1
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Mori M, Villa S, Chiarelli LR, Meneghetti F, Bellinzoni M. Structural Study of a New MbtI-Inhibitor Complex: Towards an Optimized Model for Structure-Based Drug Discovery. Pharmaceuticals (Basel) 2023; 16:1559. [PMID: 38004425 PMCID: PMC10675255 DOI: 10.3390/ph16111559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
MbtI from Mycobacterium tuberculosis (Mtb) is a Mg2+-dependent salicylate synthase, belonging to the chorismate-utilizing enzyme (CUE) family. As a fundamental player in iron acquisition, MbtI promotes the survival and pathogenicity of Mtb in the infected host. Hence, it has emerged in the last decade as an innovative, potential target for the anti-virulence therapy of tuberculosis. In this context, 5-phenylfuran-2-carboxylic acids have been identified as potent MbtI inhibitors. The first co-crystal structure of MbtI in complex with a member of this class was described in 2020, showing the enzyme adopting an open configuration. Due to the high mobility of the loop adjacent to the binding pocket, large portions of the amino acid chain were not defined in the electron density map, hindering computational efforts aimed at structure-driven ligand optimization. Herein, we report a new, high-resolution co-crystal structure of MbtI with a furan-based derivative, in which the closed configuration of the enzyme allowed tracing the entirety of the active site pocket in the presence of the bound inhibitor. Moreover, we describe a new crystal structure of MbtI in open conformation and in complex with the known inhibitor methyl-AMT, suggesting that in vitro potency is not related to the observed enzyme conformation. These findings will prove fundamental to enhance the potency of this series via rational structure-based drug-design approaches.
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Affiliation(s)
- Matteo Mori
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.M.); (S.V.); (F.M.)
| | - Stefania Villa
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.M.); (S.V.); (F.M.)
| | - Laurent R. Chiarelli
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via A. Ferrata 9, 27100 Pavia, Italy;
| | - Fiorella Meneghetti
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.M.); (S.V.); (F.M.)
| | - Marco Bellinzoni
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015 Paris, France
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2
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Yang L, Wagner T, Mechaly A, Boyko A, Bruch EM, Megrian D, Gubellini F, Alzari PM, Bellinzoni M. High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase. Nat Commun 2023; 14:4851. [PMID: 37563123 PMCID: PMC10415282 DOI: 10.1038/s41467-023-40253-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/19/2023] [Indexed: 08/12/2023] Open
Abstract
Actinobacteria possess unique ways to regulate the oxoglutarate metabolic node. Contrary to most organisms in which three enzymes compose the 2-oxoglutarate dehydrogenase complex (ODH), actinobacteria rely on a two-in-one protein (OdhA) in which both the oxidative decarboxylation and succinyl transferase steps are carried out by the same polypeptide. Here we describe high-resolution cryo-EM and crystallographic snapshots of representative enzymes from Mycobacterium smegmatis and Corynebacterium glutamicum, showing that OdhA is an 800-kDa homohexamer that assembles into a three-blade propeller shape. The obligate trimeric and dimeric states of the acyltransferase and dehydrogenase domains, respectively, are critical for maintaining the overall assembly, where both domains interact via subtle readjustments of their interfaces. Complexes obtained with substrate analogues, reaction products and allosteric regulators illustrate how these domains operate. Furthermore, we provide additional insights into the phosphorylation-dependent regulation of this enzymatic machinery by the signalling protein OdhI.
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Affiliation(s)
- Lu Yang
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
- Wuhan Institute of Biological Products Co. Ltd., Wuhan, 430207, PR China
| | - Tristan Wagner
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
- Microbial Metabolism Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, D-28359, Bremen, Germany
| | - Ariel Mechaly
- Institut Pasteur, Université Paris Cité, Plateforme de Cristallographie, F-75015, Paris, France
| | - Alexandra Boyko
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
- BostonGene, Yerevan, Armenia
| | - Eduardo M Bruch
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
- Sanofi, In vitro Biology, Integrated Drug Discovery, 350 Water St, Cambridge, MA, 02141, USA
| | - Daniela Megrian
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
| | - Francesca Gubellini
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
| | - Pedro M Alzari
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
| | - Marco Bellinzoni
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France.
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3
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Sundermeyer L, Bosco G, Gujar S, Brocker M, Baumgart M, Willbold D, Weiergräber OH, Bellinzoni M, Bott M. Characteristics of the GlnH and GlnX Signal Transduction Proteins Controlling PknG-Mediated Phosphorylation of OdhI and 2-Oxoglutarate Dehydrogenase Activity in Corynebacterium glutamicum. Microbiol Spectr 2022; 10:e0267722. [PMID: 36445153 PMCID: PMC9769921 DOI: 10.1128/spectrum.02677-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/05/2022] [Indexed: 12/03/2022] Open
Abstract
In Corynebacterium glutamicum the protein kinase PknG phosphorylates OdhI and thereby abolishes the inhibition of 2-oxoglutarate dehydrogenase activity by unphosphorylated OdhI. Our previous studies suggested that PknG activity is controlled by the periplasmic binding protein GlnH and the transmembrane protein GlnX, because ΔglnH and ΔglnX mutants showed a growth defect on glutamine similar to that of a ΔpknG mutant. We have now confirmed the involvement of GlnH and GlnX in the control of OdhI phosphorylation by analyzing the OdhI phosphorylation status and glutamate secretion in ΔglnH and ΔglnX mutants and by characterizing ΔglnX suppressor mutants. We provide evidence for GlnH being a lipoprotein and show by isothermal titration calorimetry that it binds l-aspartate and l-glutamate with moderate to low affinity, but not l-glutamine, l-asparagine, or 2-oxoglutarate. Based on a structural comparison with GlnH of Mycobacterium tuberculosis, two residues critical for the binding affinity were identified and verified. The predicted GlnX topology with four transmembrane segments and two periplasmic domains was confirmed by PhoA and LacZ fusions. A structural model of GlnX suggested that, with the exception of a poorly ordered N-terminal region, the entire protein is composed of α-helices and small loops or linkers, and it revealed similarities to other bacterial transmembrane receptors. Our results suggest that the GlnH-GlnX-PknG-OdhI-OdhA signal transduction cascade serves to adapt the flux of 2-oxoglutarate between ammonium assimilation via glutamate dehydrogenase and energy generation via the tricarboxylic acid (TCA) cycle to the availability of the amino group donors l-glutamate and l-aspartate in the environment. IMPORTANCE Actinobacteria comprise a large number of species playing important roles in biotechnology and medicine, such as Corynebacterium glutamicum, the major industrial amino acid producer, and Mycobacterium tuberculosis, the pathogen causing tuberculosis. Many actinobacteria use a signal transduction process in which the phosphorylation status of OdhI (corynebacteria) or GarA (mycobacteria) regulates the carbon flux at the 2-oxoglutarate node. Inhibition of 2-oxoglutarate dehydrogenase by unphosphorylated OdhI shifts the flux of 2-oxoglutarate from the TCA cycle toward glutamate formation and, thus, ammonium assimilation. Phosphorylation of OdhI/GarA is catalyzed by the protein kinase PknG, whose activity was proposed to be controlled by the periplasmic binding protein GlnH and the transmembrane protein GlnX. In this study, we combined genetic, biochemical, and structural modeling approaches to characterize GlnH and GlnX of C. glutamicum and confirm their roles in the GlnH-GlnX-PknG-OdhI-OdhA signal transduction cascade. These findings are relevant also to other Actinobacteria employing a similar control process.
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Affiliation(s)
- Lea Sundermeyer
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Graziella Bosco
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Srushti Gujar
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
- IBI-7: Structural Biochemistry, Institute of Biological Information Processing, Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Melanie Brocker
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Meike Baumgart
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
| | - Dieter Willbold
- IBI-7: Structural Biochemistry, Institute of Biological Information Processing, Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Oliver H. Weiergräber
- IBI-7: Structural Biochemistry, Institute of Biological Information Processing, Forschungszentrum Jülich, Jülich, Germany
| | - Marco Bellinzoni
- Institut Pasteur, Université de Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, Paris, France
| | - Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Jülich, Germany
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4
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Aleshin VA, Bunik VI, Bruch EM, Bellinzoni M. Structural Basis for the Binding of Allosteric Activators Leucine and ADP to Mammalian Glutamate Dehydrogenase. Int J Mol Sci 2022; 23:ijms231911306. [PMID: 36232607 PMCID: PMC9570180 DOI: 10.3390/ijms231911306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/26/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Glutamate dehydrogenase (GDH) plays a key role in the metabolism of glutamate, an important compound at a cross-road of carbon and nitrogen metabolism and a relevant neurotransmitter. Despite being one of the first discovered allosteric enzymes, GDH still poses challenges for structural characterization of its allosteric sites. Only the structures with ADP, and at low (3.5 Å) resolution, are available for mammalian GDH complexes with allosteric activators. Here, we aim at deciphering a structural basis for the GDH allosteric activation using bovine GDH as a model. For the first time, we report a mammalian GDH structure in a ternary complex with the activators leucine and ADP, co-crystallized with potassium ion, resolved to 2.45 Å. An improved 2.4-angstrom resolution of the GDH complex with ADP is also presented. The ternary complex with leucine and ADP differs from the binary complex with ADP by the conformation of GDH C-terminus, involved in the leucine binding and subunit interactions. The potassium site, identified in this work, may mediate interactions between the leucine and ADP binding sites. Our data provide novel insights into the mechanisms of GDH activation by leucine and ADP, linked to the enzyme regulation by (de)acetylation.
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Affiliation(s)
- Vasily A. Aleshin
- Department of Biokinetics, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Department of Biochemistry, Sechenov University, 119048 Moscow, Russia
| | - Victoria I. Bunik
- Department of Biokinetics, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Department of Biochemistry, Sechenov University, 119048 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
- Correspondence: (V.I.B.); (M.B.); Tel.: +7-495-9394484 (V.I.B.); +33-1-45688608 (M.B.)
| | - Eduardo M. Bruch
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75724 Paris, France
| | - Marco Bellinzoni
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75724 Paris, France
- Correspondence: (V.I.B.); (M.B.); Tel.: +7-495-9394484 (V.I.B.); +33-1-45688608 (M.B.)
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5
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Artiukhov AV, Kazantsev AV, Lukashev NV, Bellinzoni M, Bunik VI. Selective Inhibition of 2-Oxoglutarate and 2-Oxoadipate Dehydrogenases by the Phosphonate Analogs of Their 2-Oxo Acid Substrates. Front Chem 2021; 8:596187. [PMID: 33511099 PMCID: PMC7835950 DOI: 10.3389/fchem.2020.596187] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/10/2020] [Indexed: 11/13/2022] Open
Abstract
Phosphonate analogs of pyruvate and 2-oxoglutarate are established specific inhibitors of cognate 2-oxo acid dehydrogenases. The present work develops application of this class of compounds to specific in vivo inhibition of 2-oxoglutarate dehydrogenase (OGDH) and its isoenzyme, 2-oxoadipate dehydrogenase (OADH). The isoenzymes-enriched preparations from the rat tissues with different expression of OADH and OGDH are used to characterize their interaction with 2-oxoglutarate (OG), 2-oxoadipate (OA) and the phosphonate analogs. Despite a 100-fold difference in the isoenzymes ratio in the heart and liver, similar Michaelis saturations by OG are inherent in the enzyme preparations from these tissues (KmOG = 0.45 ± 0.06 and 0.27 ± 0.026 mM, respectively), indicating no significant contribution of OADH to the OGDH reaction, or similar affinities of the isoenzymes to OG. However, the preparations differ in the catalysis of OADH reaction. The heart preparation, where OADH/OGDH ratio is ≈ 0.01, possesses low-affinity sites to OA (KmOA = 0.55 ± 0.07 mM). The liver preparation, where OADH/OGDH ratio is ≈ 1.6, demonstrates a biphasic saturation with OA: the low-affinity sites (Km,2OA = 0.45 ± 0.12 mM) are similar to those of the heart preparation; the high-affinity sites (Km,1OA = 0.008 ± 0.001 mM), revealed in the liver preparation only, are attributed to OADH. Phosphonate analogs of C5-C7 dicarboxylic 2-oxo acids inhibit OGDH and OADH competitively to 2-oxo substrates in all sites. The high-affinity sites for OA are affected the least by the C5 analog (succinyl phosphonate) and the most by the C7 one (adipoyl phosphonate). The opposite reactivity is inherent in both the low-affinity OA-binding sites and OG-binding sites. The C6 analog (glutaryl phosphonate) does not exhibit a significant preference to either OADH or OGDH. Structural analysis of the phosphonates binding to OADH and OGDH reveals the substitution of a tyrosine residue in OGDH for a serine residue in OADH among structural determinants of the preferential binding of the bulkier ligands to OADH. The consistent kinetic and structural results expose adipoyl phosphonate as a valuable pharmacological tool for specific in vivo inhibition of the DHTKD1-encoded OADH, a new member of mammalian family of 2-oxo acid dehydrogenases, up-regulated in some cancers and associated with diabetes and obesity.
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Affiliation(s)
- Artem V Artiukhov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Department of Biokinetics, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Marco Bellinzoni
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS, Université de Paris, Paris, France
| | - Victoria I Bunik
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Department of Biokinetics, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Department of Biochemistry, Sechenov University, Moscow, Russia
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6
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Mori M, Stelitano G, Gelain A, Pini E, Chiarelli LR, Sammartino JC, Poli G, Tuccinardi T, Beretta G, Porta A, Bellinzoni M, Villa S, Meneghetti F. Shedding X-ray Light on the Role of Magnesium in the Activity of Mycobacterium tuberculosis Salicylate Synthase (MbtI) for Drug Design. J Med Chem 2020; 63:7066-7080. [PMID: 32530281 PMCID: PMC8008425 DOI: 10.1021/acs.jmedchem.0c00373] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 12/30/2022]
Abstract
![]()
The
Mg2+-dependent Mycobacterium tuberculosis salicylate synthase (MbtI) is a key enzyme involved in the biosynthesis
of siderophores. Because iron is essential for the survival and pathogenicity
of the microorganism, this protein constitutes an attractive target
for antitubercular therapy, also considering the absence of homologous
enzymes in mammals. An extension of the structure–activity
relationships of our furan-based candidates allowed us to disclose
the most potent competitive inhibitor known to date (10, Ki = 4 μM), which also proved
effective on mycobacterial cultures. By structural studies, we characterized
its unexpected Mg2+-independent binding mode. We also investigated
the role of the Mg2+ cofactor in catalysis, analyzing the
first crystal structure of the MbtI–Mg2+–salicylate
ternary complex. Overall, these results pave the way for the development
of novel antituberculars through the rational design of improved MbtI
inhibitors.
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Affiliation(s)
- Matteo Mori
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Giovanni Stelitano
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via A. Ferrata 9, 27100 Pavia, Italy
| | - Arianna Gelain
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Elena Pini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Laurent R Chiarelli
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via A. Ferrata 9, 27100 Pavia, Italy
| | - José C Sammartino
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via A. Ferrata 9, 27100 Pavia, Italy
| | - Giulio Poli
- Dipartimento di Farmacia, Università di Pisa, via Bonanno Pisano 6, 56126 Pisa, Italy
| | - Tiziano Tuccinardi
- Dipartimento di Farmacia, Università di Pisa, via Bonanno Pisano 6, 56126 Pisa, Italy.,Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Giangiacomo Beretta
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, via G. Celoria 2, 20133 Milano, Italy
| | - Alessio Porta
- Dipartimento di Chimica, Università degli Studi di Pavia, via T. Taramelli 12, 27100 Pavia, Italy
| | - Marco Bellinzoni
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS, Université de Paris, F-75015 Paris, France
| | - Stefania Villa
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Fiorella Meneghetti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
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7
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Wagner T, Boyko A, Alzari PM, Bunik VI, Bellinzoni M. Conformational transitions in the active site of mycobacterial 2-oxoglutarate dehydrogenase upon binding phosphonate analogues of 2-oxoglutarate: From a Michaelis-like complex to ThDP adducts. J Struct Biol 2019; 208:182-190. [PMID: 31476368 DOI: 10.1016/j.jsb.2019.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/22/2019] [Accepted: 08/29/2019] [Indexed: 11/17/2022]
Abstract
Mycobacterial KGD, the thiamine diphosphate (ThDP)-dependent E1o component of the 2-oxoglutarate dehydrogenase complex (OGDHC), is known to undergo significant conformational changes during catalysis with two distinct conformational states, previously named as the early and late state. In this work, we employ two phosphonate analogues of 2-oxoglutarate (OG), i.e. succinyl phosphonate (SP) and phosphono ethyl succinyl phosphonate (PESP), as tools to isolate the first catalytic steps and understand the significance of conformational transitions for the enzyme regulation. The kinetics showed a more efficient inhibition of mycobacterial E1o by SP (Ki 0.043 ± 0.013 mM) than PESP (Ki 0.88 ± 0.28 mM), consistent with the different circular dichroism spectra of the corresponding complexes. PESP allowed us to get crystallographic snapshots of the Michaelis-like complex, the first one for 2-oxo acid dehydrogenases, followed by the covalent adduction of the inhibitor to ThDP, mimicking the pre-decarboxylation complex. In addition, covalent ThDP-phosphonate complexes obtained with both compounds by co-crystallization were in the late conformational state, probably corresponding to slowly dissociating enzyme-inhibitor complexes. We discuss the relevance of these findings in terms of regulatory features of the mycobacterial E1o enzymes, and in the perspective of developing tools for species-specific metabolic regulation.
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Affiliation(s)
- Tristan Wagner
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS, Université de Paris, F-75724 Paris, France
| | - Alexandra Boyko
- A.N. Belozersky Institute of Physicochemical Biology and Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russia
| | - Pedro M Alzari
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS, Université de Paris, F-75724 Paris, France
| | - Victoria I Bunik
- A.N. Belozersky Institute of Physicochemical Biology and Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russia
| | - Marco Bellinzoni
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS, Université de Paris, F-75724 Paris, France.
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8
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Bellinzoni M, Wehenkel AM, Durán R, Alzari PM. Novel mechanistic insights into physiological signaling pathways mediated by mycobacterial Ser/Thr protein kinases. Microbes Infect 2019; 21:222-229. [PMID: 31254628 DOI: 10.1016/j.micinf.2019.06.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 12/11/2022]
Abstract
Protein phosphorylation is known to be one of the keystones of signal sensing and transduction in all living organisms. Once thought to be essentially confined to the eukaryotic kingdoms, reversible phosphorylation on serine, threonine and tyrosine residues, has now been shown to play a major role in many prokaryotes, where the number of Ser/Thr protein kinases (STPKs) equals or even exceeds that of two component systems. Mycobacterium tuberculosis, the etiological agent of tuberculosis, is one of the most studied organisms for the role of STPK-mediated signaling in bacteria. Driven by the interest and tractability of these enzymes as potential therapeutic targets, extensive studies revealed the remarkable conservation of protein kinases and their cognate phosphatases across evolution, and their involvement in bacterial physiology and virulence. Here, we present an overview of the current knowledge of mycobacterial STPKs structures and kinase activation mechanisms, and we then focus on PknB and PknG, two well-characterized STPKs that are essential for the intracellular survival of the bacillus. We summarize the mechanistic evidence that links PknB to the regulation of peptidoglycan synthesis in cell division and morphogenesis, and the major findings that establishes PknG as a master regulator of central carbon and nitrogen metabolism. Two decades after the discovery of STPKs in M. tuberculosis, the emerging landscape of O-phosphosignaling is starting to unveil how eukaryotic-like kinases can be engaged in unique, non-eukaryotic-like, signaling mechanisms in mycobacteria.
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Affiliation(s)
- Marco Bellinzoni
- Unit of Structural Microbiology, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528 & Université Paris Diderot, 25 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Anne Marie Wehenkel
- Unit of Structural Microbiology, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528 & Université Paris Diderot, 25 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Rosario Durán
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Mataojo 2020, Montevideo 11400, Uruguay
| | - Pedro M Alzari
- Unit of Structural Microbiology, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528 & Université Paris Diderot, 25 rue du Docteur Roux, 75724 Paris cedex 15, France.
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9
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Wagner T, André-Leroux G, Hindie V, Barilone N, Lisa MN, Hoos S, Raynal B, Vulliez-Le Normand B, O'Hare HM, Bellinzoni M, Alzari PM. Structural insights into the functional versatility of an FHA domain protein in mycobacterial signaling. Sci Signal 2019; 12:12/580/eaav9504. [PMID: 31064884 DOI: 10.1126/scisignal.aav9504] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Forkhead-associated (FHA) domains are modules that bind to phosphothreonine (pThr) residues in signaling cascades. The FHA-containing mycobacterial protein GarA is a central element of a phosphorylation-dependent signaling pathway that redirects metabolic flux in response to amino acid starvation or cell growth requirements. GarA acts as a phosphorylation-dependent ON/OFF molecular switch. In its nonphosphorylated ON state, the GarA FHA domain engages in phosphorylation-independent interactions with various metabolic enzymes that orchestrate nitrogen flow, such as 2-oxoglutarate decarboxylase (KGD). However, phosphorylation at the GarA N-terminal region by the protein kinase PknB or PknG triggers autoinhibition through the intramolecular association of the N-terminal domain with the FHA domain, thus blocking all downstream interactions. To investigate these different FHA binding modes, we solved the crystal structures of the mycobacterial upstream (phosphorylation-dependent) complex PknB-GarA and the downstream (phosphorylation-independent) complex GarA-KGD. Our results show that the phosphorylated activation loop of PknB serves as a docking site to recruit GarA through canonical FHA-pThr interactions. However, the same GarA FHA-binding pocket targets an allosteric site on nonphosphorylated KGD, where a key element of recognition is a phosphomimetic aspartate. Further enzymatic and mutagenesis studies revealed that GarA acted as a dynamic allosteric inhibitor of KGD by preventing crucial motions in KGD that are necessary for catalysis. Our results provide evidence for physiological phosphomimetics, supporting numerous mutagenesis studies using such approaches, and illustrate how evolution can shape a single FHA-binding pocket to specifically interact with multiple phosphorylated and nonphosphorylated protein partners.
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Affiliation(s)
- Tristan Wagner
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Gwénaëlle André-Leroux
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Valérie Hindie
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Nathalie Barilone
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - María-Natalia Lisa
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Sylviane Hoos
- Institut Pasteur, Plateforme de Biophysique Moléculaire, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Bertrand Raynal
- Institut Pasteur, Plateforme de Biophysique Moléculaire, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Brigitte Vulliez-Le Normand
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Helen M O'Hare
- Leicester Tuberculosis Research Group (LTBRG) and Leicester Institute of Structural and Chemical Biology (LISCB), Department of Respiratory Science & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Marco Bellinzoni
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France.
| | - Pedro M Alzari
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France.
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10
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Bellinzoni M, Wehenkel AM, Durán R, Alzari PM. Novel mechanistic insights into physiological signaling pathways mediated by mycobacterial Ser/Thr protein kinases. Genes Immun 2019; 20:383-393. [DOI: 10.1038/s41435-019-0069-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 12/16/2022]
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11
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Chiarelli LR, Mori M, Beretta G, Gelain A, Pini E, Sammartino JC, Stelitano G, Barlocco D, Costantino L, Lapillo M, Poli G, Caligiuri I, Rizzolio F, Bellinzoni M, Tuccinardi T, Villa S, Meneghetti F. New insight into structure-activity of furan-based salicylate synthase (MbtI) inhibitors as potential antitubercular agents. J Enzyme Inhib Med Chem 2019; 34:823-828. [PMID: 30889995 PMCID: PMC6427685 DOI: 10.1080/14756366.2019.1589462] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 02/08/2023] Open
Abstract
Starting from the analysis of the hypothetical binding mode of our previous furan-based hit (I), we successfully achieved our objective to replace the nitro moiety, leading to the disclosure of a new lead exhibiting a strong activity against MbtI. Our best candidate 1 h displayed a Ki of 8.8 µM and its antimycobacterial activity (MIC99 = 250 µM) is conceivably related to mycobactin biosynthesis inhibition. These results support the hypothesis that 5-phenylfuran-2-carboxylic derivatives are a promising class of MbtI inhibitors.
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Affiliation(s)
- Laurent R Chiarelli
- a Department of Biology and Biotechnology "L Spallanzani" , University of Pavia , Pavia , Italy
| | - Matteo Mori
- b Department of Pharmaceutical Sciences , University of Milano , Milano , Italy
| | - Giangiacomo Beretta
- c Department of Environmental Science and Policy , University of Milano , Milano , Italy
| | - Arianna Gelain
- b Department of Pharmaceutical Sciences , University of Milano , Milano , Italy
| | - Elena Pini
- b Department of Pharmaceutical Sciences , University of Milano , Milano , Italy
| | - Josè Camilla Sammartino
- a Department of Biology and Biotechnology "L Spallanzani" , University of Pavia , Pavia , Italy
| | - Giovanni Stelitano
- a Department of Biology and Biotechnology "L Spallanzani" , University of Pavia , Pavia , Italy
| | - Daniela Barlocco
- b Department of Pharmaceutical Sciences , University of Milano , Milano , Italy
| | - Luca Costantino
- d Department of Life Sciences , University of Modena e Reggio Emilia , Modena , Italy
| | | | - Giulio Poli
- e Department of Pharmacy , University of Pisa , Pisa , Italy
| | - Isabella Caligiuri
- f Pathology Unit, Department of Molecular Biology and Translational Research , National Cancer Institute and Center for Molecular Biomedicine , Aviano , Italy
| | - Flavio Rizzolio
- f Pathology Unit, Department of Molecular Biology and Translational Research , National Cancer Institute and Center for Molecular Biomedicine , Aviano , Italy.,g Department of Molecular Science and Nanosystems , Ca' Foscari University of Venezia , Venezia-Mestre , Italy
| | | | | | - Stefania Villa
- b Department of Pharmaceutical Sciences , University of Milano , Milano , Italy
| | - Fiorella Meneghetti
- b Department of Pharmaceutical Sciences , University of Milano , Milano , Italy
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12
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Mercati O, Huguet G, Danckaert A, André-Leroux G, Maruani A, Bellinzoni M, Rolland T, Gouder L, Mathieu A, Buratti J, Amsellem F, Benabou M, Van-Gils J, Beggiato A, Konyukh M, Bourgeois JP, Gazzellone MJ, Yuen RKC, Walker S, Delépine M, Boland A, Régnault B, Francois M, Van Den Abbeele T, Mosca-Boidron AL, Faivre L, Shimoda Y, Watanabe K, Bonneau D, Rastam M, Leboyer M, Scherer SW, Gillberg C, Delorme R, Cloëz-Tayarani I, Bourgeron T. CNTN6 mutations are risk factors for abnormal auditory sensory perception in autism spectrum disorders. Mol Psychiatry 2017; 22:625-633. [PMID: 27166760 PMCID: PMC5378808 DOI: 10.1038/mp.2016.61] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 02/12/2016] [Accepted: 02/17/2016] [Indexed: 12/11/2022]
Abstract
Contactin genes CNTN5 and CNTN6 code for neuronal cell adhesion molecules that promote neurite outgrowth in sensory-motor neuronal pathways. Mutations of CNTN5 and CNTN6 have previously been reported in individuals with autism spectrum disorders (ASDs), but very little is known on their prevalence and clinical impact. In this study, we identified CNTN5 and CNTN6 deleterious variants in individuals with ASD. Among the carriers, a girl with ASD and attention-deficit/hyperactivity disorder was carrying five copies of CNTN5. For CNTN6, both deletions (6/1534 ASD vs 1/8936 controls; P=0.00006) and private coding sequence variants (18/501 ASD vs 535/33480 controls; P=0.0005) were enriched in individuals with ASD. Among the rare CNTN6 variants, two deletions were transmitted by fathers diagnosed with ASD, one stop mutation CNTN6W923X was transmitted by a mother to her two sons with ASD and one variant CNTN6P770L was found de novo in a boy with ASD. Clinical investigations of the patients carrying CNTN5 or CNTN6 variants showed that they were hypersensitive to sounds (a condition called hyperacusis) and displayed changes in wave latency within the auditory pathway. These results reinforce the hypothesis of abnormal neuronal connectivity in the pathophysiology of ASD and shed new light on the genes that increase risk for abnormal sensory perception in ASD.
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Affiliation(s)
- O Mercati
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - G Huguet
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - A Danckaert
- Imagopole, Citech, Institut Pasteur, Paris, France
| | - G André-Leroux
- Institut Pasteur, Unité de Microbiologie Structurale, Paris, France
- CNRS UMR 3528, Paris, France
- INRA, Unité MaIAGE, UR1404, Jouy-en-Josas, France
| | - A Maruani
- Assistance Publique-Hôpitaux de Paris, Child and Adolescent Psychiatry Department, Robert Debré Hospital, Paris, France
| | - M Bellinzoni
- Institut Pasteur, Unité de Microbiologie Structurale, Paris, France
- CNRS UMR 3528, Paris, France
| | - T Rolland
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - L Gouder
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - A Mathieu
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - J Buratti
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - F Amsellem
- Assistance Publique-Hôpitaux de Paris, Child and Adolescent Psychiatry Department, Robert Debré Hospital, Paris, France
| | - M Benabou
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - J Van-Gils
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - A Beggiato
- Assistance Publique-Hôpitaux de Paris, Child and Adolescent Psychiatry Department, Robert Debré Hospital, Paris, France
| | - M Konyukh
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - J-P Bourgeois
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - M J Gazzellone
- Centre for Applied Genomics, Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - R K C Yuen
- Centre for Applied Genomics, Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - S Walker
- Centre for Applied Genomics, Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - M Delépine
- Centre National de Génotypage, Evry, France
| | - A Boland
- Centre National de Génotypage, Evry, France
| | - B Régnault
- Eukaryote Genotyping Platform, Genopole, Institut Pasteur, Paris, France
| | - M Francois
- Assistance Publique-Hôpitaux de Paris, ENT and Head and Neck Surgery Department, Robert Debré Hospital, Paris-VII University, Paris, France
| | - T Van Den Abbeele
- Assistance Publique-Hôpitaux de Paris, ENT and Head and Neck Surgery Department, Robert Debré Hospital, Paris-VII University, Paris, France
| | - A L Mosca-Boidron
- Département de Génétique, CHU Dijon et Université de Bourgogne, Dijon, France
| | - L Faivre
- Département de Génétique, CHU Dijon et Université de Bourgogne, Dijon, France
| | - Y Shimoda
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - K Watanabe
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - D Bonneau
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire, Angers, France
| | - M Rastam
- Department of Clinical Sciences in Lund, Lund University, Lund, Sweden
- Gillberg Neuropsychiatry Centre, University of Gothenburg, Gothenburg, Sweden
| | - M Leboyer
- INSERM U955, Psychiatrie Translationnelle, Créteil, France
- Université Paris Est, Faculté de Médecine, Créteil, France
- Assistance Publique-Hôpitaux de Paris, DHU Pe-PSY, H. Mondor Hospital, Department of Psychiatry, Créteil, France
- FondaMental Foundation, Créteil, France
| | - S W Scherer
- Centre for Applied Genomics, Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
- McLaughlin Centre, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - C Gillberg
- Gillberg Neuropsychiatry Centre, University of Gothenburg, Gothenburg, Sweden
| | - R Delorme
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
- Assistance Publique-Hôpitaux de Paris, Child and Adolescent Psychiatry Department, Robert Debré Hospital, Paris, France
| | - I Cloëz-Tayarani
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - T Bourgeron
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, France
- CNRS UMR 3571: Genes, Synapses and Cognition, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
- Gillberg Neuropsychiatry Centre, University of Gothenburg, Gothenburg, Sweden
- FondaMental Foundation, Créteil, France
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13
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Lisa MN, Wagner T, Alexandre M, Barilone N, Raynal B, Alzari PM, Bellinzoni M. The crystal structure of PknI from Mycobacterium tuberculosis shows an inactive, pseudokinase-like conformation. FEBS J 2017; 284:602-614. [PMID: 28054744 DOI: 10.1111/febs.14003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 12/10/2016] [Accepted: 01/04/2017] [Indexed: 11/27/2022]
Abstract
Eukaryotic-like Ser/Thr protein kinases (ePKs) have been identified in many bacterial species, where they are known to mediate signalling mechanisms that share several features with their eukaryotic counterparts. In Mycobacterium tuberculosis, PknI is one of the 11 predicted ePKs and it has been related to bacterial virulence. In order to better understand the molecular basis of its role in mycobacterial signalling, we solved the crystal structure of the PknI cytoplasmic domain. We found that even though PknI possesses most conserved elements characteristic of Hanks-type kinases, it is degraded in several motifs that are essential for the ePKs catalytic activity. Most notably, PknI presents a remarkably short activation segment lacking a peptide-substrate binding site. Consistent with this observation and similar to earlier findings for eukaryotic pseudokinases, no kinase activity was detected for the catalytic domain of PknI, against different substrates and in various experimental conditions. Based on these results, we conclude that PknI may rely on unconventional mechanism(s) for kinase activity and/or it could play alternative role(s) in mycobacterial signalling. DATABASE Atomic coordinates and structure factors for the catalytic domain of M. tuberculosis PknI are in the Protein Data Bank under the accession codes 5M06 (wild-type PknI + ADP), 5M07 (PknI_C20A), 5M08 (PknI_C20A_R136A) and 5M09 (PknI_C20A_R136N).
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Affiliation(s)
- María-Natalia Lisa
- Unité de Microbiologie Structurale, Institut Pasteur, Paris Cedex, France.,CNRS UMR 3528 'Biologie structurale des processus cellulaires et maladies infectieuses', Institut Pasteur, Paris Cedex, France.,Sorbonne Paris Cité, Microbiologie Structurale, Université Paris Diderot, France
| | - Tristan Wagner
- Unité de Microbiologie Structurale, Institut Pasteur, Paris Cedex, France.,CNRS UMR 3528 'Biologie structurale des processus cellulaires et maladies infectieuses', Institut Pasteur, Paris Cedex, France.,Sorbonne Paris Cité, Microbiologie Structurale, Université Paris Diderot, France
| | - Matthieu Alexandre
- Unité de Microbiologie Structurale, Institut Pasteur, Paris Cedex, France.,CNRS UMR 3528 'Biologie structurale des processus cellulaires et maladies infectieuses', Institut Pasteur, Paris Cedex, France.,Sorbonne Paris Cité, Microbiologie Structurale, Université Paris Diderot, France
| | - Nathalie Barilone
- Unité de Microbiologie Structurale, Institut Pasteur, Paris Cedex, France.,CNRS UMR 3528 'Biologie structurale des processus cellulaires et maladies infectieuses', Institut Pasteur, Paris Cedex, France.,Sorbonne Paris Cité, Microbiologie Structurale, Université Paris Diderot, France
| | - Bertrand Raynal
- CNRS UMR 3528 'Biologie structurale des processus cellulaires et maladies infectieuses', Institut Pasteur, Paris Cedex, France.,Plateforme de Biophysique Moléculaire, Institut Pasteur, Paris Cedex, France
| | - Pedro M Alzari
- Unité de Microbiologie Structurale, Institut Pasteur, Paris Cedex, France.,CNRS UMR 3528 'Biologie structurale des processus cellulaires et maladies infectieuses', Institut Pasteur, Paris Cedex, France.,Sorbonne Paris Cité, Microbiologie Structurale, Université Paris Diderot, France
| | - Marco Bellinzoni
- Unité de Microbiologie Structurale, Institut Pasteur, Paris Cedex, France.,CNRS UMR 3528 'Biologie structurale des processus cellulaires et maladies infectieuses', Institut Pasteur, Paris Cedex, France.,Sorbonne Paris Cité, Microbiologie Structurale, Université Paris Diderot, France
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14
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Le NH, Molle V, Eynard N, Miras M, Stella A, Bardou F, Galandrin S, Guillet V, André-Leroux G, Bellinzoni M, Alzari P, Mourey L, Burlet-Schiltz O, Daffé M, Marrakchi H. Ser/Thr Phosphorylation Regulates the Fatty Acyl-AMP Ligase Activity of FadD32, an Essential Enzyme in Mycolic Acid Biosynthesis. J Biol Chem 2016; 291:22793-22805. [PMID: 27590338 DOI: 10.1074/jbc.m116.748053] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 08/31/2016] [Indexed: 12/21/2022] Open
Abstract
Mycolic acids are essential components of the mycobacterial cell envelope, and their biosynthetic pathway is a well known source of antituberculous drug targets. Among the promising new targets in the pathway, FadD32 is an essential enzyme required for the activation of the long meromycolic chain of mycolic acids and is essential for mycobacterial growth. Following the in-depth biochemical, biophysical, and structural characterization of FadD32, we investigated its putative regulation via post-translational modifications. Comparison of the fatty acyl-AMP ligase activity between phosphorylated and dephosphorylated FadD32 isoforms showed that the native protein is phosphorylated by serine/threonine protein kinases and that this phosphorylation induced a significant loss of activity. Mass spectrometry analysis of the native protein confirmed the post-translational modifications and identified Thr-552 as the phosphosite. Phosphoablative and phosphomimetic FadD32 mutant proteins confirmed both the position and the importance of the modification and its correlation with the negative regulation of FadD32 activity. Investigation of the mycolic acid condensation reaction catalyzed by Pks13, involving FadD32 as a partner, showed that FadD32 phosphorylation also impacts the condensation activity. Altogether, our results bring to light FadD32 phosphorylation by serine/threonine protein kinases and its correlation with the enzyme-negative regulation, thus shedding a new horizon on the mycolic acid biosynthesis modulation and possible inhibition strategies for this promising drug target.
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Affiliation(s)
- Nguyen-Hung Le
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Virginie Molle
- the Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques, Université de Montpellier, CNRS UMR 5235, Place Eugène Bataillon, 34095 Montpellier Cedex 05, and
| | - Nathalie Eynard
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Mathieu Miras
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Alexandre Stella
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Fabienne Bardou
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Ségolène Galandrin
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Valérie Guillet
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Gwenaëlle André-Leroux
- the Institut Pasteur, Unité de Microbiologie Structurale, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Marco Bellinzoni
- the Institut Pasteur, Unité de Microbiologie Structurale, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Pedro Alzari
- the Institut Pasteur, Unité de Microbiologie Structurale, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Lionel Mourey
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Odile Burlet-Schiltz
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Mamadou Daffé
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS,
| | - Hedia Marrakchi
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS,
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15
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Mori G, Chiarelli LR, Esposito M, Makarov V, Bellinzoni M, Hartkoorn RC, Degiacomi G, Boldrin F, Ekins S, de Jesus Lopes Ribeiro AL, Marino LB, Centárová I, Svetlíková Z, Blaško J, Kazakova E, Lepioshkin A, Barilone N, Zanoni G, Porta A, Fondi M, Fani R, Baulard AR, Mikušová K, Alzari PM, Manganelli R, de Carvalho LPS, Riccardi G, Cole ST, Pasca MR. Thiophenecarboxamide Derivatives Activated by EthA Kill Mycobacterium tuberculosis by Inhibiting the CTP Synthetase PyrG. ACTA ACUST UNITED AC 2015; 22:917-27. [PMID: 26097035 PMCID: PMC4521081 DOI: 10.1016/j.chembiol.2015.05.016] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 05/25/2015] [Accepted: 05/30/2015] [Indexed: 11/06/2022]
Abstract
To combat the emergence of drug-resistant strains of Mycobacterium tuberculosis, new antitubercular agents and novel drug targets are needed. Phenotypic screening of a library of 594 hit compounds uncovered two leads that were active against M. tuberculosis in its replicating, non-replicating, and intracellular states: compounds 7947882 (5-methyl-N-(4-nitrophenyl)thiophene-2-carboxamide) and 7904688 (3-phenyl-N-[(4-piperidin-1-ylphenyl)carbamothioyl]propanamide). Mutants resistant to both compounds harbored mutations in ethA (rv3854c), the gene encoding the monooxygenase EthA, and/or in pyrG (rv1699) coding for the CTP synthetase, PyrG. Biochemical investigations demonstrated that EthA is responsible for the activation of the compounds, and by mass spectrometry we identified the active metabolite of 7947882, which directly inhibits PyrG activity. Metabolomic studies revealed that pharmacological inhibition of PyrG strongly perturbs DNA and RNA biosynthesis, and other metabolic processes requiring nucleotides. Finally, the crystal structure of PyrG was solved, paving the way for rational drug design with this newly validated drug target. Two compounds activated by EthA kill M. tuberculosis through PyrG inhibition EthA metabolite is active against PyrG and M. tuberculosis growth Definition of the mechanism of activation and validation of PyrG as a new drug target
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Affiliation(s)
- Giorgia Mori
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Marta Esposito
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Vadim Makarov
- A. N. Bakh Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia
| | - Marco Bellinzoni
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS-UMR3528, Université Paris Diderot, Sorbonne Paris Cité, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Ruben C Hartkoorn
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | - Giulia Degiacomi
- Department of Molecular Medicine, University of Padova, 35128 Padua, Italy
| | - Francesca Boldrin
- Department of Molecular Medicine, University of Padova, 35128 Padua, Italy
| | - Sean Ekins
- Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, CA 94010, USA
| | | | - Leonardo B Marino
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK; Faculty of Pharmaceutical Sciences, UNESP - Univ Estadual Paulista, Araraquara, São Paulo 14801-902, Brazil
| | - Ivana Centárová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 84215 Bratislava, Slovakia
| | - Zuzana Svetlíková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 84215 Bratislava, Slovakia
| | - Jaroslav Blaško
- Institute of Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 84215 Bratislava, Slovak Republic
| | - Elena Kazakova
- A. N. Bakh Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia
| | - Alexander Lepioshkin
- A. N. Bakh Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia
| | - Nathalie Barilone
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS-UMR3528, Université Paris Diderot, Sorbonne Paris Cité, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Giuseppe Zanoni
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Alessio Porta
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Marco Fondi
- Department of Biology, University of Florence, Sesto Fiorentino, Florence 50019, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Sesto Fiorentino, Florence 50019, Italy
| | - Alain R Baulard
- Institut Pasteur de Lille, Center for Infection and Immunity, 59019 Lille, France
| | - Katarína Mikušová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 84215 Bratislava, Slovakia
| | - Pedro M Alzari
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS-UMR3528, Université Paris Diderot, Sorbonne Paris Cité, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | | | | | - Giovanna Riccardi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Stewart T Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland.
| | - Maria Rosalia Pasca
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy.
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16
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Wagner T, Alexandre M, Duran R, Barilone N, Wehenkel A, Alzari PM, Bellinzoni M. The crystal structure of the catalytic domain of the ser/thr kinase PknA from M. tuberculosis
shows an Src-like autoinhibited conformation. Proteins 2015; 83:982-8. [DOI: 10.1002/prot.24754] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 12/12/2014] [Accepted: 12/23/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Tristan Wagner
- Institut Pasteur; Unité De Microbiologie Structurale; Paris 75724 France
- CNRS UMR 3528; Paris 75724 France
- Université Paris Diderot, Sorbonne Paris Cité; Microbiologie Structurale; Paris 75724 France
| | - Matthieu Alexandre
- Institut Pasteur; Unité De Microbiologie Structurale; Paris 75724 France
- CNRS UMR 3528; Paris 75724 France
- Université Paris Diderot, Sorbonne Paris Cité; Microbiologie Structurale; Paris 75724 France
| | - Rosario Duran
- Unidad De Bioquímica Y Proteómica Analíticas; Institut Pasteur De Montevideo; Uruguay
- Unidad De Bioquímica Y Proteómica Analíticas; Instituto De Investigaciones Biológicas Clemente Estable; Ministerio De Educación Y Cultura; Uruguay
| | - Nathalie Barilone
- Institut Pasteur; Unité De Microbiologie Structurale; Paris 75724 France
- CNRS UMR 3528; Paris 75724 France
- Université Paris Diderot, Sorbonne Paris Cité; Microbiologie Structurale; Paris 75724 France
| | - Annemarie Wehenkel
- Institut Pasteur; Unité De Microbiologie Structurale; Paris 75724 France
- CNRS UMR 3528; Paris 75724 France
- Université Paris Diderot, Sorbonne Paris Cité; Microbiologie Structurale; Paris 75724 France
| | - Pedro M. Alzari
- Institut Pasteur; Unité De Microbiologie Structurale; Paris 75724 France
- CNRS UMR 3528; Paris 75724 France
- Université Paris Diderot, Sorbonne Paris Cité; Microbiologie Structurale; Paris 75724 France
| | - Marco Bellinzoni
- Institut Pasteur; Unité De Microbiologie Structurale; Paris 75724 France
- CNRS UMR 3528; Paris 75724 France
- Université Paris Diderot, Sorbonne Paris Cité; Microbiologie Structurale; Paris 75724 France
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17
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Bellinzoni M, Haouz A, Miras I, Magnet S, André-Leroux G, Mukherjee R, Shepard W, Cole ST, Alzari PM. Structural studies suggest a peptidoglycan hydrolase function for the Mycobacterium tuberculosis Tat-secreted protein Rv2525c. J Struct Biol 2014; 188:156-64. [PMID: 25260828 DOI: 10.1016/j.jsb.2014.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [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: 06/05/2014] [Revised: 08/08/2014] [Accepted: 09/16/2014] [Indexed: 11/18/2022]
Abstract
Among the few proteins shown to be secreted by the Tat system in Mycobacterium tuberculosis, Rv2525c is of particular interest, since its gene is conserved in the minimal genome of Mycobacterium leprae. Previous evidence linked this protein to cell wall metabolism and sensitivity to β-lactams. We describe here the crystal structure of Rv2525c that shows a TIM barrel-like fold characteristic of glycoside hydrolases of the GH25 family, which includes prokaryotic and phage-encoded peptidoglycan hydrolases. Structural comparison with other members of this family combined with substrate docking suggest that, although the 'neighbouring group' catalytic mechanism proposed for this family still appears as the most plausible, the identity of residues involved in catalysis in GH25 hydrolases might need to be revised.
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Affiliation(s)
- Marco Bellinzoni
- Institut Pasteur, Unité de Microbiologie Structurale and CNRS-UMR3528, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France.
| | - Ahmed Haouz
- Institut Pasteur, Plateforme de Cristallographie (CNRS-UMR3528), 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Isabelle Miras
- Institut Pasteur, Plateforme de Cristallographie (CNRS-UMR3528), 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Sophie Magnet
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | - Gwénaëlle André-Leroux
- Institut Pasteur, Unité de Microbiologie Structurale and CNRS-UMR3528, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France; Unité Mathématique, Informatique et Génome (MIG), INRA, Domaine de Vilvert, 78352 Jouy en Josas Cedex, France
| | - Raju Mukherjee
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | - William Shepard
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, 91192 Gif-sur-Yvette Cedex, France
| | - Stewart T Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | - Pedro M Alzari
- Institut Pasteur, Unité de Microbiologie Structurale and CNRS-UMR3528, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
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18
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Ventura M, Rieck B, Boldrin F, Degiacomi G, Bellinzoni M, Barilone N, Alzaidi F, Alzari PM, Manganelli R, O'Hare HM. GarA is an essential regulator of metabolism in Mycobacterium tuberculosis. Mol Microbiol 2013; 90:356-66. [PMID: 23962235 DOI: 10.1111/mmi.12368] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2013] [Indexed: 01/16/2023]
Abstract
Alpha-ketoglutarate is a key metabolic intermediate at the crossroads of carbon and nitrogen metabolism, whose fate is tightly regulated. In mycobacteria the protein GarA regulates the tricarboxylic acid cycle and glutamate synthesis by direct binding and regulation of three enzymes that use α-ketoglutarate. GarA, in turn, is thought to be regulated via phosphorylation by protein kinase G and other kinases. We have investigated the requirement for GarA for metabolic regulation during growth in vitro and in macrophages. GarA was found to be essential to Mycobacterium tuberculosis, but dispensable in non-pathogenic Mycobacterium smegmatis. Disruption of garA caused a distinctive, nutrient-dependent phenotype, fitting with its proposed role in regulating glutamate metabolism. The data underline the importance of the TCA cycle and the balance with glutamate synthesis in M. tuberculosis and reveal vulnerability to disruption of these pathways.
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Affiliation(s)
- Marcello Ventura
- Department of Molecular Medicine, University of Padua, Via Gabelli 63, Padova, Italy
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19
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Béhar G, Bellinzoni M, Maillasson M, Paillard-Laurance L, Alzari PM, He X, Mouratou B, Pecorari F. Tolerance of the archaeal Sac7d scaffold protein to alternative library designs: characterization of anti-immunoglobulin G Affitins. Protein Eng Des Sel 2013; 26:267-75. [PMID: 23315487 DOI: 10.1093/protein/gzs106] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Engineered protein scaffolds have received considerable attention as alternatives to antibodies in both basic and applied research, as they can offer superior biophysical properties often associated with a simpler molecular organization. Sac7d has been demonstrated as an effective scaffold for molecular recognition. Here, we used the initial L1 'flat surface' library constructed by randomization of 14 residues, to identify ligands specific for human immunoglobulin G. To challenge the plasticity of the Sac7d protein scaffold, we designed the alternative L2 'flat surface & loops' library whereof only 10 residues are randomized. Representative binders (Affitins) of the two libraries exhibited affinities in the low nanomolar range and were able to recognize different epitopes within human immunoglobulin G. These Affitins were stable up to pH 12 while largely conserving other favorable properties of Sac7d protein, such as high expression yields in Escherichia coli, solubility, thermal stability up to 80.7°C, and acidic stability (pH 0). In agreement with our library designs, mutagenesis study revealed two distinct binding areas, one including loops. Together, our results indicate that the Sac7d scaffold tolerates alternative library designs, which further expands the diversity of Affitins and may provide a general way to create tailored affinity tools for demanding applications.
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Affiliation(s)
- Ghislaine Béhar
- Université de Nantes, UMR CNRS 6204, Ingénierie de la reconnaissance, F-44322 Nantes, France
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20
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Mercati O, Danckaert A, André-Leroux G, Bellinzoni M, Gouder L, Watanabe K, Shimoda Y, Grailhe R, De Chaumont F, Bourgeron T, Cloëz-Tayarani I. Contactin 4, -5 and -6 differentially regulate neuritogenesis while they display identical PTPRG binding sites. Biol Open 2013; 2:324-34. [PMID: 23519440 PMCID: PMC3603414 DOI: 10.1242/bio.20133343] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [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: 10/12/2012] [Accepted: 11/28/2012] [Indexed: 12/22/2022] Open
Abstract
The neural cell-adhesion molecules contactin 4, contactin 5 and contactin 6 are involved in brain development, and disruptions in contactin genes may confer increased risk for autism spectrum disorders (ASD). We describe a co-culture of rat cortical neurons and HEK293 cells overexpressing and delivering the secreted forms of rat contactin 4-6. We quantified their effects on the length and branching of neurites. Contactin 4-6 effects were different depending on the contactin member and duration of co-culture. At 4 days in culture, contactin 4 and -6 increased the length of neurites, while contactin 5 increased the number of roots. Up to 8 days in culture, contactin 6 progressively increased the length of neurites while contactin 5 was more efficient on neurite branching. We studied the molecular sites of interaction between human contactin 4, -5 or -6 and the human Protein Tyrosine Phosphatase Receptor Gamma (PTPRG), a contactin partner, by modeling their 3D structures. As compared to contactin 4, we observed differences in the Ig2 and Ig3 domains of contactin 5 and -6 with the appearance of an omega loop that could adopt three distinct conformations. However, interactive residues between human contactin 4-6 and PTPRG were strictly conserved. We did not observe any differences in PTPRG binding on contactin 5 and -6 either. Our data suggest that the differential contactin effects on neurite outgrowth do not result from distinct interactions with PTPRG. A better understanding of the contactin cellular properties should help elucidate their roles in ASD.
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Affiliation(s)
- Oriane Mercati
- Human Genetics and Cognitive Functions, Institut Pasteur , 75015 Paris , France ; CNRS URA 2182 'Genes, synapses and cognition', Institut Pasteur , 75015 Paris , France ; Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions , 75013 Paris , France
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21
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Mechaly AE, Haouz A, Miras I, Barilone N, Weber P, Shepard W, Alzari PM, Bellinzoni M. Conformational changes upon ligand binding in the essential class II fumarase Rv1098c fromMycobacterium tuberculosis. FEBS Lett 2012; 586:1606-11. [DOI: 10.1016/j.febslet.2012.04.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 03/31/2012] [Accepted: 04/19/2012] [Indexed: 12/17/2022]
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Wagner T, Bellinzoni M, Wehenkel A, O'Hare HM, Alzari PM. Functional plasticity and allosteric regulation of α-ketoglutarate decarboxylase in central mycobacterial metabolism. ACTA ACUST UNITED AC 2011; 18:1011-20. [PMID: 21867916 DOI: 10.1016/j.chembiol.2011.06.004] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 05/24/2011] [Accepted: 06/07/2011] [Indexed: 11/18/2022]
Abstract
The α-ketoglutarate dehydrogenase (KDH) complex is a major regulatory point of aerobic energy metabolism. Mycobacterium tuberculosis was reported to lack KDH activity, and the putative KDH E1o component, α-ketoglutarate decarboxylase (KGD), was instead assigned as a decarboxylase or carboligase. Here, we show that this protein does in fact sustain KDH activity, as well as the additional two reactions, and these multifunctional properties are shared by the Escherichia coli homolog, SucA. We also show that the mycobacterial enzyme is finely regulated by an additional acyltransferase-like domain and by the action of acetyl-CoA, a powerful allosteric activator able to enhance the concerted protein motions observed during catalysis. Our results uncover the functional plasticity of a crucial node in bacterial metabolism, which may be important for M. tuberculosis during host infection.
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Affiliation(s)
- Tristan Wagner
- Institut Pasteur, Unité de Biochimie Structurale (CNRS URA 2185), 25 rue du Dr. Roux, 75724 Paris, France
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23
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Urresti S, Giganti D, Bellinzoni M, Jackson M, Alzari PM, Guerin ME. A model of action for peripheral membrane-associated GT-B glycosyltransferases. Acta Crystallogr A 2011. [DOI: 10.1107/s010876731108799x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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24
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Mechaly AE, Haouz A, Miras I, Alzari PM, Bellinzoni M. Insights into the fumarase reaction mechanism from crystal structures of Rv1098c. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311080184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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25
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Bellinzoni M, Bastard K, Perret A, Zaparucha A, Perchat N, Vergne C, Wagner T, de Melo-Minardi RC, Artiguenave F, Cohen GN, Weissenbach J, Salanoubat M, Alzari PM. 3-Keto-5-aminohexanoate cleavage enzyme: a common fold for an uncommon Claisen-type condensation. J Biol Chem 2011; 286:27399-405. [PMID: 21632536 PMCID: PMC3149333 DOI: 10.1074/jbc.m111.253260] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [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: 04/20/2011] [Revised: 05/17/2011] [Indexed: 11/06/2022] Open
Abstract
The exponential increase in genome sequencing output has led to the accumulation of thousands of predicted genes lacking a proper functional annotation. Among this mass of hypothetical proteins, enzymes catalyzing new reactions or using novel ways to catalyze already known reactions might still wait to be identified. Here, we provide a structural and biochemical characterization of the 3-keto-5-aminohexanoate cleavage enzyme (Kce), an enzymatic activity long known as being involved in the anaerobic fermentation of lysine but whose catalytic mechanism has remained elusive so far. Although the enzyme shows the ubiquitous triose phosphate isomerase (TIM) barrel fold and a Zn(2+) cation reminiscent of metal-dependent class II aldolases, our results based on a combination of x-ray snapshots and molecular modeling point to an unprecedented mechanism that proceeds through deprotonation of the 3-keto-5-aminohexanoate substrate, nucleophilic addition onto an incoming acetyl-CoA, intramolecular transfer of the CoA moiety, and final retro-Claisen reaction leading to acetoacetate and 3-aminobutyryl-CoA. This model also accounts for earlier observations showing the origin of carbon atoms in the products, as well as the absence of detection of any covalent acyl-enzyme intermediate. Kce is the first representative of a large family of prokaryotic hypothetical proteins, currently annotated as the "domain of unknown function" DUF849.
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Affiliation(s)
- Marco Bellinzoni
- From the Unité de Microbiologie Structurale, Institut Pasteur, and CNRS-URA2185, 25 rue du Dr. Roux, 75724 Paris Cedex 15
| | - Karine Bastard
- the Direction des Sciences du Vivant, Commissariat à l'Energie Atomique (CEA), Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, 91057 Evry
- CNRS-UMR8030, 2 rue Gaston Crémieux, 91057 Evry
- the Université d'Evry Val d'Essonne, boulevard François Mitterrand, 91057 Evry, and
| | - Alain Perret
- the Direction des Sciences du Vivant, Commissariat à l'Energie Atomique (CEA), Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, 91057 Evry
- CNRS-UMR8030, 2 rue Gaston Crémieux, 91057 Evry
- the Université d'Evry Val d'Essonne, boulevard François Mitterrand, 91057 Evry, and
| | - Anne Zaparucha
- the Direction des Sciences du Vivant, Commissariat à l'Energie Atomique (CEA), Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, 91057 Evry
- CNRS-UMR8030, 2 rue Gaston Crémieux, 91057 Evry
- the Université d'Evry Val d'Essonne, boulevard François Mitterrand, 91057 Evry, and
| | - Nadia Perchat
- the Direction des Sciences du Vivant, Commissariat à l'Energie Atomique (CEA), Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, 91057 Evry
- CNRS-UMR8030, 2 rue Gaston Crémieux, 91057 Evry
- the Université d'Evry Val d'Essonne, boulevard François Mitterrand, 91057 Evry, and
| | - Carine Vergne
- the Direction des Sciences du Vivant, Commissariat à l'Energie Atomique (CEA), Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, 91057 Evry
- CNRS-UMR8030, 2 rue Gaston Crémieux, 91057 Evry
- the Université d'Evry Val d'Essonne, boulevard François Mitterrand, 91057 Evry, and
| | - Tristan Wagner
- From the Unité de Microbiologie Structurale, Institut Pasteur, and CNRS-URA2185, 25 rue du Dr. Roux, 75724 Paris Cedex 15
| | - Raquel C. de Melo-Minardi
- the Direction des Sciences du Vivant, Commissariat à l'Energie Atomique (CEA), Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, 91057 Evry
- CNRS-UMR8030, 2 rue Gaston Crémieux, 91057 Evry
- the Université d'Evry Val d'Essonne, boulevard François Mitterrand, 91057 Evry, and
| | - François Artiguenave
- the Direction des Sciences du Vivant, Commissariat à l'Energie Atomique (CEA), Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, 91057 Evry
- CNRS-UMR8030, 2 rue Gaston Crémieux, 91057 Evry
- the Université d'Evry Val d'Essonne, boulevard François Mitterrand, 91057 Evry, and
| | - Georges N. Cohen
- the Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Jean Weissenbach
- the Direction des Sciences du Vivant, Commissariat à l'Energie Atomique (CEA), Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, 91057 Evry
- CNRS-UMR8030, 2 rue Gaston Crémieux, 91057 Evry
- the Université d'Evry Val d'Essonne, boulevard François Mitterrand, 91057 Evry, and
| | - Marcel Salanoubat
- the Direction des Sciences du Vivant, Commissariat à l'Energie Atomique (CEA), Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, 91057 Evry
- CNRS-UMR8030, 2 rue Gaston Crémieux, 91057 Evry
- the Université d'Evry Val d'Essonne, boulevard François Mitterrand, 91057 Evry, and
| | - Pedro M. Alzari
- From the Unité de Microbiologie Structurale, Institut Pasteur, and CNRS-URA2185, 25 rue du Dr. Roux, 75724 Paris Cedex 15
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Manina G, Bellinzoni M, Pasca MR, Neres J, Milano A, Ribeiro ALDJL, Buroni S, Skovierová H, Dianišková P, Mikušová K, Marák J, Makarov V, Giganti D, Haouz A, Lucarelli AP, Degiacomi G, Piazza A, Chiarelli LR, De Rossi E, Salina E, Cole ST, Alzari PM, Riccardi G. Biological and structural characterization of the Mycobacterium smegmatis nitroreductase NfnB, and its role in benzothiazinone resistance. Mol Microbiol 2011; 77:1172-85. [PMID: 20624223 DOI: 10.1111/j.1365-2958.2010.07277.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Tuberculosis is still a leading cause of death in developing countries, for which there is an urgent need for new pharmacological agents. The synthesis of the novel antimycobacterial drug class of benzothiazinones (BTZs) and the identification of their cellular target as DprE1 (Rv3790), a component of the decaprenylphosphoryl-β-d-ribose 2'-epimerase complex, have been reported recently. Here, we describe the identification and characterization of a novel resistance mechanism to BTZ in Mycobacterium smegmatis. The overexpression of the nitroreductase NfnB leads to the inactivation of the drug by reduction of a critical nitro-group to an amino-group. The direct involvement of NfnB in the inactivation of the lead compound BTZ043 was demonstrated by enzymology, microbiological assays and gene knockout experiments. We also report the crystal structure of NfnB in complex with the essential cofactor flavin mononucleotide, and show that a common amino acid stretch between NfnB and DprE1 is likely to be essential for the interaction with BTZ. We performed docking analysis of NfnB-BTZ in order to understand their interaction and the mechanism of nitroreduction. Although Mycobacterium tuberculosis seems to lack nitroreductases able to inactivate these drugs, our findings are valuable for the design of new BTZ molecules, which may be more effective in vivo.
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Affiliation(s)
- Giulia Manina
- Dipartimento di Genetica e Microbiologia, Università degli Studi di Pavia, via Ferrata, 1, 27100 Pavia, Italy
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27
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Martinez MA, Zaballa ME, Schaeffer F, Bellinzoni M, Albanesi D, Schujman GE, Vila AJ, Alzari PM, de Mendoza D. A novel role of malonyl-ACP in lipid homeostasis. Biochemistry 2010; 49:3161-7. [PMID: 20201588 DOI: 10.1021/bi100136n] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The FapR protein of Bacillus subtilis has been shown to play an important role in membrane lipid homeostasis. FapR acts as a repressor of many genes involved in fatty acid and phospholipid metabolism (the fap regulon). FapR binding to DNA is antagonized by malonyl-CoA, and thus FapR acts as a sensor of the status of fatty acid biosynthesis. However, malonyl-CoA is utilized for fatty acid synthesis only following its conversion to malonyl-ACP, which plays a central role in the initiation and elongation cycles carried out by the type II fatty acid synthase. Using in vitro transcription studies and isothermal titration calorimetry, we show here that malonyl-ACP binds FapR, disrupting the repressor-operator complex with an affinity similar to that of its precursor malonyl-CoA. NMR experiments reveal that there is no protein-protein recognition between ACP and FapR. These findings are consistent with the crystal structure of malonyl-ACP, which shows that the malonyl-phosphopantetheine moiety protrudes away from the protein core and thus can act as an effector ligand. Therefore, FapR regulates the expression of the fap regulon in response to the composition of the malonyl-phosphopantetheine pool. This mechanism ensures that fatty acid biosynthesis in B. subtilis is finely regulated at the transcriptional level by sensing the concentrations of the two first intermediates (malonyl-CoA and malonyl-ACP) in order to balance the production of membrane phospholipids.
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Affiliation(s)
- Mariano A Martinez
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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28
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Graña M, Bellinzoni M, Bellalou J, Haouz A, Miras I, Buschiazzo A, Winter N, Alzari PM. Crystal structure of Mycobacterium tuberculosis LppA, a lipoprotein confined to pathogenic mycobacteria. Proteins 2010; 78:769-72. [PMID: 19899167 DOI: 10.1002/prot.22603] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Martin Graña
- Unité de Biochimie Structurale & URA 2185 CNRS, Institut Pasteur, 75724 Paris, France
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29
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Graña M, Bellinzoni M, Miras I, Fiez-Vandal C, Haouz A, Shepard W, Buschiazzo A, Alzari PM. Structure of Mycobacterium tuberculosis Rv2714, a representative of a duplicated gene family in Actinobacteria. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:972-7. [PMID: 19851001 DOI: 10.1107/s1744309109035027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Accepted: 09/01/2009] [Indexed: 11/10/2022]
Abstract
The gene Rv2714 from Mycobacterium tuberculosis, which codes for a hypothetical protein of unknown function, is a representative member of a gene family that is largely confined to the order Actinomycetales of Actinobacteria. Sequence analysis indicates the presence of two paralogous genes in most mycobacterial genomes and suggests that gene duplication was an ancient event in bacterial evolution. The crystal structure of Rv2714 has been determined at 2.6 A resolution, revealing a trimer in which the topology of the protomer core is similar to that observed in a functionally diverse set of enzymes, including purine nucleoside phosphorylases, some carboxypeptidases, bacterial peptidyl-tRNA hydrolases and even the plastidic form of an intron splicing factor. However, some structural elements, such as a beta-hairpin insertion involved in protein oligomerization and a C-terminal alpha-helical domain that serves as a lid to the putative substrate-binding (or ligand-binding) site, are only found in Rv2714 bacterial homologues and represent specific signatures of this protein family.
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Affiliation(s)
- Martin Graña
- Institut Pasteur, Unité de Biochimie Structurale, URA CNRS 2185, 25 Rue du Dr Roux, 75724 Paris, France
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30
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Bellinzoni M, Alzari PM. Bacterial Metabolism under FHA Control. Structure 2009; 17:487-8. [DOI: 10.1016/j.str.2009.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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O'Hare HM, Durán R, Cerveñansky C, Bellinzoni M, Wehenkel AM, Pritsch O, Obal G, Baumgartner J, Vialaret J, Johnsson K, Alzari PM. Regulation of glutamate metabolism by protein kinases in mycobacteria. Mol Microbiol 2008; 70:1408-23. [PMID: 19019160 DOI: 10.1111/j.1365-2958.2008.06489.x] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Protein kinase G of Mycobacterium tuberculosis has been implicated in virulence and in regulation of glutamate metabolism. Here we show that this kinase undergoes a pattern of autophosphorylation that is distinct from that of other M. tuberculosis protein kinases characterized to date and we identify GarA as a substrate for phosphorylation by PknG. Autophosphorylation of PknG has little effect on kinase activity but promotes binding to GarA, an interaction that is also detected in living mycobacteria. PknG phosphorylates GarA at threonine 21, adjacent to the residue phosphorylated by PknB (T22), and these two phosphorylation events are mutually exclusive. Like the homologue OdhI from Corynebacterium glutamicum, the unphosphorylated form of GarA is shown to inhibit alpha-ketoglutarate decarboxylase in the TCA cycle. Additionally GarA is found to bind and modulate the activity of a large NAD(+)-specific glutamate dehydrogenase with an unusually low affinity for glutamate. Previous reports of a defect in glutamate metabolism caused by pknG deletion may thus be explained by the effect of unphosphorylated GarA on these two enzyme activities, which may also contribute to the attenuation of virulence.
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Affiliation(s)
- Helen M O'Hare
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
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32
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Wehenkel A, Bellinzoni M, Schaeffer F, Villarino A, Alzari PM. Structural and Binding Studies of the Three-metal Center in Two Mycobacterial PPM Ser/Thr Protein Phosphatases. J Mol Biol 2007; 374:890-8. [DOI: 10.1016/j.jmb.2007.09.076] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Revised: 09/25/2007] [Accepted: 09/26/2007] [Indexed: 10/22/2022]
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Wehenkel A, Bellinzoni M, Graña M, Duran R, Villarino A, Fernandez P, Andre-Leroux G, England P, Takiff H, Cerveñansky C, Cole ST, Alzari PM. Mycobacterial Ser/Thr protein kinases and phosphatases: physiological roles and therapeutic potential. Biochim Biophys Acta 2007; 1784:193-202. [PMID: 17869195 DOI: 10.1016/j.bbapap.2007.08.006] [Citation(s) in RCA: 144] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Revised: 08/01/2007] [Accepted: 08/03/2007] [Indexed: 11/19/2022]
Abstract
Reversible protein phosphorylation is a major regulation mechanism of fundamental biological processes, not only in eukaryotes but also in bacteria. A growing body of evidence suggests that Ser/Thr phosphorylation play important roles in the physiology and virulence of Mycobacterium tuberculosis, the etiological agent of tuberculosis. This pathogen uses 'eukaryotic-like' Ser/Thr protein kinases and phosphatases not only to regulate many intracellular metabolic processes, but also to interfere with signaling pathways of the infected host cell. Disrupting such processes by means of selective inhibitors may thus provide new pharmaceutical weapons to combat the disease. Here we review the current knowledge on Ser/Thr protein kinases and phosphatases in M. tuberculosis, their regulation mechanisms and putative substrates, and we explore their therapeutic potential as possible targets for the development of new anti-mycobacterial compounds.
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Affiliation(s)
- Annemarie Wehenkel
- Unité de Biochimie Structurale, URA 2185 CNRS, Institut Pasteur, 25 rue du Docteur Roux, F-75724, Paris Cedex 15, France
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34
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Bellinzoni M, Wehenkel A, Shepard W, Alzari PM. Insights into the Catalytic Mechanism of PPM Ser/Thr Phosphatases from the Atomic Resolution Structures of a Mycobacterial Enzyme. Structure 2007; 15:863-72. [PMID: 17637345 DOI: 10.1016/j.str.2007.06.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Revised: 06/07/2007] [Accepted: 06/10/2007] [Indexed: 01/11/2023]
Abstract
Serine/threonine-specific phosphatases (PPs) represent, after protein tyrosine phosphatases, the second major class of enzymes that catalyze the dephosphorylation of proteins. They are classed in two large families, known as PPP and PPM, on the basis of sequence similarities, metal ion dependence, and inhibitor sensitivity. Despite their wide species distribution and broad physiological roles, the catalytic mechanism of PPM phosphatases has been primarily inferred from studies of a single enzyme, human PP2Calpha. Here, we report the biochemical characterization and the atomic resolution structures of a soluble PPM phosphatase from the saprophyte Mycobacterium smegmatis in complex with different ligands. The structures provide putative snapshots along the catalytic cycle, which support an associative reaction mechanism that differs in some important aspects from the currently accepted model and reinforces the hypothesis of convergent evolution in PPs.
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Affiliation(s)
- Marco Bellinzoni
- Unité de Biochimie Structurale, CNRS-URA 2185, Institut Pasteur, 75724 Paris Cedex 15, France
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35
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Bellinzoni M, Haouz A, Graña M, Munier-Lehmann H, Shepard W, Alzari PM. The crystal structure of Mycobacterium tuberculosis adenylate kinase in complex with two molecules of ADP and Mg2+ supports an associative mechanism for phosphoryl transfer. Protein Sci 2006; 15:1489-93. [PMID: 16672241 PMCID: PMC2242552 DOI: 10.1110/ps.062163406] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The crystal structure of Mycobacterium tuberculosis adenylate kinase (MtAK) in complex with two ADP molecules and Mg2+ has been determined at 1.9 A resolution. Comparison with the solution structure of the enzyme, obtained in the absence of substrates, shows significant conformational changes of the LID and NMP-binding domains upon substrate binding. The ternary complex represents the state of the enzyme at the start of the backward reaction (ATP synthesis). The structure is consistent with a direct nucleophilic attack of a terminal oxygen from the acceptor ADP molecule on the beta-phosphate from the donor substrate, and both the geometry and the distribution of positive charge in the active site support the hypothesis of an associative mechanism for phosphoryl transfer.
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Affiliation(s)
- Marco Bellinzoni
- Unité de Biochimie Structurale, CNRS-URA 2185, Institut Pasteur, F-75724 Paris, France
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36
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Wehenkel A, Fernandez P, Bellinzoni M, Catherinot V, Barilone N, Labesse G, Jackson M, Alzari PM. The structure of PknB in complex with mitoxantrone, an ATP-competitive inhibitor, suggests a mode of protein kinase regulation in mycobacteria. FEBS Lett 2006; 580:3018-22. [PMID: 16674948 DOI: 10.1016/j.febslet.2006.04.046] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2006] [Revised: 04/15/2006] [Accepted: 04/18/2006] [Indexed: 10/24/2022]
Abstract
Mycobacterium tuberculosis PknB is an essential receptor-like protein kinase involved in cell growth control. Here, we demonstrate that mitoxantrone, an anthraquinone derivative used in cancer therapy, is a PknB inhibitor capable of preventing mycobacterial growth. The structure of the complex reveals that mitoxantrone partially occupies the adenine-binding pocket in PknB, providing a framework for the design of compounds with potential therapeutic applications. PknB crystallizes as a 'back-to-back' homodimer identical to those observed in other structures of PknB in complex with ATP analogs. This organization resembles that of the RNA-dependent protein kinase PKR, suggesting a mechanism for kinase activation in mycobacteria.
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Affiliation(s)
- Annemarie Wehenkel
- Unité de Biochimie Structurale and CNRS URA2185, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris, France
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37
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Durán R, Villarino A, Bellinzoni M, Wehenkel A, Fernandez P, Boitel B, Cole ST, Alzari PM, Cerveñansky C. Conserved autophosphorylation pattern in activation loops and juxtamembrane regions of Mycobacterium tuberculosis Ser/Thr protein kinases. Biochem Biophys Res Commun 2005; 333:858-67. [PMID: 15967413 DOI: 10.1016/j.bbrc.2005.05.173] [Citation(s) in RCA: 66] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2005] [Accepted: 05/25/2005] [Indexed: 10/25/2022]
Abstract
The identification of phosphorylation sites in proteins provides a powerful tool to study signal transduction pathways and to establish interaction networks involving signaling elements. Using different strategies to identify phosphorylated residues, we report here mass spectrometry studies of the entire intracellular regions of four 'receptor-like' protein kinases from Mycobacterium tuberculosis (PknB, PknD, PknE, and PknF), each consisting of an N-terminal kinase domain and a juxtamembrane region of varying length (26-100 residues). The enzymes were observed to incorporate different numbers of phosphates, from five in PknB up to 11 in PknD or PknE, and all detected sites were dephosphorylated by the cognate mycobacterial phosphatase PstP. Comparison of the phosphorylation patterns reveals two recurrent clusters of pThr/pSer residues, respectively, in their activation loops and juxtamembrane regions, which have a distinct effect on kinase activity. All studied kinases have at least two conserved phosphorylated residues in their activation loop and mutations of these residues in PknB significantly decreased the kinase activity, whereas deletion of the entire juxtamembrane regions in PknB and PknF had little effect on their activities. These results reinforce the hypothesis that mycobacterial kinase regulation includes a conserved activation loop mechanism, and suggest that phosphorylation sites in the juxtamembrane region might be involved in putative kinase-mediated signaling cascades.
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Affiliation(s)
- Rosario Durán
- Laboratorio de Bioquímica Analítica, Instituto de Investigaciones Biológicas Clemente Estable and Facultad de Ciencias, Montevideo, Uruguay
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38
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Wehenkel A, Villarino A, Fernandez P, Bellinzoni M, England P, Alzari PM. Structural studies of mycobacterial protein kinases and phosphatases. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305090100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Bellinzoni M, Buroni S, Pasca MR, Guglierame P, Arcesi F, De Rossi E, Riccardi G. Glutamine amidotransferase activity of NAD+ synthetase from Mycobacterium tuberculosis depends on an amino-terminal nitrilase domain. Res Microbiol 2005; 156:173-7. [PMID: 15748981 DOI: 10.1016/j.resmic.2004.08.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2004] [Accepted: 08/23/2004] [Indexed: 11/24/2022]
Abstract
NAD(+) synthetase (NadE; E.C. 6.3.5.1) from Mycobacterium tuberculosis utilizes both glutamine and ammonia to catalyze NAD(+) production, in contrast to the corresponding NH(3)-dependent enzymes from other prokaryotes. Here we report the site-directed mutagenesis of amino acids located in the N-terminal domain and predicted to be essential for glutamine hydrolysis. The residues forming the putative catalytic triad (Cys176, Glu52 and Lys121) were replaced by alanine; the mutated enzymes were expressed in the Escherichia coli Origami (DE3) strain and purified. The three mutants completely lost their glutamine-dependent activity, clearly indicating that Cys176, Glu52 and Lys121 are crucial for this activity. In contrast, the C176A and E52A variants, respectively, retained 90 and 30% of the original NH(3)-dependent specific activity, while the K121A mutant lost this activity. The results show that glutamine-amidotransferase activity is mediated by an N-terminal domain belonging to the superfamily of nitrilases. This domain, a new type of glutamine amide transfer (GAT) domain, is the first to be characterized in bacterial NAD(+) synthetases.
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Affiliation(s)
- Marco Bellinzoni
- Dipartimento di Genetica e Microbiologia, University of Pavia, Via Ferrata 1, 27100 Pavia, Italy.
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40
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Pasca MR, Guglierame P, Arcesi F, Bellinzoni M, De Rossi E, Riccardi G. Rv2686c-Rv2687c-Rv2688c, an ABC fluoroquinolone efflux pump in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2004; 48:3175-8. [PMID: 15273144 PMCID: PMC478549 DOI: 10.1128/aac.48.8.3175-3178.2004] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Mycobacterium tuberculosis Rv2686c-Rv2687c-Rv2688c operon, encoding an ABC transporter, conferred resistance to ciprofloxacin and, to a lesser extent, norfloxacin, moxifloxacin, and sparfloxacin to Mycobacterium smegmatis. The resistance level decreased in the presence of the efflux pump inhibitors reserpine, carbonyl cyanide m-chlorophenylhydrazone, and verapamil. Energy-dependent efflux of ciprofloxacin from M. smegmatis cells containing the Rv2686c-Rv2687c-Rv2688c operon was observed.
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Affiliation(s)
- Maria Rosalia Pasca
- Department of Genetics and Microbiology, University of Pavia, 27100 Pavia, Italy
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41
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Terwilliger TC, Park MS, Waldo GS, Berendzen J, Hung LW, Kim CY, Smith CV, Sacchettini JC, Bellinzoni M, Bossi R, De Rossi E, Mattevi A, Milano A, Riccardi G, Rizzi M, Roberts MM, Coker AR, Fossati G, Mascagni P, Coates ARM, Wood SP, Goulding CW, Apostol MI, Anderson DH, Gill HS, Eisenberg DS, Taneja B, Mande S, Pohl E, Lamzin V, Tucker P, Wilmanns M, Colovos C, Meyer-Klaucke W, Munro AW, McLean KJ, Marshall KR, Leys D, Yang JK, Yoon HJ, Lee BI, Lee MG, Kwak JE, Han BW, Lee JY, Baek SH, Suh SW, Komen MM, Arcus VL, Baker EN, Lott JS, Jacobs W, Alber T, Rupp B. The TB structural genomics consortium: a resource for Mycobacterium tuberculosis biology. Tuberculosis (Edinb) 2004; 83:223-49. [PMID: 12906835 DOI: 10.1016/s1472-9792(03)00051-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The TB Structural Genomics Consortium is an organization devoted to encouraging, coordinating, and facilitating the determination and analysis of structures of proteins from Mycobacterium tuberculosis. The Consortium members hope to work together with other M. tuberculosis researchers to identify M. tuberculosis proteins for which structural information could provide important biological information, to analyze and interpret structures of M. tuberculosis proteins, and to work collaboratively to test ideas about M. tuberculosis protein function that are suggested by structure or related to structural information. This review describes the TB Structural Genomics Consortium and some of the proteins for which the Consortium is in the progress of determining three-dimensional structures.
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Affiliation(s)
- T C Terwilliger
- Los Alamos National Laboratory, Bioscience Division, Mail Stop M888, Los Alamos, NM 87545, USA.
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42
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Affiliation(s)
- Marco Bellinzoni
- Dipartimento di Genetica e Microbiologia, Università di Pavia, via Ferrata, 1, 27100, Pavia, Italy
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De Rossi E, Arrigo P, Bellinzoni M, Silva PAE, Martín C, Aínsa JA, Guglierame P, Riccardi G. The multidrug transporters belonging to major facilitator superfamily in Mycobacterium tuberculosis. Mol Med 2002; 8:714-24. [PMID: 12520088 PMCID: PMC2039957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023] Open
Abstract
BACKGROUND Both intrinsic and acquired multidrug resistance play an important role in the insurgence of tuberculosis. Detailed knowledge of the molecular basis of drug recognition and transport by multidrug transport systems is required for the development of new antibiotics that are not extruded or of inhibitors that block the multidrug transporter and allow traditional antibiotics to be effective. MATERIALS AND METHODS We have undertaken the inventory of the drug transporters subfamily, included in the major facilitator superfamily (MFS), encoded by the complete genome of Mycobacterium tuberculosis (MTB). These proteins were identified on the basis of their characteristic stretches of amino acids and transmembrane segments (TMS) number. CONCLUSIONS Genome analysis and searches of homology between the identified transporters and proteins characterized in other organisms revealed 16 open reading frames encoding putative drug efflux pumps belonging to MFS. In the case of two of them, we also have demonstrated that they function as drug efflux proteins.
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Affiliation(s)
- Edda De Rossi
- Dipartimento di Genetica e Microbiologia, Università degli Studi di Pavia, Italy.
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44
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De Rossi E, Arrigo P, Bellinzoni M, Silva PEA, Martin C, Aínsa JA, Guglierame P, Riccardi G. The Multidrug Transporters Belonging to Major Facilitator Superfamily (MFS) in Mycobacterium tuberculosis. Mol Med 2002. [DOI: 10.1007/bf03402035] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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45
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Almici C, Imberti L, Lanfranchi A, Verardi R, Bellinzoni M, Berta S, Izzi T. Reconstitution of T-cell receptor repertoire diversity following non-myeloablative allogeneic stem cell transplantation in an acute myeloid leukemia patient. Haematologica 2002; 87:ECR31. [PMID: 12368174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023] Open
MESH Headings
- Adult
- Antigens, Differentiation, T-Lymphocyte/chemistry
- Blood Transfusion, Autologous
- Humans
- Leukemia, Myeloid, Acute/immunology
- Leukemia, Myeloid, Acute/metabolism
- Lymphocyte Subsets
- Male
- Neutrophils/metabolism
- Polymorphism, Genetic
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/immunology
- Stem Cell Transplantation/methods
- T-Lymphocytes/chemistry
- T-Lymphocytes/immunology
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Affiliation(s)
- Camillo Almici
- Department of Internal Medicine-Hematology, BMT Unit, Spedali Civili di Brescia, Italy.
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Pirovano S, Bellinzoni M, Matteelli A, Ballerini C, Albertini A, Imberti L. High prevalence of a variant of SENV in intravenous drug user HIV-infected patients. J Med Virol 2002; 68:18-23. [PMID: 12210426 DOI: 10.1002/jmv.10165] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The prevalence, route of transmission, and clinical significance of SEN virus (SENV) infection was evaluated in 715 samples obtained from 150 blood donors, 165 patients infected by HIV, 150 with HCV/HBV infection, 80 with autoimmune diseases, 40 with Primary Immunodeficiency, 40 with sexually transmitted diseases, 40 polytransfused, and from 50 unselected patients. The identification of SENV-DNA was performed by polymerase chain reaction and hybridization, followed by an immunoenzymatic method that identify different SENV strains. SENV-A variant is largely represented among HIV-infected patients, being found in 71% of HIV(+) intravenous drug users and in 26% of individuals that had acquired HIV through sex. A high prevalence of SENV-A was observed also in HIV- polytransfused (27%) or in patients with sexually transmitted diseases (30%). These percentages are significantly higher than those observed in an unselected population and in blood donors. Prevalence of SENV-A is, therefore, high among HIV(+) patients with parental risk of exposure, but this infection does not appear to influence the clinical or immune status of HIV(+) patients.
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Affiliation(s)
- Silvia Pirovano
- Terzo Servizio Analisi and Institute of Chemistry, Spedali Civili of Brescia, Italy
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Bellinzoni M, De Rossi E, Branzoni M, Milano A, Peverali FA, Rizzi M, Riccardi G. Heterologous expression, purification, and enzymatic activity of Mycobacterium tuberculosis NAD(+) synthetase. Protein Expr Purif 2002; 25:547-57. [PMID: 12182838 DOI: 10.1016/s1046-5928(02)00041-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The enzyme NAD(+) synthetase (NadE) catalyzes the last step of NAD biosynthesis. Given NAD vital role in cell metabolism, the enzyme represents a valid target for the development of new antimycobacterial agents. In the present study we expressed and purified two putative forms of Mycobacterium tuberculosis NAD(+) synthetase, differing in the polypeptide chain length (NadE-738 and NadE-679). Furthermore, we evaluated several systems for the heterologous expression and large scale purification of the enzyme. In particular, we compared the efficiency of production, the yield of purification, and the catalytic activity of recombinant enzyme in different hosts, ranging from Escherichia coli strains to cultured High Five (Trichoplusia ni BTI-TN-5B1-4) insect cells. Among the systems assayed, we found that the expression of a thioredoxin-NadE fusion protein in E. coli Origami(DE3) is the best system in obtaining highly pure, active NAD(+) synthetase. The recombinant enzyme maintained its activity even after proteolytic cleavage of thioredoxin moiety. Biochemical evidence suggests that the shorter form (NadE-679) may be the real M. tuberculosis NAD(+) synthetase. These results enable us to obtain a purified product for structure-function analysis and high throughput assays for rapid screening of compounds which inhibit enzymatic activity.
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Affiliation(s)
- Marco Bellinzoni
- Dipartimento di Genetica e Microbiologia, Universitá di Pavia, Via Ferrata 1, 27100 Pavia, Italy.
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Abstract
Sera from 30 women at high risk for infection, one half of which were SEN virus positive (SENV(+)), were collected at delivery to study SENV mother-to child transmission. Thirteen of their babies were positive for at least one SENV strain: one baby was SENV(+) at birth, eight became positive within 6 months from delivery, and four became positive in the following months. Our data indicate that vertical transmission of SENV does occur, presumably, at delivery, but it may not induce persistent viremia. This is supported by the fact that, generally, SENV is not detected at birth, by the high SENV homology in the sequences found in the mothers and in their children, by a lack of other risk factors for infection of the babies, and by the irregular detection of SENV in the follow-up. No clinical events surely linked to SENV infection were found, but transient elevations of alanine aminotransferase were observed in babies followed for a long period of time.
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Affiliation(s)
- Silvia Pirovano
- III Laboratory of Clinical Chemistry, Hospital of Brescia, Institute of Chemistry and Department of Pediatrics, University of Brescia, Brescia, Italy
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