS and detected two distinct adenosine triphosphate (ATP)-dependent steps occurring in the course of the synthesis. Our data, together with recent reconstitution of an in vitro bacterial system, indicated that t6A cannot be catalysed by Sua5/YrdC and Kae1/YgjD alone but requires accessory proteins that are not universal. Remarkably, we observed interdomain complementation when bacterial, archaeal and eukaryotic proteins were combined in vitro, suggesting a conserved catalytic mechanism for the biosynthesis of t6A in nature. These findings shed light on the reaction mechanism of t6A synthesis and evolution of molecular systems that promote translation fidelity in present-day cells.
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Affiliation(s)
- Ludovic Perrochia
- Institut de Génétique et Microbiologie, Université Paris-Sud, IFR115, UMR8621-CNRS, 91405 Orsay, France
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31
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Barreteau H, Tiouajni M, Graille M, Josseaume N, Bouhss A, Patin D, Blanot D, Fourgeaud M, Mainardi JL, Arthur M, van Tilbeurgh H, Mengin-Lecreulx D, Touzé T. Functional and structural characterization of PaeM, a colicin M-like bacteriocin produced by Pseudomonas aeruginosa. J Biol Chem 2012; 287:37395-405. [PMID: 22977250 DOI: 10.1074/jbc.m112.406439] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Colicin M (ColM) is the only enzymatic colicin reported to date that inhibits cell wall peptidoglycan biosynthesis. It catalyzes the specific degradation of the lipid intermediates involved in this pathway, thereby provoking lysis of susceptible Escherichia coli cells. A gene encoding a homologue of ColM was detected within the exoU-containing genomic island A carried by certain pathogenic Pseudomonas aeruginosa strains. This bacteriocin (pyocin) that we have named PaeM was crystallized, and its structure with and without an Mg(2+) ion bound was solved. In parallel, site-directed mutagenesis of conserved PaeM residues from the C-terminal domain was performed, confirming their essentiality for the protein activity both in vitro (lipid II-degrading activity) and in vivo (cytotoxicity against a susceptible P. aeruginosa strain). Although PaeM is structurally similar to ColM, the conformation of their active sites differs radically; in PaeM, residues essential for enzymatic activity and cytotoxicity converge toward a same pocket, whereas in ColM they are spread along a particularly elongated active site. We have also isolated a minimal domain corresponding to the C-terminal half of the PaeM protein and exhibiting a 70-fold higher enzymatic activity as compared with the full-length protein. This isolated domain of the PaeM bacteriocin was further shown to kill E. coli cells when addressed to the periplasm of these bacteria.
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Affiliation(s)
- Hélène Barreteau
- Université Paris-Sud, Institut de Biochimie et Biophysique Moléculaire et Cellulaire, UMR 8619, F-91405 Orsay, France
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32
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Boudes M, Lazar N, Graille M, Durand D, Gaidenko TA, Stewart V, van Tilbeurgh H. The structure of the NasR transcription antiterminator reveals a one-component system with a NIT nitrate receptor coupled to an ANTAR RNA-binding effector. Mol Microbiol 2012; 85:431-44. [PMID: 22690729 DOI: 10.1111/j.1365-2958.2012.08111.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The nitrate- and nitrite-sensing NIT domain is present in diverse signal-transduction proteins across a wide range of bacterial species. NIT domain function was established through analysis of the Klebsiella oxytoca NasR protein, which controls expression of the nasF operon encoding enzymes for nitrite and nitrate assimilation. In the presence of nitrate or nitrite, the NasR protein inhibits transcription termination at the factor-independent terminator site in the nasF operon transcribed leader region. We present here the crystal structure of the intact NasR protein in the apo state. The dimeric all-helical protein contains a large amino-terminal NIT domain that associates two four-helix bundles, and a carboxyl-terminal ANTAR (AmiR and NasR transcription antitermination regulator) domain. The analysis reveals unexpectedly that the NIT domain is structurally similar to the periplasmic input domain of the NarX two-component sensor that regulates nitrate and nitrite respiration. This similarity suggests that the NIT domain binds nitrate and nitrite between two invariant arginyl residues located on adjacent alpha helices, and results from site-specific mutagenesis showed that these residues are critical for NasR function. The resulting structural movements in the NIT domain would provoke an active configuration of the ANTAR domains necessary for specific leader mRNA binding.
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Affiliation(s)
- Marion Boudes
- IBBMC-CNRS UMR8619, Bât. 430, Université Paris-Sud, 91405 Orsay, France
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33
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Affiliation(s)
- Valley Stewart
- Department of Microbiology, University of California Davis, Davis, California, United States of America
- * E-mail: (VS); (Hvt)
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34
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Durand D, Li de la Sierra-Gallay I, Brooks MA, Thompson AW, Lazar N, Lisboa J, van Tilbeurgh H, Quevillon-Cheruel S. Expression, purification and preliminary structural analysis of Escherichia coli MatP in complex with the matS DNA site. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:638-43. [PMID: 22684059 DOI: 10.1107/s1744309112011062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 03/13/2012] [Indexed: 11/10/2022]
Abstract
The Escherichia coli chromosome is organized into four macrodomains which are found in the replication-origin region (Ori), at the terminus (Ter) and on both its sides (Right and Left). The localization of the macrodomains is subject to programmed changes during the cell cycle. The compaction of the 800 kb Ter macrodomain relies on the binding of the MatP protein to a 13 bp matS motif repeated 23 times. MatP is a small DNA-binding protein of about 18 kDa that shares homology in its C-terminal region with the ribbon-helix-helix (RHH) motifs present in regulatory DNA-binding proteins such as CopG. In order to understand the DNA-compaction mechanism of MatP at an atomic level, it was decided to study the structure of apo MatP and of the nucleoprotein complex MatP-matS by both X-ray diffraction and SAXS analysis. It was demonstrated that MatP forms dimers that bind a single matS motif. Complete native X-ray data sets were collected and phasing of the diffraction data is under way.
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Affiliation(s)
- Dominique Durand
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université de Paris-Sud, UMR8619 du CNRS, Bâtiment 430, 91405 Orsay, France
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35
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Barreteau H, El Ghachi M, Barnéoud-Arnoulet A, Sacco E, Touzé T, Duché D, Gérard F, Brooks M, Patin D, Bouhss A, Blanot D, van Tilbeurgh H, Arthur M, Lloubès R, Mengin-Lecreulx D. Characterization of colicin M and its orthologs targeting bacterial cell wall peptidoglycan biosynthesis. Microb Drug Resist 2012; 18:222-9. [PMID: 22432709 DOI: 10.1089/mdr.2011.0230] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
For a long time, colicin M was known for killing susceptible Escherichia coli cells by interfering with cell wall peptidoglycan biosynthesis, but its precise mode of action was only recently elucidated: this bacterial toxin was demonstrated to be an enzyme that catalyzes the specific degradation of peptidoglycan lipid intermediate II, thereby provoking the arrest of peptidoglycan synthesis and cell lysis. The discovery of this activity renewed the interest in this colicin and opened the way for biochemical and structural analyses of this new class of enzyme (phosphoesterase). The identification of a few orthologs produced by pathogenic strains of Pseudomonas further enlarged the field of investigation. The present article aims at reviewing recently acquired knowledge on the biology of this small family of bacteriocins.
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Affiliation(s)
- Hélène Barreteau
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris-Sud , UMR 8619 CNRS, Orsay, France
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36
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Walbott H, Machado-Pinilla R, Liger D, Blaud M, Réty S, Grozdanov PN, Godin K, van Tilbeurgh H, Varani G, Meier UT, Leulliot N. The H/ACA RNP assembly factor SHQ1 functions as an RNA mimic. Genes Dev 2011; 25:2398-408. [PMID: 22085966 DOI: 10.1101/gad.176834.111] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
SHQ1 is an essential assembly factor for H/ACA ribonucleoproteins (RNPs) required for ribosome biogenesis, pre-mRNA splicing, and telomere maintenance. SHQ1 binds dyskerin/NAP57, the catalytic subunit of human H/ACA RNPs, and this interaction is modulated by mutations causing X-linked dyskeratosis congenita. We report the crystal structure of the C-terminal domain of yeast SHQ1, Shq1p, and its complex with yeast dyskerin/NAP57, Cbf5p, lacking its catalytic domain. The C-terminal domain of Shq1p interacts with the RNA-binding domain of Cbf5p and, through structural mimicry, uses the RNA-protein-binding sites to achieve a specific protein-protein interface. We propose that Shq1p operates as a Cbf5p chaperone during RNP assembly by acting as an RNA placeholder, thereby preventing Cbf5p from nonspecific RNA binding before association with an H/ACA RNA and the other core RNP proteins.
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Affiliation(s)
- Hélène Walbott
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université de Paris-Sud, Orsay Cedex, France
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Rispal D, Henri J, van Tilbeurgh H, Graille M, Séraphin B. Structural and functional analysis of Nro1/Ett1: a protein involved in translation termination in S. cerevisiae and in O2-mediated gene control in S. pombe. RNA 2011; 17:1213-1224. [PMID: 21610214 PMCID: PMC3138559 DOI: 10.1261/rna.2697111] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 04/01/2011] [Indexed: 05/30/2023]
Abstract
In Saccharomyces cerevisiae, the putative 2-OG-Fe(II) dioxygenase Tpa1 and its partner Ett1 have been shown to impact mRNA decay and translation. Hence, inactivation of these factors was shown to influence stop codon read-though. In addition, Tpa1 represses, by an unknown mechanism, genes regulated by Hap1, a transcription factor involved in the response to levels of heme and O(2). The Schizosaccharomyces pombe orthologs of Tpa1 and Ett1, Ofd1, and its partner Nro1, respectively, have been shown to regulate the stability of the Sre1 transcription factor in response to oxygen levels. To gain insight into the function of Nro1/Ett1, we have solved the crystal structure of the S. pombe Nro1 protein deleted of its 54 N-terminal residues. Nro1 unexpectedly adopts a Tetratrico Peptide Repeat (TPR) fold, a motif often responsible for protein or peptide binding. Two ligands, a sulfate ion and an unknown molecule, interact with a cluster of highly conserved amino acids on the protein surface. Mutation of these residues demonstrates that these ligand binding sites are essential for Ett1 function in S. cerevisiae, as investigated by assaying for efficient translation termination.
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Affiliation(s)
- Delphine Rispal
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, Inserm U964, and Université de Strasbourg, Strasbourg, Illkirch F-67000, France
- Centre de Génétique Moléculaire (CGM), CNRS, F-91198 Gif-sur-Yvette Cedex, France
| | - Julien Henri
- Equipe “Fonction et Architecture des Assemblages Macromoléculaires”, IBBMC (Institut de Biochimie et Biophysique Moléculaire et Cellulaire), CNRS, UMR8619, Bat 430, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Herman van Tilbeurgh
- Equipe “Fonction et Architecture des Assemblages Macromoléculaires”, IBBMC (Institut de Biochimie et Biophysique Moléculaire et Cellulaire), CNRS, UMR8619, Bat 430, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Marc Graille
- Equipe “Fonction et Architecture des Assemblages Macromoléculaires”, IBBMC (Institut de Biochimie et Biophysique Moléculaire et Cellulaire), CNRS, UMR8619, Bat 430, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Bertrand Séraphin
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, Inserm U964, and Université de Strasbourg, Strasbourg, Illkirch F-67000, France
- Centre de Génétique Moléculaire (CGM), CNRS, F-91198 Gif-sur-Yvette Cedex, France
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Liger D, Mora L, Lazar N, Figaro S, Henri J, Scrima N, Buckingham RH, van Tilbeurgh H, Heurgué-Hamard V, Graille M. Mechanism of activation of methyltransferases involved in translation by the Trm112 'hub' protein. Nucleic Acids Res 2011; 39:6249-59. [PMID: 21478168 PMCID: PMC3152332 DOI: 10.1093/nar/gkr176] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [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: 12/02/2022] Open
Abstract
Methylation is a common modification encountered in DNA, RNA and proteins. It plays a central role in gene expression, protein function and mRNA translation. Prokaryotic and eukaryotic class I translation termination factors are methylated on the glutamine of the essential and universally conserved GGQ motif, in line with an important cellular role. In eukaryotes, this modification is performed by the Mtq2-Trm112 holoenzyme. Trm112 activates not only the Mtq2 catalytic subunit but also two other tRNA methyltransferases (Trm9 and Trm11). To understand the molecular mechanisms underlying methyltransferase activation by Trm112, we have determined the 3D structure of the Mtq2-Trm112 complex and mapped its active site. Using site-directed mutagenesis and in vivo functional experiments, we show that this structure can also serve as a model for the Trm9-Trm112 complex, supporting our hypothesis that Trm112 uses a common strategy to activate these three methyltransferases.
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Affiliation(s)
- Dominique Liger
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, IFR115, CNRS UMR 8619, Orsay Cedex F-91405, France
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39
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Daugeron MC, Lenstra TL, Frizzarin M, El Yacoubi B, Liu X, Baudin-Baillieu A, Lijnzaad P, Decourty L, Saveanu C, Jacquier A, Holstege FCP, de Crécy-Lagard V, van Tilbeurgh H, Libri D. Gcn4 misregulation reveals a direct role for the evolutionary conserved EKC/KEOPS in the t6A modification of tRNAs. Nucleic Acids Res 2011; 39:6148-60. [PMID: 21459853 PMCID: PMC3152333 DOI: 10.1093/nar/gkr178] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [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: 11/28/2022] Open
Abstract
The EKC/KEOPS complex is universally conserved in Archaea and Eukarya and has been implicated in several cellular processes, including transcription, telomere homeostasis and genomic instability. However, the molecular function of the complex has remained elusive so far. We analyzed the transcriptome of EKC/KEOPS mutants and observed a specific profile that is highly enriched in targets of the Gcn4p transcriptional activator. GCN4 expression was found to be activated at the translational level in mutants via the defective recognition of the inhibitory upstream ORFs (uORFs) present in its leader. We show that EKC/KEOPS mutants are defective for the N6-threonylcarbamoyl adenosine modification at position 37 (t6A37) of tRNAs decoding ANN codons, which affects initiation at the inhibitory uORFs and provokes Gcn4 de-repression. Structural modeling reveals similarities between Kae1 and bacterial enzymes involved in carbamoylation reactions analogous to t6A37 formation, supporting a direct role for the EKC in tRNA modification. These findings are further supported by strong genetic interactions of EKC mutants with a translation initiation factor and with threonine biosynthesis genes. Overall, our data provide a novel twist to understanding the primary function of the EKC/KEOPS and its impact on several essential cellular functions like transcription and telomere homeostasis.
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Affiliation(s)
- Marie-Claire Daugeron
- LEA Laboratory of Nuclear RNA metabolism, Centre de Génétique Moléculaire, CNRS-FRE3144, 1 av de la Terrasse, 91190 Gif sur Yvette, France
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40
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Brooks MA, Gewartowski K, Mitsiki E, Létoquart J, Pache RA, Billier Y, Bertero M, Corréa M, Czarnocki-Cieciura M, Dadlez M, Henriot V, Lazar N, Delbos L, Lebert D, Piwowarski J, Rochaix P, Böttcher B, Serrano L, Séraphin B, van Tilbeurgh H, Aloy P, Perrakis A, Dziembowski A. Systematic bioinformatics and experimental validation of yeast complexes reduces the rate of attrition during structural investigations. Structure 2011; 18:1075-82. [PMID: 20826334 DOI: 10.1016/j.str.2010.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2010] [Revised: 06/30/2010] [Accepted: 08/07/2010] [Indexed: 10/19/2022]
Abstract
For high-throughput structural studies of protein complexes of composition inferred from proteomics data, it is crucial that candidate complexes are selected accurately. Herein, we exemplify a procedure that combines a bioinformatics tool for complex selection with in vivo validation, to deliver structural results in a medium-throughout manner. We have selected a set of 20 yeast complexes, which were predicted to be feasible by either an automated bioinformatics algorithm, by manual inspection of primary data, or by literature searches. These complexes were validated with two straightforward and efficient biochemical assays, and heterologous expression technologies of complex components were then used to produce the complexes to assess their feasibility experimentally. Approximately one-half of the selected complexes were useful for structural studies, and we detail one particular success story. Our results underscore the importance of accurate target selection and validation in avoiding transient, unstable, or simply nonexistent complexes from the outset.
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Affiliation(s)
- Mark A Brooks
- IBBMC-CNRS UMR8619, IFR 115, Bât. 430, Université Paris-Sud, 91405 Orsay, France
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41
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Martin T, Lu SW, van Tilbeurgh H, Ripoll DR, Dixelius C, Turgeon BG, Debuchy R. Tracing the origin of the fungal α1 domain places its ancestor in the HMG-box superfamily: implication for fungal mating-type evolution. PLoS One 2010; 5:e15199. [PMID: 21170349 PMCID: PMC2999568 DOI: 10.1371/journal.pone.0015199] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2010] [Accepted: 10/29/2010] [Indexed: 11/19/2022] Open
Abstract
Background Fungal mating types in self-incompatible Pezizomycotina are specified by one of two alternate sequences occupying the same locus on corresponding chromosomes. One sequence is characterized by a gene encoding an HMG protein, while the hallmark of the other is a gene encoding a protein with an α1 domain showing similarity to the Matα1p protein of Saccharomyces cerevisiae. DNA-binding HMG proteins are ubiquitous and well characterized. In contrast, α1 domain proteins have limited distribution and their evolutionary origin is obscure, precluding a complete understanding of mating-type evolution in Ascomycota. Although much work has focused on the role of the S. cerevisiae Matα1p protein as a transcription factor, it has not yet been placed in any of the large families of sequence-specific DNA-binding proteins. Methodology/Principal Findings We present sequence comparisons, phylogenetic analyses, and in silico predictions of secondary and tertiary structures, which support our hypothesis that the α1 domain is related to the HMG domain. We have also characterized a new conserved motif in α1 proteins of Pezizomycotina. This motif is immediately adjacent to and downstream of the α1 domain and consists of a core sequence Y-[LMIF]-x(3)-G-[WL] embedded in a larger conserved motif. Conclusions/Significance Our data suggest that extant α1-box genes originated from an ancestral HMG gene, which confirms the current model of mating-type evolution within the fungal kingdom. We propose to incorporate α1 proteins in a new subclass of HMG proteins termed MATα_HMG.
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Affiliation(s)
- Tom Martin
- Department of Plant Biology and Forest Genetics, Uppsala Biocenter, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Shun-Wen Lu
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Herman van Tilbeurgh
- Univ Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR8619 Univ Paris-Sud CNRS, Orsay, France
| | - Daniel R. Ripoll
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Christina Dixelius
- Department of Plant Biology and Forest Genetics, Uppsala Biocenter, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - B. Gillian Turgeon
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Robert Debuchy
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR8621 Univ Paris-Sud CNRS, Orsay, France
- CNRS, Institut de Génétique et Microbiologie, UMR8621 Univ Paris-Sud CNRS, Orsay, France
- * E-mail:
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42
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Urvoas A, Guellouz A, Valerio-Lepiniec M, Graille M, Durand D, Desravines DC, van Tilbeurgh H, Desmadril M, Minard P. Design, Production and Molecular Structure of a New Family of Artificial Alpha-helicoidal Repeat Proteins (αRep) Based on Thermostable HEAT-like Repeats. J Mol Biol 2010; 404:307-27. [DOI: 10.1016/j.jmb.2010.09.048] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 09/15/2010] [Accepted: 09/21/2010] [Indexed: 01/07/2023]
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43
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Henri J, Rispal D, Bayart E, van Tilbeurgh H, Séraphin B, Graille M. Structural and functional insights into Saccharomyces cerevisiae Tpa1, a putative prolylhydroxylase influencing translation termination and transcription. J Biol Chem 2010; 285:30767-78. [PMID: 20630870 DOI: 10.1074/jbc.m110.106864] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Efficiency of translation termination relies on the specific recognition of the three stop codons by the eukaryotic translation termination factor eRF1. To date only a few proteins are known to be involved in translation termination in eukaryotes. Saccharomyces cerevisiae Tpa1, a largely conserved but uncharacterized protein, has been described to associate with a messenger ribonucleoprotein complex located at the 3' end of mRNAs that contains at least eRF1, eRF3, and Pab1. Deletion of the TPA1 gene results in a decrease of translation termination efficacy and an increase in mRNAs half-lives and longer mRNA poly(A) tails. In parallel, Schizosaccharomyces pombe Ofd1, a Tpa1 ortholog, and its partner Nro1 have been implicated in the regulation of the stability of a transcription factor that regulates genes essential for the cell response to hypoxia. To gain insight into Tpa1/Ofd1 function, we have solved the crystal structure of S. cerevisiae Tpa1 protein. This protein is composed of two equivalent domains with the double-stranded β-helix fold. The N-terminal domain displays a highly conserved active site with strong similarities with prolyl-4-hydroxylases. Further functional studies show that the integrity of Tpa1 active site as well as the presence of Yor051c/Ett1 (the S. cerevisiae Nro1 ortholog) are essential for correct translation termination. In parallel, we show that Tpa1 represses the expression of genes regulated by Hap1, a transcription factor involved in the response to levels of heme and oxygen. Altogether, our results support that Tpa1 is a putative enzyme acting as an oxygen sensor and influencing several distinct regulatory pathways.
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Affiliation(s)
- Julien Henri
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, CNRS UMR8619 Bat 430 Université Paris Sud, 91405 Orsay Cedex, France
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44
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Soler N, Marguet E, Cortez D, Desnoues N, Keller J, van Tilbeurgh H, Sezonov G, Forterre P. Two novel families of plasmids from hyperthermophilic archaea encoding new families of replication proteins. Nucleic Acids Res 2010; 38:5088-104. [PMID: 20403814 PMCID: PMC2926602 DOI: 10.1093/nar/gkq236] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Thermococcales (phylum Euryarchaeota) are model organisms for physiological and molecular studies of hyperthermophiles. Here we describe three new plasmids from Thermococcales that could provide new tools and model systems for genetic and molecular studies in Archaea. The plasmids pTN2 from Thermococcus nautilus sp. 30-1 and pP12-1 from Pyrococcus sp. 12-1 belong to the same family. They have similar size (∼12 kb) and share six genes, including homologues of genes encoded by the virus PAV1 from Pyrococcus abyssi. The plasmid pT26-2 from Thermococcus sp. 26-2 (21.5 kb), that corresponds to another plasmid family, encodes many proteins having homologues in virus-like elements integrated in several genomes of Thermococcales and Methanococcales. Our analyses confirm that viruses and plasmids are evolutionary related and co-evolve with their hosts. Whereas all plasmids previously isolated from Thermococcales replicate by the rolling circle mechanism, the three plasmids described here probably replicate by the theta mechanism. The plasmids pTN2 and pP12-1 encode a putative helicase of the SFI superfamily and a new family of DNA polymerase, whose activity was demonstrated in vitro, whereas pT26-2 encodes a putative new type of helicase. This strengthens the idea that plasmids and viruses are a reservoir of novel protein families involved in DNA replication.
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Affiliation(s)
- Nicolas Soler
- Institut de Génétique et Microbiologie, Univ Paris-Sud, 91405 Orsay Cedex, CNRS UMR 8621, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, IFR115, UMR8619-CNRS, 91405 Orsay and Université Pierre et Marie Curie, 4 place Jussieu, 75005 Paris, France
- *To whom correspondence should be addressed. Tel: +33 1 40 51 65 76; Fax: +0033 140516570;
| | - Evelyne Marguet
- Institut de Génétique et Microbiologie, Univ Paris-Sud, 91405 Orsay Cedex, CNRS UMR 8621, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, IFR115, UMR8619-CNRS, 91405 Orsay and Université Pierre et Marie Curie, 4 place Jussieu, 75005 Paris, France
| | - Diego Cortez
- Institut de Génétique et Microbiologie, Univ Paris-Sud, 91405 Orsay Cedex, CNRS UMR 8621, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, IFR115, UMR8619-CNRS, 91405 Orsay and Université Pierre et Marie Curie, 4 place Jussieu, 75005 Paris, France
| | - Nicole Desnoues
- Institut de Génétique et Microbiologie, Univ Paris-Sud, 91405 Orsay Cedex, CNRS UMR 8621, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, IFR115, UMR8619-CNRS, 91405 Orsay and Université Pierre et Marie Curie, 4 place Jussieu, 75005 Paris, France
| | - Jenny Keller
- Institut de Génétique et Microbiologie, Univ Paris-Sud, 91405 Orsay Cedex, CNRS UMR 8621, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, IFR115, UMR8619-CNRS, 91405 Orsay and Université Pierre et Marie Curie, 4 place Jussieu, 75005 Paris, France
| | - Herman van Tilbeurgh
- Institut de Génétique et Microbiologie, Univ Paris-Sud, 91405 Orsay Cedex, CNRS UMR 8621, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, IFR115, UMR8619-CNRS, 91405 Orsay and Université Pierre et Marie Curie, 4 place Jussieu, 75005 Paris, France
| | - Guennadi Sezonov
- Institut de Génétique et Microbiologie, Univ Paris-Sud, 91405 Orsay Cedex, CNRS UMR 8621, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, IFR115, UMR8619-CNRS, 91405 Orsay and Université Pierre et Marie Curie, 4 place Jussieu, 75005 Paris, France
| | - Patrick Forterre
- Institut de Génétique et Microbiologie, Univ Paris-Sud, 91405 Orsay Cedex, CNRS UMR 8621, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, IFR115, UMR8619-CNRS, 91405 Orsay and Université Pierre et Marie Curie, 4 place Jussieu, 75005 Paris, France
- *To whom correspondence should be addressed. Tel: +33 1 40 51 65 76; Fax: +0033 140516570;
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Goulet A, Spinelli S, Blangy S, van Tilbeurgh H, Leulliot N, Basta T, Prangishvili D, Cambillau C, Campanacci V. The thermo- and acido-stable ORF-99 from the archaeal virus AFV1. Protein Sci 2009; 18:1316-20. [PMID: 19472363 DOI: 10.1002/pro.122] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Acidianus Filamentous Virus 1 (AFV1), isolated from acidic hot springs, is an enveloped lipid-containing archaeal filamentous virus with a linear double-stranded DNA genome. It infects Acidianus, which is a hyperthermostable archaea growing at 85 degrees C and acidic pHs, below pH 3. AFV1-99, a protein of 99 amino acids of unknown function, has homologues in the archaeal virus families Lipothrixviridae and Rudiviridae. We determined the crystal structure of AFV1-99 at 2.05 A resolution. AFV1-99 has a new fold, is hyperthermostable (up to 95 degrees C) and resists to extreme pH (between pH 0 and 11) and to the combination of high temperature (95 degrees C) and low pH (pH 0). It possesses characteristics of hyperthermostable proteins, such as a high content of charged residues.
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Affiliation(s)
- Adeline Goulet
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d'Aix-Marseille I & II, 163 avenue de Luminy, Marseille cedex 9, France
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46
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Keller J, Leulliot N, Collinet B, Campanacci V, Cambillau C, Pranghisvilli D, van Tilbeurgh H. Crystal structure of AFV1-102, a protein from the acidianus filamentous virus 1. Protein Sci 2009; 18:845-9. [PMID: 19319936 DOI: 10.1002/pro.79] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Viruses infecting hyperthermophilic archaea have intriguing morphologies and genomic properties. The vast majority of their genes do not have homologs other than in other hyperthermophilic viruses, and the biology of these viruses is poorly understood. As part of a structural genomics project on the proteins of these viruses, we present here the structure of a 102 amino acid protein from acidianus filamentous virus 1 (AFV1-102). The structure shows that it is made of two identical motifs that have poor sequence similarity. Although no function can be proposed from structural analysis, tight binding of the gateway tag peptide in a groove between the two motifs suggests AFV1-102 is involved in protein protein interactions.
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Affiliation(s)
- Jenny Keller
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, IFR115, UMR8619-CNRS, 91405 Orsay, France
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47
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Godin KS, Walbott H, Leulliot N, van Tilbeurgh H, Varani G. The box H/ACA snoRNP assembly factor Shq1p is a chaperone protein homologous to Hsp90 cochaperones that binds to the Cbf5p enzyme. J Mol Biol 2009; 390:231-44. [PMID: 19426738 DOI: 10.1016/j.jmb.2009.04.076] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Revised: 04/27/2009] [Accepted: 04/28/2009] [Indexed: 11/15/2022]
Abstract
Box H/ACA small nucleolar (sno) ribonucleoproteins (RNPs) are responsible for the formation of pseudouridine in a variety of RNAs and are essential for ribosome biogenesis, modification of spliceosomal RNAs, and telomerase stability. A mature snoRNP has been reconstituted in vitro and is composed of a single RNA and four proteins. However, snoRNP biogenesis in vivo requires multiple factors to coordinate a complex and poorly understood assembly and maturation process. Among the factors required for snoRNP biogenesis in yeast is Shq1p, an essential protein necessary for stable expression of box H/ACA snoRNAs. We have found that Shq1p consists of two independent domains that contain casein kinase 1 phosphorylation sites. We also demonstrate that Shq1p binds the pseudourydilating enzyme Cbf5p through the C-terminal domain, in synergy with the N-terminal domain. The NMR solution structure of the N-terminal domain has striking homology to the 'Chord and Sgt1' domain of known Hsp90 cochaperones, yet Shq1p does not interact with the yeast Hsp90 homologue in vitro. Surprisingly, Shq1p has stand-alone chaperone activity in vitro. This activity is harbored by the C-terminal domain, but it is increased by the presence of the N-terminal domain. These results provide the first evidence of a specific biochemical activity for Shq1p and a direct link to the H/ACA snoRNP.
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Affiliation(s)
- Katherine S Godin
- Department of Chemistry, University of Washington, Seattle, 98195, USA
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48
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Goulet A, Spinelli S, Blangy S, van Tilbeurgh H, Leulliot N, Basta T, Prangishvili D, Cambillau C, Campanacci V. The crystal structure of ORF14 from Sulfolobus islandicus
filamentous virus. Proteins 2009; 76:1020-2. [DOI: 10.1002/prot.22448] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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49
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Leulliot N, Cladière L, Lecointe F, Durand D, Hübscher U, van Tilbeurgh H. The family X DNA polymerase from Deinococcus radiodurans adopts a non-standard extended conformation. J Biol Chem 2009; 284:11992-9. [PMID: 19251692 DOI: 10.1074/jbc.m809342200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [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
Deinococcus radiodurans is an extraordinarily radioresistant bacterium that is able to repair hundreds of radiation-induced double-stranded DNA breaks. One of the players in this pathway is an X family DNA polymerase (PolX(Dr)). Deletion of PolX(Dr) has been shown to decrease the rate of repair of double-stranded DNA breaks and increase cell sensitivity to gamma-rays. A 3'-->5' exonuclease activity that stops cutting close to DNA loops has also been demonstrated. The present crystal structure of PolX(Dr) solved at 2.46-A resolution reveals that PolX(Dr) has a novel extended conformation in stark contrast to the closed "right hand" conformation commonly observed for DNA polymerases. This extended conformation is stabilized by the C-terminal PHP domain, whose putative nuclease active site is obstructed by its interaction with the polymerase domain. The overall conformation and the presence of non standard residues in the active site of the polymerase X domain makes PolX(Dr) the founding member of a novel class of polymerases involved in DNA repair but whose detailed mode of action still remains enigmatic.
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Affiliation(s)
- Nicolas Leulliot
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université de Paris-Sud, CNRS, UMR8619, IFR115, Bât 430, Orsay 91405 Cedex, France
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50
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Hecker A, Lopreiato R, Graille M, Collinet B, Forterre P, Libri D, van Tilbeurgh H. Structure of the archaeal Kae1/Bud32 fusion protein MJ1130: a model for the eukaryotic EKC/KEOPS subcomplex. EMBO J 2009; 27:2340-51. [PMID: 19172740 DOI: 10.1038/emboj.2008.157] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The EKC/KEOPS yeast complex is involved in telomere maintenance and transcription. The Bud32p and kinase-associated endopeptidase 1 (Kaelp) components of the complex are totally conserved in eukarya and archaea. Their genes are fused in several archaeal genomes, suggesting that they physically interact. We report here the structure of the Methanocaldococcus jannaschii Kae1/Bud32 fusion protein MJ1130. Kae1 is an iron protein with an ASKHA fold and Bud32 is an atypical small RIO-type kinase. The structure MJ1130 suggests that association with Kae1 maintains the Bud32 kinase in an inactive state. We indeed show that yeast Kae1p represses the kinase activity of yeast Bud32p. Extensive conserved interactions between MjKae1 and MjBud32 suggest that Kae1p and Bud32p directly interact in both yeast and archaea. Mutations that disrupt the Kae1p/Bud32p interaction in the context of the yeast complex have dramatic effects in vivo and in vitro, similar to those observed with deletion mutations of the respective components. Direct interaction between Kae1p and Bud32p in yeast is required both for the transcription and the telomere homeostasis function of EKC/KEOPS.
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Affiliation(s)
- Arnaud Hecker
- Institut de Génétique et Microbiologie, Université Paris-Sud, IFR115 UMR8621-CNR, Orsay, France
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