1
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Papkou A, Garcia-Pastor L, Escudero JA, Wagner A. A rugged yet easily navigable fitness landscape. Science 2023; 382:eadh3860. [PMID: 37995212 DOI: 10.1126/science.adh3860] [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: 03/01/2023] [Accepted: 09/29/2023] [Indexed: 11/25/2023]
Abstract
Fitness landscape theory predicts that rugged landscapes with multiple peaks impair Darwinian evolution, but experimental evidence is limited. In this study, we used genome editing to map the fitness of >260,000 genotypes of the key metabolic enzyme dihydrofolate reductase in the presence of the antibiotic trimethoprim, which targets this enzyme. The resulting landscape is highly rugged and harbors 514 fitness peaks. However, its highest peaks are accessible to evolving populations via abundant fitness-increasing paths. Different peaks share large basins of attraction that render the outcome of adaptive evolution highly contingent on chance events. Our work shows that ruggedness need not be an obstacle to Darwinian evolution but can reduce its predictability. If true in general, the complexity of optimization problems on realistic landscapes may require reappraisal.
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Affiliation(s)
- Andrei Papkou
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Lucia Garcia-Pastor
- Departamento de Sanidad Animal and VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
| | - José Antonio Escudero
- Departamento de Sanidad Animal and VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, NM, USA
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2
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Lemay-St-Denis C, Pelletier JN. From a binding module to essential catalytic activity: how nature stumbled on a good thing. Chem Commun (Camb) 2023; 59:12560-12572. [PMID: 37791701 DOI: 10.1039/d3cc04209j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Enzymes are complex macromolecules capable of catalyzing a wide variety of chemical reactions with high efficiency. Nonetheless, biological catalysis can be rudimentary. Here, we describe an enzyme that is built from a simple protein fold. This short protein sequence - almost a peptide - belongs to the ancient SH3 family of binding modules. Surprisingly, this binding module catalyzes the specific reduction of dihydrofolate using NADPH as a reducing cofactor, making this a dihydrofolate reductase. Too small to provide all the required binding and catalytic machinery on its own, it homotetramerizes, thus creating a large, central active site environment. Remarkably, none of the active site residues is essential to the catalytic function. Instead, backbone interactions juxtapose the reducing cofactor proximal to the target imine of the folate substrate, and a specific motion of the substrate promotes formation of the transition state. In this feature article, we describe the features that make this small protein a functional enzyme capable of catalyzing a metabolically essential reaction, highlighting the characteristics that make it a model for the evolution of primitive enzymes from binding modules.
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Affiliation(s)
- Claudèle Lemay-St-Denis
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
| | - Joelle N Pelletier
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
- Chemistry Department, Université de Montréal, Montreal, QC, Canada.
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3
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Kneis D, Lemay-St-Denis C, Cellier-Goetghebeur S, Elena AX, Berendonk TU, Pelletier JN, Heß S. Trimethoprim resistance in surface and wastewater is mediated by contrasting variants of the dfrB gene. THE ISME JOURNAL 2023; 17:1455-1466. [PMID: 37369703 PMCID: PMC10432401 DOI: 10.1038/s41396-023-01460-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023]
Abstract
Trimethoprim (TMP) is a low-cost, widely prescribed antibiotic. Its effectiveness is increasingly challenged by the spread of genes coding for TMP-resistant dihydrofolate reductases: dfrA, and the lesser-known, evolutionarily unrelated dfrB. Despite recent reports of novel variants conferring high level TMP resistance (dfrB10 to dfrB21), the prevalence of dfrB is still unknown due to underreporting, heterogeneity of the analyzed genetic material in terms of isolation sources, and limited bioinformatic processing. In this study, we explored a coherent set of shotgun metagenomic sequences to quantitatively estimate the abundance of dfrB gene variants in aquatic environments. Specifically, we scanned sequences originating from influents and effluents of municipal sewage treatment plants as well as river-borne microbiomes. Our analyses reveal an increased prevalence of dfrB1, dfrB2, dfrB3, dfrB4, dfrB5, and dfrB7 in wastewater microbiomes as compared to freshwater. These gene variants were frequently found in genomic neighborship with other resistance genes, transposable elements, and integrons, indicating their mobility. By contrast, the relative abundances of the more recently discovered variants dfrB9, dfrB10, and dfrB13 were significantly higher in freshwater than in wastewater microbiomes. Moreover, their direct neighborship with other resistance genes or markers of mobile genetic elements was significantly less likely. Our findings suggest that natural freshwater communities form a major reservoir of the recently discovered dfrB gene variants. Their proliferation and mobilization in response to the exposure of freshwater communities to selective TMP concentrations may promote the prevalence of high-level TMP resistance and thus limit the future effectiveness of antimicrobial therapies.
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Affiliation(s)
- David Kneis
- TU Dresden, Institute of Hydrobiology, 01062, Dresden, Germany.
| | - Claudèle Lemay-St-Denis
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
- Department of Biochemistry & Molecular Medicine, University of Montréal, Montréal, QC, H3T 1J4, Canada
| | - Stella Cellier-Goetghebeur
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
- Department of Biochemistry & Molecular Medicine, University of Montréal, Montréal, QC, H3T 1J4, Canada
| | - Alan X Elena
- TU Dresden, Institute of Hydrobiology, 01062, Dresden, Germany
| | | | - Joelle N Pelletier
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
- Department of Biochemistry & Molecular Medicine, University of Montréal, Montréal, QC, H3T 1J4, Canada
- Chemistry Department, University of Montréal, Montréal, QC, H2V 0B3, Canada
| | - Stefanie Heß
- TU Dresden, Institute of Microbiology, 01062, Dresden, Germany
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4
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Lemay-St-Denis C, Alejaldre L, Jemouai Z, Lafontaine K, St-Aubin M, Hitache K, Valikhani D, Weerasinghe NW, Létourneau M, Thibodeaux CJ, Doucet N, Baron C, Copp JN, Pelletier JN. A conserved SH3-like fold in diverse putative proteins tetramerizes into an oxidoreductase providing an antimicrobial resistance phenotype. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220040. [PMID: 36633286 PMCID: PMC9835603 DOI: 10.1098/rstb.2022.0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
We present a potential mechanism for emergence of catalytic activity that is essential for survival, from a non-catalytic protein fold. The type B dihydrofolate reductase (DfrB) family of enzymes were first identified in pathogenic bacteria because their dihydrofolate reductase activity is sufficient to provide trimethoprim (TMP) resistance. DfrB enzymes are described as poorly evolved as a result of their unusual structural and kinetic features. No characterized protein shares sequence homology with DfrB enzymes; how they evolved to emerge in the modern resistome is unknown. In this work, we identify DfrB homologues from a database of putative and uncharacterized proteins. These proteins include an SH3-like fold homologous to the DfrB enzymes, embedded in a variety of additional structural domains. By means of functional, structural and biophysical characterization, we demonstrate that these distant homologues and their extracted SH3-like fold can display dihydrofolate reductase activity and confer TMP resistance. We provide evidence of tetrameric assembly and catalytic mechanism analogous to that of DfrB enzymes. These results contribute, to our knowledge, the first insights into a potential evolutionary path taken by this SH3-like fold to emerge in the modern resistome following introduction of TMP. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Claudèle Lemay-St-Denis
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, Québec G1V 0A6, Canada,CGCC, Center in Green Chemistry and Catalysis, Montréal, Québec H2V 0B3, Canada,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Lorea Alejaldre
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, Québec G1V 0A6, Canada,CGCC, Center in Green Chemistry and Catalysis, Montréal, Québec H2V 0B3, Canada,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Zakaria Jemouai
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Kiana Lafontaine
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, Québec G1V 0A6, Canada,CGCC, Center in Green Chemistry and Catalysis, Montréal, Québec H2V 0B3, Canada,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Maxime St-Aubin
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, Québec G1V 0A6, Canada,CGCC, Center in Green Chemistry and Catalysis, Montréal, Québec H2V 0B3, Canada,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Katia Hitache
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, Québec G1V 0A6, Canada,CGCC, Center in Green Chemistry and Catalysis, Montréal, Québec H2V 0B3, Canada,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Donya Valikhani
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, Québec G1V 0A6, Canada,CGCC, Center in Green Chemistry and Catalysis, Montréal, Québec H2V 0B3, Canada,Chemistry Department, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Nuwani W. Weerasinghe
- Department of Chemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, Québec H3A 0B8, Canada
| | - Myriam Létourneau
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, Québec G1V 0A6, Canada,Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Québec H7V 1B7, Canada
| | - Christopher J. Thibodeaux
- Department of Chemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, Québec H3A 0B8, Canada
| | - Nicolas Doucet
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, Québec G1V 0A6, Canada,Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Québec H7V 1B7, Canada
| | - Christian Baron
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec H3C 3J7, Canada,Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Janine N. Copp
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Joelle N. Pelletier
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, Québec G1V 0A6, Canada,CGCC, Center in Green Chemistry and Catalysis, Montréal, Québec H2V 0B3, Canada,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec H3C 3J7, Canada,Chemistry Department, Université de Montréal, Montréal, Québec H3C 3J7, Canada
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5
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Cisneros AF, Gagnon-Arsenault I, Dubé AK, Després PC, Kumar P, Lafontaine K, Pelletier JN, Landry CR. Epistasis between promoter activity and coding mutations shapes gene evolvability. SCIENCE ADVANCES 2023; 9:eadd9109. [PMID: 36735790 PMCID: PMC9897669 DOI: 10.1126/sciadv.add9109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 12/22/2022] [Indexed: 06/01/2023]
Abstract
The evolution of protein-coding genes proceeds as mutations act on two main dimensions: regulation of transcription level and the coding sequence. The extent and impact of the connection between these two dimensions are largely unknown because they have generally been studied independently. By measuring the fitness effects of all possible mutations on a protein complex at various levels of promoter activity, we show that promoter activity at the optimal level for the wild-type protein masks the effects of both deleterious and beneficial coding mutations. Mutations that are deleterious at low activity but masked at optimal activity are slightly destabilizing for individual subunits and binding interfaces. Coding mutations that increase protein abundance are beneficial at low expression but could potentially incur a cost at high promoter activity. We thereby demonstrate that promoter activity in interaction with protein properties can dictate which coding mutations are beneficial, neutral, or deleterious.
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Affiliation(s)
- Angel F. Cisneros
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, G1V 0A6, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Québec, Canada
- Centre de recherche sur les données massives, Université Laval, G1V 0A6, Québec, Canada
| | - Isabelle Gagnon-Arsenault
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, G1V 0A6, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Québec, Canada
- Centre de recherche sur les données massives, Université Laval, G1V 0A6, Québec, Canada
- Département de biologie, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada
| | - Alexandre K. Dubé
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, G1V 0A6, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Québec, Canada
- Centre de recherche sur les données massives, Université Laval, G1V 0A6, Québec, Canada
- Département de biologie, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada
| | - Philippe C. Després
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, G1V 0A6, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Québec, Canada
- Centre de recherche sur les données massives, Université Laval, G1V 0A6, Québec, Canada
| | - Pradum Kumar
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Kiana Lafontaine
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Québec, Canada
- Département de biochimie et de médecine moléculaire, Faculté de médecine, Université de Montréal, H3C 3J7, Montréal, Canada
| | - Joelle N. Pelletier
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Québec, Canada
- Département de biochimie et de médecine moléculaire, Faculté de médecine, Université de Montréal, H3C 3J7, Montréal, Canada
- Département de chimie, Faculté des arts et des sciences, Université de Montréal, H3C 3J7, Montréal, Canada
| | - Christian R. Landry
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada
- Institut de biologie intégrative et des systèmes, Université Laval, G1V 0A6, Québec, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Québec, Canada
- Centre de recherche sur les données massives, Université Laval, G1V 0A6, Québec, Canada
- Département de biologie, Faculté des sciences et de génie, Université Laval, G1V 0A6, Québec, Canada
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6
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Cellier-Goetghebeur S, Lafontaine K, Lemay-St-Denis C, Tsamo P, Bonneau-Burke A, Copp JN, Pelletier JN. Discovery of Highly Trimethoprim-Resistant DfrB Dihydrofolate Reductases in Diverse Environmental Settings Suggests an Evolutionary Advantage Unrelated to Antibiotic Resistance. Antibiotics (Basel) 2022; 11:antibiotics11121768. [PMID: 36551425 PMCID: PMC9774602 DOI: 10.3390/antibiotics11121768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022] Open
Abstract
Type B dihydrofolate reductases (DfrB) are intrinsically highly resistant to the widely used antibiotic trimethoprim, posing a threat to global public health. The ten known DfrB family members have been strongly associated with genetic material related to the application of antibiotics. Several dfrB genes were associated with multidrug resistance contexts and mobile genetic elements, integrated both in chromosomes and plasmids. However, little is known regarding their presence in other environments. Here, we investigated the presence of dfrB beyond the traditional areas of enquiry by conducting metagenomic database searches from environmental settings where antibiotics are not prevalent. Thirty putative DfrB homologues that share 62 to 95% identity with characterized DfrB were identified. Expression of ten representative homologues verified trimethoprim resistance in all and dihydrofolate reductase activity in most. Contrary to samples associated with the use of antibiotics, the newly identified dfrB were rarely associated with mobile genetic elements or antibiotic resistance genes. Instead, association with metabolic enzymes was observed, suggesting an evolutionary advantage unrelated to antibiotic resistance. Our results are consistent with the hypothesis that multiple dfrB exist in diverse environments from which dfrB were mobilized into the clinically relevant resistome. Our observations reinforce the need to closely monitor their progression.
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Affiliation(s)
- Stella Cellier-Goetghebeur
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
| | - Kiana Lafontaine
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
| | - Claudèle Lemay-St-Denis
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
| | - Princesse Tsamo
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
| | - Alexis Bonneau-Burke
- The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
- Chemistry Department, Université de Montréal, Montréal, QC H2V 0B3, Canada
| | - Janine N. Copp
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Joelle N. Pelletier
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
- Chemistry Department, Université de Montréal, Montréal, QC H2V 0B3, Canada
- Correspondence:
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7
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Computational Development of Inhibitors of Plasmid-Borne Bacterial Dihydrofolate Reductase. Antibiotics (Basel) 2022; 11:antibiotics11060779. [PMID: 35740185 PMCID: PMC9220120 DOI: 10.3390/antibiotics11060779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 12/03/2022] Open
Abstract
Resistance to trimethoprim and other antibiotics targeting dihydrofolate reductase may arise in bacteria harboring an atypical, plasmid-encoded, homotetrameric dihydrofolate reductase, called R67 DHFR. Although developing inhibitors to this enzyme may be expected to be promising drugs to fight trimethoprim-resistant strains, there is a paucity of reports describing the development of such molecules. In this manuscript, we describe the design of promising lead compounds to target R67 DHFR. Density-functional calculations were first used to identify the modifications of the pterin core that yielded derivatives likely to bind the enzyme and not susceptible to being acted upon by it. These unreactive molecules were then docked to the active site, and the stability of the docking poses of the best candidates was analyzed through triplicate molecular dynamics simulations, and compared to the binding stability of the enzyme–substrate complex. Molecule 32 ([6-(methoxymethyl)-4-oxo-3,7-dihydro-4H-pyrano[2,3-d]pyrimidin-2-yl]methyl-guanidinium) was shown by this methodology to afford extremely stable binding towards R67 DHFR and to prevent simultaneous binding to the substrate. Additional docking and molecular dynamics simulations further showed that this candidate also binds strongly to the canonical prokaryotic dihydrofolate reductase and to human DHFR, and is therefore likely to be useful to the development of chemotherapeutic agents and of dual-acting antibiotics that target the two types of bacterial dihydrofolate reductase.
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8
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Antibiotics Resistance in Escherichia coli Isolated from Livestock in the Emirate of Abu Dhabi, UAE, 2014–2019. Int J Microbiol 2022; 2022:3411560. [PMID: 35519508 PMCID: PMC9064518 DOI: 10.1155/2022/3411560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/07/2022] [Indexed: 11/17/2022] Open
Abstract
Escherichia coli (E. coli) is a zoonotic pathogen that showed growing resistance to antibiotics. No descriptive analysis highlights the threat of antimicrobial-resistant (AMR) of E. coli among livestock in the United Arab Emirates (UAE). Herein, we conducted phenotypic and genotypic resistance studies on E. coli isolates from livestock samples in the Emirate of Abu Dhabi based on routine diagnosis between the periods 2014–2019. Bacterial culture and disk diffusion methods were used for bacterial isolation and phenotypic resistance analysis. Resistance mechanism was studied by PCR targeting the most commonly resistance genes: ampicillin (blaSHV, blaCMY, and blaTEM-1B), tetracyclines (tetA and tetB), co-trimoxazole [sulfamethoxazole (sul1, sul2, and sul3) + trimethoprim (dfrA1 and dfrA17)], aminoglycosides [aph(3'')-Ia, aph(6)-Id, and aac(3)-IV], and fluoroquinolones (qnrA and aac(6’)-Ib-cr). Analysis of 165 E. coli isolates showed resistant to ampicillin, tetracycline, co-trimoxazole, gentamicin, and enrofloxacin by 157/165 (95.4%), 154/165 (93.6%), 141/165 (86%), 139/165 (85%), and 135/165 (82.7%), respectively. Predominant resistance gene/s detected by PCR were blaCMY (119/160, 72%) and blaTEM-1B (154/160, 96.3%) for ampicillin; tetA (162/164, 98.8%) and tetB (112/164, 68.3%) for tetracyclines; sul2 (156/164, 95%), sul3 (138/164, 84%), and dfra17 (74/164, 44.5%) for co-trimoxazole; aph(3'')-Ia (134/164, 82.1%) and aph(6)-Id (161/164, 98.2%) for aminoglycosides; and aac(6’)-Ib-cr (61/61, 100%) for enrofloxacin. Both phenotypic and genotypic analyses revealed that all E. coli isolates were multidrug-resistant (resistance to 3, 4, and 5 antibiotics classes by 3.6%, 57.6%, and 38.8%, respectively) carrying one or more resistance gene/s for the same antibiotic. PCR profiling confirmed the presence of resistance genes corresponding to their antibiotic profile. Results of the study will highlight the knowledge based on E. coli AMR related to livestock in UAE that may call for interventions.
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9
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Karimi E, Heshmati E, Khalifeh K. Evolutionary adaptation of DHFR via expression of enzyme isoforms with various binding properties and dynamics behavior: a bioinformatics and computational study. Biol Chem 2021; 403:643-652. [PMID: 34905670 DOI: 10.1515/hsz-2021-0346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/04/2021] [Indexed: 11/15/2022]
Abstract
We compared the binding properties and dynamics of three experimentally reviewed isoforms of human dihydrofolate reductase (DHFR). The cytoplasmic variants including isoforms1 and 2 (iso1 and iso2) are produced by alternative splicing; while the mitochondrial form is located in the mitochondria. The iso1 as the canonical sequence contains 187 residues, and iso2 differs from the iso1, where it has 1-52 residues missing at the N-terminus of canonical sequence. Here, the structural models of the iso2 and mitochondrial forms were constructed by the MODELLER program using the crystal structure of the iso1 as the template. Bioinformatics analysis on ligand-bearing structures demonstrates that mitochondrial variant forms more stable complex with ligands compared with iso1 and 2, indicating their different binding properties. The root mean square fluctuation (RMSF) data suggest that C-terminus of iso1 contains two representative highly flexible fragments, while iso2 contains a highly flexible fragment at N-terminus end. Interestingly, both ends of mitochondrial variant have a degree of rigidity. Finally, the observation of differences in structural dynamics and binding properties predicts that the simultaneous existence of enzyme isoforms is a way to increase the speed of the enzyme maneuver in response to various environmental conditions. This prediction needs to be tested experimentally.
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Affiliation(s)
- Elahe Karimi
- Department of Biology, Faculty of Sciences, University of Zanjan, University Blvd., Zanjan 45371-38791, Iran
| | - Emran Heshmati
- Department of Biology, Faculty of Sciences, University of Zanjan, University Blvd., Zanjan 45371-38791, Iran
| | - Khosrow Khalifeh
- Department of Biology, Faculty of Sciences, University of Zanjan, University Blvd., Zanjan 45371-38791, Iran.,Department of Biotechnology, Research Institute of Modern Biological Techniques, University of Zanjan, Zanjan, Iran
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10
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Singh P, Vandemeulebroucke A, Li J, Schulenburg C, Fortunato G, Kohen A, Hilvert D, Cheatum CM. Evolution of the Chemical Step in Enzyme Catalysis. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00442] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Priyanka Singh
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | | | - Jiayue Li
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Cindy Schulenburg
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Gabriel Fortunato
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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11
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Lemay-St-Denis C, Diwan SS, Pelletier JN. The Bacterial Genomic Context of Highly Trimethoprim-Resistant DfrB Dihydrofolate Reductases Highlights an Emerging Threat to Public Health. Antibiotics (Basel) 2021; 10:antibiotics10040433. [PMID: 33924456 PMCID: PMC8103504 DOI: 10.3390/antibiotics10040433] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/08/2021] [Accepted: 04/12/2021] [Indexed: 01/21/2023] Open
Abstract
Type B dihydrofolate reductase (dfrb) genes were identified following the introduction of trimethoprim in the 1960s. Although they intrinsically confer resistance to trimethoprim (TMP) that is orders of magnitude greater than through other mechanisms, the distribution and prevalence of these short (237 bp) genes is unknown. Indeed, this knowledge has been hampered by systematic biases in search methodologies. Here, we investigate the genomic context of dfrbs to gain information on their current distribution in bacterial genomes. Upon searching publicly available databases, we identified 61 sequences containing dfrbs within an analyzable genomic context. The majority (70%) of those sequences also harbor virulence genes and 97% of the dfrbs are found near a mobile genetic element, representing a potential risk for antibiotic resistance genes. We further identified and confirmed the TMP-resistant phenotype of two new members of the family, dfrb10 and dfrb11. Dfrbs are found both in Betaproteobacteria and Gammaproteobacteria, a majority (59%) being in Pseudomonas aeruginosa. Previously labelled as strictly plasmid-borne, we found 69% of dfrbs in the chromosome of pathogenic bacteria. Our results demonstrate that the intrinsically TMP-resistant dfrbs are a potential emerging threat to public health and justify closer surveillance of these genes.
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Affiliation(s)
- Claudèle Lemay-St-Denis
- Department of Biochemistry and Molecular Medecine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
| | - Sarah-Slim Diwan
- Department of Biochemistry and Molecular Medecine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
| | - Joelle N Pelletier
- Department of Biochemistry and Molecular Medecine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
- Chemistry Department, Université de Montréal, Montréal, QC H2V 0B3, Canada
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12
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Willms IM, Grote M, Kocatürk M, Singhoff L, Kraft AA, Bolz SH, Nacke H. Novel Soil-Derived Beta-Lactam, Chloramphenicol, Fosfomycin and Trimethoprim Resistance Genes Revealed by Functional Metagenomics. Antibiotics (Basel) 2021; 10:antibiotics10040378. [PMID: 33916668 PMCID: PMC8066302 DOI: 10.3390/antibiotics10040378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 11/16/2022] Open
Abstract
Antibiotic resistance genes (ARGs) in soil are considered to represent one of the largest environmental resistomes on our planet. As these genes can potentially be disseminated among microorganisms via horizontal gene transfer (HGT) and in some cases are acquired by clinical pathogens, knowledge about their diversity, mobility and encoded resistance spectra gained increasing public attention. This knowledge offers opportunities with respect to improved risk prediction and development of strategies to tackle antibiotic resistance, and might help to direct the design of novel antibiotics, before further resistances reach hospital settings or the animal sector. Here, metagenomic libraries, which comprise genes of cultivated microorganisms, but, importantly, also those carried by the uncultured microbial majority, were screened for novel ARGs from forest and grassland soils. We detected three new beta-lactam, a so far unknown chloramphenicol, a novel fosfomycin, as well as three previously undiscovered trimethoprim resistance genes. These ARGs were derived from phylogenetically diverse soil bacteria and predicted to encode antibiotic inactivation, antibiotic efflux, or alternative variants of target enzymes. Moreover, deduced gene products show a minimum identity of ~21% to reference database entries and confer high-level resistance. This highlights the vast potential of functional metagenomics for the discovery of novel ARGs from soil ecosystems.
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13
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Nguyen H, Abramov M, Eremeeva E, Herdewijn P. In Vivo Expression of Genetic Information from Phosphoramidate-DNA. Chembiochem 2021; 21:272-278. [PMID: 31868979 DOI: 10.1002/cbic.201900712] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Indexed: 12/31/2022]
Abstract
Chemically modified genes and genomes with customized properties will become a valuable tool in numerous fields, including synthetic biology, biotechnology, and medicine. These genetic materials are meant to store and exchange information with DNA and RNA while tuning their functionality. Herein, we outline the development of an alternative genetic system carrying phosphoramidate linkages that successfully propagates genetic information in bacteria and at the same time is labile to acidic conditions. The P3'→N5' phosphoramidate-containing DNA (PN-DNA) was enzymatically synthesized by using 5'-amino-2',5'-deoxycytidine 5'-N-triphosphates (NH-dCTPs) as substrates for DNA polymerases and employed to encode antibiotic resistance in Escherichia coli. The resulting PN-DNA can be efficiently destroyed by mild acidic conditions, whereas an unmodified counterpart remains intact. A cloning strategy was proposed for assembling modified fragments into a genome. This method can be of interest to scientists working in the field of orthogonal nucleic acid genes and genomes.
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Affiliation(s)
- Hoai Nguyen
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000, Leuven, Belgium
| | - Mikhail Abramov
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000, Leuven, Belgium
| | - Elena Eremeeva
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000, Leuven, Belgium
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000, Leuven, Belgium
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14
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Fuente-Gómez GJ, Kellum CL, Miranda AC, Duff MR, Howell EE. Differentiation of the binding of two ligands to a tetrameric protein with a single symmetric active site by 19 F NMR. Protein Sci 2020; 30:477-484. [PMID: 33269489 PMCID: PMC7784773 DOI: 10.1002/pro.4007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/20/2020] [Accepted: 11/26/2020] [Indexed: 01/31/2023]
Abstract
R67 dihydrofolate reductase (R67 DHFR) is a plasmid‐encoded enzyme that confers resistance to the antibacterial drug trimethoprim. R67 DHFR is a tetramer with a single active site that is unusual as both cofactor and substrate are recognized by symmetry‐related residues. Such promiscuity has limited our previous efforts to differentiate ligand binding by NMR. To address this problem, we incorporated fluorine at positions 4, 5, 6, or 7 of the indole rings of tryptophans 38 and 45 and characterized the spectra to determine which probe was optimal for studying ligand binding. Two resonances were observed for all apo proteins. Unexpectedly, the W45 resonance appeared broad, and truncation of the disordered N‐termini resulted in the appearance of one sharp W45 resonance. These results are consistent with interaction of the N‐terminus with W45. Binding of the cofactor broadened W38 for all fluorine probes, whereas substrate, dihydrofolate, binding resulted in the appearance of three new resonances for 4‐ and 5‐fluoroindole labeled protein and severe line broadening for 6‐ and 7‐fluoroindole R67 DHFR. W45 became slightly broader upon ligand binding. With only two peaks in the 19F NMR spectra, our data were able to differentiate cofactor and substrate binding to the single, symmetric active site of R67 DHFR and yield binding affinities.
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Affiliation(s)
- Gabriel J Fuente-Gómez
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee, USA
| | - Creighton L Kellum
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee, USA
| | - Alexis C Miranda
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee, USA
| | - Michael R Duff
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee, USA
| | - Elizabeth E Howell
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee, USA
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15
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Toulouse JL, Shi G, Lemay-St-Denis C, Ebert MCCJC, Deon D, Gagnon M, Ruediger E, Saint-Jacques K, Forge D, Vanden Eynde JJ, Marinier A, Ji X, Pelletier JN. Dual-Target Inhibitors of the Folate Pathway Inhibit Intrinsically Trimethoprim-Resistant DfrB Dihydrofolate Reductases. ACS Med Chem Lett 2020; 11:2261-2267. [PMID: 33214838 DOI: 10.1021/acsmedchemlett.0c00393] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/28/2020] [Indexed: 12/11/2022] Open
Abstract
Trimethoprim (TMP) is widely used to treat infections in humans and in livestock, accelerating the incidence of TMP resistance. The emergent and largely untracked type II dihydrofolate reductases (DfrBs) are intrinsically TMP-resistant plasmid-borne Dfrs that are structurally and evolutionarily unrelated to chromosomal Dfrs. We report kinetic characterization of the known DfrB family members. Their kinetic constants are conserved and all are poorly inhibited by TMP, consistent with TMP resistance. We investigate their inhibition with known and novel bisubstrate inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK). Importantly, all are inhibited by the HPPK inhibitors, making these molecules dual-target inhibitors of two folate pathway enzymes that are strictly microbial.
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Affiliation(s)
- Jacynthe L. Toulouse
- Département de biochimie, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
- PROTEO, Quebec G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, Quebec H2V 0B3, Canada
| | - Genbin Shi
- Macromolecular Crystallography Laboratory, NCI, Frederick, Maryland 21702, United States
| | - Claudèle Lemay-St-Denis
- Département de biochimie, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
- PROTEO, Quebec G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, Quebec H2V 0B3, Canada
| | | | - Daniel Deon
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Marc Gagnon
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Edward Ruediger
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Kévin Saint-Jacques
- Département de chimie, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Delphine Forge
- Laboratoire de chimie organique, Université de Mons, 7000 Mons, Belgium
| | | | - Anne Marinier
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Xinhua Ji
- Macromolecular Crystallography Laboratory, NCI, Frederick, Maryland 21702, United States
| | - Joelle N. Pelletier
- Département de biochimie, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
- PROTEO, Quebec G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, Quebec H2V 0B3, Canada
- Département de biochimie, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
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16
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A novel method to determine antibiotic sensitivity in Bdellovibrio bacteriovorus reveals a DHFR-dependent natural trimethoprim resistance. Sci Rep 2020; 10:5315. [PMID: 32210253 PMCID: PMC7093396 DOI: 10.1038/s41598-020-62014-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
Bdellovibrio bacteriovorus is a small Gram-negative bacterium and an obligate predator of other Gram-negative bacteria. Prey resistance to B. bacteriovorus attack is rare and transient. This consideration together with its safety and low immunogenicity makes B. bacteriovorus a valid alternative to antibiotics, especially in the treatment of multidrug resistant pathogens. In this study we developed a novel technique to estimate B. bacteriovorus sensitivity against antibiotics in order to make feasible the development and testing of co-therapies with antibiotics that would increase its antimicrobial efficacy and at the same time reduce the development of drug resistance. Results from tests performed with this technique show that among all tested antibiotics, trimethoprim has the lowest antimicrobial effect on B. bacteriovorus. Additional experiments revealed that the mechanism of trimethoprim resistance in B. bacteriovorus depends on the low affinity of this compound for the B. bacteriovorus dihydrofolate reductase (Bd DHFR).
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17
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Toulouse J, Yachnin BJ, Ruediger EH, Deon D, Gagnon M, Saint-Jacques K, Ebert MCCC, Forge D, Bastien D, Colin DY, Vanden Eynde JJ, Marinier A, Berghuis AM, Pelletier JN. Structure-Based Design of Dimeric Bisbenzimidazole Inhibitors to an Emergent Trimethoprim-Resistant Type II Dihydrofolate Reductase Guides the Design of Monomeric Analogues. ACS OMEGA 2019; 4:10056-10069. [PMID: 31460098 PMCID: PMC6648814 DOI: 10.1021/acsomega.9b00640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/22/2019] [Indexed: 05/18/2023]
Abstract
The worldwide use of the broad-spectrum antimicrobial trimethoprim (TMP) has induced the rise of TMP-resistant microorganisms. In addition to resistance-causing mutations of the microbial chromosomal dihydrofolate reductase (Dfr), the evolutionarily and structurally unrelated type II Dfrs (DfrBs) have been identified in TMP-resistant microorganisms. DfrBs are intrinsically TMP-resistant and allow bacterial proliferation when the microbial chromosomal Dfr is TMP-inhibited, making these enzymes important targets for inhibitor development. Furthermore, DfrBs occur in multiresistance plasmids, potentially accelerating their dissemination. We previously reported symmetrical bisbenzimidazoles that are the first selective inhibitors of the only well-characterized DfrB, DfrB1. Here, their diversification provides a new series of inhibitors (K i = 1.7-12.0 μM). Our results reveal two prominent features: terminal carboxylates and inhibitor length allow the establishment of essential interactions with DfrB1. Two crystal structures demonstrate the simultaneous binding of two inhibitor molecules in the symmetrical active site. Observations of those dimeric inhibitors inspired the design of monomeric analogues, binding in a single copy yet offering similar inhibition potency (K i = 1.1 and 7.4 μM). Inhibition of a second member of the DfrB family, DfrB4, suggests the generality of these inhibitors. These results provide key insights into inhibition of the highly TMP-resistant DfrBs, opening avenues to downstream development of antibiotics for combatting this emergent source of resistance.
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Affiliation(s)
- Jacynthe
L. Toulouse
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
- PROTEO,
the Québec Network for Research on Protein, Function, Engineering
and Applications, Quebec G1V 0A6, Canada
- CGCC,
The Center in Green Chemistry and Catalysis, Montréal H3A
0B8, Quebec, Canada
| | - Brahm J. Yachnin
- PROTEO,
the Québec Network for Research on Protein, Function, Engineering
and Applications, Quebec G1V 0A6, Canada
- Department
of Biochemistry, McGill University, Montréal H3A 0G4, Quebec, Canada
| | - Edward H. Ruediger
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
| | - Daniel Deon
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
| | - Marc Gagnon
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
| | - Kévin Saint-Jacques
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
- Département
de Chimie, Université de Sherbrooke, Sherbrooke J1K 0A5, Quebec, Canada
| | | | - Delphine Forge
- Laboratoire
de Chimie Organique, Université de
Mons, Mons 7000, Belgium
| | - Dominic Bastien
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
- PROTEO,
the Québec Network for Research on Protein, Function, Engineering
and Applications, Quebec G1V 0A6, Canada
- CGCC,
The Center in Green Chemistry and Catalysis, Montréal H3A
0B8, Quebec, Canada
| | - Damien Y. Colin
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
- PROTEO,
the Québec Network for Research on Protein, Function, Engineering
and Applications, Quebec G1V 0A6, Canada
- CGCC,
The Center in Green Chemistry and Catalysis, Montréal H3A
0B8, Quebec, Canada
| | | | - Anne Marinier
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
| | - Albert M. Berghuis
- PROTEO,
the Québec Network for Research on Protein, Function, Engineering
and Applications, Quebec G1V 0A6, Canada
- Department
of Biochemistry, McGill University, Montréal H3A 0G4, Quebec, Canada
| | - Joelle N. Pelletier
- Département
de Biochimie, Institute for Research in Immunology and Cancer
(IRIC), and Département de Chimie, Université
de Montréal, Montreal H3C 3J7, Quebec, Canada
- PROTEO,
the Québec Network for Research on Protein, Function, Engineering
and Applications, Quebec G1V 0A6, Canada
- CGCC,
The Center in Green Chemistry and Catalysis, Montréal H3A
0B8, Quebec, Canada
- E-mail: . Phone: 514-343-2124. Fax: 514-343-7586
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18
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Duff MR, Desai N, Craig MA, Agarwal PK, Howell EE. Crowders Steal Dihydrofolate Reductase Ligands through Quinary Interactions. Biochemistry 2019; 58:1198-1213. [PMID: 30724552 DOI: 10.1021/acs.biochem.8b01110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydrofolate reductase (DHFR) reduces dihydrofolate (DHF) to tetrahydrofolate using NADPH as a cofactor. Due to its role in one carbon metabolism, chromosomal DHFR is the target of the antibacterial drug, trimethoprim. Resistance to trimethoprim has resulted in a type II DHFR that is not structurally related to the chromosomal enzyme target. Because of its metabolic significance, understanding DHFR kinetics and ligand binding behavior in more cell-like conditions, where the total macromolecule concentration can be as great as 300 mg/mL, is important. The progress-curve kinetics and ligand binding properties of the drug target (chromosomal E. coli DHFR) and the drug resistant (R67 DHFR) enzymes were studied in the presence of macromolecular cosolutes. There were varied effects on NADPH oxidation and binding to the two DHFRs, with some cosolutes increasing affinity and others weakening binding. However, DHF binding and reduction in both DHFRs decreased in the presence of all cosolutes. The decreased binding of ligands is mostly attributed to weak associations with the macromolecules, as opposed to crowder effects on the DHFRs. Computer simulations found weak, transient interactions for both ligands with several proteins. The net charge of protein cosolutes correlated with effects on NADP+ binding, with near neutral and positively charged proteins having more detrimental effects on binding. For DHF binding, effects correlated more with the size of binding pockets on the protein crowders. These nonspecific interactions between DHFR ligands and proteins predict that the in vivo efficiency of DHFRs may be much lower than expected from their in vitro rates.
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Affiliation(s)
- Michael R Duff
- Department of Biochemistry & Cellular and Molecular Biology Department , University of Tennessee-Knoxville , Knoxville , Tennessee 37996 , United States
| | - Nidhi Desai
- Department of Biochemistry & Cellular and Molecular Biology Department , University of Tennessee-Knoxville , Knoxville , Tennessee 37996 , United States
| | - Michael A Craig
- Department of Biochemistry & Cellular and Molecular Biology Department , University of Tennessee-Knoxville , Knoxville , Tennessee 37996 , United States
| | - Pratul K Agarwal
- Department of Biochemistry & Cellular and Molecular Biology Department , University of Tennessee-Knoxville , Knoxville , Tennessee 37996 , United States
| | - Elizabeth E Howell
- Department of Biochemistry & Cellular and Molecular Biology Department , University of Tennessee-Knoxville , Knoxville , Tennessee 37996 , United States
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19
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In Vivo Titration of Folate Pathway Enzymes. Appl Environ Microbiol 2018; 84:AEM.01139-18. [PMID: 30030232 DOI: 10.1128/aem.01139-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/18/2018] [Indexed: 12/12/2022] Open
Abstract
How enzymes behave in cells is likely different from how they behave in the test tube. Previous in vitro studies find that osmolytes interact weakly with folate. Removal of the osmolyte from the solvation shell of folate is more difficult than removal of water, which weakens binding of folate to its enzyme partners. To examine if this phenomenon occurs in vivo, osmotic stress titrations were performed with Escherichia coli Two strategies were employed: resistance to an antibacterial drug and complementation of a knockout strain by the appropriate gene cloned into a plasmid that allows tight control of expression levels as well as labeling by a degradation tag. The abilities of the knockout and complemented strains to grow under osmotic stress were compared. Typically, the knockout strain could grow to high osmolalities on supplemented medium, while the complemented strain stopped growing at lower osmolalities on minimal medium. This pattern was observed for an R67 dihydrofolate reductase clone rescuing a ΔfolA strain, for a methylenetetrahydrofolate reductase clone rescuing a ΔmetF strain, and for a serine hydroxymethyltransferase clone rescuing a ΔglyA strain. Additionally, an R67 dihydrofolate reductase clone allowed E. coli DH5α to grow in the presence of trimethoprim until an osmolality of ∼0.81 is reached, while cells in a control titration lacking antibiotic could grow to 1.90 osmol.IMPORTANCEE. coli can survive in drought and flooding conditions and can tolerate large changes in osmolality. However, the cell processes that limit bacterial growth under high osmotic stress conditions are not known. In this study, the dose of four different enzymes in E. coli was decreased by using deletion strains complemented by the gene carried in a tunable plasmid. Under conditions of limiting enzyme concentration (lower than that achieved by chromosomal gene expression), cell growth can be blocked by osmotic stress conditions that are normally tolerated. These observations indicate that E. coli has evolved to deal with variations in its osmotic environment and that normal protein levels are sufficient to buffer the cell from environmental changes. Additional factors involved in the osmotic pressure response may include altered protein concentration/activity levels, weak solute interactions with ligands which can make it more difficult for proteins to bind their substrates/inhibitors/cofactors in vivo, and/or viscosity effects.
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20
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Toulouse JL, Abraham SMJ, Kadnikova N, Bastien D, Gauchot V, Schmitzer AR, Pelletier JN. Investigation of Classical Organic and Ionic Liquid Cosolvents for Early-Stage Screening in Fragment-Based Inhibitor Design with Unrelated Bacterial and Human Dihydrofolate Reductases. Assay Drug Dev Technol 2017; 15:141-153. [PMID: 28426233 DOI: 10.1089/adt.2016.768] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Drug design by methods such as fragment screening requires effective solubilization of millimolar concentrations of small organic compounds while maintaining the properties of the biological target. We investigate four organic solvents and three 1-butyl-3-methylimidazolium (BMIm)-based ionic liquids (ILs) as cosolvents to establish conditions for screening two structurally unrelated dihydrofolate reductases (DHFRs) that are prime drug targets. Moderate concentrations (10%-15%) of cosolvents had little effect on inhibition of the microbial type II R67 DHFR and of human DHFR (hDHFR), while higher concentrations of organic cosolvents generally decreased activity of both DHFRs. In contrast, a specific IL conserved the activity of one DHFR, while severely reducing the activity of the other, and vice versa, illustrating the differing effect of ILs on distinct protein folds. Most of the cosolvents investigated preserved the fold of R67 DHFR and had little effect on binding of the cofactor NADPH, but reduced the productive affinity for its substrate. In contrast, cosolvents resulted in modest structural destabilization of hDHFR with little effect on productive affinity. We conclude that the organic cosolvents, methanol, dimethylformamide, and dimethylsulfoxide, offer the most balanced conditions for early-stage compound screening as they maintain sufficient biological activity of both DHFRs while allowing for compound dissolution in the millimolar range. However, IL cosolvents showed poor capacity to solubilize organic compounds at millimolar concentrations, mitigating their utility in early-stage screening. Nonetheless, ILs could provide an alternative to classical organic cosolvents when low concentrations of inhibitors are used, as when characterizing higher affinity inhibitors.
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Affiliation(s)
- Jacynthe L Toulouse
- 1 Département de Biochimie, Université de Montréal , Québec, Canada .,2 CGCC, The Center in Green Chemistry and Catalysis , Montréal, Québec, Canada .,3 PROTEO , The Québec Network for Protein Function, Structure and Engineering, Québec, Canada
| | - Sarah M J Abraham
- 2 CGCC, The Center in Green Chemistry and Catalysis , Montréal, Québec, Canada .,3 PROTEO , The Québec Network for Protein Function, Structure and Engineering, Québec, Canada .,4 Département de Chimie, Université de Montréal , Québec, Canada
| | - Natalia Kadnikova
- 2 CGCC, The Center in Green Chemistry and Catalysis , Montréal, Québec, Canada .,3 PROTEO , The Québec Network for Protein Function, Structure and Engineering, Québec, Canada .,4 Département de Chimie, Université de Montréal , Québec, Canada
| | - Dominic Bastien
- 1 Département de Biochimie, Université de Montréal , Québec, Canada .,2 CGCC, The Center in Green Chemistry and Catalysis , Montréal, Québec, Canada .,3 PROTEO , The Québec Network for Protein Function, Structure and Engineering, Québec, Canada
| | - Vincent Gauchot
- 2 CGCC, The Center in Green Chemistry and Catalysis , Montréal, Québec, Canada .,4 Département de Chimie, Université de Montréal , Québec, Canada
| | - Andreea R Schmitzer
- 2 CGCC, The Center in Green Chemistry and Catalysis , Montréal, Québec, Canada .,4 Département de Chimie, Université de Montréal , Québec, Canada
| | - Joelle N Pelletier
- 1 Département de Biochimie, Université de Montréal , Québec, Canada .,2 CGCC, The Center in Green Chemistry and Catalysis , Montréal, Québec, Canada .,3 PROTEO , The Québec Network for Protein Function, Structure and Engineering, Québec, Canada .,4 Département de Chimie, Université de Montréal , Québec, Canada
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21
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Bhojane P, Duff MR, Bafna K, Rimmer GP, Agarwal PK, Howell EE. Aspects of Weak Interactions between Folate and Glycine Betaine. Biochemistry 2016; 55:6282-6294. [PMID: 27768285 PMCID: PMC5198541 DOI: 10.1021/acs.biochem.6b00873] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/19/2016] [Indexed: 01/22/2023]
Abstract
Folate, or vitamin B9, is an important compound in one-carbon metabolism. Previous studies have found weaker binding of dihydrofolate to dihydrofolate reductase in the presence of osmolytes. In other words, osmolytes are more difficult to remove from the dihydrofolate solvation shell than water; this shifts the equilibrium toward the free ligand and protein species. This study uses vapor-pressure osmometry to explore the interaction of folate with the model osmolyte, glycine betaine. This method yields a preferential interaction potential (μ23/RT value). This value is concentration-dependent as folate dimerizes. The μ23/RT value also tracks the deprotonation of folate's N3-O4 keto-enol group, yielding a pKa of 8.1. To determine which folate atoms interact most strongly with betaine, the interaction of heterocyclic aromatic compounds (as well as other small molecules) with betaine was monitored. Using an accessible surface area approach coupled with osmometry measurements, deconvolution of the μ23/RT values into α values for atom types was achieved. This allows prediction of μ23/RT values for larger molecules such as folate. Molecular dynamics simulations of folate show a variety of structures from extended to L-shaped. These conformers possess μ23/RT values from -0.18 to 0.09 m-1, where a negative value indicates a preference for solvation by betaine and a positive value indicates a preference for water. This range of values is consistent with values observed in osmometry and solubility experiments. As the average predicted folate μ23/RT value is near zero, this indicates folate interacts almost equally well with betaine and water. Specifically, the glutamate tail prefers to interact with water, while the aromatic rings prefer betaine. In general, the more protonated species in our small molecule survey interact better with betaine as they provide a source of hydrogens (betaine is not a hydrogen bond donor). Upon deprotonation of the small molecule, the preference swings toward water interaction because of its hydrogen bond donating capacities.
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Affiliation(s)
- Purva
P. Bhojane
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
| | - Michael R. Duff
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
| | - Khushboo Bafna
- Genome
Science and Technology Program, University
of Tennessee, Knoxville, Tennessee 37996-0840, United States
| | - Gabriella P. Rimmer
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
| | - Pratul K. Agarwal
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
- Genome
Science and Technology Program, University
of Tennessee, Knoxville, Tennessee 37996-0840, United States
- Computer
Science and Mathematics Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Elizabeth E. Howell
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
- Genome
Science and Technology Program, University
of Tennessee, Knoxville, Tennessee 37996-0840, United States
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22
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Eremeeva E, Abramov M, Margamuljana L, Rozenski J, Pezo V, Marlière P, Herdewijn P. Chemical Morphing of DNA Containing Four Noncanonical Bases. Angew Chem Int Ed Engl 2016; 55:7515-9. [PMID: 27159019 DOI: 10.1002/anie.201601529] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Indexed: 01/04/2023]
Abstract
The ability of alternative nucleic acids, in which all four nucleobases are substituted, to replicate in vitro and to serve as genetic templates in vivo was evaluated. A nucleotide triphosphate set of 5-chloro-2'-deoxyuridine, 7-deaza-2'-deoxyadenosine, 5-fluoro-2'-deoxycytidine, and 7-deaza-2'deoxyguanosine successfully underwent polymerase chain reaction (PCR) amplification using templates of different lengths (57 or 525mer) and Taq or Vent (exo-) DNA polymerases as catalysts. Furthermore, a fully morphed gene encoding a dihydrofolate reductase was generated by PCR using these fully substituted nucleotides and was shown to transform and confer trimethoprim resistance to E. coli. These results demonstrated that fully modified templates were accurately read by the bacterial replication machinery and provide the first example of a long fully modified DNA molecule being functional in vivo.
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Affiliation(s)
- Elena Eremeeva
- Laboratory of Medicinal Chemistry, Rega, Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Michail Abramov
- Laboratory of Medicinal Chemistry, Rega, Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Lia Margamuljana
- Laboratory of Medicinal Chemistry, Rega, Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Jef Rozenski
- Laboratory of Medicinal Chemistry, Rega, Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Valerie Pezo
- ISSB, Génopole, Genavenir 6, Equipe Xénome, 5 rue Henri Desbruères, 91030, Evry Cedex, France
| | - Philippe Marlière
- ISSB, Génopole, Genavenir 6, Equipe Xénome, 5 rue Henri Desbruères, 91030, Evry Cedex, France
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega, Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium. .,ISSB, Génopole, Genavenir 6, Equipe Xénome, 5 rue Henri Desbruères, 91030, Evry Cedex, France.
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23
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Eremeeva E, Abramov M, Margamuljana L, Rozenski J, Pezo V, Marlière P, Herdewijn P. Chemical Morphing of DNA Containing Four Noncanonical Bases. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601529] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Elena Eremeeva
- Laboratory of Medicinal Chemistry, Rega; Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 3000 Leuven Belgium
| | - Michail Abramov
- Laboratory of Medicinal Chemistry, Rega; Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 3000 Leuven Belgium
| | - Lia Margamuljana
- Laboratory of Medicinal Chemistry, Rega; Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 3000 Leuven Belgium
| | - Jef Rozenski
- Laboratory of Medicinal Chemistry, Rega; Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 3000 Leuven Belgium
| | - Valerie Pezo
- ISSB; Génopole; Genavenir 6; Equipe Xénome; 5 rue Henri Desbruères 91030 Evry Cedex France
| | - Philippe Marlière
- ISSB; Génopole; Genavenir 6; Equipe Xénome; 5 rue Henri Desbruères 91030 Evry Cedex France
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega; Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 3000 Leuven Belgium
- ISSB; Génopole; Genavenir 6; Equipe Xénome; 5 rue Henri Desbruères 91030 Evry Cedex France
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24
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Duff MR, Chopra S, Strader MB, Agarwal PK, Howell EE. Tales of Dihydrofolate Binding to R67 Dihydrofolate Reductase. Biochemistry 2015; 55:133-45. [PMID: 26637016 PMCID: PMC5147970 DOI: 10.1021/acs.biochem.5b00981] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Homotetrameric R67 dihydrofolate reductase possesses 222 symmetry and a single active site pore. This situation results in a promiscuous binding site that accommodates either the substrate, dihydrofolate (DHF), or the cofactor, NADPH. NADPH interacts more directly with the protein as it is larger than the substrate. In contrast, the p-aminobenzoyl-glutamate tail of DHF, as monitored by nuclear magnetic resonance and crystallography, is disordered when bound. To explore whether smaller active site volumes (which should decrease the level of tail disorder by confinement effects) alter steady state rates, asymmetric mutations that decreased the half-pore volume by ∼35% were constructed. Only minor effects on k(cat) were observed. To continue exploring the role of tail disorder in catalysis, 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide-mediated cross-linking between R67 DHFR and folate was performed. A two-folate, one-tetramer complex results in the loss of enzyme activity where two symmetry-related K32 residues in the protein are cross-linked to the carboxylates of two bound folates. The tethered folate could be reduced, although with a ≤30-fold decreased rate, suggesting decreased dynamics and/or suboptimal positioning of the cross-linked folate for catalysis. Computer simulations that restrain the dihydrofolate tail near K32 indicate that cross-linking still allows movement of the p-aminobenzoyl ring, which allows the reaction to occur. Finally, a bis-ethylene-diamine-α,γ-amide folate adduct was synthesized; both negatively charged carboxylates in the glutamate tail were replaced with positively charged amines. The K(i) for this adduct was ∼9-fold higher than for folate. These various results indicate a balance between folate tail disorder, which helps the enzyme bind substrate while dynamics facilitates catalysis.
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Affiliation(s)
- Michael R Duff
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996-0840, United States
| | - Shaileja Chopra
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996-0840, United States
| | - Michael Brad Strader
- Laboratory of Biochemistry and Vascular Biology, Center for Biologics Evaluation and Research, Food and Drug Administration , Silver Spring, Maryland 20993, United States
| | - Pratul K Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996-0840, United States.,Computer Science and Mathematics Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Elizabeth E Howell
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996-0840, United States
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25
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26
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Ebert MCCJC, Morley KL, Volpato JP, Schmitzer AR, Pelletier JN. Asymmetric mutations in the tetrameric R67 dihydrofolate reductase reveal high tolerance to active-site substitutions. Protein Sci 2014; 24:495-507. [PMID: 25401264 DOI: 10.1002/pro.2602] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 11/07/2014] [Accepted: 11/10/2014] [Indexed: 11/08/2022]
Abstract
Type II R67 dihydrofolate reductase (DHFR) is a bacterial plasmid-encoded enzyme that is intrinsically resistant to the widely-administered antibiotic trimethoprim. R67 DHFR is genetically and structurally unrelated to E. coli chromosomal DHFR and has an unusual architecture, in that four identical protomers form a single symmetrical active site tunnel that allows only one substrate binding/catalytic event at any given time. As a result, substitution of an active-site residue has as many as four distinct consequences on catalysis, constituting an atypical model of enzyme evolution. Although we previously demonstrated that no single residue of the native active site is indispensable for function, library selection here revealed a strong bias toward maintenance of two native protomers per mutated tetramer. A variety of such "half-native" tetramers were shown to procure native-like catalytic activity, with similar KM values but kcat values 5- to 33-fold lower, illustrating a high tolerance for active-site substitutions. The selected variants showed a reduced thermal stability (Tm ∼12°C lower), which appears to result from looser association of the protomers, but generally showed a marked increase in resilience to heat denaturation, recovering activity to a significantly greater extent than the variant with no active-site substitutions. Our results suggest that the presence of two native protomers in the R67 DHFR tetramer is sufficient to provide native-like catalytic rate and thus ensure cellular proliferation.
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Affiliation(s)
- Maximilian C C J C Ebert
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, Québec, H3C 3J7, Canada; PROTEO, the Québec Network for Protein Function, Structure and Engineering, Québec, Canada; CGCC, the Center for Green Chemistry and Catalysis, Montréal, Canada
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27
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Timson MJ, Duff MR, Dickey G, Saxton AM, Reyes-De-Corcuera JI, Howell EE. Further studies on the role of water in R67 dihydrofolate reductase. Biochemistry 2013; 52:2118-27. [PMID: 23458706 DOI: 10.1021/bi301544k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previous osmotic pressure studies of two nonhomologous dihydrofolate reductase (DHFR) enzymes found tighter binding of the nicotinamide adenine dinucleotide phosphate cofactor upon addition of neutral osmolytes. This result is consistent with water release accompanying binding. In contrast, osmotic stress studies found weaker binding of the dihydrofolate (DHF) substrate for both type I and type II DHFRs in the presence of osmolytes; this observation can be explained if dihydrofolate interacts with osmolytes and shifts the equilibrium from the enzyme-bound state toward the unbound substrate. Nuclear magnetic resonance experiments support this hypothesis, finding that osmolytes interact with dihydrofolate. To consider binding without added osmolytes, a high-pressure approach was used. In this study, the type II enzyme, R67 DHFR, was subjected to high hydrostatic pressure (HHP). Both enzyme activity and fluorescence measurements find the protein tolerates pressures up to 200 MPa. Binding of the cofactor to R67 DHFR weakens with increasing pressure, and a positive association volume of 11.4 ± 0.5 cm(3)/mol was measured. Additionally, an activation volume of 3.3 ± 0.5 cm(3)/mol describing k(cat)/K(m(DHF)) was determined from progress curve analysis. Results from these HHP experiments suggest water release accompanies binding of both the cofactor and DHF to R67 DHFR. In an additional set of experiments, isothermal titration calorimetry studies in H2O and D2O find that water reorganization dominates the enthalpy associated with binding of DHF to R67 DHFR·NADP(+), while no obvious effects occur for cofactor binding. The combined results indicate that water plays an active role in ligand binding to R67 DHFR.
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Affiliation(s)
- Mary Jane Timson
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996-0840, United States
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28
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Roberts MC, Schwarz S, Aarts HJM. Erratum: Acquired antibiotic resistance genes: an overview. Front Microbiol 2012; 3:384. [PMID: 23162539 PMCID: PMC3499791 DOI: 10.3389/fmicb.2012.00384] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 10/15/2012] [Indexed: 11/13/2022] Open
Affiliation(s)
- Marilyn C Roberts
- Department of Environmental and Occupational Health Sciences, School of Public Health Seattle, WA, USA
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29
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Bastien D, Ebert MCCJC, Forge D, Toulouse J, Kadnikova N, Perron F, Mayence A, Huang TL, Vanden Eynde JJ, Pelletier JN. Fragment-Based Design of Symmetrical Bis-benzimidazoles as Selective Inhibitors of the Trimethoprim-Resistant, Type II R67 Dihydrofolate Reductase. J Med Chem 2012; 55:3182-92. [DOI: 10.1021/jm201645r] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dominic Bastien
- Département de Biochimie, Université de Montréal, C.P. 6128, Succ.
Centre-ville Montréal, Québec H3C 3J7, Canada
| | - Maximilian C. C. J. C. Ebert
- Département de Biochimie, Université de Montréal, C.P. 6128, Succ.
Centre-ville Montréal, Québec H3C 3J7, Canada
| | - Delphine Forge
- Laboratoire de Chimie Organique, Université de Mons-UMONS, 20 Place du Parc,
B-7000 Mons, Belgium
| | - Jacynthe Toulouse
- Département de Biochimie, Université de Montréal, C.P. 6128, Succ.
Centre-ville Montréal, Québec H3C 3J7, Canada
| | - Natalia Kadnikova
- Département
de Chimie, Université de Montréal, C.P. 6128, Succursale
Centre-ville Montréal, Québec H3C 3J7, Canada
| | - Florent Perron
- Laboratoire de Chimie Organique, Université de Mons-UMONS, 20 Place du Parc,
B-7000 Mons, Belgium
| | - Annie Mayence
- Division of Basic Pharmaceutical
Sciences, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125, United States
| | - Tien L. Huang
- Division of Basic Pharmaceutical
Sciences, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125, United States
| | | | - Joelle N. Pelletier
- Département de Biochimie, Université de Montréal, C.P. 6128, Succ.
Centre-ville Montréal, Québec H3C 3J7, Canada
- Département
de Chimie, Université de Montréal, C.P. 6128, Succursale
Centre-ville Montréal, Québec H3C 3J7, Canada
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30
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Duff MR, Grubbs J, Serpersu E, Howell EE. Weak interactions between folate and osmolytes in solution. Biochemistry 2012; 51:2309-18. [PMID: 22369433 DOI: 10.1021/bi3000947] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Previous osmotic stress studies on the role of solvent in two structurally unrelated dihydrofolate reductases (DHFRs) found weaker binding of dihydrofolate (DHF) to either enzyme in the presence of osmolytes. To explain these unusual results, weak interactions between DHF and osmolytes were proposed, with a competition between osmolyte and DHFR for DHF. High osmolyte concentrations will inhibit binding of the cognate pair. To evaluate this hypothesis, we devised a small molecule approach. Dimerization of folate, monitored by nuclear magnetic resonance, was weakened 2-3-fold upon addition of betaine or dimethyl sulfoxide (DMSO), supporting preferential interaction of either osmolyte with the monomer (as it possesses a larger surface area). Nuclear Overhauser effect (NOE) spectroscopy experiments found a positive NOE for the interaction of the C3'/C5' benzoyl ring protons with the C9 proton in buffer; however, a negative NOE was observed upon addition of betaine or DMSO. This change indicated a decreased tumbling rate, consistent with osmolyte interaction. Osmotic stress experiments also showed that betaine, DMSO, and sucrose preferentially interact with folate. Further, studies with the folate fragments, p-aminobenzoic acid and pterin 6-carboxylate, revealed interactions for both model compounds with betaine and sucrose. In contrast, DMSO was strongly excluded from the pterin ring but preferentially interacted with the p-aminobenzoyl moiety. These interactions are likely to be important in vivo because of the crowded conditions of the cell where weak contacts can more readily compete with specific binding interactions.
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Affiliation(s)
- Michael R Duff
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
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31
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Wide variation in antibiotic resistance proteins identified by functional metagenomic screening of a soil DNA library. Appl Environ Microbiol 2012; 78:1708-14. [PMID: 22247132 DOI: 10.1128/aem.06759-11] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Most genes for antibiotic resistance present in soil microbes remain unexplored because most environmental microbes cannot be cultured. Only recently has the identification of these genes become feasible through the use of culture-independent methods. We screened a soil metagenomic DNA library in an Escherichia coli host for genes that can confer resistance to kanamycin, gentamicin, rifampin, trimethoprim, chloramphenicol, or tetracycline. The screen revealed 41 genes that encode novel protein variants of eight protein families, including aminoglycoside acetyltransferases, rifampin ADP-ribosyltransferases, dihydrofolate reductases, and transporters. Several proteins of the same protein family deviate considerably from each other yet confer comparable resistance. For example, five dihydrofolate reductases sharing at most 44% amino acid sequence identity in pairwise comparisons were equivalent in conferring trimethoprim resistance. We identified variants of aminoglycoside acetyltransferases and transporters that differ in the specificity of the drugs for which they confer resistance. We also found wide variation in protein structure. Two forms of rifampin ADP-ribosyltransferases, one twice the size of the other, were similarly effective at conferring rifampin resistance, although the short form was expressed at a much lower level. Functional metagenomic screening provides insight into the large variability in antibiotic resistance protein sequences, revealing divergent variants that preserve protein function.
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32
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Evolutionarily conserved linkage between enzyme fold, flexibility, and catalysis. PLoS Biol 2011; 9:e1001193. [PMID: 22087074 PMCID: PMC3210774 DOI: 10.1371/journal.pbio.1001193] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 09/27/2011] [Indexed: 11/19/2022] Open
Abstract
Proteins are intrinsically flexible molecules. The role of internal motions in a protein's designated function is widely debated. The role of protein structure in enzyme catalysis is well established, and conservation of structural features provides vital clues to their role in function. Recently, it has been proposed that the protein function may involve multiple conformations: the observed deviations are not random thermodynamic fluctuations; rather, flexibility may be closely linked to protein function, including enzyme catalysis. We hypothesize that the argument of conservation of important structural features can also be extended to identification of protein flexibility in interconnection with enzyme function. Three classes of enzymes (prolyl-peptidyl isomerase, oxidoreductase, and nuclease) that catalyze diverse chemical reactions have been examined using detailed computational modeling. For each class, the identification and characterization of the internal protein motions coupled to the chemical step in enzyme mechanisms in multiple species show identical enzyme conformational fluctuations. In addition to the active-site residues, motions of protein surface loop regions (>10 Å away) are observed to be identical across species, and networks of conserved interactions/residues connect these highly flexible surface regions to the active-site residues that make direct contact with substrates. More interestingly, examination of reaction-coupled motions in non-homologous enzyme systems (with no structural or sequence similarity) that catalyze the same biochemical reaction shows motions that induce remarkably similar changes in the enzyme–substrate interactions during catalysis. The results indicate that the reaction-coupled flexibility is a conserved aspect of the enzyme molecular architecture. Protein motions in distal areas of homologous and non-homologous enzyme systems mediate similar changes in the active-site enzyme–substrate interactions, thereby impacting the mechanism of catalyzed chemistry. These results have implications for understanding the mechanism of allostery, and for protein engineering and drug design.
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33
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van Hoek AHAM, Mevius D, Guerra B, Mullany P, Roberts AP, Aarts HJM. Acquired antibiotic resistance genes: an overview. Front Microbiol 2011; 2:203. [PMID: 22046172 PMCID: PMC3202223 DOI: 10.3389/fmicb.2011.00203] [Citation(s) in RCA: 348] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 09/08/2011] [Indexed: 01/18/2023] Open
Abstract
In this review an overview is given on antibiotic resistance (AR) mechanisms with special attentions to the AR genes described so far preceded by a short introduction on the discovery and mode of action of the different classes of antibiotics. As this review is only dealing with acquired resistance, attention is also paid to mobile genetic elements such as plasmids, transposons, and integrons, which are associated with AR genes, and involved in the dispersal of antimicrobial determinants between different bacteria.
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Affiliation(s)
- Angela H. A. M. van Hoek
- Laboratory for Zoonoses and Environmental Microbiology, Centre for Infectious Disease Control, National Institute of Public Health and the EnvironmentUtrecht, Netherlands
| | - Dik Mevius
- Central Veterinary Institute of Wageningen URLelystad, Netherlands
- Department of Infectious Diseases and Immunology, Utrecht UniversityUtrecht, Netherlands
| | - Beatriz Guerra
- National Salmonella Reference Laboratory, Federal Institute for Risk AssessmentBerlin, Germany
| | - Peter Mullany
- Department of Microbial Diseases, University College London Eastman Dental Institute, University College LondonLondon, UK
| | - Adam Paul Roberts
- Department of Microbial Diseases, University College London Eastman Dental Institute, University College LondonLondon, UK
| | - Henk J. M. Aarts
- Laboratory for Zoonoses and Environmental Microbiology, Centre for Infectious Disease Control, National Institute of Public Health and the EnvironmentUtrecht, Netherlands
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Sen A, Yahashiri A, Kohen A. Triple isotopic labeling and kinetic isotope effects: exposing H-transfer steps in enzymatic systems. Biochemistry 2011; 50:6462-8. [PMID: 21688781 DOI: 10.1021/bi2003873] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Kinetic isotope effect (KIE) studies can provide insight into the mechanism and kinetics of specific chemical steps in complex catalytic cascades. Recent results from hydrogen KIE measurements have examined correlations between enzyme dynamics and catalytic function, leading to a surge of studies in this area. Unfortunately, most enzymatic H-transfer reactions are not rate limiting, and the observed KIEs do not reliably reflect the intrinsic KIEs on the chemical step of interest. Given their importance to understanding the chemical step under study, accurate determination of the intrinsic KIE from the observed data is essential. In 1975, Northrop developed an elegant method to assess intrinsic KIEs from their observed values [Northrop, D. B. (1975) Steady-state analysis of kinetic isotope effects in enzymic reactions. Biochemistry 14, 2644-2651]. The Northrop method involves KIE measurements using all three hydrogen isotopes, where one of them serves as the reference isotope. This method has been successfully used with different combinations of observed KIEs over the years, but criteria for a rational choice of reference isotope have never before been experimentally determined. Here we compare different reference isotopes (and hence distinct experimental designs) using the reduction of dihydrofolate and dihydrobiopterin by two dissimilar enzymes as model reactions. A number of isotopic labeling patterns have been applied to facilitate the comparative study of reference isotopes. The results demonstrate the versatility of the Northrop method and that such experiments are limited only by synthetic techniques, availability of starting materials, and the experimental error associated with the use of distinct combinations of isotopologues.
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Affiliation(s)
- Arundhuti Sen
- The Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, USA
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35
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Grubbs J, Rahmanian S, DeLuca A, Padmashali C, Jackson M, Duff MR, Howell EE. Thermodynamics and solvent effects on substrate and cofactor binding in Escherichia coli chromosomal dihydrofolate reductase. Biochemistry 2011; 50:3673-85. [PMID: 21462996 DOI: 10.1021/bi2002373] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Chromosomal dihydrofolate reductase from Escherichia coli catalyzes the reduction of dihydrofolate to tetrahydrofolate using NADPH as a cofactor. The thermodynamics of ligand binding were examined using an isothermal titration calorimetry approach. Using buffers with different heats of ionization, zero to a small, fractional proton release was observed for dihydrofolate binding, while a proton was released upon NADP(+) binding. The role of water in binding was additionally monitored using a number of different osmolytes. Binding of NADP(+) is accompanied by the net release of ∼5-24 water molecules, with a dependence on the identity of the osmolyte. In contrast, binding of dihydrofolate is weakened in the presence of osmolytes, consistent with "water uptake". Different effects are observed depending on the identity of the osmolyte. The net uptake of water upon dihydrofolate binding was previously observed in the nonhomologous R67-encoded dihydrofolate reductase (dfrB or type II enzyme) [Chopra, S., et al. (2008) J. Biol. Chem. 283, 4690-4698]. As R67 dihydrofolate reductase possesses a nonhomologous sequence and forms a tetrameric structure with a single active site pore, the observation of weaker DHF binding in the presence of osmolytes in both enzymes implicates cosolvent effects on free dihydrofolate. Consistent with this analysis, stopped flow experiments find betaine mostly affects DHF binding via changes in k(on), while betaine mostly affects NADPH binding via changes in k(off). Finally, nonadditive enthalpy terms when binary and ternary cofactor binding events are compared suggest the presence of long-lived conformational transitions that are not included in a simple thermodynamic cycle.
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Affiliation(s)
- Jordan Grubbs
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, USA
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36
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Torres-Cortés G, Millán V, Ramírez-Saad HC, Nisa-Martínez R, Toro N, Martínez-Abarca F. Characterization of novel antibiotic resistance genes identified by functional metagenomics on soil samples. Environ Microbiol 2011; 13:1101-14. [PMID: 21281423 DOI: 10.1111/j.1462-2920.2010.02422.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The soil microbial community is highly complex and contains a high density of antibiotic-producing bacteria, making it a likely source of diverse antibiotic resistance determinants. We used functional metagenomics to search for antibiotic resistance genes in libraries generated from three different soil samples, containing 3.6 Gb of DNA in total. We identified 11 new antibiotic resistance genes: 3 conferring resistance to ampicillin, 2 to gentamicin, 2 to chloramphenicol and 4 to trimethoprim. One of the clones identified was a new trimethoprim resistance gene encoding a 26.8 kDa protein closely resembling unassigned reductases of the dihydrofolate reductase group. This protein, Tm8-3, conferred trimethoprim resistance in Escherichia coli and Sinorhizobium meliloti (γ- and α-proteobacteria respectively). We demonstrated that this gene encoded an enzyme with dihydrofolate reductase activity, with kinetic constants similar to other type I and II dihydrofolate reductases (K(m) of 8.9 µM for NADPH and 3.7 µM for dihydrofolate and IC(50) of 20 µM for trimethoprim). This is the first description of a new type of reductase conferring resistance to trimethoprim. Our results indicate that soil bacteria display a high level of genetic diversity and are a reservoir of antibiotic resistance genes, supporting the use of this approach for the discovery of novel enzymes with unexpected activities unpredictable from their amino acid sequences.
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Affiliation(s)
- Gloria Torres-Cortés
- Genetic Ecology Group, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Calle Profesor Albareda 1, 18008 Granada, Spain
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37
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Kamath G, Howell EE, Agarwal PK. The Tail Wagging the Dog: Insights into Catalysis in R67 Dihydrofolate Reductase. Biochemistry 2010; 49:9078-88. [DOI: 10.1021/bi1007222] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ganesh Kamath
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Elizabeth E. Howell
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Pratul K. Agarwal
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
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Feng J, Grubbs J, Dave A, Goswami S, Horner CG, Howell EE. Radical redesign of a tandem array of four R67 dihydrofolate reductase genes yields a functional, folded protein possessing 45 substitutions. Biochemistry 2010; 49:7384-92. [PMID: 20684560 DOI: 10.1021/bi1005943] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
R67 dihydrofolate reductase (DHFR) is a plasmid-encoded, type II enzyme. Four monomers (78 amino acids long) assemble into a homotetramer possessing 222 symmetry. In previous studies, a tandem array of four R67 DHFR gene copies was fused in frame to generate a functional monomer named Quad1. This protein possessed the essential tertiary structure of the R67 "parent". To facilitate mutagenesis reactions, restriction enzyme sites were introduced in the tandem gene array. S59A and H362L mutations were also added to minimize possible folding topologies; this protein product, named Quad3, possesses 10 substitutions and is functional. Since R67 DHFR possesses a stable scaffold, a large jump in sequence space was performed by the further addition of 45 amino acid substitutions. The mutational design utilized alternate sequences from other type II DHFRs. In addition, most of the mutations were positioned on the surface of the protein as well as in the disordered N-terminal sequence, which serves as the linker between the fused domains. The resulting Quad4 protein is quite functional; however, it is less stable than Quad1, suffering a DeltaDeltaG loss of 5 kcal/mol at pH 5. One unexpected result was formation of Quad4 dimers and higher order oligomers at pH 8. R67 DHFR, and its derivative Quad proteins, possesses a robust scaffold, capable of withstanding introduction of >or=55 substitutions.
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Affiliation(s)
- Jian Feng
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, USA
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39
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Yahashiri A, Nimrod G, Ben-Tal N, Howell EE, Kohen A. The effect of electrostatic shielding on H tunneling in R67 dihydrofolate reductase. Chembiochem 2010; 10:2620-3. [PMID: 19774544 DOI: 10.1002/cbic.200900451] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Atsushi Yahashiri
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
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40
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Stojković V, Kohen A. Enzymatic H Transfers: Quantum Tunneling and Coupled Motion from Kinetic Isotope Effect Studies. Isr J Chem 2009. [DOI: 10.1560/ijc.49.2.163] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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41
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Spina M, Cuccioloni M, Mozzicafreddo M, Montecchia F, Pucciarelli S, Eleuteri AM, Fioretti E, Angeletti M. Mechanism of inhibition of wt-dihydrofolate reductase from E. coli by tea epigallocatechin-gallate. Proteins 2008; 72:240-51. [PMID: 18214969 DOI: 10.1002/prot.21914] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Dihydrofolate reductase (DHFR) is a ubiquitous enzyme involved in major biological process, including DNA synthesis and cancer inhibition, and its modulation is the object of extensive structural, kinetic, and pharmacological studies. In particular, earlier studies showed that green tea catechins are powerful inhibitors of bovine liver and chicken liver DHFR. In this article, we report the results of inhibition kinetics for the enzyme from another source (DHFR from E. coli) exerted by (-)-epigallocatechingallate (EGCG). Using different analytical techniques, we reported that EGCG acts as a bisubstrate inhibitor on the bacterial DHFR. Moreover, the combined approach of biosensor, kinetic, and molecular modelling analysis disclosed the ability of EGCG to bind to the enzyme both on substrate (DHF) and cofactor (NADPH) site. Collectively, our data have confirmed the selectivity of antifolate compounds with respect to the different source of enzyme (bacterial or mammalian DHFR) and the possible role of tea catechins as chemopreventive agents.
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Affiliation(s)
- Michele Spina
- Department of Molecular, Cellular and Animal Biology, University of Camerino, Via Gentile III da Varano, 62032, Camerino (MC), Italy.
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42
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Yahashiri A, Howell EE, Kohen A. Tuning of the H-transfer coordinate in primitive versus well-evolved enzymes. Chemphyschem 2008; 9:980-2. [PMID: 18444258 DOI: 10.1002/cphc.200800067] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Atsushi Yahashiri
- Department of Chemistry, University of Iowa, Iowa City, IA, 52242-1294, USA
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43
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Krahn JM, Jackson MR, DeRose EF, Howell EE, London RE. Crystal structure of a type II dihydrofolate reductase catalytic ternary complex. Biochemistry 2007; 46:14878-88. [PMID: 18052202 PMCID: PMC3743094 DOI: 10.1021/bi701532r] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Type II dihydrofolate reductase (DHFR) is a plasmid-encoded enzyme that confers resistance to bacterial DHFR-targeted antifolate drugs. It forms a symmetric homotetramer with a central pore which functions as the active site. Its unusual structure, which results in a promiscuous binding surface that accommodates either the dihydrofolate (DHF) substrate or the NADPH cofactor, has constituted a significant limitation to efforts to understand its substrate specificity and reaction mechanism. We describe here the first structure of a ternary R67 DHFR.DHF.NADP+ catalytic complex, resolved to 1.26 A. This structure provides the first clear picture of how this enzyme, which lacks the active site carboxyl residue that is ubiquitous in Type I DHFRs, is able to function. In the catalytic complex, the polar backbone atoms of two symmetry-related I68 residues provide recognition motifs that interact with the carboxamide on the nicotinamide ring, and the N3-O4 amide function on the pteridine ring. This set of interactions orients the aromatic rings of substrate and cofactor in a relative endo geometry in which the reactive centers are held in close proximity. Additionally, a central, hydrogen-bonded network consisting of two pairs of Y69-Q67-Q67'-Y69' residues provides an unusually tight interface, which appears to serve as a "molecular clamp" holding the substrates in place in an orientation conducive to hydride transfer. In addition to providing the first clear insight regarding how this extremely unusual enzyme is able to function, the structure of the ternary complex provides general insights into how a mutationally challenged enzyme, i.e., an enzyme whose evolution is restricted to four-residues-at-a-time active site mutations, overcomes this fundamental limitation.
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Affiliation(s)
- Joseph M. Krahn
- Laboratory of Structural Biology, MR-01, National Institute of Environmental Health Sciences, National Institutes of Health, Box 12233, Research Triangle Park, North Carolina 27709
| | - Michael R. Jackson
- Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996-0840
| | - Eugene F. DeRose
- Laboratory of Structural Biology, MR-01, National Institute of Environmental Health Sciences, National Institutes of Health, Box 12233, Research Triangle Park, North Carolina 27709
| | - Elizabeth E. Howell
- Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996-0840
| | - Robert E. London
- Laboratory of Structural Biology, MR-01, National Institute of Environmental Health Sciences, National Institutes of Health, Box 12233, Research Triangle Park, North Carolina 27709
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Chopra S, Dooling RM, Horner CG, Howell EE. A balancing act between net uptake of water during dihydrofolate binding and net release of water upon NADPH binding in R67 dihydrofolate reductase. J Biol Chem 2007; 283:4690-8. [PMID: 18086667 DOI: 10.1074/jbc.m709443200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
R67 dihydrofolate reductase (DHFR) catalyzes the reduction of dihydrofolate (DHF) to tetrahydrofolate using NADPH as a cofactor. This enzyme is a homotetramer possessing 222 symmetry, and a single active site pore traverses the length of the protein. A promiscuous binding surface can accommodate either DHF or NADPH, thus two nonproductive complexes can form (2NADPH or 2DHF) as well as a productive complex (NADPH.DHF). The role of water in binding was monitored using a number of different osmolytes. From isothermal titration calorimetry (ITC) studies, binding of NADPH is accompanied by the net release of 38 water molecules. In contrast, from both steady state kinetics and ITC studies, binding of DHF is accompanied by the net uptake of water. Although different osmolytes have similar effects on NADPH binding, variable results are observed when DHF binding is probed. Sensitivity to water activity can also be probed by an in vivo selection using the antibacterial drug, trimethoprim, where the water content of the media is decreased by increasing concentrations of sorbitol. The ability of wild type and mutant clones of R67 DHFR to allow host Escherichia coli to grow in the presence of trimethoprim plus added sorbitol parallels the catalytic efficiency of the DHFR clones, indicating water content strongly correlates with the in vivo function of R67 DHFR.
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Affiliation(s)
- Shaileja Chopra
- Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, USA
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45
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Divya N, Grifith E, Narayana N. Structure of the Q67H mutant of R67 dihydrofolate reductase-NADP+ complex reveals a novel cofactor binding mode. Protein Sci 2007; 16:1063-8. [PMID: 17473013 PMCID: PMC2206676 DOI: 10.1110/ps.062740907] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Plasmid-encoded bacterial R67 dihydrofolate reductase (DHFR) is a NADPH-dependent enzyme unrelated to chromosomal DHFR in amino acid sequence and structure. R67 DHFR is insensitive to the bacterial drug trimethoprim in contrast to chromosomal DHFR. The crystal structure of Q67H mutant of R67 DHFR bound to NADP(+) has been determined at 1.15 angstroms resolution. The cofactor assumes an extended conformation with the nicotinamide ring bound near the center of the active site pore, the ribose and pyrophosphate group (PP(i)) extending toward the outer pore. The ribonicotinamide exhibits anti conformation as in chromosomal DHFR complexes. The relative orientation between the PP(i) and the nicotinamide ribose differs from that observed in chromosomal DHFR-NADP(+) complexes. The coenzyme displays symmetrical binding mode with several water-mediated hydrogen bonds with the protein besides ionic, stacking, and van der Waals interactions. The structure provides a molecular basis for the observed stoichiometry and cooperativity in ligand binding. The ternary model based on the present structure and the previous R67 DHFR-folate complex provides insight into the catalytic mechanism and indicates that the relative orientation of the reactants in plasmid DHFR is different from that seen in chromosomal DHFRs.
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Affiliation(s)
- N Divya
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA
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46
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Levin I, Mevarech M, Palfey BA. Characterization of a novel bifunctional dihydropteroate synthase/dihydropteroate reductase enzyme from Helicobacter pylori. J Bacteriol 2007; 189:4062-9. [PMID: 17416665 PMCID: PMC1913416 DOI: 10.1128/jb.01878-06] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tetrahydrofolate is a ubiquitous C(1) carrier in many biosynthetic pathways in bacteria, importantly, in the biosynthesis of formylmethionyl tRNA(fMet), which is essential for the initiation of translation. The final step in the biosynthesis of tetrahydrofolate is carried out by the enzyme dihydrofolate reductase (DHFR). A search of the complete genome sequence of Helicobacter pylori failed to reveal any sequence that encodes DHFR. Previous studies demonstrated that the H. pylori dihydropteroate synthase gene folP can complement an Escherichia coli strain in which folA and folM, encoding two distinct DHFRs, are deleted. It was also shown that H. pylori FolP possesses an additional N-terminal domain that binds flavin mononucleotide (FMN). Homologous domains are found in FolP proteins of other microorganisms that do not possess DHFR. In this study, we demonstrated that H. pylori FolP is also a dihydropteroate reductase that derives its reducing power from soluble flavins, reduced FMN and reduced flavin adenine dinucleotide. We also determined the stoichiometry of the enzyme-bound flavin and showed that half of the bound flavin is exchangeable with the soluble flavins. Finally, site-directed mutagenesis of the most conserved amino acid residues in the N-terminal domain indicated the importance of these residues for the activity of the enzyme as a dihydropteroate reductase.
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Affiliation(s)
- Itay Levin
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
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47
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New integron-associated gene cassette encoding a trimethoprim-resistant DfrB-type dihydrofolate reductase. Antimicrob Agents Chemother 2006; 50:2863-5. [PMID: 16870788 DOI: 10.1128/aac.00449-06] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A sixth gene cassette containing a dfrB-type gene, dfrB6, was found in a dfrB6-aadA1 cassette array in class 1 integrons. This array was isolated from several multiply antibiotic-resistant Salmonella enterica serovar Infantis strains that appear to be clonally related. The DfrB6 dihydrofolate reductase conferred resistance to trimethoprim.
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48
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Alonso H, Gready JE. Integron-sequestered dihydrofolate reductase: a recently redeployed enzyme. Trends Microbiol 2006; 14:236-42. [PMID: 16584884 DOI: 10.1016/j.tim.2006.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2005] [Revised: 03/01/2006] [Accepted: 03/21/2006] [Indexed: 11/21/2022]
Abstract
The introduction and wide use of antibacterial drugs has resulted in the emergence of resistant organisms. DfrB dihydrofolate reductase (DHFR) is a bacterial enzyme that is uniquely associated with mobile gene cassettes within integrons, and confers resistance to the drug trimethoprim. This enzyme has intrigued microbiologists since it was discovered more than thirty years ago because of its simple structure, enzymatic inefficiency and its virtual insensitivity to trimethoprim. Here, for the first time, a comprehensive discussion of genetic, evolutionary, structural and functional studies of this enzyme is presented together. This information supports the ideas that DfrB DHFR is a poorly adapted catalyst and has recently been recruited to perform a novel enzymatic activity in response to selective pressure.
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Affiliation(s)
- Hernán Alonso
- Division of Molecular Bioscience, John Curtin School of Medical Research, Australian National University, Canberra, ACT 0200, Australia
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