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Perkins SW, Hlaing MZ, Hicks KA, Rajakovich LJ, Snider MJ. Mechanism of the Multistep Catalytic Cycle of 6-Hydroxynicotinate 3-Monooxygenase Revealed by Global Kinetic Analysis. Biochemistry 2023; 62:1553-1567. [PMID: 37130364 DOI: 10.1021/acs.biochem.2c00514] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The class A flavoenzyme 6-hydroxynicotinate 3-monooxygenase (NicC) catalyzes a rare decarboxylative hydroxylation reaction in the degradation of nicotinate by aerobic bacteria. While the structure and critical residues involved in catalysis have been reported, the mechanism of this multistep enzyme has yet to be determined. A kinetic understanding of the NicC mechanism would enable comparison to other phenolic hydroxylases and illuminate its bioengineering potential for remediation of N-heterocyclic aromatic compounds. Toward these goals, transient state kinetic analyses by stopped-flow spectrophotometry were utilized to follow rapid changes in flavoenzyme absorbance spectra during all three stages of NicC catalysis: (1) 6-HNA binding; (2) NADH binding and FAD reduction; and (3) O2 binding with C4a-adduct formation, substrate hydroxylation, and FAD regeneration. Global kinetic simulations by numeric integration were used to supplement analytical fitting of time-resolved data and establish a kinetic mechanism. Results indicate that 6-HNA binding is a two-step process that substantially increases the affinity of NicC for NADH and enables the formation of a charge-transfer-complex intermediate to enhance the rate of flavin reduction. Singular value decomposition of the time-resolved spectra during the reaction of the substrate-bound, reduced enzyme with dioxygen provides evidence for the involvement of C4a-hydroperoxy-flavin and C4a-hydroxy-flavin intermediates in NicC catalysis. Global analysis of the full kinetic mechanism suggests that steady-state catalytic turnover is partially limited by substrate hydroxylation and C4a-hydroxy-flavin dehydration to regenerate the flavoenzyme. Insights gleaned from the kinetic model and determined microscopic rate constants provide a fundamental basis for understanding NicC's substrate specificity and reactivity.
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Affiliation(s)
- Scott W Perkins
- Department of Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
| | - May Z Hlaing
- Department of Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
| | - Katherine A Hicks
- Department of Chemistry, The State University of New York College at Cortland, Cortland, New York 13045, United States
| | - Lauren J Rajakovich
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Mark J Snider
- Department of Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
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2
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Tassoulas LJ, Elias MH, Wackett LP. Discovery of an ultraspecific triuret hydrolase (TrtA) establishes the triuret biodegradation pathway. J Biol Chem 2020; 296:100055. [PMID: 33172891 PMCID: PMC7948467 DOI: 10.1074/jbc.ra120.015631] [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: 08/12/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 12/25/2022] Open
Abstract
Triuret (carbonyldiurea) is an impurity found in industrial urea fertilizer (<0.1% w/w) that is applied, worldwide, around 300 million pounds each year on agricultural lands. In addition to anthropogenic sources, endogenous triuret has been identified in amoeba and human urine, the latter being diagnostic for hypokalemia. The present study is the first to describe the metabolic breakdown of triuret, which funnels into biuret metabolism. We identified the gene responsible for triuret decomposition (trtA) in bacterial genomes, clustered with biuH, which encodes biuret hydrolase and has close protein sequence homology. TrtA is a member of the isochorismatase-like hydrolase (IHL) protein family, similarly to BiuH, and has a catalytic efficiency (kcat/KM) of 6 x 105 M−1s−1, a KM for triuret of 20 μM, and exquisite substrate specificity. Indeed, TrtA has four orders of magnitude less activity with biuret. Crystal structures of TrtA in apo and holo form were solved and compared with the BiuH structure. The high substrate selectivity was found to be conveyed by second shell residues around each active site. Mutagenesis of residues conserved in TrtA to the alternate consensus found in BiuHs revealed residues critical to triuret hydrolase activity but no single mutant evolved more biuret activity, and likely a combination of mutations is required to interconvert between TrtA, BiuH functions. TrtA-mediated triuret metabolism is relatively rare in recorded genomes (1–2%), but is largely found in plant-associated, nodulating, and endophytic bacteria. This study suggests functions for triuret hydrolase in certain eukaryotic intermediary processes and prokaryotic intermediary or biodegradative metabolism
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Affiliation(s)
- Lambros J Tassoulas
- Department of Biochemistry, Biophysics & Molecular Biology, University of Minnesota, Minneapolis, Minnesota, USA; BioTechnology Institute, University of Minnesota, St Paul, Minnesota, USA
| | - Mikael H Elias
- Department of Biochemistry, Biophysics & Molecular Biology, University of Minnesota, Minneapolis, Minnesota, USA; BioTechnology Institute, University of Minnesota, St Paul, Minnesota, USA
| | - Lawrence P Wackett
- Department of Biochemistry, Biophysics & Molecular Biology, University of Minnesota, Minneapolis, Minnesota, USA; BioTechnology Institute, University of Minnesota, St Paul, Minnesota, USA.
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3
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Díaz-García D, Ardiles PR, Díaz-Sánchez M, Mena-Palomo I, Del Hierro I, Prashar S, Rodríguez-Diéguez A, Páez PL, Gómez-Ruiz S. Copper-functionalized nanostructured silica-based systems: Study of the antimicrobial applications and ROS generation against gram positive and gram negative bacteria. J Inorg Biochem 2019; 203:110912. [PMID: 31743886 DOI: 10.1016/j.jinorgbio.2019.110912] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/26/2019] [Accepted: 11/07/2019] [Indexed: 12/29/2022]
Abstract
A series of copper-functionalized SBA-15 (Santa Barbara Amorphous) materials containing the ligands triethoxysilylpropylmaleamic acid (maleamic) or triethoxy-3-(2-imidazolin-1-yl)propylsilane (imidazoline) have been prepared. The nanostructured silica-based systems SBA-maleamic, SBA-imidazoline, SBA-maleamic-Cu and SBA-imidazoline-Cu were characterized by several methods observing that the functionalization took place mainly inside the pores of the mesoporous system. The antimicrobial behaviour of the synthesized materials against Staphylococcus aureus and Escherichia coli was tested observing a very potent activity of the copper-functionalized systems (minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values for SBA-maleamic-Cu of ca. 31.25 μg/mL, which correspond with ca. 1.13 μg/mL of Cu). A study of the oxidative stress promoted by the synthesized materials showed that the SBA-maleamic-Cu and the SBA-imidazoline-Cu were able to increase the reactive oxygen species (ROS) production in S. aureus by 427% and 373%, respectively, while this increase was slightly lower in E. coli (387 and 324%, respectively). Furthermore, an electrochemical study was carried out in order to determine if these materials interact with lysine or alanine to validate a potential antimicrobial mechanism based on the inhibition of the synthesis of the peptidoglycan of the bacterial wall. Finally, these studies were also performed to determine the potential interaction of the copper-containing materials with glutathione in order to assess if they are able to perturb the metabolism of this tripeptide.
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Affiliation(s)
- Diana Díaz-García
- COMET-NANO Group, Departamento de Biología y Geología, Física y Química Inorgánica, ESCET, Universidad Rey Juan Carlos, Calle Tulipán s/n, E-28933 Móstoles, Madrid, Spain
| | - Perla R Ardiles
- Departamento de Ciencias Farmacéuticas. Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Haya de la Torre y Medina Allende, X5000HUA Córdoba, Argentina
| | - Miguel Díaz-Sánchez
- COMET-NANO Group, Departamento de Biología y Geología, Física y Química Inorgánica, ESCET, Universidad Rey Juan Carlos, Calle Tulipán s/n, E-28933 Móstoles, Madrid, Spain
| | - Irene Mena-Palomo
- COMET-NANO Group, Departamento de Biología y Geología, Física y Química Inorgánica, ESCET, Universidad Rey Juan Carlos, Calle Tulipán s/n, E-28933 Móstoles, Madrid, Spain
| | - Isabel Del Hierro
- COMET-NANO Group, Departamento de Biología y Geología, Física y Química Inorgánica, ESCET, Universidad Rey Juan Carlos, Calle Tulipán s/n, E-28933 Móstoles, Madrid, Spain
| | - Sanjiv Prashar
- COMET-NANO Group, Departamento de Biología y Geología, Física y Química Inorgánica, ESCET, Universidad Rey Juan Carlos, Calle Tulipán s/n, E-28933 Móstoles, Madrid, Spain
| | - Antonio Rodríguez-Diéguez
- Departamento de Química Inorgánica, C/Severo Ochoa s/n, Universidad de Granada, 18071 Granada, Spain
| | - Paulina L Páez
- Departamento de Ciencias Farmacéuticas. Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Haya de la Torre y Medina Allende, X5000HUA Córdoba, Argentina.
| | - Santiago Gómez-Ruiz
- COMET-NANO Group, Departamento de Biología y Geología, Física y Química Inorgánica, ESCET, Universidad Rey Juan Carlos, Calle Tulipán s/n, E-28933 Móstoles, Madrid, Spain.
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4
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Ion BF, Meister PJ, Gauld JW. Multiscale Computational Study on the Catalytic Mechanism of the Nonmetallo Amidase Maleamate Amidohydrolase (NicF). J Phys Chem A 2019; 123:7710-7719. [DOI: 10.1021/acs.jpca.9b05914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bogdan F. Ion
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Paul J. Meister
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - James W. Gauld
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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Díaz-García D, Ardiles PR, Prashar S, Rodríguez-Diéguez A, Páez PL, Gómez-Ruiz S. Preparation and Study of the Antibacterial Applications and Oxidative Stress Induction of Copper Maleamate-Functionalized Mesoporous Silica Nanoparticles. Pharmaceutics 2019; 11:E30. [PMID: 30646534 PMCID: PMC6359009 DOI: 10.3390/pharmaceutics11010030] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 02/06/2023] Open
Abstract
Mesoporous silica nanoparticles (MSNs) are an interesting class of nanomaterials with potential applications in different therapeutic areas and that have been extensively used as drug carriers in different fields of medicine. The present work is focused on the synthesis of MSNs containing a maleamato ligand (MSN-maleamic) and the subsequent coordination of copper(II) ions (MSN-maleamic-Cu) for the exploration of their potential application as antibacterial agents. The Cu-containing nanomaterials have been characterized by different techniques and the preliminary antibacterial effect of the supported maleamato-copper(II) complexes has been tested against two types of bacteria (Gram positive and Gram negative) in different assays to determine the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). The biological results showed a moderate antibacterial activity against Escherichia coli which motivated a more detailed study of the antibacterial mechanism of action of the synthesized maleamate-containing nanosystems and whose findings showed oxidative stress generation in bacterial cells. All the prepared nanomaterials were also tested as catalysts in the "solvent free" selective oxidation of benzyl alcohol, to observe if there is a potential correlation between the catalytic oxidation capacity of the materials and the observed oxidative stress in bacteria. This may help in the future, for a more accurate rational design of antibacterial nanosystems, based on their observed catalytic oxidation activity.
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Affiliation(s)
- Diana Díaz-García
- Departamento de Biología y Geología, Física y Química Inorgánica, ESCET, Universidad Rey Juan Carlos, Calle Tulipán s/n, E-28933 Móstoles (Madrid), Spain.
| | - Perla R Ardiles
- Departamento de Ciencias Farmacéuticas. Facultad de Ciencias Químicas, Universidad Nacional de Córdoba. Ciudad Universitaria, Haya de la Torre y Medina Allende, X5000HUA Córdoba, Argentina.
| | - Sanjiv Prashar
- Departamento de Biología y Geología, Física y Química Inorgánica, ESCET, Universidad Rey Juan Carlos, Calle Tulipán s/n, E-28933 Móstoles (Madrid), Spain.
| | - Antonio Rodríguez-Diéguez
- Departamento de Química Inorgánica, Universidad de Granada, Facultad de Ciencias, Campus de Fuentenueva, Avda. Fuentenueva s/n, E-18071 Granada, Spain.
| | - Paulina L Páez
- Departamento de Ciencias Farmacéuticas. Facultad de Ciencias Químicas, Universidad Nacional de Córdoba. Ciudad Universitaria, Haya de la Torre y Medina Allende, X5000HUA Córdoba, Argentina.
| | - Santiago Gómez-Ruiz
- Departamento de Biología y Geología, Física y Química Inorgánica, ESCET, Universidad Rey Juan Carlos, Calle Tulipán s/n, E-28933 Móstoles (Madrid), Spain.
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6
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Li H, Xu M, Zhu J. Headspace Gas Monitoring of Gut Microbiota Using Targeted and Globally Optimized Targeted Secondary Electrospray Ionization Mass Spectrometry. Anal Chem 2018; 91:854-863. [DOI: 10.1021/acs.analchem.8b03517] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Haorong Li
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, Ohio 45056, United States
| | - Mengyang Xu
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, Ohio 45056, United States
| | - Jiangjiang Zhu
- Department of Chemistry and Biochemistry, Miami University, 651 E. High Street, Oxford, Ohio 45056, United States
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7
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Guragain M, Jennings-Gee J, Cattelan N, Finger M, Conover MS, Hollis T, Deora R. The Transcriptional Regulator BpsR Controls the Growth of Bordetella bronchiseptica by Repressing Genes Involved in Nicotinic Acid Degradation. J Bacteriol 2018; 200:JB.00712-17. [PMID: 29581411 PMCID: PMC5971473 DOI: 10.1128/jb.00712-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 03/19/2018] [Indexed: 12/12/2022] Open
Abstract
Many of the pathogenic species of the genus Bordetella have an absolute requirement for nicotinic acid (NA) for laboratory growth. These Gram-negative bacteria also harbor a gene cluster homologous to the nic cluster of Pseudomonas putida which is involved in the aerobic degradation of NA and its transcriptional control. We report here that BpsR, a negative regulator of biofilm formation and Bps polysaccharide production, controls the growth of Bordetella bronchiseptica by repressing the expression of nic genes. The severe growth defect of the ΔbpsR strain in Stainer-Scholte medium was restored by supplementation with NA, which also functioned as an inducer of nic genes at low micromolar concentrations that are usually present in animals and humans. Purified BpsR protein bound to the nic promoter region, and its DNA binding activity was inhibited by 6-hydroxynicotinic acid (6-HNA), the first metabolite of the NA degradative pathway. Reporter assays with the isogenic mutant derivative of the wild-type (WT) strain harboring deletion in nicA, which encodes a putative nicotinic acid hydroxylase responsible for conversion of NA to 6-HNA, showed that 6-HNA is the actual inducer of the nic genes in the bacterial cell. Gene expression profiling further showed that BpsR dually activated and repressed the expression of genes associated with pathogenesis, transcriptional regulation, metabolism, and other cellular processes. We discuss the implications of these findings with respect to the selection of pyridines such as NA and quinolinic acid for optimum bacterial growth depending on the ecological niche.IMPORTANCE BpsR, the previously described regulator of biofilm formation and Bps polysaccharide production, controls Bordetella bronchiseptica growth by regulating the expression of genes involved in the degradation of nicotinic acid (NA). 6-Hydroxynicotinic acid (6-HNA), the first metabolite of the NA degradation pathway prevented BpsR from binding to DNA and was the actual in vivo inducer. We hypothesize that BpsR enables Bordetella bacteria to efficiently and selectively utilize NA for their survival depending on the environment in which they reside. The results reported herein lay the foundation for future investigations of how BpsR and the alteration of its activity by NA orchestrate the control of Bordetella growth, metabolism, biofilm formation, and pathogenesis.
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Affiliation(s)
- Manita Guragain
- Department of Microbial Infection and Immunity, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jamie Jennings-Gee
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Natalia Cattelan
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
- Facultad de Ciencias Exactas, Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI, CONICET-CCT-La Plata), Universidad Nacional de La Plata, La Plata, Argentina
| | - Mary Finger
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Matt S Conover
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Thomas Hollis
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Rajendar Deora
- Department of Microbial Infection and Immunity, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
- Department of Microbiology, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
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8
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Robinson SL, Badalamenti JP, Dodge AG, Tassoulas LJ, Wackett LP. Microbial biodegradation of biuret: defining biuret hydrolases within the isochorismatase superfamily. Environ Microbiol 2018. [PMID: 29528550 DOI: 10.1111/1462-2920.14094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Biuret is a minor component of urea fertilizer and an intermediate in s-triazine herbicide biodegradation. The microbial metabolism of biuret has never been comprehensively studied. Here, we enriched and isolated bacteria from a potato field that grew on biuret as a sole nitrogen source. We sequenced the genome of the fastest-growing isolate, Herbaspirillum sp. BH-1 and identified genes encoding putative biuret hydrolases (BHs). We purified and characterized a functional BH enzyme from Herbaspirillum sp. BH-1 and two other bacteria from divergent phyla. The BH enzymes reacted exclusively with biuret in the range of 2-11 µmol min-1 mg-1 protein. We then constructed a global protein superfamily network to map structure-function relationships in the BH subfamily and used this to mine > 7000 genomes. High-confidence BH sequences were detected in Actinobacteria, Alpha- and Beta-proteobacteria, and some fungi, archaea and green algae, but not animals or land plants. Unexpectedly, no cyanuric acid hydrolase homologs were detected in > 90% of genomes with BH homologs, suggesting BHs may have arisen independently of s-triazine ring metabolism. This work links genotype to phenotype by enabling accurate genome-mining to predict microbial utilization of biuret. Importantly, it advances understanding of the microbial capacity for biuret biodegradation in agricultural systems.
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Affiliation(s)
- Serina L Robinson
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, - Twin Cities, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - Jonathan P Badalamenti
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, - Twin Cities, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - Anthony G Dodge
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, - Twin Cities, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - Lambros J Tassoulas
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, - Twin Cities, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - Lawrence P Wackett
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, - Twin Cities, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
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9
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Brickman TJ, Armstrong SK. The Bordetella bronchiseptica nic locus encodes a nicotinic acid degradation pathway and the 6-hydroxynicotinate-responsive regulator BpsR. Mol Microbiol 2018; 108:397-409. [PMID: 29485696 DOI: 10.1111/mmi.13943] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2018] [Indexed: 01/01/2023]
Abstract
The classical Bordetella species use amino acids as carbon sources and can catabolize organic acids and tricarboxylic acid cycle intermediates. They are also auxotrophic for nicotinamide adenine dinucleotide (NAD) pathway precursors such as nicotinic acid. Bordetellae have a putative nicotinate catabolism gene locus highly similar to that characterized in Pseudomonas putida KT2440. This study determined the distribution of the nic genes among Bordetella species and analyzed the regulation of this nicotinic acid degradation system. Transcription of the Bordetella bronchiseptica nicC gene was repressed by the NicR ortholog, BpsR, previously shown to regulate extracellular polysaccharide synthesis genes. nicC expression was derepressed by nicotinic acid or by the first product of the degradation pathway, 6-hydroxynicotinic acid, which was shown to be the inducer. Results using mutants with either a hyperactivated pathway or an inactivated pathway showed a marked effect on growth on nicotinic acid that indicated this degradation pathway influences NAD biosynthesis. Pathway dysregulation also affected Bordetella BvgAS-mediated virulence gene regulation, demonstrating that fluctuation of intracellular nicotinic acid pools impacts Bvg phase transition responses.
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Affiliation(s)
- Timothy J Brickman
- Department of Microbiology and Immunology, University of Minnesota Medical School, 3-117 Microbiology Research Facility, 689 23rd Ave. S.E, Minneapolis, MN 55455-1507, USA
| | - Sandra K Armstrong
- Department of Microbiology and Immunology, University of Minnesota Medical School, 3-117 Microbiology Research Facility, 689 23rd Ave. S.E, Minneapolis, MN 55455-1507, USA
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10
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Esquirol L, Peat TS, Wilding M, Lucent D, French NG, Hartley CJ, Newman J, Scott C. Structural and biochemical characterization of the biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841. PLoS One 2018; 13:e0192736. [PMID: 29425231 PMCID: PMC5806882 DOI: 10.1371/journal.pone.0192736] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/29/2018] [Indexed: 11/24/2022] Open
Abstract
Biuret deamination is an essential step in cyanuric acid mineralization. In the well-studied atrazine degrading bacterium Pseudomonas sp. strain ADP, the amidase AtzE catalyzes this step. However, Rhizobium leguminosarum bv. viciae 3841 uses an unrelated cysteine hydrolase, BiuH, instead. Herein, structures of BiuH, BiuH with bound inhibitor and variants of BiuH are reported. The substrate is bound in the active site by a hydrogen bonding network that imparts high substrate specificity. The structure of the inactive Cys175Ser BiuH variant with substrate bound in the active site revealed that an active site cysteine (Cys175), aspartic acid (Asp36) and lysine (Lys142) form a catalytic triad, which is consistent with biochemical studies of BiuH variants. Finally, molecular dynamics simulations highlighted the presence of three channels from the active site to the enzyme surface: a persistent tunnel gated by residues Val218 and Gln215 forming a potential substrate channel and two smaller channels formed by Val28 and a mobile loop (including residues Phe41, Tyr47 and Met51) that may serve as channels for co-product (ammonia) or co-substrate (water).
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Affiliation(s)
- Lygie Esquirol
- CSIRO Biocatalysis and Synthetic Biology, Canberra, Australian Capital Territory, Australia
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Thomas S. Peat
- CSIRO Biomedical Manufacturing, Parkville, Melbourne, Victoria, Australia
| | - Matthew Wilding
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
- CSIRO Biomedical Manufacturing, Parkville, Melbourne, Victoria, Australia
| | - Del Lucent
- Department of Electrical Engineering and Physics, Wilkes University, Wilkes-Barre, Pennsylvania, United States of America
| | - Nigel G. French
- CSIRO Biocatalysis and Synthetic Biology, Canberra, Australian Capital Territory, Australia
| | - Carol J. Hartley
- CSIRO Biocatalysis and Synthetic Biology, Canberra, Australian Capital Territory, Australia
| | - Janet Newman
- CSIRO Biomedical Manufacturing, Parkville, Melbourne, Victoria, Australia
| | - Colin Scott
- CSIRO Biocatalysis and Synthetic Biology, Canberra, Australian Capital Territory, Australia
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11
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Ion BF, Aboelnga MM, Gauld JW. Insights from molecular dynamics on substrate binding and effects of active site mutations in Δ1-pyrroline-5-carboxylate dehydrogenase. CAN J CHEM 2016. [DOI: 10.1139/cjc-2016-0286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The NAD+-dependent enzyme, Δ1-pyrroline-5-carboxylate dehydrogenase (P5CDH), has an important role in proline and hydroxyproline catabolism for humans. Specifically, this aldehyde dehydrogenase is responsible for the oxidation of both l-glutamate-γ-semialdehyde (GSA) and 4-erythro-hydroxy-l-glutamate-γ-semialdehyde (4-OH-GSA) to their respective l-glutamate product forms. We have performed a detailed molecular dynamics (MD) study of both the reactant and product complex structures of P5CDH to gain insights into ligand binding (i.e., GSA, 4-OH-GSA, NAD+, GLU) in the active site. Moreover, our investigations were further extended to examine the structural impact of S352L, S352A, and E314A mutations on the deficiency in the P5CDH enzymatic activity. Our in silico mutation analysis indicated that the conserved Glu447 has significantly shifted in both the S352L and E314A mutants, causing NAD+ to be displaced from its predictive orientation in the binding site and hence forming a catalytically inactive enzyme. However in the case of S352A, the catalytic site including the oxyanion hole and Cys348 remain virtually unchanged, and the coenzyme maintains its binding position.
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Affiliation(s)
- Bogdan F. Ion
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Mohamed M. Aboelnga
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - James W. Gauld
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
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Xu H, Chakrabarty Y, Philmus B, Mehta AP, Bhandari D, Hohmann HP, Begley TP. Identification of the First Riboflavin Catabolic Gene Cluster Isolated from Microbacterium maritypicum G10. J Biol Chem 2016; 291:23506-23515. [PMID: 27590337 PMCID: PMC5095406 DOI: 10.1074/jbc.m116.729871] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 08/31/2016] [Indexed: 11/06/2022] Open
Abstract
Riboflavin is a common cofactor, and its biosynthetic pathway is well characterized. However, its catabolic pathway, despite intriguing hints in a few distinct organisms, has never been established. This article describes the isolation of a Microbacterium maritypicum riboflavin catabolic strain, and the cloning of the riboflavin catabolic genes. RcaA, RcaB, RcaD, and RcaE were overexpressed and biochemically characterized as riboflavin kinase, riboflavin reductase, ribokinase, and riboflavin hydrolase, respectively. Based on these activities, a pathway for riboflavin catabolism is proposed.
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Affiliation(s)
- Hui Xu
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Yindrila Chakrabarty
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Benjamin Philmus
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Angad P Mehta
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Dhananjay Bhandari
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Hans-Peter Hohmann
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Tadhg P Begley
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843
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Hicks KA, Yuen ME, Zhen WF, Gerwig TJ, Story RW, Kopp MC, Snider MJ. Structural and Biochemical Characterization of 6-Hydroxynicotinic Acid 3-Monooxygenase, A Novel Decarboxylative Hydroxylase Involved in Aerobic Nicotinate Degradation. Biochemistry 2016; 55:3432-46. [DOI: 10.1021/acs.biochem.6b00105] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Katherine A. Hicks
- Department
of Chemistry, SUNY Cortland, Cortland, New York 13045, United States
| | - Meigan E. Yuen
- Department
of Chemistry, SUNY Cortland, Cortland, New York 13045, United States
| | - Wei Feng Zhen
- Department
of Chemistry, SUNY Cortland, Cortland, New York 13045, United States
| | - Tyler J. Gerwig
- Department
of Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
| | - Ryan W. Story
- Department
of Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
| | - Megan C. Kopp
- Department
of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Mark J. Snider
- Department
of Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
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14
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Torres A, Luke JD, Kullas AL, Kapilashrami K, Botbol Y, Koller A, Tonge PJ, Chen EI, Macian F, van der Velden AWM. Asparagine deprivation mediated by Salmonella asparaginase causes suppression of activation-induced T cell metabolic reprogramming. J Leukoc Biol 2015; 99:387-98. [PMID: 26497246 DOI: 10.1189/jlb.4a0615-252r] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 10/02/2015] [Indexed: 01/09/2023] Open
Abstract
Salmonellae are pathogenic bacteria that induce immunosuppression by mechanisms that remain largely unknown. Previously, we showed that a putative type II l-asparaginase produced by Salmonella Typhimurium inhibits T cell responses and mediates virulence in a murine model of infection. Here, we report that this putative L-asparaginase exhibits L-asparagine hydrolase activity required for Salmonella Typhimurium to inhibit T cells. We show that L-asparagine is a nutrient important for T cell activation and that L-asparagine deprivation, such as that mediated by the Salmonella Typhimurium L-asparaginase, causes suppression of activation-induced mammalian target of rapamycin signaling, autophagy, Myc expression, and L-lactate secretion. We also show that L-asparagine deprivation mediated by the Salmonella Typhimurium L-asparaginase causes suppression of cellular processes and pathways involved in protein synthesis, metabolism, and immune response. Our results advance knowledge of a mechanism used by Salmonella Typhimurium to inhibit T cell responses and mediate virulence, and provide new insights into the prerequisites of T cell activation. We propose a model in which l-asparagine deprivation inhibits T cell exit from quiescence by causing suppression of activation-induced metabolic reprogramming.
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Affiliation(s)
- AnnMarie Torres
- *Department of Molecular Genetics and Microbiology and Center for Infectious Diseases, Graduate Program in Genetics, Department of Chemistry and Institute for Chemical Biology and Drug Discovery, Proteomics Center, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA; and Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Joanna D Luke
- *Department of Molecular Genetics and Microbiology and Center for Infectious Diseases, Graduate Program in Genetics, Department of Chemistry and Institute for Chemical Biology and Drug Discovery, Proteomics Center, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA; and Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Amy L Kullas
- *Department of Molecular Genetics and Microbiology and Center for Infectious Diseases, Graduate Program in Genetics, Department of Chemistry and Institute for Chemical Biology and Drug Discovery, Proteomics Center, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA; and Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Kanishk Kapilashrami
- *Department of Molecular Genetics and Microbiology and Center for Infectious Diseases, Graduate Program in Genetics, Department of Chemistry and Institute for Chemical Biology and Drug Discovery, Proteomics Center, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA; and Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Yair Botbol
- *Department of Molecular Genetics and Microbiology and Center for Infectious Diseases, Graduate Program in Genetics, Department of Chemistry and Institute for Chemical Biology and Drug Discovery, Proteomics Center, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA; and Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Antonius Koller
- *Department of Molecular Genetics and Microbiology and Center for Infectious Diseases, Graduate Program in Genetics, Department of Chemistry and Institute for Chemical Biology and Drug Discovery, Proteomics Center, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA; and Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Peter J Tonge
- *Department of Molecular Genetics and Microbiology and Center for Infectious Diseases, Graduate Program in Genetics, Department of Chemistry and Institute for Chemical Biology and Drug Discovery, Proteomics Center, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA; and Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Emily I Chen
- *Department of Molecular Genetics and Microbiology and Center for Infectious Diseases, Graduate Program in Genetics, Department of Chemistry and Institute for Chemical Biology and Drug Discovery, Proteomics Center, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA; and Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Fernando Macian
- *Department of Molecular Genetics and Microbiology and Center for Infectious Diseases, Graduate Program in Genetics, Department of Chemistry and Institute for Chemical Biology and Drug Discovery, Proteomics Center, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA; and Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Adrianus W M van der Velden
- *Department of Molecular Genetics and Microbiology and Center for Infectious Diseases, Graduate Program in Genetics, Department of Chemistry and Institute for Chemical Biology and Drug Discovery, Proteomics Center, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA; and Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
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15
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Wu G, Chen D, Tang H, Ren Y, Chen Q, Lv Y, Zhang Z, Zhao YL, Yao Y, Xu P. Structural insights into the specific recognition of N-heterocycle biodenitrogenation-derived substrates by microbial amide hydrolases. Mol Microbiol 2014; 91:1009-21. [PMID: 24397579 DOI: 10.1111/mmi.12511] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2014] [Indexed: 11/28/2022]
Abstract
N-heterocyclic compounds from industrial wastes, including nicotine, are environmental pollutants or toxicants responsible for a variety of health problems. Microbial biodegradation is an attractive strategy for the removal of N-heterocyclic pollutants, during which carbon-nitrogen bonds in N-heterocycles are converted to amide bonds and subsequently severed by amide hydrolases. Previous studies have failed to clarify the molecular mechanism through which amide hydrolases selectively recognize diverse amide substrates and complete the biodenitrogenation process. In this study, structural, computational and enzymatic analyses showed how the N-formylmaleamate deformylase Nfo and the maleamate amidase Ami, two pivotal amide hydrolases in the nicotine catabolic pathway of Pseudomonas putida S16, specifically recognize their respective substrates. In addition, comparison of the α-β-α groups of amidases, which include Ami, pinpointed several subgroup-characteristic residues differentiating the two classes of amide substrates as containing either carboxylate groups or aromatic rings. Furthermore, this study reveals the molecular mechanism through which the specially tailored active sites of deformylases and amidases selectively recognize their unique substrates. Our work thus provides a thorough elucidation of the molecular mechanism through which amide hydrolases accomplish substrate-specific recognition in the microbial N-heterocycles biodenitrogenation pathway.
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Affiliation(s)
- Geng Wu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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