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Jaroensuk J, Chuaboon L, Kesornpun C, Chaiyen P. Enzymes in riboflavin biosynthesis: Potential antibiotic drug targets. Arch Biochem Biophys 2023; 748:109762. [PMID: 37739114 DOI: 10.1016/j.abb.2023.109762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/13/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
The rapid resistance of pathogens to antibiotics has emerged as a major threat to global health. Identification of new antibiotic targets is thus needed for developing alternative drugs. Genes encoding enzymes involved in the biosynthesis of riboflavin and flavin cofactors (FMN/FAD) are attractive targets because these enzymatic reactions are necessary for most bacteria to synthesize flavin cofactors for use in their central metabolic reactions. Moreover, humans lack most of these enzymes because we uptake riboflavin from our diet. This review discusses the current knowledge of enzymes involved in bacterial biosynthesis of riboflavin and other flavin cofactors, as well as the functions of the FMN riboswitch. Here, we highlight recent progress in the structural and mechanistic characterization, and inhibition of GTP cyclohydrolase II (GCH II), lumazine synthase (LS), riboflavin synthase (RFS), FAD synthetase (FADS), and FMN riboswitch, which have been identified as plausible antibiotic targets. As the structures and functions of these enzymes and regulatory systems are not completely understood, they are attractive as subjects for future in-depth biochemical and biophysical analysis.
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Affiliation(s)
- Juthamas Jaroensuk
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Wangchan, Rayong, 21210, Thailand
| | - Litavadee Chuaboon
- School of Pharmacy and Biomass and Oil Palm Center of Excellence, Walailak University, Nakhon Si Thammarat, 80160, Thailand
| | - Chatchai Kesornpun
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Wangchan, Rayong, 21210, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Wangchan, Rayong, 21210, Thailand.
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Iglesias Rando MR, Gorojovsky N, Zylberman V, Goldbaum FA, Craig PO. Improvement of Cellulomonas fimi endoglucanase CenA by multienzymatic display on a decameric structural scaffold. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12581-6. [PMID: 37212884 DOI: 10.1007/s00253-023-12581-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/27/2023] [Accepted: 05/06/2023] [Indexed: 05/23/2023]
Abstract
The development of multifunctional particles using polymeric scaffolds is an emerging technology for many nanobiotechnological applications. Here we present a system for the production of multifunctional complexes, based on the high affinity non-covalent interaction of cohesin and dockerin modules complementary fused to decameric Brucella abortus lumazine synthase (BLS) subunits, and selected target proteins, respectively. The cohesin-BLS scaffold was solubly expressed in high yield in Escherichia coli, and revealed a high thermostability. The production of multienzymatic particles using this system was evaluated using the catalytic domain of Cellulomonas fimi endoglucanase CenA recombinantly fused to a dockerin module. Coupling of the enzyme to the scaffold was highly efficient and occurred with the expected stoichiometry. The decavalent enzymatic complexes obtained showed higher cellulolytic activity and association to the substrate compared to equivalent amounts of the free enzyme. This phenomenon was dependent on the multiplicity and proximity of the enzymes coupled to the scaffold, and was attributed to an avidity effect in the polyvalent enzyme interaction with the substrate. Our results highlight the usefulness of the scaffold presented in this work for the development of multifunctional particles, and the improvement of lignocellulose degradation among other applications. KEY POINTS: • New system for multifunctional particle production using the BLS scaffold • Higher cellulolytic activity of polyvalent endoglucanase compared to the free enzyme • Amount of enzyme associated to cellulose is higher for the polyvalent endoglucanase.
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Affiliation(s)
- Matías R Iglesias Rando
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina
| | - Natalia Gorojovsky
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina
| | - Vanesa Zylberman
- Inmunova SA, Gral. San Martín, 25 de Mayo 1021 (CP 1650), Villa Lynch, Buenos Aires, Argentina
| | - Fernando A Goldbaum
- Inmunova SA, Gral. San Martín, 25 de Mayo 1021 (CP 1650), Villa Lynch, Buenos Aires, Argentina
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (CP 1405), Buenos Aires, Argentina
- Centro de Rediseño e Ingeniería de Proteínas (CRIP), UNSAM Campus Miguelete, 25 de Mayo y Francia (CP 1650), Gral. San Martín, Buenos Aires, Argentina
| | - Patricio O Craig
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina.
- CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina.
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Sosa S, Rossi AH, Szalai AM, Klinke S, Rinaldi J, Farias A, Berguer PM, Nadra AD, Stefani FD, Goldbaum FA, Bonomi HR. Asymmetric bifunctional protein nanoparticles through redesign of self-assembly. NANOSCALE ADVANCES 2019; 1:1833-1846. [PMID: 36134238 PMCID: PMC9419478 DOI: 10.1039/c8na00375k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 02/14/2019] [Indexed: 05/05/2023]
Abstract
Engineering oligomeric protein self-assembly is an attractive approach to fabricate nanostructures with well-defined geometries, stoichiometry and functions. The homodecamer Brucella Lumazine Synthase (BLS) is a highly stable and immunogenic protein nanoparticle (PNP). Here, we engineered the BLS protein scaffold to display two functions in spatially opposite regions of its structure yielding a Janus-like nanoparticle. An in silico analysis of the BLS head-to-head dimer of homopentamers shows major inter-pentameric interactions located in the equatorial interface. Based on this analysis, two BLS protomer variants were designed to interrupt pentamer self-dimerization and promote heteropentameric dimers. This strategy enabled us to generate a decameric particle with two distinct sides formed by two independent pentamers. The versatility of this new self-assembly nanofabrication strategy is illustrated with two example applications. First, a bifunctional BLS bearing Alexa Fluor 488 fluorophores on one side and sialic acid binding domains on the other side was used for labelling murine and human cells and analyzed by flow cytometry and confocal microscopy. Second, multichromophoric FRET nanoparticles were fabricated and characterized at the single molecule level, showing discrete energy transfer events. The engineered BLS variants constitute a general platform for displaying two functions in a controlled manner within the same PNP with potential applications in various areas such as biomedicine, biotechnology and nanotechnology.
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Affiliation(s)
- Santiago Sosa
- Fundación Instituto Leloir, IIBBA-CONICET Av. Patricias Argentinas 435, (C1405BWE) Ciudad Autónoma de Buenos Aires Argentina
- Centro de Investigaciones en Bionanociencias (CIBION)-CONICET Godoy Cruz 2390 (C1425FQD), Ciudad Autónoma de Buenos Aires Argentina
| | - Andrés H Rossi
- Fundación Instituto Leloir, IIBBA-CONICET Av. Patricias Argentinas 435, (C1405BWE) Ciudad Autónoma de Buenos Aires Argentina
| | - Alan M Szalai
- Centro de Investigaciones en Bionanociencias (CIBION)-CONICET Godoy Cruz 2390 (C1425FQD), Ciudad Autónoma de Buenos Aires Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET Av. Patricias Argentinas 435, (C1405BWE) Ciudad Autónoma de Buenos Aires Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM Av. Patricias Argentinas 435 (C1405BWE) Ciudad Autónoma de Buenos Aires Argentina
| | - Jimena Rinaldi
- Fundación Instituto Leloir, IIBBA-CONICET Av. Patricias Argentinas 435, (C1405BWE) Ciudad Autónoma de Buenos Aires Argentina
| | - Ana Farias
- Fundación Instituto Leloir, IIBBA-CONICET Av. Patricias Argentinas 435, (C1405BWE) Ciudad Autónoma de Buenos Aires Argentina
| | - Paula M Berguer
- Fundación Instituto Leloir, IIBBA-CONICET Av. Patricias Argentinas 435, (C1405BWE) Ciudad Autónoma de Buenos Aires Argentina
| | - Alejandro D Nadra
- Departamento de Fisiología, Biología Molecular y Celular, Departamento de Química Biológica and IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pabellón 2 (C1428EHA), Ciudad Autónoma de Buenos Aires Argentina
| | - Fernando D Stefani
- Centro de Investigaciones en Bionanociencias (CIBION)-CONICET Godoy Cruz 2390 (C1425FQD), Ciudad Autónoma de Buenos Aires Argentina
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 1 Ciudad Universitaria (C1428EHA) Ciudad Autónoma de Buenos Aires Argentina
| | - Fernando A Goldbaum
- Fundación Instituto Leloir, IIBBA-CONICET Av. Patricias Argentinas 435, (C1405BWE) Ciudad Autónoma de Buenos Aires Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM Av. Patricias Argentinas 435 (C1405BWE) Ciudad Autónoma de Buenos Aires Argentina
| | - Hernán R Bonomi
- Fundación Instituto Leloir, IIBBA-CONICET Av. Patricias Argentinas 435, (C1405BWE) Ciudad Autónoma de Buenos Aires Argentina
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Serer MI, Carrica MDC, Trappe J, López Romero S, Bonomi HR, Klinke S, Cerutti ML, Goldbaum FA. A high-throughput screening for inhibitors of riboflavin synthase identifies novel antimicrobial compounds to treat brucellosis. FEBS J 2019; 286:2522-2535. [PMID: 30927485 DOI: 10.1111/febs.14829] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/26/2019] [Accepted: 03/29/2019] [Indexed: 10/27/2022]
Abstract
Brucella spp. are pathogenic intracellular Gram-negative bacteria adapted to life within cells of several mammals, including humans. These bacteria are the causative agent of brucellosis, one of the zoonotic infections with the highest incidence in the world and for which a human vaccine is still unavailable. Current therapeutic treatments against brucellosis are based on the combination of two or more antibiotics for prolonged periods, which may lead to antibiotic resistance in the population. Riboflavin (vitamin B2) is biosynthesized by microorganisms and plants but mammals, including humans, must obtain it from dietary sources. Owing to the absence of the riboflavin biosynthetic enzymes in animals, this pathway is nowadays regarded as a rich resource of targets for the development of new antimicrobial agents. In this work, we describe a high-throughput screening approach to identify inhibitors of the enzymatic activity of riboflavin synthase, the last enzyme in this pathway. We also provide evidence for their subsequent validation as potential drug candidates in an in vitro brucellosis infection model. From an initial set of 44 000 highly diverse low molecular weight compounds with drug-like properties, we were able to identify ten molecules with 50% inhibitory concentrations in the low micromolar range. Further Brucella culture and intramacrophagic replication experiments showed that the most effective bactericidal compounds share a 2-Phenylamidazo[2,1-b][1,3]benzothiazole chemical scaffold. Altogether, these findings set up the basis for the subsequent lead optimization process and represent a promising advancement in the pursuit of novel and effective antimicrobial compounds against brucellosis.
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Affiliation(s)
- María Inés Serer
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | | | - Jörg Trappe
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | | | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina.,Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - María Laura Cerutti
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina.,Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Fernando Alberto Goldbaum
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina.,Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
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5
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Alzogaray V, Urrutia M, Berguer P, Rossi A, Zylberman V, Pardo R, Bonomi HR, Goldbaum FA. Characterization of folding-sensitive nanobodies as tools to study the expression and quality of protein particle immunogens. J Biotechnol 2019; 293:17-23. [PMID: 30690101 DOI: 10.1016/j.jbiotec.2019.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 12/04/2018] [Accepted: 01/07/2019] [Indexed: 01/05/2023]
Abstract
Vaccination is as one of the most beneficial biopharmaceutical interventions against pathogens due to its ability to induce adaptive immunity through targeted activation of the immune system. Each vaccine needs a tailor-made set of tests in order to monitor its quality throughout the development and manufacturing. The analysis of the conformational state of protein nanoparticles is one of the key steps in vaccine quality control. The enzyme lumazine synthase from Brucella spp. (BLS) acts as a potent oral and systemic immunogen. BLS has been used as a carrier of foreign peptides, protein domains and whole proteins, serving as a versatile platform for vaccine engineering purposes. Here, we show the generation and characterization of four families of nanobodies (Nbs) which only recognize BLS in its native conformational state and that bind to its active site. The present results support the use of conformation-sensitive Nbs as molecular probes during the development and production of vaccines based on the BLS platform. Finally, we propose Nbs as useful molecular tools targeting other protein scaffolds with potential applications in nano-and biotechnology.
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Affiliation(s)
- Vanina Alzogaray
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435 (C1405BWE), Ciudad de Buenos Aires, Argentina
| | - Mariela Urrutia
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435 (C1405BWE), Ciudad de Buenos Aires, Argentina
| | - Paula Berguer
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435 (C1405BWE), Ciudad de Buenos Aires, Argentina
| | - Andrés Rossi
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435 (C1405BWE), Ciudad de Buenos Aires, Argentina
| | - Vanesa Zylberman
- INMUNOVA, 25 de Mayo 1021 (B1650HMI), San Martin, Buenos Aires, Argentina
| | - Romina Pardo
- INMUNOVA, 25 de Mayo 1021 (B1650HMI), San Martin, Buenos Aires, Argentina
| | - Hernán R Bonomi
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435 (C1405BWE), Ciudad de Buenos Aires, Argentina
| | - Fernando A Goldbaum
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435 (C1405BWE), Ciudad de Buenos Aires, Argentina.
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Wei Y, Kumar P, Wahome N, Mantis NJ, Middaugh CR. Biomedical Applications of Lumazine Synthase. J Pharm Sci 2018; 107:2283-2296. [DOI: 10.1016/j.xphs.2018.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/02/2018] [Accepted: 05/02/2018] [Indexed: 10/16/2022]
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Abstract
Riboflavin derivatives are essential cofactors for a myriad of flavoproteins. In bacteria, flavins importance extends beyond their role as intracellular protein cofactors, as secreted flavins are a key metabolite in a variety of physiological processes. Bacteria obtain riboflavin through the endogenous riboflavin biosynthetic pathway (RBP) or by the use of importer proteins. Bacteria frequently encode multiple paralogs of the RBP enzymes and as for other micronutrient supply pathways, biosynthesis and uptake functions largely coexist. It is proposed that bacteria shut down biosynthesis and would rather uptake riboflavin when the vitamin is environmentally available. Recently, the overlap of riboflavin provisioning elements has gained attention and the functions of duplicated paralogs of RBP enzymes started to be addressed. Results point towards the existence of a modular structure in the bacterial riboflavin supply pathways. Such structure uses subsets of RBP genes to supply riboflavin for specific functions. Given the importance of riboflavin in intra and extracellular bacterial physiology, this complex array of riboflavin provision pathways may have developed to contend with the various riboflavin requirements. In riboflavin-prototrophic bacteria, riboflavin transporters could represent a module for riboflavin provision for particular, yet unidentified processes, rather than substituting for the RBP as usually assumed.
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Affiliation(s)
- Víctor Antonio García-Angulo
- a Microbiology and Mycology Program, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile , Santiago , Chile
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Haase I, Gräwert T, Illarionov B, Bacher A, Fischer M. Recent advances in riboflavin biosynthesis. Methods Mol Biol 2014; 1146:15-40. [PMID: 24764086 DOI: 10.1007/978-1-4939-0452-5_2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Riboflavin is biosynthesized from GTP and ribulose 5-phosphate. Whereas the early reactions conducing to 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate show significant taxonomic variation, the subsequent reaction steps are universal in all taxonomic kingdoms. With the exception of a hitherto elusive phosphatase, all enzymes of the pathway have been characterized in some detail at the structural and mechanistic level. Some of the pathway enzymes (GTP cycloyhdrolase II, 3,4-dihydroxy-2-butanone 4-phosphate synthase, riboflavin synthase) have exceptionally complex reaction mechanisms. The commercial production of the vitamin is now entirely based on highly productive fermentation processes. Due to their absence in animals, the pathway enzymes are potential targets for the development of novel anti-infective drugs.
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Affiliation(s)
- Ilka Haase
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146, Hamburg, Germany
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Serer MI, Bonomi HR, Guimarães BG, Rossi RC, Goldbaum FA, Klinke S. Crystallographic and kinetic study of riboflavin synthase from Brucella abortus, a chemotherapeutic target with an enhanced intrinsic flexibility. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1419-34. [PMID: 24816110 PMCID: PMC4014124 DOI: 10.1107/s1399004714005161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 03/06/2014] [Indexed: 11/11/2022]
Abstract
Riboflavin synthase (RS) catalyzes the last step of riboflavin biosynthesis in microorganisms and plants, which corresponds to the dismutation of two molecules of 6,7-dimethyl-8-ribityllumazine to yield one molecule of riboflavin and one molecule of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. Owing to the absence of this enzyme in animals and the fact that most pathogenic bacteria show a strict dependence on riboflavin biosynthesis, RS has been proposed as a potential target for antimicrobial drug development. Eubacterial, fungal and plant RSs assemble as homotrimers lacking C3 symmetry. Each monomer can bind two substrate molecules, yet there is only one active site for the whole enzyme, which is located at the interface between two neighbouring chains. This work reports the crystallographic structure of RS from the pathogenic bacterium Brucella abortus (the aetiological agent of the disease brucellosis) in its apo form, in complex with riboflavin and in complex with two different product analogues, being the first time that the structure of an intact RS trimer with bound ligands has been solved. These crystal models support the hypothesis of enhanced flexibility in the particle and also highlight the role of the ligands in assembling the unique active site. Kinetic and binding studies were also performed to complement these findings. The structural and biochemical information generated may be useful for the rational design of novel RS inhibitors with antimicrobial activity.
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Affiliation(s)
- María I. Serer
- Fundación Instituto Leloir, IIBBA–CONICET, Avenida Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
| | - Hernán R. Bonomi
- Fundación Instituto Leloir, IIBBA–CONICET, Avenida Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
| | - Beatriz G. Guimarães
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin BP 48, 91192 Gif-sur-Yvette CEDEX, France
| | - Rolando C. Rossi
- Instituto de Química y Fisicoquímica Biológicas y Departamento de Química Biológica, IQUIFIB–UBA–CONICET, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD Buenos Aires, Argentina
| | - Fernando A. Goldbaum
- Fundación Instituto Leloir, IIBBA–CONICET, Avenida Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA–CONICET, Avenida Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
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Identification and characterization of RibN, a novel family of riboflavin transporters from Rhizobium leguminosarum and other proteobacteria. J Bacteriol 2013; 195:4611-9. [PMID: 23935051 DOI: 10.1128/jb.00644-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Rhizobia are symbiotic bacteria able to invade and colonize the roots of legume plants, inducing the formation of nodules, where bacteria reduce atmospheric nitrogen (N2) to ammonia (NH3). Riboflavin availability influences the capacity of rhizobia to survive in the rhizosphere and to colonize roots. In this study, we identified the RL1692 gene of Rhizobium leguminosarum downstream of a flavin mononucleotide (FMN) riboswitch. RL1692 encodes a putative transmembrane permease with two EamA domains. The presence of an FMN riboswitch regulating a transmembrane protein is usually observed in riboflavin transporters, suggesting that RL1692 may be involved in riboflavin uptake. The product of RL1692, which we named RibN, is conserved in members of the alpha-, beta-, and gammaproteobacteria and shares no significant identity with any riboflavin transporter previously identified. In this work, we show that RibN is localized in the membrane cellular fraction and its expression is downregulated by riboflavin. By heterologous expression in a Brucella abortus mutant auxotrophic for riboflavin, we demonstrate that RibN possesses flavin transport activity. Similarly, we also demonstrate that RibN orthologues from Ochrobactrum anthropi and Vibrio cholerae (which lacks the FMN riboswitch) are able to transport riboflavin. An R. leguminosarum ribN null mutant exhibited lower nodule occupancy levels in pea plants during symbiosis assays. Thus, we propose that RibN and its homologues belong to a novel family of riboflavin transporters. This work provides the first experimental description of riboflavin transporters in Gram-negative bacteria.
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Shankar M, Wilbanks SM, Nakatani Y, Monk BC, Tyndall JDA. Catalysis product captured in lumazine synthase from the fungal pathogenCandida glabrata. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1580-6. [DOI: 10.1107/s0907444913010949] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 04/23/2013] [Indexed: 02/05/2023]
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Ladenstein R, Fischer M, Bacher A. The lumazine synthase/riboflavin synthase complex: shapes and functions of a highly variable enzyme system. FEBS J 2013; 280:2537-63. [PMID: 23551830 DOI: 10.1111/febs.12255] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 03/01/2013] [Accepted: 03/04/2013] [Indexed: 11/30/2022]
Abstract
The xylene ring of riboflavin (vitamin B2 ) is assembled from two molecules of 3,4-dihydroxy-2-butanone 4-phosphate by a mechanistically complex process that is jointly catalyzed by lumazine synthase and riboflavin synthase. In Bacillaceae, these enzymes form a structurally unique complex comprising an icosahedral shell of 60 lumazine synthase subunits and a core of three riboflavin synthase subunits, whereas many other bacteria have empty lumazine synthase capsids, fungi, Archaea and some eubacteria have pentameric lumazine synthases, and the riboflavin synthases of Archaea are paralogs of lumazine synthase. The structures of the molecular ensembles have been studied in considerable detail by X-ray crystallography, X-ray small-angle scattering and electron microscopy. However, certain mechanistic aspects remain unknown. Surprisingly, the quaternary structure of the icosahedral β subunit capsids undergoes drastic changes, resulting in formation of large, quasi-spherical capsids; this process is modulated by sequence mutations. The occurrence of large shells consisting of 180 or more lumazine synthase subunits has recently generated interest for protein engineering topics, particularly the construction of encapsulation systems.
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Affiliation(s)
- Rudolf Ladenstein
- Department of Bioscience and Nutrition, Karolinska Institutet NOVUM, SE-14183 Huddinge, Sweden.
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Craig PO, Alzogaray V, Goldbaum FA. Polymeric Display of Proteins through High Affinity Leucine Zipper Peptide Adaptors. Biomacromolecules 2012; 13:1112-21. [PMID: 22372794 DOI: 10.1021/bm201875p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The polymeric display of proteins is a method that could be used to increase the immunogenicity of antigens and to enhance the interaction strength of binding domains for their target ligands through an avidity effect. However, the coupling of proteins to oligomeric scaffolds is challenging. The chemical conjugation and recombinant fusion techniques have limitations that prevent their general use. In this work we describe a simple and effective method for coupling proteins to the decameric structure of Brucella abortus Lumazine Synthase based on the use of a pair of high affinity heterodimeric coiled coil peptides complementary fused to the scaffold and the target protein. Results obtained with a series of proteins demonstrate the capability of this approach to generate polyvalent particles. Furthermore, we show that the method is able to increase the immunogenicity of antigens and produce polyfunctional particles with promising biomedical and nanotechnological applications.
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Affiliation(s)
- Patricio O Craig
- Fundación Instituto Leloir e Instituto de Investigaciones Bioquímicas de Buenos Aires, IIBBA-CONICET, Buenos Aires, Argentina
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Fischer M, Bacher A. Biosynthesis of Vitamin B2: A Unique Way to Assemble a Xylene Ring. Chembiochem 2011; 12:670-80. [DOI: 10.1002/cbic.201000681] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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15
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Ainciart N, Zylberman V, Craig P, Nygaard D, Bonomi H, Cauerhff A, Goldbaum F. Sensing the dissociation of a polymeric enzyme by means of an engineered intrinsic probe. Proteins 2011; 79:1079-88. [DOI: 10.1002/prot.22945] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 10/29/2010] [Accepted: 11/07/2010] [Indexed: 01/09/2023]
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Abstract
The biosynthesis of riboflavin requires 1 equivalent of GTP and 2 equivalents of ribulose phosphate. The first committed reactions of the convergent pathway are catalyzed by GTP hydrolase II and 3,4-dihydroxy-2-butanone 4-phosphate synthase. The initial reaction steps afford 5-amino-6-ribitylaminopyrimidine 5'-phosphate, which needs to be dephosphorylated by a hitherto elusive hydrolase. The dephosphorylated pyrimidine is condensed with the carbohydrate precursor, 3,4-dihydroxy-2-butanone 4-phosphate. The resulting 6,7-dimethyl-8-ribityllumazine affords riboflavin by a mechanistically unique dismutation, i.e., by formation of a pentacyclic dimer that is subsequently fragmented.
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Morgunova E, Illarionov B, Saller S, Popov A, Sambaiah T, Bacher A, Cushman M, Fischer M, Ladenstein R. Structural study and thermodynamic characterization of inhibitor binding to lumazine synthase from Bacillus anthracis. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:1001-11. [PMID: 20823551 PMCID: PMC2935281 DOI: 10.1107/s0907444910029690] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 07/26/2010] [Indexed: 11/10/2022]
Abstract
The crystal structure of lumazine synthase from Bacillus anthracis was solved by molecular replacement and refined to R(cryst) = 23.7% (R(free) = 28.4%) at a resolution of 3.5 A. The structure reveals the icosahedral symmetry of the enzyme and specific features of the active site that are unique in comparison with previously determined orthologues. The application of isothermal titration calorimetry in combination with enzyme kinetics showed that three designed pyrimidine derivatives bind to lumazine synthase with micromolar dissociation constants and competitively inhibit the catalytic reaction. Structure-based modelling suggested the binding modes of the inhibitors in the active site and allowed an estimation of the possible contacts formed upon binding. The results provide a structural framework for the design of antibiotics active against B. anthracis.
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Affiliation(s)
- Ekaterina Morgunova
- Karolinska Institutet NOVUM, Center of Structural Biochemistry, Hälsovägen 7–9, 141 57 Huddinge, Sweden
| | - Boris Illarionov
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Sabine Saller
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Aleksander Popov
- European Synchrotron Radiation Facility, BP 220, F-38043 Grenoble CEDEX 09, France
| | - Thota Sambaiah
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, USA
| | - Adelbert Bacher
- Chemistry Department, Technical University of Munich, 85747 Garching, Germany
| | - Mark Cushman
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, USA
| | - Markus Fischer
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Rudolf Ladenstein
- Karolinska Institutet NOVUM, Center of Structural Biochemistry, Hälsovägen 7–9, 141 57 Huddinge, Sweden
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Talukdar A, Morgunova E, Duan J, Meining W, Foloppe N, Nilsson L, Bacher A, Illarionov B, Fischer M, Ladenstein R, Cushman M. Virtual screening, selection and development of a benzindolone structural scaffold for inhibition of lumazine synthase. Bioorg Med Chem 2010; 18:3518-34. [PMID: 20430628 PMCID: PMC2868945 DOI: 10.1016/j.bmc.2010.03.072] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Revised: 03/24/2010] [Accepted: 03/25/2010] [Indexed: 10/19/2022]
Abstract
Virtual screening of a library of commercially available compounds versus the structure of Mycobacterium tuberculosis lumazine synthase identified 2-(2-oxo-1,2-dihydrobenzo[cd]indole-6-sulfonamido)acetic acid (9) as a possible lead compound. Compound 9 proved to be an effective inhibitor of M. tuberculosis lumazine synthase with a K(i) of 70microM. Lead optimization through replacement of the carboxymethylsulfonamide sidechain with sulfonamides substituted with alkyl phosphates led to a four-carbon phosphate 38 that displayed a moderate increase in enzyme inhibitory activity (K(i) 38microM). Molecular modeling based on known lumazine synthase/inhibitor crystal structures suggests that the main forces stabilizing the present benzindolone/enzyme complexes involve pi-pi stacking interactions with Trp27 and hydrogen bonding of the phosphates with Arg128, the backbone nitrogens of Gly85 and Gln86, and the side chain hydroxyl of Thr87.
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Affiliation(s)
- Arindam Talukdar
- Department of Medicinal Chemistry and Molecular Pharmacology, School of Pharmacy and Pharmaceutical Sciences, and The Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Ekaterina Morgunova
- Karolinska Institute, Department of Bioscience, Hälsovägen 7-9, S-14157 Huddinge, Sweden
| | - Jianxin Duan
- Anterio Consult & Research GmbH, Augustaanlage 23, 68165 Mannheim, Germany
| | - Winfried Meining
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85350 Freising-Weihenstephan, Germany
| | - Nicolas Foloppe
- Karolinska Institute, Department of Bioscience, Hälsovägen 7-9, S-14157 Huddinge, Sweden
| | - Lennart Nilsson
- Karolinska Institute, Department of Bioscience, Hälsovägen 7-9, S-14157 Huddinge, Sweden
| | - Adelbert Bacher
- Institute of Biochemistry and Food Chemistry, Food Chemistry Division, University of Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
| | - Boris Illarionov
- Institute of Biochemistry and Food Chemistry, Food Chemistry Division, University of Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
| | - Markus Fischer
- Institute of Biochemistry and Food Chemistry, Food Chemistry Division, University of Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
| | - Rudolf Ladenstein
- Karolinska Institute, Department of Bioscience, Hälsovägen 7-9, S-14157 Huddinge, Sweden
| | - Mark Cushman
- Department of Medicinal Chemistry and Molecular Pharmacology, School of Pharmacy and Pharmaceutical Sciences, and The Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, 47907, USA
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Long Q, Ji L, Wang H, Xie J. Riboflavin Biosynthetic and Regulatory Factors as Potential Novel Anti-Infective Drug Targets. Chem Biol Drug Des 2010; 75:339-47. [DOI: 10.1111/j.1747-0285.2010.00946.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Bonomi HR, Marchesini MI, Klinke S, Ugalde JE, Zylberman V, Ugalde RA, Comerci DJ, Goldbaum FA. An atypical riboflavin pathway is essential for Brucella abortus virulence. PLoS One 2010; 5:e9435. [PMID: 20195542 PMCID: PMC2828483 DOI: 10.1371/journal.pone.0009435] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 02/04/2010] [Indexed: 11/30/2022] Open
Abstract
Brucellosis is a worldwide zoonosis that affects livestock and humans and is caused by closely related Brucella spp., which are adapted to intracellular life within cells of a large variety of mammals. Brucella can be considered a furtive pathogen that infects professional and non-professional phagocytes. In these cells Brucella survives in a replicative niche, which is characterized for having a very low oxygen tension and being deprived from nutrients such as amino acids and vitamins. Among these vitamins, we have focused on riboflavin (vitamin B2). Flavin metabolism has been barely implicated in bacterial virulence. We have recently described that Brucella and other Rhizobiales bear an atypical riboflavin metabolic pathway. In the present work we analyze the role of the flavin metabolism on Brucella virulence. Mutants on the two lumazine synthases (LS) isoenzymes RibH1 and RibH2 and a double RibH mutant were generated. These mutants and different complemented strains were tested for viability and virulence in cells and in mice. In this fashion we have established that at least one LS must be present for B. abortus survival and that RibH2 and not RibH1 is essential for intracellular survival due to its LS activity in vivo. In summary, we show that riboflavin biosynthesis is essential for Brucella survival inside cells or in mice. These results highlight the potential use of flavin biosynthetic pathway enzymes as targets for the chemotherapy of brucellosis.
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Affiliation(s)
| | - María Inés Marchesini
- Instituto de Investigaciones Biotecnológicas-CONICET, Universidad Nacional de General San Martín, San Martín, Buenos Aires, Argentina
| | | | - Juan E. Ugalde
- Instituto de Investigaciones Biotecnológicas-CONICET, Universidad Nacional de General San Martín, San Martín, Buenos Aires, Argentina
| | | | - Rodolfo A. Ugalde
- Instituto de Investigaciones Biotecnológicas-CONICET, Universidad Nacional de General San Martín, San Martín, Buenos Aires, Argentina
| | - Diego J. Comerci
- Instituto de Investigaciones Biotecnológicas-CONICET, Universidad Nacional de General San Martín, San Martín, Buenos Aires, Argentina
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22
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Survey of large protein complexes in D. vulgaris reveals great structural diversity. Proc Natl Acad Sci U S A 2009; 106:16580-5. [PMID: 19805340 DOI: 10.1073/pnas.0813068106] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An unbiased survey has been made of the stable, most abundant multi-protein complexes in Desulfovibrio vulgaris Hildenborough (DvH) that are larger than Mr approximately 400 k. The quaternary structures for 8 of the 16 complexes purified during this work were determined by single-particle reconstruction of negatively stained specimens, a success rate approximately 10 times greater than that of previous "proteomic" screens. In addition, the subunit compositions and stoichiometries of the remaining complexes were determined by biochemical methods. Our data show that the structures of only two of these large complexes, out of the 13 in this set that have recognizable functions, can be modeled with confidence based on the structures of known homologs. These results indicate that there is significantly greater variability in the way that homologous prokaryotic macromolecular complexes are assembled than has generally been appreciated. As a consequence, we suggest that relying solely on previously determined quaternary structures for homologous proteins may not be sufficient to properly understand their role in another cell of interest.
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Rodríguez-Fernández L, López-Jaramillo FJ, Bacher A, Fischer M, Weinkauf S. Improvement of the quality of lumazine synthase crystals by protein engineering. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:625-8. [PMID: 18607092 PMCID: PMC2443968 DOI: 10.1107/s1744309108015728] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2008] [Accepted: 05/25/2008] [Indexed: 11/10/2022]
Abstract
Icosahedral macromolecules have a wide spectrum of potential nanotechnological applications, the success of which relies on the level of accuracy at which the molecular structure is known. Lumazine synthase from Bacillus subtilis forms a 150 A icosahedral capsid consisting of 60 subunits and crystallizes in space group P6(3)22 or C2. However, the quality of these crystals is poor and structural information is only available at 2.4 A resolution. As classical strategies for growing better diffracting crystals have so far failed, protein engineering has been employed in order to improve the overexpression and purification of the molecule as well as to obtain new crystal forms. Two cysteines were replaced to bypass misfolding problems and a charged surface residue was replaced to force different molecular packings. The mutant protein crystallizes in space group R3, with unit-cell parameters a = b = 313.02, c = 365.77 A, alpha = beta = 90.0, gamma = 120 degrees , and diffracts to 1.6 A resolution.
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Affiliation(s)
- Lidia Rodríguez-Fernández
- Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - F. Javier López-Jaramillo
- Institute of Biotechnology, Department of Organic Chemistry, University of Granada, Campus Fuentenueva, 18071 Granada, Spain
| | - Adelbert Bacher
- Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Markus Fischer
- Institute of Biochemistry and Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Sevil Weinkauf
- Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
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Klinke S, Zylberman V, Bonomi HR, Haase I, Guimarães BG, Braden BC, Bacher A, Fischer M, Goldbaum FA. Structural and kinetic properties of lumazine synthase isoenzymes in the order Rhizobiales. J Mol Biol 2007; 373:664-80. [PMID: 17854827 DOI: 10.1016/j.jmb.2007.08.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2007] [Revised: 08/06/2007] [Accepted: 08/09/2007] [Indexed: 11/27/2022]
Abstract
6,7-Dimethyl-8-ribityllumazine synthase (lumazine synthase; LS) catalyzes the penultimate step in the biosynthesis of riboflavin in plants and microorganisms. This protein is known to exhibit different quaternary assemblies between species, existing as free pentamers, decamers (dimers of pentamers) and icosahedrally arranged dodecamers of pentamers. A phylogenetic analysis on eubacterial, fungal and plant LSs allowed us to classify them into two categories: Type I LSs (pentameric or icosahedral) and Type II LSs (decameric). The Rhizobiales represent an order of alpha-proteobacteria that includes, among others, the genera Mesorhizobium, Agrobacterium and Brucella. Here, we present structural and kinetic studies on several LSs from Rhizobiales. Interestingly, Mesorhizobium and Brucella encode both a Type-I LS and a Type-II LS called RibH1 and RibH2, respectively. We show that Type II LSs appear to be almost inactive, whereas Type I LSs present a highly variable catalytic activity according to the genus. Additionally, we have solved four RibH1/RibH2 crystallographic structures from the genera Mesorhizobium and Brucella. The relationship between the active-site architecture and catalytic properties in these isoenzymes is discussed, and a model that describes the enzymatic behavior is proposed. Furthermore, sequence alignment studies allowed us to extend our results to the genus Agrobacterium. Our results suggest that the selective pressure controlling the riboflavin pathway favored the evolution of catalysts with low reaction rates, since the excess of flavins in the intracellular pool in Rhizobiales could act as a negative factor when these bacteria are exposed to oxidative or nitrosative stress.
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Affiliation(s)
- Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, C1405BWE, Buenos Aires, Argentina.
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25
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Morgunova E, Saller S, Haase I, Cushman M, Bacher A, Fischer M, Ladenstein R. Lumazine synthase from Candida albicans as an anti-fungal target enzyme: structural and biochemical basis for drug design. J Biol Chem 2007; 282:17231-41. [PMID: 17446177 DOI: 10.1074/jbc.m701724200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lumazine synthase is an enzyme involved in riboflavin biosynthesis in many plants and microorganisms, including numerous human pathogens. The fact that the enzymes of the riboflavin biosynthesis pathway are not present in the human or animal host makes them potential targets for anti-infective agents. The crystal structure of lumazine synthase from Candida albicans was solved by molecular replacement and refined at 2.5-Angstrom resolution. The results of crystallographic investigations and sedimentation equilibrium experiments clearly indicated the presence of pentameric assemblies of the enzyme either in crystals or in solution. Isothermal titration calorimetry measurements of the binding reactions of four different inhibitors revealed high affinity for all four compounds with binding constants in the micromolar range. Structural comparison with previously determined structures of the enzyme.ligand complexes of other orthologue allowed modeling of the binding of four different inhibitors into the active site of lumazine synthase from Candida albicans.
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Affiliation(s)
- Ekaterina Morgunova
- Karolinska Institutet, NOVUM, Centre for Structural Biochemistry, Halsovagen 7-9, S-14157 Huddinge, Sweden.
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Zylberman V, Klinke S, Haase I, Bacher A, Fischer M, Goldbaum FA. Evolution of vitamin B2 biosynthesis: 6,7-dimethyl-8-ribityllumazine synthases of Brucella. J Bacteriol 2006; 188:6135-42. [PMID: 16923880 PMCID: PMC1595393 DOI: 10.1128/jb.00207-06] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The penultimate step in the biosynthesis of riboflavin (vitamin B2) involves the condensation of 3,4-dihydroxy-2-butanone 4-phosphate with 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, which is catalyzed by 6,7-dimethyl-8-ribityllumazine synthase (lumazine synthase). Pathogenic Brucella species adapted to an intracellular lifestyle have two genes involved in riboflavin synthesis, ribH1 and ribH2, which are located on different chromosomes. The ribH2 gene was shown previously to specify a lumazine synthase (type II lumazine synthase) with an unusual decameric structure and a very high Km for 3,4-dihydroxy-2-butanone 4-phosphate. Moreover, the protein was found to be an immunodominant Brucella antigen and was able to generate strong humoral as well as cellular immunity against Brucella abortus in mice. We have now cloned and expressed the ribH1 gene, which is located inside a small riboflavin operon, together with two other putative riboflavin biosynthesis genes and the nusB gene, specifying an antitermination factor. The RibH1 protein (type I lumazine synthase) is a homopentamer catalyzing the formation of 6,7-dimethyl-8-ribityllumazine at a rate of 18 nmol mg(-1) min(-1). Sequence comparison of lumazine synthases from archaea, bacteria, plants, and fungi suggests a family of proteins comprising archaeal lumazine and riboflavin synthases, type I lumazine synthases, and the eubacterial type II lumazine synthases.
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Morgunova E, Illarionov B, Sambaiah T, Haase I, Bacher A, Cushman M, Fischer M, Ladenstein R. Structural and thermodynamic insights into the binding mode of five novel inhibitors of lumazine synthase from Mycobacterium tuberculosis. FEBS J 2006; 273:4790-804. [PMID: 16984393 DOI: 10.1111/j.1742-4658.2006.05481.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Recently published genomic investigations of the human pathogen Mycobacterium tuberculosis have revealed that genes coding the proteins involved in riboflavin biosynthesis are essential for the growth of the organism. Because the enzymes involved in cofactor biosynthesis pathways are not present in humans, they appear to be promising candidates for the development of therapeutic drugs. The substituted purinetrione compounds have demonstrated high affinity and specificity to lumazine synthase, which catalyzes the penultimate step of riboflavin biosynthesis in bacteria and plants. The structure of M. tuberculosis lumazine synthase in complex with five different inhibitor compounds is presented, together with studies of the binding reactions by isothermal titration calorimetry. The inhibitors showed the association constants in the micromolar range. The analysis of the structures demonstrated the specific features of the binding of different inhibitors. The comparison of the structures and binding modes of five different inhibitors allows us to propose the ribitylpurinetrione compounds with C4-C5 alkylphosphate chains as most promising leads for further development of therapeutic drugs against M. tuberculosis.
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Affiliation(s)
- Ekaterina Morgunova
- Karolinska Institutet, NOVUM, Centre for Structural Biochemistry, Huddinge, Sweden.
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Mack M, Grill S. Riboflavin analogs and inhibitors of riboflavin biosynthesis. Appl Microbiol Biotechnol 2006; 71:265-75. [PMID: 16607521 DOI: 10.1007/s00253-006-0421-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2006] [Revised: 03/06/2006] [Accepted: 03/06/2006] [Indexed: 11/30/2022]
Abstract
Flavins are active components of many enzymes. In most cases, riboflavin (vitamin B(2)) as a coenzyme represents the catalytic part of the holoenzyme. Riboflavin is an amphiphatic molecule and allows a large variety of different interactions with the enzyme itself and also with the substrate. A great number of active riboflavin analogs can readily be synthesized by chemical methods and, thus, a large number of possible inhibitors for many different enzyme targets is conceivable. As mammalian and especially human biochemistry depends on flavins as well, the target of the inhibiting flavin analog has to be carefully selected to avoid unwanted effects. In addition to flavoproteins, enzymes, which are involved in the biosynthesis of flavins, are possible targets for anti-infectives. Only a few flavin analogs or inhibitors of flavin biosynthesis have been subjected to detailed studies to evaluate their biological activity. Nevertheless, flavin analogs certainly have the potential to serve as basic structures for the development of novel anti-infectives and it is possible that, in the future, the urgent need for new molecules to fight multiresistant microorganisms will be met.
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Affiliation(s)
- Matthias Mack
- Institute for Technical Microbiology, Mannheim University of Applied Sciences, Germany.
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