1
|
Yang G, Pećanac O, Wijma HJ, Rozeboom HJ, de Gonzalo G, Fraaije MW, Mascotti ML. Evolution of the catalytic mechanism at the dawn of the Baeyer-Villiger monooxygenases. Cell Rep 2024; 43:114130. [PMID: 38640062 DOI: 10.1016/j.celrep.2024.114130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/15/2024] [Accepted: 04/04/2024] [Indexed: 04/21/2024] Open
Abstract
Enzymes are crucial for the emergence and sustenance of life on earth. How they became catalytically active during their evolution is still an open question. Two opposite explanations are plausible: acquiring a mechanism in a series of discrete steps or all at once in a single evolutionary event. Here, we use molecular phylogeny, ancestral sequence reconstruction, and biochemical characterization to follow the evolution of a specialized group of flavoprotein monooxygenases, the bacterial Baeyer-Villiger monooxygenases (BVMOs). These enzymes catalyze an intricate chemical reaction relying on three different elements: a reduced nicotinamide cofactor, dioxygen, and a substrate. Characterization of ancestral BVMOs shows that the catalytic mechanism evolved in a series of steps starting from a FAD-binding protein and further acquiring reactivity and specificity toward each of the elements participating in the reaction. Together, the results of our work portray how an intrinsically complex catalytic mechanism emerged during evolution.
Collapse
Affiliation(s)
- Guang Yang
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Ognjen Pećanac
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Hein J Wijma
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Henriëtte J Rozeboom
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Gonzalo de Gonzalo
- Departamento de Química Orgánica, Universidad de Sevilla, and Centro de Innovación en Química Avanzada (ORFEO-CINQA), 41012 Sevilla, Spain
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Maria Laura Mascotti
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands; IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina.
| |
Collapse
|
2
|
Phintha A, Chaiyen P. Unifying and versatile features of flavin-dependent monooxygenases: Diverse catalysis by a common C4a-(hydro)peroxyflavin. J Biol Chem 2023; 299:105413. [PMID: 37918809 PMCID: PMC10696468 DOI: 10.1016/j.jbc.2023.105413] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/18/2023] [Accepted: 10/22/2023] [Indexed: 11/04/2023] Open
Abstract
Flavin-dependent monooxygenases (FDMOs) are known for their remarkable versatility and for their crucial roles in various biological processes and applications. Extensive research has been conducted to explore the structural and functional relationships of FDMOs. The majority of reported FDMOs utilize C4a-(hydro)peroxyflavin as a reactive intermediate to incorporate an oxygen atom into a wide range of compounds. This review discusses and analyzes recent advancements in our understanding of the structural and mechanistic features governing the enzyme functions. State-of-the-art discoveries related to common and distinct structural properties governing the catalytic versatility of the C4a-(hydro)peroxyflavin intermediate in selected FDMOs are discussed. Specifically, mechanisms of hydroxylation, dehalogenation, halogenation, and light-emitting reactions by FDMOs are highlighted. We also provide new analysis based on the structural and mechanistic features of these enzymes to gain insights into how the same intermediate can be harnessed to perform a wide variety of reactions. Challenging questions to obtain further breakthroughs in the understanding of FDMOs are also proposed.
Collapse
Affiliation(s)
- Aisaraphon Phintha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, Thailand.
| |
Collapse
|
3
|
Interconnected Set of Enzymes Provide Lysine Biosynthetic Intermediates and Ornithine Derivatives as Key Precursors for the Biosynthesis of Bioactive Secondary Metabolites. Antibiotics (Basel) 2023; 12:antibiotics12010159. [PMID: 36671360 PMCID: PMC9854754 DOI: 10.3390/antibiotics12010159] [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: 12/15/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Bacteria, filamentous fungi, and plants synthesize thousands of secondary metabolites with important biological and pharmacological activities. The biosynthesis of these metabolites is performed by networks of complex enzymes such as non-ribosomal peptide synthetases, polyketide synthases, and terpenoid biosynthetic enzymes. The efficient production of these metabolites is dependent upon the supply of precursors that arise from primary metabolism. In the last decades, an impressive array of biosynthetic enzymes that provide specific precursors and intermediates leading to secondary metabolites biosynthesis has been reported. Suitable knowledge of the elaborated pathways that synthesize these precursors or intermediates is essential for advancing chemical biology and the production of natural or semisynthetic biological products. Two of the more prolific routes that provide key precursors in the biosynthesis of antitumor, immunosuppressant, antifungal, or antibacterial compounds are the lysine and ornithine pathways, which are involved in the biosynthesis of β-lactams and other non-ribosomal peptides, and bacterial and fungal siderophores. Detailed analysis of the molecular genetics and biochemistry of the enzyme system shows that they are formed by closely related components. Particularly the focus of this study is on molecular genetics and the enzymatic steps that lead to the formation of intermediates of the lysine pathway, such as α-aminoadipic acid, saccharopine, pipecolic acid, and related compounds, and of ornithine-derived molecules, such as N5-Acetyl-N5-Hydroxyornithine and N5-anhydromevalonyl-N5-hydroxyornithine, which are precursors of siderophores. We provide evidence that shows interesting functional relationships between the genes encoding the enzymes that synthesize these products. This information will contribute to a better understanding of the possibilities of advancing the industrial applications of synthetic biology.
Collapse
|
4
|
Lyons NS, Bogner AN, Tanner JJ, Sobrado P. Kinetic and Structural Characterization of a Flavin-Dependent Putrescine N-Hydroxylase from Acinetobacter baumannii. Biochemistry 2022; 61:2607-2620. [DOI: 10.1021/acs.biochem.2c00493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Noah S. Lyons
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Alexandra N. Bogner
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - John J. Tanner
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
- Department of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Pablo Sobrado
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
| |
Collapse
|
5
|
Shyam Mohan AH, Rao SN, D S, Rajeswari N. In silico structural, phylogenetic and drug target analysis of putrescine monooxygenase from Shewanella putrefaciens-95. J Genet Eng Biotechnol 2022; 20:57. [PMID: 35412199 PMCID: PMC9005580 DOI: 10.1186/s43141-022-00338-z] [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: 10/21/2021] [Accepted: 03/22/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND The enormous and irresponsible use of antibiotics has led to the emergence of resistant strains of bacteria globally. A new approach to combat this crisis has been nutritional immunity limiting the availability of nutrients to pathogens. Targeting the siderophore biosynthetic pathway that helps in iron acquisition, an essential microelement in the bacterial system has been the topic of interest in recent days that backs the concept of nutritional immunity. Supporting this view, we have chosen to study a key enzyme in the biosynthetic pathway of putrebactin called putrescine monooxygenase (SpPMO) from Shewanella putrefaciens. In our previous study, we co-expressed putrescine monooxygenase recombinantly in Escherichia coli BL21 Star (DE3). The bioinformatic analysis and screening of inhibitors will broaden the scope of SpPMO as a drug target. RESULTS In the present study, we have analysed the physicochemical properties of the target enzyme and other N-hydroxylating monooxygenases (NMOs) using ExPASy server. The target enzyme SpPMO and most of the selected NMOs have a slightly acidic isoelectric point and are medially thermostable and generally insoluble. The multiple sequence alignment identified the GXGXX(N/A), DXXXFATGYXXXXP motives and conserved amino acids involved in FAD binding, NADP binding, secondary structure formation and substrate binding. The phylogenetic analysis indicated the distribution of the monooxygenases into different clades according to their substrate specificity. Further, a 3D model of SpPMO was predicted using I-TASSER online tool with DfoA from Erwinia amylovora as a template. The model was validated using the SAVES server and deposited to the Protein Model Database with the accession number PM0082222. The molecular docking analysis with different substrates revealed the presence of a putrescine binding pocket made of conserved amino acids and another binding pocket present on the surface of the protein wherein all other ligands interact with high binding affinity. The molecular docking of naturally occurring inhibitor molecules with SpPMO 3D model identified curcumin and niazirin with 1.83 and 2.81 μM inhibition constants as two promising inhibitors. Further studies on kinetic parameters of curcumin and niazirin inhibitors in vitro determined the Ki to be 2.6±0.0036 μM and 18.38±0.008 μM respectively. CONCLUSION This analysis will help us understand the structural, phylogenetic and drug target aspects of putrescine monooxygenase from Shewanella putrefaciens-95 in detail. It sheds light on the precautionary measures that can be developed to inhibit the enzyme and thereby the secondary infections caused by them.
Collapse
Affiliation(s)
- Anil H Shyam Mohan
- Department of Biotechnology, Dayananda Sagar College of Engineering, Kumaraswamy Layout, Shavige Malleswara Hills, Bengaluru-78, Karnataka, India
| | - Saroja Narsing Rao
- Pesticide Residue and Food Quality Analysis Laboratory, University of Agricultural Sciences, Raichur, Karnataka, 584104, India.
| | - Srividya D
- Department of Biotechnology, Davangere University, Shivagangothri, Davangere, Karnataka, 577007, India
| | - N Rajeswari
- Department of Biotechnology, Dayananda Sagar College of Engineering, Kumaraswamy Layout, Shavige Malleswara Hills, Bengaluru-78, Karnataka, India
| |
Collapse
|
6
|
Valentino H, Sobrado P. Characterization of a Nitro-Forming Enzyme Involved in Fosfazinomycin Biosynthesis. Biochemistry 2021; 60:2851-2864. [PMID: 34516102 DOI: 10.1021/acs.biochem.1c00512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N-hydroxylating monooxygenases (NMOs) are a subclass of flavin-dependent enzymes that hydroxylate nitrogen atoms. Recently, unique NMOs that perform multiple reactions on one substrate molecule have been identified. Fosfazinomycin M (FzmM) is one such NMO, forming nitrosuccinate from aspartate (Asp) in the fosfazinomycin biosynthetic pathway in some Streptomyces sp. This work details the biochemical and kinetic analysis of FzmM. Steady-state kinetic investigation shows that FzmM performs a coupled reaction with Asp (kcat, 3.0 ± 0.01 s-1) forming nitrosuccinate, which can be converted to fumarate and nitrite by the action of FzmL. FzmM displays a 70-fold higher kcat/KM value for NADPH compared to NADH and has a narrow optimal pH range (7.5-8.0). Contrary to other NMOs where the kred is rate-limiting, FzmM exhibits a very fast kred (50 ± 0.01 s-1 at 4 °C) with NADPH. NADPH binds at a KD value of ∼400 μM, and hydride transfer occurs with pro-R stereochemistry. Oxidation of FzmM in the absence of Asp exhibits a spectrum with a shoulder at ∼370 nm, consistent with the formation of a C(4a)-hydroperoxyflavin intermediate, which decays into oxidized flavin and hydrogen peroxide at a rate 100-fold slower than the kcat. This reaction is enhanced in the presence of Asp with a slightly faster kox than the kcat, suggesting that flavin dehydration or Asp oxidation is partially rate limiting. Multiple sequence analyses of FzmM to NMOs identified conserved residues involved in flavin binding but not for NADPH. Additional sequence analysis to related monooxygenases suggests that FzmM shares sequence motifs absent in other NMOs.
Collapse
Affiliation(s)
- Hannah Valentino
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States.,Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States.,Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
| |
Collapse
|
7
|
Hernández VM, Arteaga A, Dunn MF. Diversity, properties and functions of bacterial arginases. FEMS Microbiol Rev 2021; 45:6308370. [PMID: 34160574 DOI: 10.1093/femsre/fuab034] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/17/2021] [Indexed: 02/07/2023] Open
Abstract
The metalloenzyme arginase hydrolyzes L-arginine to produce L-ornithine and urea. In bacteria, arginase has important functions in basic nitrogen metabolism and redistribution, production of the key metabolic precursor L-ornithine, stress resistance and pathogenesis. We describe the regulation and specific functions of the arginase pathway as well as summarize key characteristics of related arginine catabolic pathways. The use of arginase-derived ornithine as a precursor molecule is reviewed. We discuss the biochemical and transcriptional regulation of arginine metabolism, including arginase, with the latter topic focusing on the RocR and AhrC transcriptional regulators in the model organism Bacillus subtilis. Finally, we consider similarities and contrasts in the structure and catalytic mechanism of the arginases from Bacillus caldovelox and Helicobacter pylori. The overall aim of this review is to provide a panorama of the diversity of physiological functions, regulation, and biochemical features of arginases in a variety of bacterial species.
Collapse
Affiliation(s)
- Victor M Hernández
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas-Universidad Nacional Autonoma de México, Cuernavaca, Morelos, C.P. 62210, Mexico
| | - Alejandra Arteaga
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas-Universidad Nacional Autonoma de México, Cuernavaca, Morelos, C.P. 62210, Mexico
| | - Michael F Dunn
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas-Universidad Nacional Autonoma de México, Cuernavaca, Morelos, C.P. 62210, Mexico
| |
Collapse
|
8
|
Giddings LA, Lountos GT, Kim KW, Brockley M, Needle D, Cherry S, Tropea JE, Waugh DS. Characterization of a broadly specific cadaverine N-hydroxylase involved in desferrioxamine B biosynthesis in Streptomyces sviceus. PLoS One 2021; 16:e0248385. [PMID: 33784308 PMCID: PMC8009421 DOI: 10.1371/journal.pone.0248385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023] Open
Abstract
N-hydroxylating flavin-dependent monooxygenases (FMOs) are involved in the biosynthesis of hydroxamate siderophores, playing a key role in microbial virulence. Herein, we report the first structural and kinetic characterization of a novel alkyl diamine N-hydroxylase DesB from Streptomyces sviceus (SsDesB). This enzyme catalyzes the first committed step in the biosynthesis of desferrioxamine B, a clinical drug used to treat iron overload disorders. X-ray crystal structures of the SsDesB holoenzyme with FAD and the ternary complex with bound NADP+ were solved at 2.86 Å and 2.37 Å resolution, respectively, providing a structural view of the active site environment. SsDesB crystallized as a tetramer and the structure of the individual protomers closely resembles the structures of homologous N-hydroxylating FMOs from Erwinia amylovora (DfoA), Pseudomonas aeruginosa (PvdA), and Aspergillus fumigatus (SidA). Using NADPH oxidation, oxygen consumption, and product formation assays, kinetic parameters were determined for various substrates with SsDesB. SsDesB exhibited typical saturation kinetics with substrate inhibition at high concentrations of NAD(P)H as well as cadaverine. The apparent kcat values for NADPH in steady-state NADPH oxidation and oxygen consumption assays were 0.28 ± 0.01 s-1 and 0.24 ± 0.01 s-1, respectively. However, in product formation assays used to measure the rate of N-hydroxylation, the apparent kcat for NADPH (0.034 ± 0.008 s-1) was almost 10-fold lower under saturating FAD and cadaverine concentrations, reflecting an uncoupled reaction, and the apparent NADPH KM was 33 ± 24 μM. Under saturating FAD and NADPH concentrations, the apparent kcat and KM for cadaverine in Csaky assays were 0.048 ± 0.004 s-1 and 19 ± 9 μM, respectively. SsDesB also N-hydroxylated putrescine, spermidine, and L-lysine substrates but not alkyl (di)amines that were branched or had fewer than four methylene units in an alkyl chain. These data demonstrate that SsDesB has wider substrate scope compared to other well-studied ornithine and lysine N-hydroxylases, making it an amenable biocatalyst for the production of desferrioxamine B, derivatives, and other N-substituted products.
Collapse
Affiliation(s)
- Lesley-Ann Giddings
- Department of Chemistry, Smith College, Northampton, MA, United States of America
- Department of Chemistry & Biochemistry, Middlebury College, Middlebury, VT, United States of America
| | - George T. Lountos
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America
| | - Kang Woo Kim
- Department of Chemistry & Biochemistry, Middlebury College, Middlebury, VT, United States of America
| | - Matthew Brockley
- Department of Chemistry & Biochemistry, Middlebury College, Middlebury, VT, United States of America
| | - Danielle Needle
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States of America
| | - Scott Cherry
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States of America
| | - Joseph E. Tropea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States of America
| | - David S. Waugh
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States of America
| |
Collapse
|
9
|
Nóbile ML, Stricker AM, Marchesano L, Iribarren AM, Lewkowicz ES. N-oxygenation of amino compounds: Early stages in its application to the biocatalyzed preparation of bioactive compounds. Biotechnol Adv 2021; 51:107726. [PMID: 33675955 DOI: 10.1016/j.biotechadv.2021.107726] [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: 11/16/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 10/22/2022]
Abstract
Among the compounds that contain unusual functional groups, nitro is perhaps one of the most interesting due to the valuable properties it confers on pharmaceuticals and explosives. Traditional chemistry has for many years used environmentally unfriendly strategies; in contrast, the biocatalyzed production of this type of products offers a promising alternative. The small family of enzymes formed by N-oxygenases allows the conversion of an amino group to a nitro through the sequential addition of oxygen. These enzymes also make it possible to obtain other less oxidized N-O functions, such as hydroxylamine or nitroso, present in intermediate or final products. The current substrates on which these enzymes are reported to work encompass a few aromatic molecules and sugars. The unique characteristics of N-oxygenases and the great economic value of the products that they could generate, place them in a position of very high scientific and industrial interest. The most important and best studied N-oxygenases will be presented here.
Collapse
Affiliation(s)
- Matías L Nóbile
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Biocatalysis and Biotransformation Laboratory, Roque Sáenz Peña 352, Bernal 1876, Buenos Aires, Argentina.
| | - Abigail M Stricker
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Biocatalysis and Biotransformation Laboratory, Roque Sáenz Peña 352, Bernal 1876, Buenos Aires, Argentina
| | - Lucas Marchesano
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Biocatalysis and Biotransformation Laboratory, Roque Sáenz Peña 352, Bernal 1876, Buenos Aires, Argentina
| | - Adolfo M Iribarren
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Biocatalysis and Biotransformation Laboratory, Roque Sáenz Peña 352, Bernal 1876, Buenos Aires, Argentina
| | - Elizabeth S Lewkowicz
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Biocatalysis and Biotransformation Laboratory, Roque Sáenz Peña 352, Bernal 1876, Buenos Aires, Argentina
| |
Collapse
|
10
|
|
11
|
Misslinger M, Hortschansky P, Brakhage AA, Haas H. Fungal iron homeostasis with a focus on Aspergillus fumigatus. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118885. [PMID: 33045305 DOI: 10.1016/j.bbamcr.2020.118885] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/15/2020] [Accepted: 10/01/2020] [Indexed: 02/08/2023]
Abstract
To maintain iron homeostasis, fungi have to balance iron acquisition, storage, and utilization to ensure sufficient supply and to avoid toxic excess of this essential trace element. As pathogens usually encounter iron limitation in the host niche, this metal plays a particular role during virulence. Siderophores are iron-chelators synthesized by most, but not all fungal species to sequester iron extra- and intracellularly. In recent years, the facultative human pathogen Aspergillus fumigatus has become a model for fungal iron homeostasis of siderophore-producing fungal species. This article summarizes the knowledge on fungal iron homeostasis and its links to virulence with a focus on A. fumigatus. It covers mechanisms for iron acquisition, storage, and detoxification, as well as the modes of transcriptional iron regulation and iron sensing in A. fumigatus in comparison to other fungal species. Moreover, potential translational applications of the peculiarities of fungal iron metabolism for treatment and diagnosis of fungal infections is addressed.
Collapse
Affiliation(s)
- Matthias Misslinger
- Institute of Molecular Biology - Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Peter Hortschansky
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany; Department Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Hubertus Haas
- Institute of Molecular Biology - Biocenter, Medical University of Innsbruck, Innsbruck, Austria.
| |
Collapse
|
12
|
Mügge C, Heine T, Baraibar AG, van Berkel WJH, Paul CE, Tischler D. Flavin-dependent N-hydroxylating enzymes: distribution and application. Appl Microbiol Biotechnol 2020; 104:6481-6499. [PMID: 32504128 PMCID: PMC7347517 DOI: 10.1007/s00253-020-10705-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/18/2020] [Accepted: 05/24/2020] [Indexed: 02/06/2023]
Abstract
Amino groups derived from naturally abundant amino acids or (di)amines can be used as "shuttles" in nature for oxygen transfer to provide intermediates or products comprising N-O functional groups such as N-hydroxy, oxazine, isoxazolidine, nitro, nitrone, oxime, C-, S-, or N-nitroso, and azoxy units. To this end, molecular oxygen is activated by flavin, heme, or metal cofactor-containing enzymes and transferred to initially obtain N-hydroxy compounds, which can be further functionalized. In this review, we focus on flavin-dependent N-hydroxylating enzymes, which play a major role in the production of secondary metabolites, such as siderophores or antimicrobial agents. Flavoprotein monooxygenases of higher organisms (among others, in humans) can interact with nitrogen-bearing secondary metabolites or are relevant with respect to detoxification metabolism and are thus of importance to understand potential medical applications. Many enzymes that catalyze N-hydroxylation reactions have specific substrate scopes and others are rather relaxed. The subsequent conversion towards various N-O or N-N comprising molecules is also described. Overall, flavin-dependent N-hydroxylating enzymes can accept amines, diamines, amino acids, amino sugars, and amino aromatic compounds and thus provide access to versatile families of compounds containing the N-O motif. Natural roles as well as synthetic applications are highlighted. Key points • N-O and N-N comprising natural and (semi)synthetic products are highlighted. • Flavin-based NMOs with respect to mechanism, structure, and phylogeny are reviewed. • Applications in natural product formation and synthetic approaches are provided. Graphical abstract .
Collapse
Affiliation(s)
- Carolin Mügge
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Thomas Heine
- Environmental Microbiology, Faculty of Chemistry and Physics, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Alvaro Gomez Baraibar
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany
- Rottendorf Pharma GmbH, Ostenfelder Str. 51-61, 59320, Ennigerloh, Germany
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | - Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, HZ 2629, Delft, The Netherlands
| | - Dirk Tischler
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany.
| |
Collapse
|
13
|
Campbell AC, Stiers KM, Martin Del Campo JS, Mehra-Chaudhary R, Sobrado P, Tanner JJ. Trapping conformational states of a flavin-dependent N-monooxygenase in crystallo reveals protein and flavin dynamics. J Biol Chem 2020; 295:13239-13249. [PMID: 32723870 DOI: 10.1074/jbc.ra120.014750] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/21/2020] [Indexed: 11/06/2022] Open
Abstract
The siderophore biosynthetic enzyme A (SidA) ornithine hydroxylase from Aspergillus fumigatus is a fungal disease drug target involved in the production of hydroxamate-containing siderophores, which are used by the pathogen to sequester iron. SidA is an N-monooxygenase that catalyzes the NADPH-dependent hydroxylation of l-ornithine through a multistep oxidative mechanism, utilizing a C4a-hydroperoxyflavin intermediate. Here we present four new crystal structures of SidA in various redox and ligation states, including the first structure of oxidized SidA without NADP(H) or l-ornithine bound (resting state). The resting state structure reveals a new out active site conformation characterized by large rotations of the FAD isoalloxazine around the C1-'C2' and N10-C1' bonds, coupled to a 10-Å movement of the Tyr-loop. Additional structures show that either flavin reduction or the binding of NADP(H) is sufficient to drive the FAD to the in conformation. The structures also reveal protein conformational changes associated with the binding of NADP(H) and l-ornithine. Some of these residues were probed using site-directed mutagenesis. Docking was used to explore the active site of the out conformation. These calculations identified two potential ligand-binding sites. Altogether, our results provide new information about conformational dynamics in flavin-dependent monooxygenases. Understanding the different active site conformations that appear during the catalytic cycle may allow fine-tuning of inhibitor discovery efforts.
Collapse
Affiliation(s)
- Ashley C Campbell
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Kyle M Stiers
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | | | | | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA.
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA; Department of Chemistry, University of Missouri, Columbia, Missouri, USA.
| |
Collapse
|
14
|
Abstract
Flavin-dependent monooxygenases (FMOs) are ancient enzymes present in all kingdoms of life. FMOs typically catalyze the incorporation of an oxygen atom from molecular oxygen into small molecules. To date, the majority of functional characterization studies have been performed on mammalian, fungal and bacterial FMOs, showing that they play fundamental roles in drug and xenobiotic metabolism. By contrast, our understanding of FMOs across the plant kingdom is very limited, despite plants possessing far greater FMO diversity compared to both bacteria and other multicellular organisms. Here, we review the progress of plant FMO research, with a focus on FMO diversity and functionality. Significantly, of the FMOs characterized to date, they all perform oxygenation reactions that are crucial steps within hormone metabolism, pathogen resistance, signaling and chemical defense. This demonstrates the fundamental role FMOs have within plant metabolism, and presents significant opportunities for future research pursuits and downstream applications.
Collapse
|
15
|
Kenjić N, Hoag MR, Moraski GC, Caperelli CA, Moran GR, Lamb AL. PvdF of pyoverdin biosynthesis is a structurally unique N 10-formyltetrahydrofolate-dependent formyltransferase. Arch Biochem Biophys 2019; 664:40-50. [PMID: 30689984 DOI: 10.1016/j.abb.2019.01.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 11/17/2022]
Abstract
The hydroxyornithine transformylase from Pseudomonas aeruginosa is known by the gene name pvdF, and has been hypothesized to use N10-formyltetrahydrofolate (N10-fTHF) as a co-substrate formyl donor to convert N5-hydroxyornithine (OHOrn) to N5-formyl- N5-hydroxyornithine (fOHOrn). PvdF is in the biosynthetic pathway for pyoverdin biosynthesis, a siderophore generated under iron-limiting conditions that has been linked to virulence, quorum sensing and biofilm formation. The structure of PvdF was determined by X-ray crystallography to 2.3 Å, revealing a formyltransferase fold consistent with N10-formyltetrahydrofolate dependent enzymes, such as the glycinamide ribonucleotide transformylases, N-sugar transformylases and methionyl-tRNA transformylases. Whereas the core structure, including the catalytic triad, is conserved, PvdF has three insertions of 18 or more amino acids, which we hypothesize are key to binding the OHOrn substrate. Steady state kinetics revealed a non-hyperbolic rate curve, promoting the hypothesis that PvdF uses a random-sequential mechanism, and favors folate binding over OHOrn.
Collapse
Affiliation(s)
- Nikola Kenjić
- Department of Molecular Biosciences, 1200 Sunnyside Ave, University of Kansas, Lawrence, KS, 66045, USA
| | - Matthew R Hoag
- Department of Chemistry and Biochemistry, 3210 N Cramer St, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA
| | - Garrett C Moraski
- Department of Chemistry and Biochemistry, 103 Chemistry and Biochemistry Building, Montana State University, Bozeman, MT, 59717, USA
| | - Carol A Caperelli
- Winkle College of Pharmacy, University of Cincinnati, ML 0514, 231 Albert Sabin Way, MSB 3109B, Cincinnati, OH, 45267, USA
| | - Graham R Moran
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Audrey L Lamb
- Department of Molecular Biosciences, 1200 Sunnyside Ave, University of Kansas, Lawrence, KS, 66045, USA.
| |
Collapse
|
16
|
Saroja NR, Mohan AHS, Srividya D, Supreetha K. Chaperone-assisted expression and purification of putrescine monooxygenase from Shewanella putrefaciens-95. Protein Expr Purif 2019; 157:9-16. [PMID: 30654014 DOI: 10.1016/j.pep.2019.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 01/09/2019] [Accepted: 01/09/2019] [Indexed: 01/22/2023]
Abstract
A putrescine monooxygenase from Shewanella putrefaciens 95 (SpPMO) is the initial enzyme catalyzing the hydroxylation of putrescine to N-hydroxyl putrescine, the precursor for the synthesis of a siderophore putrebactin was identified. This PMO clustered together with known characterized NMOs from Shewanella baltica, Bordetella pertussis, Erwinia amylovora, Streptomyces sp. Gordonia rubripertincta, Pseudomonas aeruginosa and outgrouped from Escherichia coli, Nocardia farcinica, and Rhodococcus erythropolis. The deduced SpPMO protein showed 53% and 36% sequence identity with other characterized bacterial NMOs from Erwinia amylovora and Gordonia rubripertincta respectively. In this investigation, we have cloned the complete 1518bp coding sequence of pubA from Shewanella putrefaciens 95 encoding the corresponding protein SpPMO. It comprises 505 amino acid residues in length and has approximately a molecular weight of 54 kDa. Chaperone-assisted heterologous expression of SpPMO in pET151Topo expression vector under the control of bacteriophage T7 promoter permitted a stringent IPTG dependent expression. It has been successfully cloned, overexpressed and purified as a soluble His6 -tagged enzyme using E. coli as a cloning and expression host. The expression of recombinant SpPMO was confirmed by Western blotting using anti-His6 antibody. The purified protein showed FAD and NADPH dependent N-hydroxylation activity. This study has paved a way to understand the hydroxylation step of putrebactin synthesis which can be further investigated by studying its kinetic mechanism and physiological role.
Collapse
Affiliation(s)
- Narsing Rao Saroja
- Pesticide Residue and Food Quality Analysis Laboratory, University of Agricultural Sciences, Raichur, 584104, Karnataka, India.
| | - Anil H Shyam Mohan
- Department of Biotechnology, Dayananda Sagar College of Engineering, Kumaraswamy Layout, Shavige Malleswara Hills, Bengaluru, 78, Karnataka, India
| | - D Srividya
- Pesticide Residue and Food Quality Analysis Laboratory, University of Agricultural Sciences, Raichur, 584104, Karnataka, India
| | - K Supreetha
- Department of Biotechnology, Dayananda Sagar College of Engineering, Kumaraswamy Layout, Shavige Malleswara Hills, Bengaluru, 78, Karnataka, India
| |
Collapse
|
17
|
Hartmann M, Zeier J. l-lysine metabolism to N-hydroxypipecolic acid: an integral immune-activating pathway in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:5-21. [PMID: 30035374 DOI: 10.1111/tpj.14037] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/22/2018] [Accepted: 07/03/2018] [Indexed: 05/03/2023]
Abstract
l-lysine catabolic routes in plants include the saccharopine pathway to α-aminoadipate and decarboxylation of lysine to cadaverine. The current review will cover a third l-lysine metabolic pathway having a major role in plant systemic acquired resistance (SAR) to pathogen infection that was recently discovered in Arabidopsis thaliana. In this pathway, the aminotransferase AGD2-like defense response protein (ALD1) α-transaminates l-lysine and generates cyclic dehydropipecolic (DP) intermediates that are subsequently reduced to pipecolic acid (Pip) by the reductase SAR-deficient 4 (SARD4). l-pipecolic acid, which occurs ubiquitously in the plant kingdom, is further N-hydroxylated to the systemic acquired resistance (SAR)-activating metabolite N-hydroxypipecolic acid (NHP) by flavin-dependent monooxygenase1 (FMO1). N-hydroxypipecolic acid induces the expression of a set of major plant immune genes to enhance defense readiness, amplifies resistance responses, acts synergistically with the defense hormone salicylic acid, promotes the hypersensitive cell death response and primes plants for effective immune mobilization in cases of future pathogen challenge. This pathogen-inducible NHP biosynthetic pathway is activated at the transcriptional level and involves feedback amplification. Apart from FMO1, some cytochrome P450 monooxygenases involved in secondary metabolism catalyze N-hydroxylation reactions in plants. In specific taxa, pipecolic acid might also serve as a precursor in the biosynthesis of specialized natural products, leading to C-hydroxylated and otherwise modified piperidine derivatives, including indolizidine alkaloids. Finally, we show that NHP is glycosylated in Arabidopsis to form a hexose-conjugate, and then discuss open questions in Pip/NHP-related research.
Collapse
Affiliation(s)
- Michael Hartmann
- Department of Biology, Institute for Molecular Ecophysiology of Plants, Heinrich Heine University, Universitätsstraße 1, D-40225, Düsseldorf, Germany
| | - Jürgen Zeier
- Department of Biology, Institute for Molecular Ecophysiology of Plants, Heinrich Heine University, Universitätsstraße 1, D-40225, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstraße 1, D-40225, Düsseldorf, Germany
| |
Collapse
|
18
|
Robinson RM, Klancher CA, Rodriguez PJ, Sobrado P. Flavin oxidation in flavin-dependent N-monooxygenases. Protein Sci 2018; 28:90-99. [PMID: 30098072 DOI: 10.1002/pro.3487] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 07/14/2018] [Accepted: 07/23/2018] [Indexed: 01/08/2023]
Abstract
Siderophore A (SidA) from Aspergillus fumigatus is a flavin-containing monooxygenase that hydroxylates ornithine (Orn) at the amino group of the side chain. Lysine (Lys) also binds to the active site of SidA; however, hydroxylation is not efficient and H2 O2 is the main product. The effect of pH on steady-state kinetic parameters was measured and the results were consistent with Orn binding with the side chain amino group in the neutral form. From the pH dependence on flavin oxidation in the absence of Orn, a pKa value >9 was determined and assigned to the FAD-N5 atom. In the presence of Orn, the pH dependence displayed a pKa value of 6.7 ±0.1 and of 7.70 ±0.10 in the presence of Lys. Q102 interacts with NADPH and, upon mutation to alanine, leads to destabilization of the C4a-hydroperoxyflavin (FADOOH ). Flavin oxidation with Q102A showed a pKa value of ~8.0. The data are consistent with the pKa of the FAD N5-atom being modulated to a value >9 in the absence of Orn, which aids in the stabilization of FADOOH . Changes in the FAD-N5 environment lead to a decrease in the pKa value, which facilitates elimination of H2 O2 or H2 O. These findings are supported by solvent kinetic isotope effect experiments, which show that proton transfer from the FAD N5-atom is rate limiting in the absence of a substrate, however, is significantly less rate limiting in the presence of Orn and or Lys.
Collapse
Affiliation(s)
- Reeder M Robinson
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia, 24061
| | - Catherine A Klancher
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia, 24061
| | - Pedro J Rodriguez
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia, 24061
| | - Pablo Sobrado
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia, 24061
| |
Collapse
|
19
|
Telfer TJ, Codd R. Fluorinated Analogues of Desferrioxamine B from Precursor-Directed Biosynthesis Provide New Insight into the Capacity of DesBCD. ACS Chem Biol 2018; 13:2456-2471. [PMID: 30081629 DOI: 10.1021/acschembio.8b00340] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The siderophore desferrioxamine B (DFOB, 1) native to Streptomyces pilosus is biosynthesized by the DesABCD enzyme cluster. DesA-mediated decarboxylation of l-lysine gives 1,5-diaminopentane (DP) for processing by DesBCD. S. pilosus culture medium was supplemented with rac-1,4-diamino-2-fluorobutane ( rac-FDB) to compete against DP to generate fluorinated analogues of DFOB, as agents of potential clinical interest. LC-MS/MS analysis identified fluorinated analogues of DFOB with one, two, or three DP units (binary notation: 0) exchanged for one (DFOA-F1[001] (2), DFOA-F1[010] (3), DFOA-F1[100] (4)), two (DFOA-F2[011] (5), DFOA-F2[110] (6), DFOA-F2[101] (7)), or three (DFOA-F3[111] (8)) rac-FDB units (binary notation: 1). The two sets of constitutional isomers 2-4 and 5-7 arose from the position of the substrates in the N-acetyl, internal, or amine-containing regions of the DFOB trimer. N-Acetylated fluorinated DFOB analogues were formed where the rac-FDB substrate was positioned in the amine region ( e.g., N-Ac-DFOA-F1[001] (2a)). Other analogues contained two hydroxamic acid groups and three amide bonds. Experiments using rac-FDB, R-FDB, or S-FDB showed a similar species profile between rac-FDB and R-FDB. These data are consistent with the following. (i) DesB can act on rac-FDB. (ii) DesC can act directly on rac-FDB. (iii) The products of DesBC or DesC catalysis of rac-FDB can undergo a second round of DesC catalysis at the free amine. (iv) DesD catalysis of these products gives N, N'-diacetylated compounds. (v) A minimum of two hydroxamic acid groups is required to form a viable DesD-substrate(s) precomplex. (vi) One or more DesBCD-catalyzed steps in DFOB biosynthesis is enantioselective. This work has provided a potential path to access fluorinated analogues of DFOB and new insight into its biosynthesis.
Collapse
Affiliation(s)
- Thomas J. Telfer
- School of Medical Sciences (Pharmacology), The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Rachel Codd
- School of Medical Sciences (Pharmacology), The University of Sydney, Sydney, New South Wales 2006, Australia
| |
Collapse
|
20
|
Active site variants provide insight into the nature of conformational changes that accompany the cyclohexanone monooxygenase catalytic cycle. Arch Biochem Biophys 2018; 654:85-96. [DOI: 10.1016/j.abb.2018.07.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 01/31/2023]
|
21
|
Hartmann M, Zeier T, Bernsdorff F, Reichel-Deland V, Kim D, Hohmann M, Scholten N, Schuck S, Bräutigam A, Hölzel T, Ganter C, Zeier J. Flavin Monooxygenase-Generated N-Hydroxypipecolic Acid Is a Critical Element of Plant Systemic Immunity. Cell 2018; 173:456-469.e16. [PMID: 29576453 DOI: 10.1016/j.cell.2018.02.049] [Citation(s) in RCA: 227] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/16/2018] [Accepted: 02/20/2018] [Indexed: 12/21/2022]
Abstract
Following a previous microbial inoculation, plants can induce broad-spectrum immunity to pathogen infection, a phenomenon known as systemic acquired resistance (SAR). SAR establishment in Arabidopsis thaliana is regulated by the Lys catabolite pipecolic acid (Pip) and flavin-dependent-monooxygenase1 (FMO1). Here, we show that elevated Pip is sufficient to induce an FMO1-dependent transcriptional reprogramming of leaves that is reminiscent of SAR. In planta and in vitro analyses demonstrate that FMO1 functions as a pipecolate N-hydroxylase, catalyzing the biochemical conversion of Pip to N-hydroxypipecolic acid (NHP). NHP systemically accumulates in plants after microbial attack. When exogenously applied, it overrides the defect of NHP-deficient fmo1 in acquired resistance and acts as a potent inducer of plant immunity to bacterial and oomycete infection. Our work has identified a pathogen-inducible L-Lys catabolic pathway in plants that generates the N-hydroxylated amino acid NHP as a critical regulator of systemic acquired resistance to pathogen infection.
Collapse
Affiliation(s)
- Michael Hartmann
- Institute for Molecular Ecophysiology of Plants, Department of Biology, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Tatyana Zeier
- Institute for Molecular Ecophysiology of Plants, Department of Biology, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Friederike Bernsdorff
- Institute for Molecular Ecophysiology of Plants, Department of Biology, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vanessa Reichel-Deland
- Institute for Molecular Ecophysiology of Plants, Department of Biology, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Denis Kim
- Institute for Molecular Ecophysiology of Plants, Department of Biology, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Michele Hohmann
- Institute for Molecular Ecophysiology of Plants, Department of Biology, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Nicola Scholten
- Institute for Molecular Ecophysiology of Plants, Department of Biology, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Stefan Schuck
- Institute for Molecular Ecophysiology of Plants, Department of Biology, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Andrea Bräutigam
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany; Institute for Plant Biochemistry, Department of Biology, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Torsten Hölzel
- Institute of Inorganic and Structural Chemistry, Department of Chemistry, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Christian Ganter
- Institute of Inorganic and Structural Chemistry, Department of Chemistry, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Jürgen Zeier
- Institute for Molecular Ecophysiology of Plants, Department of Biology, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany.
| |
Collapse
|
22
|
Contrasting roles of fungal siderophores in maintaining iron homeostasis in Epichloë festucae. Fungal Genet Biol 2018; 111:60-72. [DOI: 10.1016/j.fgb.2017.11.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 11/11/2017] [Accepted: 11/14/2017] [Indexed: 11/23/2022]
|
23
|
Bufkin K, Sobrado P. Characterization of the Ornithine Hydroxylation Step in Albachelin Biosynthesis. Molecules 2017; 22:E1652. [PMID: 28974024 PMCID: PMC6151521 DOI: 10.3390/molecules22101652] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 11/16/2022] Open
Abstract
N-Hydroxylating monooxygenases (NMOs) are involved in siderophore biosynthesis. Siderophores are high affinity iron chelators composed of catechol and hydroxamate functional groups that are synthesized and secreted by microorganisms and plants. Recently, a new siderophore named albachelin was isolated from a culture of Amycolatopsis alba growing under iron-limiting conditions. This work focuses on the expression, purification, and characterization of the NMO, abachelin monooxygenase (AMO) from A. alba. This enzyme was purified and characterized in its holo (FAD-bound) and apo (FAD-free) forms. The apo-AMO could be reconstituted by addition of free FAD. The two forms of AMO hydroxylate ornithine, while lysine increases oxidase activity but is not hydroxylated and display low affinity for NADPH.
Collapse
Affiliation(s)
- Kendra Bufkin
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA.
- Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, USA.
| |
Collapse
|
24
|
Waldman AJ, Ng TL, Wang P, Balskus EP. Heteroatom-Heteroatom Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5784-5863. [PMID: 28375000 PMCID: PMC5534343 DOI: 10.1021/acs.chemrev.6b00621] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Natural products that contain functional groups with heteroatom-heteroatom linkages (X-X, where X = N, O, S, and P) are a small yet intriguing group of metabolites. The reactivity and diversity of these structural motifs has captured the interest of synthetic and biological chemists alike. Functional groups containing X-X bonds are found in all major classes of natural products and often impart significant biological activity. This review presents our current understanding of the biosynthetic logic and enzymatic chemistry involved in the construction of X-X bond containing functional groups within natural products. Elucidating and characterizing biosynthetic pathways that generate X-X bonds could both provide tools for biocatalysis and synthetic biology, as well as guide efforts to uncover new natural products containing these structural features.
Collapse
Affiliation(s)
- Abraham J. Waldman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Tai L. Ng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Peng Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| |
Collapse
|
25
|
Identification and characterization of a FAD-dependent putrescine N-hydroxylase (GorA) from Gordonia rubripertincta CWB2. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.08.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
26
|
Balhara M, Chaudhary R, Ruhil S, Singh B, Dahiya N, Parmar VS, Jaiwal PK, Chhillar AK. Siderophores; iron scavengers: the novel & promising targets for pathogen specific antifungal therapy. Expert Opin Ther Targets 2016; 20:1477-1489. [PMID: 27797604 DOI: 10.1080/14728222.2016.1254196] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION The recent emergence of resistance, toxicity paradigm and limited efficacy of conventional antifungal drugs necessitate the identification of de novo targets in fungal metabolism. One of the most critical physiological processes during in vivo pathogenesis is maintenance of iron homeostasis. The most life threatening opportunistic human fungal pathogens like Aspergillus, Candida and Cryptococcus exploit the siderophore mediated iron uptake mechanism either for survival, virulence, propagation or resistance to oxidative stress envisaged in vivo during infection. Areas covered: In this review, we will highlight the metabolic pathways; specifically siderophore biosynthesis, uptake and utilisation, triggered in the fungal pathogens in iron starving conditions and the various putative targets viable in these pathways to be recruited as novel therapeutic antidotes either via biosynthetic enzymes catalytic site inhibitors or as drug conjugates through trojan horse approach and further role in the development of fungal specific reliable diagnostic markers. Expert opinion: Siderophores are the weapons released by a pathogen to conquer the battle for iron acquisition. Hence, the fungal siderophore biosynthetic pathways along with their uptake and utilisation mechanisms represent an ideal target for pathogen specific, host friendly therapeutic strategy which would block the proliferation of parasite without causing any harm to the mammalian host.
Collapse
Affiliation(s)
- Meenakshi Balhara
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Renu Chaudhary
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Sonam Ruhil
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Bharat Singh
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Nisha Dahiya
- b Division of Epidemiology and Communicable Diseases , Indian Council of Medical Research , Delhi , India
| | - Virinder S Parmar
- c Bioorganic Laboratory, Department of Chemistry , University of Delhi , Delhi , India
| | - Pawan K Jaiwal
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Anil K Chhillar
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
| |
Collapse
|
27
|
Li B, Lowe-Power T, Kurihara S, Gonzales S, Naidoo J, MacMillan JB, Allen C, Michael AJ. Functional Identification of Putrescine C- and N-Hydroxylases. ACS Chem Biol 2016; 11:2782-2789. [PMID: 27541336 DOI: 10.1021/acschembio.6b00629] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The small polyamine putrescine (1,4-diaminobutane) is ubiquitously and abundantly found in all three domains of life. It is a precursor, through N-aminopropylation or N-aminobutylation, for biosynthesis of the longer polyamines spermidine, sym-homospermidine, spermine, and thermospermine and longer and branched chain polyamines. Putrescine is also biochemically modified for purposes of metabolic regulation and catabolism, e.g. N-acetylation and N-glutamylation, and for incorporation into specialized metabolites, e.g. N-methylation, N-citrylation, N-palmitoylation, N-hydroxylation, and N-hydroxycinnamoylation. Only one example is known where putrescine is modified on a methylene carbon: the formation of 2-hydroxyputrescine by an unknown C-hydroxylase. Here, we report the functional identification of a previously undescribed putrescine 2-hydroxylase, a Rieske-type nonheme iron sulfur protein from the β-proteobacteria Bordetella bronchiseptica and Ralstonia solanacearum. Identification of the putrescine 2-hydroxylase will facilitate investigation of the physiological functions of 2-hydroxyputrescine. One known role of 2-hydroxyputrescine has direct biomedical relevance: its role in the biosynthesis of the cyclic hydroxamate siderophore alcaligin, a potential virulence factor of the causative agent of whooping cough, Bordetella pertussis. We also report the functional identification of a putrescine N-hydroxylase from the γ-proteobacterium Shewanella oneidensis, which is homologous to FAD- and NADPH-dependent ornithine and lysine N-monooxygenases involved in siderophore biosynthesis. Heterologous expression of the putrescine N-hydroxylase in E. coli produced free N-hydroxyputrescine, never detected previously in a biological system. Furthermore, the putrescine C- and N-hydroxylases identified here could contribute new functionality to polyamine structural scaffolds, including C-H bond functionalization in synthetic biology strategies.
Collapse
Affiliation(s)
| | - Tiffany Lowe-Power
- Deptartment of Plant Pathology, University of Wisconsin, Madison, Wisconsin, United States
| | | | | | | | | | - Caitilyn Allen
- Deptartment of Plant Pathology, University of Wisconsin, Madison, Wisconsin, United States
| | | |
Collapse
|
28
|
Abdelwahab H, Robinson R, Rodriguez P, Adly C, El-Sohaimy S, Sobrado P. Identification of structural determinants of NAD(P)H selectivity and lysine binding in lysine N(6)-monooxygenase. Arch Biochem Biophys 2016; 606:180-8. [PMID: 27503802 DOI: 10.1016/j.abb.2016.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/22/2016] [Accepted: 08/01/2016] [Indexed: 11/26/2022]
Abstract
l-lysine (l-Lys) N(6)-monooxygenase (NbtG), from Nocardia farcinica, is a flavin-dependent enzyme that catalyzes the hydroxylation of l-Lys in the presence of oxygen and NAD(P)H in the biosynthetic pathway of the siderophore nocobactin. NbtG displays only a 3-fold preference for NADPH over NADH, different from well-characterized related enzymes, which are highly selective for NADPH. The structure of NbtG with bound NAD(P)(+) or l-Lys is currently not available. Herein, we present a mutagenesis study targeting M239, R301, and E216. These amino acids are conserved and located in either the NAD(P)H binding domain or the l-Lys binding pocket. M239R resulted in high production of hydrogen peroxide and little hydroxylation with no change in coenzyme selectivity. R301A caused a 300-fold decrease on kcat/Km value with NADPH but no change with NADH. E216Q increased the Km value for l-Lys by 30-fold with very little change on the kcat value or in the binding of NAD(P)H. These results suggest that R301 plays a major role in NADPH selectivity by interacting with the 2'-phosphate of the adenine-ribose moiety of NADPH, while E216 plays a role in l-Lys binding.
Collapse
Affiliation(s)
- Heba Abdelwahab
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA; Department of Chemistry, Faculty of Science, Damietta University, Damietta, 34517, Egypt
| | - Reeder Robinson
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - Pedro Rodriguez
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - Camelia Adly
- Department of Chemistry, Faculty of Science, Damietta University, Damietta, 34517, Egypt
| | - Sohby El-Sohaimy
- Department of Food Technology, Arid Lands Cultivation Research Institute, City of Scientific Research and Technological Applications, Alexandria, 21934, Egypt
| | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA; Fralin Life Science Institute, Virginia Tech, Blacksburg, VA 24061, USA; Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, USA.
| |
Collapse
|
29
|
Robinson R, Qureshi IA, Klancher CA, Rodriguez PJ, Tanner JJ, Sobrado P. Contribution to catalysis of ornithine binding residues in ornithine N5-monooxygenase. Arch Biochem Biophys 2015; 585:25-31. [PMID: 26375201 PMCID: PMC6467063 DOI: 10.1016/j.abb.2015.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 08/22/2015] [Accepted: 09/10/2015] [Indexed: 10/23/2022]
Abstract
The SidA ornithine N5-monooxygenase from Aspergillus fumigatus is a flavin monooxygenase that catalyzes the NADPH-dependent hydroxylation of ornithine. Herein we report a mutagenesis study targeting four residues that contact ornithine in crystal structures of SidA: Lys107, Asn293, Asn323, and Ser469. Mutation of Lys107 to Ala abolishes activity as measured in steady-state oxygen consumption and ornithine hydroxylation assays, indicating that the ionic interaction of Lys107 with the carboxylate of ornithine is essential for catalysis. Mutation of Asn293, Asn323, or Ser469 individually to Ala results in >14-fold increases in Km values for ornithine. Asn323 to Ala also increases the rate constant for flavin reduction by NADPH by 18-fold. Asn323 is unique among the four ornithine binding residues in that it also interacts with NADPH by forming a hydrogen bond with the nicotinamide ribose. The crystal structure of N323A complexed with NADP(+) and ornithine shows that the nicontinamide riboside group of NADP is disordered. This result suggests that the increase in flavin reduction rate results from an increase in conformational space available to the enzyme-bound NADP(H). Asn323 thus facilitates ornithine binding at the expense of hindering flavin reduction, which demonstrates the delicate balance that exists within protein-ligand interaction networks in enzyme active sites.
Collapse
Affiliation(s)
- Reeder Robinson
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - Insaf A Qureshi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | | | - Pedro J Rodriguez
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - John J Tanner
- Departments of Biochemistry and Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA.
| | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA.
| |
Collapse
|
30
|
Sartor L, Ibarra C, Al-Mestarihi A, Bachmann BO, Vey JL. Structure of DnmZ, a nitrososynthase in the Streptomyces peucetius anthracycline biosynthetic pathway. Acta Crystallogr F Struct Biol Commun 2015; 71:1205-14. [PMID: 26457508 PMCID: PMC4601581 DOI: 10.1107/s2053230x15014272] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 07/28/2015] [Indexed: 11/10/2022] Open
Abstract
The anthracyclines are a class of highly effective natural product chemotherapeutics and are used to treat a range of cancers, including leukemia. The toxicity of the anthracyclines has stimulated efforts to further diversify the scaffold of the natural product, which has led to renewed interest in the biosynthetic pathway responsible for the formation and modification of this family of molecules. DnmZ is an N-hydroxylating flavin monooxygenase (a nitrososynthase) that catalyzes the oxidation of the exocyclic amine of the sugar nucleotide dTDP-L-epi-vancosamine to its nitroso form. Its specific role in the anthracycline biosynthetic pathway involves the synthesis of the seven-carbon acetal moiety attached to C4 of L-daunosamine observed in the anthracycline baumycin. Here, X-ray crystallography was used to elucidate the three-dimensional structure of DnmZ. Two crystal structures of DnmZ were yielded: that of the enzyme alone, solved to 3.00 Å resolution, and that of the enzyme in complex with thymidine diphosphate, the nucleotide carrier portion of the substrate, solved to 2.74 Å resolution. These models add insights into the structural features involved in substrate specificity and conformational changes involved in thymidine diphosphate binding by the nitrososynthases.
Collapse
Affiliation(s)
- Lauren Sartor
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA 91330, USA
| | - Charmaine Ibarra
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA 91330, USA
| | - Ahmad Al-Mestarihi
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Brian O. Bachmann
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jessica L. Vey
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA 91330, USA
| |
Collapse
|
31
|
The Origin and Evolution of Baeyer-Villiger Monooxygenases (BVMOs): An Ancestral Family of Flavin Monooxygenases. PLoS One 2015; 10:e0132689. [PMID: 26161776 PMCID: PMC4498894 DOI: 10.1371/journal.pone.0132689] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 06/18/2015] [Indexed: 12/13/2022] Open
Abstract
The Baeyer-Villiger Monooxygenases (BVMOs) are enzymes belonging to the "Class B" of flavin monooxygenases and are capable of performing exquisite selective oxidations. These enzymes have been studied from a biotechnological perspective, but their physiological substrates and functional roles are widely unknown. Here, we investigated the origin, taxonomic distribution and evolutionary history of the BVMO genes. By using in silico approaches, 98 BVMO encoding genes were detected in the three domains of life: Archaea, Bacteria and Eukarya. We found evidence for the presence of these genes in Metazoa (Hydra vulgaris, Oikopleura dioica and Adineta vaga) and Haptophyta (Emiliania huxleyi) for the first time. Furthermore, a search for other "Class B" monooxygenases (flavoprotein monooxygenases--FMOs--and N-hydroxylating monooxygenases--NMOs) was conducted. These sequences were also found in the three domains of life. Phylogenetic analyses of all "Class B" monooxygenases revealed that NMOs and BVMOs are monophyletic, whereas FMOs form a paraphyletic group. Based on these results, we propose that BVMO genes were already present in the last universal common ancestor (LUCA) and their current taxonomic distribution is the result of differential duplication and loss of paralogous genes.
Collapse
|
32
|
Binda C, Robinson RM, Martin Del Campo JS, Keul ND, Rodriguez PJ, Robinson HH, Mattevi A, Sobrado P. An unprecedented NADPH domain conformation in lysine monooxygenase NbtG provides insights into uncoupling of oxygen consumption from substrate hydroxylation. J Biol Chem 2015; 290:12676-88. [PMID: 25802330 DOI: 10.1074/jbc.m114.629485] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Indexed: 01/01/2023] Open
Abstract
N-Hydroxylating monooxygenases are involved in the biosynthesis of iron-chelating hydroxamate-containing siderophores that play a role in microbial virulence. These flavoenzymes catalyze the NADPH- and oxygen-dependent hydroxylation of amines such as those found on the side chains of lysine and ornithine. In this work we report the biochemical and structural characterization of Nocardia farcinica Lys monooxygenase (NbtG), which has similar biochemical properties to mycobacterial homologs. NbtG is also active on d-Lys, although it binds l-Lys with a higher affinity. Differently from the ornithine monooxygenases PvdA, SidA, and KtzI, NbtG can use both NADH and NADPH and is highly uncoupled, producing more superoxide and hydrogen peroxide than hydroxylated Lys. The crystal structure of NbtG solved at 2.4 Å resolution revealed an unexpected protein conformation with a 30° rotation of the NAD(P)H domain with respect to the flavin adenine dinucleotide (FAD) domain that precludes binding of the nicotinamide cofactor. This "occluded" structure may explain the biochemical properties of NbtG, specifically with regard to the substantial uncoupling and limited stabilization of the C4a-hydroperoxyflavin intermediate. Biological implications of these findings are discussed.
Collapse
Affiliation(s)
- Claudia Binda
- From the Department of Biology and Biotechnology, University of Pavia, Pavia 27100, Italy
| | - Reeder M Robinson
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, and
| | | | - Nicholas D Keul
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, and
| | - Pedro J Rodriguez
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, and
| | - Howard H Robinson
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973
| | - Andrea Mattevi
- From the Department of Biology and Biotechnology, University of Pavia, Pavia 27100, Italy,
| | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, and
| |
Collapse
|
33
|
Badieyan S, Bach RD, Sobrado P. Mechanism of N-Hydroxylation Catalyzed by Flavin-Dependent Monooxygenases. J Org Chem 2015; 80:2139-47. [DOI: 10.1021/jo502651v] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Somayesadat Badieyan
- Department
of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Robert D. Bach
- Departments
of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Pablo Sobrado
- Department
of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
| |
Collapse
|
34
|
Frederick RE, Ojha S, Lamb A, Dubois JL. How pH modulates the reactivity and selectivity of a siderophore-associated flavin monooxygenase. Biochemistry 2014; 53:2007-16. [PMID: 24490904 PMCID: PMC3985866 DOI: 10.1021/bi401256b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
Flavin-containing
monooxygenases (FMOs) catalyze the oxygenation
of diverse organic molecules using O2, NADPH, and the flavin
adenine dinucleotide (FAD) cofactor. The fungal FMO SidA initiates
peptidic siderophore biosynthesis via the highly selective hydroxylation
of l-ornithine, while the related amino acid l-lysine
is a potent effector of reaction uncoupling to generate H2O2. We hypothesized that protonation states could critically
influence both substrate-selective hydroxylation and H2O2 release, and therefore undertook a study of SidA’s
pH-dependent reaction kinetics. Consistent with other FMOs that stabilize
a C4a-OO(H) intermediate, SidA’s reductive half reaction is
pH independent. The rate constant for the formation of the reactive
C4a-OO(H) intermediate from reduced SidA and O2 is likewise
independent of pH. However, the rate constants for C4a-OO(H) reactions,
either to eliminate H2O2 or to hydroxylate l-Orn, were strongly pH-dependent and influenced by the nature
of the bound amino acid. Solvent kinetic isotope effects of 6.6 ±
0.3 and 1.9 ± 0.2 were measured for the C4a-OOH/H2O2 conversion in the presence and absence of l-Lys, respectively. A model is proposed in which l-Lys accelerates
H2O2 release via an acid–base mechanism
and where side-chain position determines whether H2O2 or the hydroxylation product is observed.
Collapse
Affiliation(s)
- Rosanne E Frederick
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | | | | | | |
Collapse
|
35
|
Bosello M, Zeyadi M, Kraas FI, Linne U, Xie X, Marahiel MA. Structural characterization of the heterobactin siderophores from Rhodococcus erythropolis PR4 and elucidation of their biosynthetic machinery. JOURNAL OF NATURAL PRODUCTS 2013; 76:2282-2290. [PMID: 24274668 DOI: 10.1021/np4006579] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In this study, the isolation, the structural characterization, and the elucidation of the biosynthetic origin of heterobactins, catecholate-hydroxamate mixed-type siderophores from Rhodococcus erythropolis PR4, are reported. The structure elucidation of heterobactin A was accomplished via MS(n) analysis and NMR spectroscopy and revealed the noteworthy presence of a peptide bond between the guanidine group of an arginine residue and a 2,3-dihydroxybenzoate moiety. The two heterobactin S1 and S2 variants are derivatives of heterobactin A that have sulfonation modifications on the aromatic rings. The bioinformatic analysis of the R. erythropolis PR4 genome and the subsequent genetic and biochemical characterization of the putative biosynthetic machinery identified the gene cluster responsible for the biosynthesis of the heterobactins. Interestingly, the HtbG NRPS presents an unprecedented C-PCP-A domain organization within the second module of the synthetase that may help the correct elongation of the peptide intermediate. Finally, the present work revises the structure of heterobactin A that was described by Carrano et al. in 2001.
Collapse
Affiliation(s)
- Mattia Bosello
- Biochemistry, Department of Chemistry, Philipps-University Marburg , Hans-Meerwein-Strasse D-35043 Marburg, Germany
| | | | | | | | | | | |
Collapse
|
36
|
Huijbers MME, Montersino S, Westphal AH, Tischler D, van Berkel WJH. Flavin dependent monooxygenases. Arch Biochem Biophys 2013; 544:2-17. [PMID: 24361254 DOI: 10.1016/j.abb.2013.12.005] [Citation(s) in RCA: 364] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/06/2013] [Accepted: 12/09/2013] [Indexed: 11/29/2022]
Abstract
Flavin-dependent monooxygenases catalyze a wide variety of chemo-, regio- and enantioselective oxygenation reactions. As such, they are involved in key biological processes ranging from catabolism, detoxification and biosynthesis, to light emission and axon guidance. Based on fold and function, flavin-dependent monooxygenases can be distributed into eight groups. Groups A and B comprise enzymes that rely on NAD(P)H as external electron donor. Groups C-F are two-protein systems, composed of a monooxygenase and a flavin reductase. Groups G and H comprise internal monooxygenases that reduce the flavin cofactor through substrate oxidation. Recently, many new flavin-dependent monooxygenases have been discovered. In addition to posing basic enzymological questions, these proteins attract attention of pharmaceutical and fine-chemical industries, given their importance as regio- and enantioselective biocatalysts. In this review we present an update of the classification of flavin-dependent monooxygenases and summarize the latest advances in our understanding of their catalytic and structural properties.
Collapse
Affiliation(s)
- Mieke M E Huijbers
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Stefania Montersino
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Dirk Tischler
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands; Interdisciplinary Ecological Center, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany
| | - Willem J H van Berkel
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands.
| |
Collapse
|
37
|
Shirey C, Badieyan S, Sobrado P. Role of Ser-257 in the sliding mechanism of NADP(H) in the reaction catalyzed by the Aspergillus fumigatus flavin-dependent ornithine N5-monooxygenase SidA. J Biol Chem 2013; 288:32440-32448. [PMID: 24072704 DOI: 10.1074/jbc.m113.487181] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SidA (siderophore A) is a flavin-dependent N-hydroxylating monooxygenase that is essential for virulence in Aspergillus fumigatus. SidA catalyzes the NADPH- and oxygen-dependent formation of N(5)-hydroxyornithine. In this reaction, NADPH reduces the flavin, and the resulting NADP(+) is the last product to be released. The presence of NADP(+) is essential for activity, as it is required for stabilization of the C4a-hydroperoxyflavin, which is the hydroxylating species. As part of our efforts to determine the molecular details of the role of NADP(H) in catalysis, we targeted Ser-257 for site-directed mutagenesis and performed extensive characterization of the S257A enzyme. Using a combination of steady-state and stopped-flow kinetic experiments, substrate analogs, and primary kinetic isotope effects, we show that the interaction between Ser-257 and NADP(H) is essential for stabilization of the C4a-hydroperoxyflavin. Molecular dynamics simulation results suggest that Ser-257 functions as a pivot point, allowing the nicotinamide of NADP(+) to slide into position for stabilization of the C4a-hydroperoxyflavin.
Collapse
Affiliation(s)
| | | | - Pablo Sobrado
- From the Department of Biochemistry; the Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061.
| |
Collapse
|
38
|
Franke J, Ishida K, Ishida-Ito M, Hertweck C. Nitro versus Hydroxamate in Siderophores of Pathogenic Bacteria: Effect of Missing Hydroxylamine Protection in Malleobactin Biosynthesis. Angew Chem Int Ed Engl 2013; 52:8271-5. [DOI: 10.1002/anie.201303196] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Indexed: 01/13/2023]
|
39
|
Franke J, Ishida K, Ishida-Ito M, Hertweck C. Nitro versus Hydroxamate in Siderophores of Pathogenic Bacteria: Effect of Missing Hydroxylamine Protection in Malleobactin Biosynthesis. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303196] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
40
|
Riebel A, de Gonzalo G, Fraaije MW. Expanding the biocatalytic toolbox of flavoprotein monooxygenases from Rhodococcus jostii RHA1. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2012.11.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
41
|
Chaiyen P, Fraaije MW, Mattevi A. The enigmatic reaction of flavins with oxygen. Trends Biochem Sci 2012; 37:373-80. [DOI: 10.1016/j.tibs.2012.06.005] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 06/19/2012] [Accepted: 06/28/2012] [Indexed: 10/28/2022]
|
42
|
Burrell M, Hanfrey CC, Kinch LN, Elliott KA, Michael AJ. Evolution of a novel lysine decarboxylase in siderophore biosynthesis. Mol Microbiol 2012; 86:485-99. [PMID: 22906379 DOI: 10.1111/j.1365-2958.2012.08208.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2012] [Indexed: 12/30/2022]
Abstract
Structural backbones of iron-scavenging siderophore molecules include polyamines 1,3-diaminopropane and 1,5-diaminopentane (cadaverine). For the cadaverine-based desferroxiamine E siderophore in Streptomyces coelicolor, the corresponding biosynthetic gene cluster contains an ORF encoded by desA that was suspected of producing the cadaverine (decarboxylated lysine) backbone. However, desA encodes an l-2,4-diaminobutyrate decarboxylase (DABA DC) homologue and not any known form of lysine decarboxylase (LDC). The only known function of DABA DC is, together with l-2,4-aminobutyrate aminotransferase (DABA AT), to synthesize 1,3-diaminopropane. We show here that S. coelicolor desA encodes a novel LDC and we hypothesized that DABA DC homologues present in siderophore biosynthetic clusters in the absence of DABA AT ORFs would be novel LDCs. We confirmed this by correctly predicting the LDC activity of a DABA DC homologue from a Yersinia pestis siderophore biosynthetic pathway. The corollary was confirmed for a DABA DC homologue, adjacent to a DABA AT ORF in a siderophore pathway in the cyanobacterium Anabaena variabilis, which was shown to be a bona fide DABA DC. These findings enable prediction of whether a siderophore pathway will utilize 1,3-diaminopropane or cadaverine, and suggest that the majority of bacteria use DABA AT and DABA DC for siderophore, rather than norspermidine/polyamine biosynthesis.
Collapse
|
43
|
Bosello M, Mielcarek A, Giessen TW, Marahiel MA. An enzymatic pathway for the biosynthesis of the formylhydroxyornithine required for rhodochelin iron coordination. Biochemistry 2012; 51:3059-66. [PMID: 22439765 DOI: 10.1021/bi201837f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhodochelin, a mixed catecholate-hydroxamate type siderophore isolated from Rhodococcus jostii RHA1, holds two L-δ-N-formyl-δ-N-hydroxyornithine (L-fhOrn) moieties essential for proper iron coordination. Previously, bioinformatic and genetic analysis proposed rmo and rft as the genes required for the tailoring of the L-ornithine (L-Orn) precursor [Bosello, M. (2011) J. Am. Chem. Soc.133, 4587-4595]. In order to investigate if both Rmo and Rft constitute a pathway for L-fhOrn biosynthesis, the enzymes were heterologously produced and assayed in vitro. In the presence of molecular oxygen, NADPH and FAD, Rmo monooxygenase was able to convert L-Orn into L-δ-N-hydroxyornithine (L-hOrn). As confirmed in a coupled reaction assay, this hydroxylated intermediate serves as a substrate for the subsequent N(10)-formyl-tetrahydrofolate-dependent (N(10)-fH(4)F) Rtf-catalyzed formylation reaction, establishing a route for the L-fhOrn biosynthesis, prior to its incorporation by the NRPS assembly line. It is of particular interest that a major improvement to this study has been reached with the use of an alternative approach to the chemoenzymatic FolD-dependent N(10)-fH(4)F conversion, also rescuing the previously inactive CchA, the Rft-homologue in coelichelin assembly line [Buchenau, B. (2004) Arch. Microbiol.182, 313-325; Pohlmann, V. (2008) Org. Biomol. Chem.6, 1843-1848].
Collapse
Affiliation(s)
- Mattia Bosello
- Biochemistry, Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse, D-35043 Marburg, Germany
| | | | | | | |
Collapse
|
44
|
Montersino S, van Berkel WJH. Functional annotation and characterization of 3-hydroxybenzoate 6-hydroxylase from Rhodococcus jostii RHA1. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1824:433-42. [PMID: 22207056 DOI: 10.1016/j.bbapap.2011.12.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 12/09/2011] [Accepted: 12/14/2011] [Indexed: 12/11/2022]
Abstract
The genome of Rhodococcus jostii RHA1 contains an unusually large number of oxygenase encoding genes. Many of these genes have yet an unknown function, implying that a notable part of the biochemical and catabolic biodiversity of this Gram-positive soil actinomycete is still elusive. Here we present a multiple sequence alignment and phylogenetic analysis of putative R. jostii RHA1 flavoprotein hydroxylases. Out of 18 candidate sequences, three hydroxylases are absent in other available Rhodococcus genomes. In addition, we report the biochemical characterization of 3-hydroxybenzoate 6-hydroxylase (3HB6H), a gentisate-producing enzyme originally mis-annotated as salicylate hydroxylase. R. jostii RHA1 3HB6H expressed in Escherichia coli is a homodimer with each 47kDa subunit containing a non-covalently bound FAD cofactor. The enzyme has a pH optimum around pH 8.3 and prefers NADH as external electron donor. 3HB6H is active with a series of 3-hydroxybenzoate analogues, bearing substituents in ortho- or meta-position of the aromatic ring. Gentisate, the physiological product, is a non-substrate effector of 3HB6H. This compound is not hydroxylated but strongly stimulates the NADH oxidase activity of the enzyme.
Collapse
|