1
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Teufel R. Oxygen-transfer reactions by enzymatic flavin-N 5 oxygen adducts-Oxidation is not a must. Curr Opin Chem Biol 2024; 80:102464. [PMID: 38739969 DOI: 10.1016/j.cbpa.2024.102464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/16/2024]
Abstract
Flavoenzymes catalyze numerous redox reactions including the transfer of an O2-derived oxygen atom to organic substrates, while the other one is reduced to water. Investigation of some of these monooxygenases led to a detailed understanding of their catalytic cycle, which involves the flavin-C4α-(hydro)peroxide as hallmark oxygenating species, and newly discovered flavoprotein monooxygenases were generally assumed to operate similarly. However, discoveries in recent years revealed a broader mechanistic versatility, including enzymes that utilize flavin-N5 oxygen adducts for catalysis in the form of the flavin-N5-(hydro)peroxide and the flavin-N5-oxide species. In this review, I will highlight recent developments in that area, including noncanonical flavoenzymes from natural product biosynthesis and sulfur metabolism that provide first insights into the chemical properties of these species. Remarkably, some enzymes may even combine the flavin-N5-peroxide and the flavin-N5-oxide species for consecutive oxygen-transfers to the same substrate and thereby in essence operate as dioxygenases.
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Affiliation(s)
- Robin Teufel
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland.
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2
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Love AC, Purdy TN, Hubert FM, Kirwan EJ, Holland DC, Moore BS. Discovery of Latent Cannabichromene Cyclase Activity in Marine Bacterial Flavoenzymes. ACS Synth Biol 2024; 13:1343-1354. [PMID: 38459634 PMCID: PMC11031283 DOI: 10.1021/acssynbio.4c00051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Abstract
Production of phytocannabinoids remains an area of active scientific interest due to the growing use of cannabis by the public and the underexplored therapeutic potential of the over 100 minor cannabinoids. While phytocannabinoids are biosynthesized by Cannabis sativa and other select plants and fungi, structural analogs and stereoisomers can only be accessed synthetically or through heterologous expression. To date, the bioproduction of cannabinoids has required eukaryotic hosts like yeast since key, native oxidative cyclization enzymes do not express well in bacterial hosts. Here, we report that two marine bacterial flavoenzymes, Clz9 and Tcz9, perform oxidative cyclization reactions on phytocannabinoid precursors to efficiently generate cannabichromene scaffolds. Furthermore, Clz9 and Tcz9 express robustly in bacteria and display significant tolerance to organic solvent and high substrate loading, thereby enabling fermentative production of cannabichromenic acid in Escherichia coli and indicating their potential for biocatalyst development.
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Affiliation(s)
- Anna C. Love
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Trevor N. Purdy
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Felix M. Hubert
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Ella J. Kirwan
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Darren C. Holland
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
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3
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Rehpenn A, Hindelang S, Truong KN, Pöthig A, Storch G. Enhancing Flavins Photochemical Activity in Hydrogen Atom Abstraction and Triplet Sensitization through Ring-Contraction. Angew Chem Int Ed Engl 2024; 63:e202318590. [PMID: 38339882 DOI: 10.1002/anie.202318590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024]
Abstract
The isoalloxazine heterocycle of flavin cofactors reacts with various nucleophiles to form covalent adducts with important functions in enzymes. Molecular flavin models allow for the characterization of such adducts and the study of their properties. A fascinating set of reactions occurs when flavins react with hydroxide base, which leads to imidazolonequinoxalines, ring-contracted flavins, with so far unexplored activity. We report a systematic study of the photophysical properties of this new chromophore by absorption and emission spectroscopy as well as cyclic voltammetry. Excited, ring-contracted flavins are significantly stronger hydrogen atom abstractors when compared to the parent flavins, which allowed the direct trifluoromethylthiolation of aliphatic methine positions (bond dissociation energy (BDE) of 400.8 kJ mol-1). In an orthogonal activity, their increased triplet energy (E(S0←T1)=244 kJ mol-1) made sensitized reactions possible which exceeded the power of standard flavins. Combining both properties, ring-contracted flavin catalysts enabled the one-pot, five-step transformation of α-tropolone into trans-3,4-disubstituted cyclopentanones. We envision this new class of flavin-derived chromophores to open up new modes of reactivity that are currently impossible with unmodified flavins.
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Affiliation(s)
- Andreas Rehpenn
- Technical University of Munich (TUM), School of Natural Sciences and Catalysis Research Center (CRC), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Stephan Hindelang
- Technical University of Munich (TUM), School of Natural Sciences and Catalysis Research Center (CRC), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Khai-Nghi Truong
- Rigaku Europe SE, Hugenottenallee 167, 63263, Neu-Isenburg, Germany
| | - Alexander Pöthig
- Technical University of Munich (TUM), School of Natural Sciences and Catalysis Research Center (CRC), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Golo Storch
- Technical University of Munich (TUM), School of Natural Sciences and Catalysis Research Center (CRC), Lichtenbergstr. 4, 85747, Garching, Germany
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4
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Zhang Q, Chen Q, Shaik S, Wang B. Flavin-N5OOH Functions as both a Powerful Nucleophile and a Base in the Superfamily of Flavoenzymes. Angew Chem Int Ed Engl 2024; 63:e202318629. [PMID: 38299700 DOI: 10.1002/anie.202318629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/02/2024]
Abstract
Flavoenzymes can mediate a large variety of oxidation reactions through the activation of oxygen. However, the O2 activation chemistry of flavin enzymes is not yet fully exploited. Normally, the O2 activation occurs at the C4a site of the flavin cofactor, yielding the flavin C4a-(hydro)hydroperoxyl species in monooxygenases or oxidases. Using extensive MD simulations, QM/MM calculations and QM calculations, our studies reveal the formation of the common nucleophilic species, Flavin-N5OOH, in two distinct flavoenzymes (RutA and EncM). Our studies show that Flavin-N5OOH acts as a powerful nucleophile that promotes C-N cleavage of uracil in RutA, and a powerful base in the deprotonation of substrates in EncM. We reason that Flavin-N5OOH can be a common reactive species in the superfamily of flavoenzymes, which accomplish generally selective general base catalysis and C-X (X=N, S, Cl, O) cleavage reactions that are otherwise challenging with solvated hydroxide ion base. These results expand our understanding of the chemistry and catalysis of flavoenzymes.
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Affiliation(s)
- Qiaoyu Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Qianqian Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
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5
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Montua N, Thye P, Hartwig P, Kühle M, Sewald N. Enzymatic Peptide and Protein Bromination: The BromoTrp Tag. Angew Chem Int Ed Engl 2024; 63:e202314961. [PMID: 38009455 DOI: 10.1002/anie.202314961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 11/28/2023]
Abstract
Bio-orthogonal reactions for modification of proteins and unprotected peptides are of high value in chemical biology. The combination of enzymatic halogenation with transition metal-catalyzed cross-coupling provides a feasible approach for the modification of proteins and unprotected peptides. By a semirational protein engineering approach, variants of the tryptophan 6-halogenase Thal were identified that enable efficient bromination of peptides with a C-terminal tryptophan residue. The substrate scope was explored using di-, tri-, and tetrapeptide arrays, leading to the identification of an optimized peptide tag we named BromoTrp tag. This tag was introduced into three model proteins. Preparative scale post-translational bromination was possible with only a single cultivation and purification step using the brominating E. coli coexpression system Brocoli. Palladium-catalyzed Suzuki-Miyaura cross-coupling of the bromoarene was achieved with Pd nanoparticle catalysts at 37 °C, highlighting the rich potential of this strategy for bio-orthogonal functionalization and conjugation.
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Affiliation(s)
- Nicolai Montua
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Paula Thye
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Pia Hartwig
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Matthias Kühle
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
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6
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Kwon S. Structural Insight into the Working Mechanism of the FAD Synthetase from the Human Pathogen Streptococcus pneumoniae: A Molecular Docking Simulation Study. Int J Mol Sci 2023; 24:ijms24043121. [PMID: 36834532 PMCID: PMC9962085 DOI: 10.3390/ijms24043121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/29/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Flavin adenine dinucleotide synthetases (FADSs) catalyze FAD biosynthesis through two consecutive catalytic reactions, riboflavin (RF) phosphorylation and flavin mononucleotide (FMN) adenylylation. Bacterial FADSs have RF kinase (RFK) and FMN adenylyltransferase (FMNAT) domains, whereas the two domains are separated into two independent enzymes in human FADSs. Bacterial FADSs have attracted considerable attention as drug targets due to the fact that they differ from human FADSs in structure and domain combinations. In this study, we analyzed the putative FADS structure from the human pathogen Streptococcus pneumoniae (SpFADS) determined by Kim et al., including conformational changes of key loops in the RFK domain upon substrate binding. Structural analysis and comparisons with a homologous FADS structure revealed that SpFADS corresponds to a hybrid between open and closed conformations of the key loops. Surface analysis of SpFADS further revealed its unique biophysical properties for substrate attraction. In addition, our molecular docking simulations predicted possible substrate-binding modes at the active sites of the RFK and FMNAT domains. Our results provide a structural basis to understand the catalytic mechanism of SpFADS and develop novel SpFADS inhibitors.
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Affiliation(s)
- Sunghark Kwon
- Department of Biotechnology, Konkuk University, Chungju 27478, Chungbuk, Republic of Korea;
- Research Institute for Biomedical & Health Science, Konkuk University, Chungju 27478, Chungbuk, Republic of Korea
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7
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Zhang L, Toplak M, Saleem-Batcha R, Höing L, Jakob R, Jehmlich N, von Bergen M, Maier T, Teufel R. Bacterial Dehydrogenases Facilitate Oxidative Inactivation and Bioremediation of Chloramphenicol. Chembiochem 2023; 24:e202200632. [PMID: 36353978 DOI: 10.1002/cbic.202200632] [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: 11/02/2022] [Revised: 11/09/2022] [Indexed: 11/11/2022]
Abstract
Antimicrobial resistance represents a major threat to human health and knowledge of the underlying mechanisms is therefore vital. Here, we report the discovery and characterization of oxidoreductases that inactivate the broad-spectrum antibiotic chloramphenicol via dual oxidation of the C3-hydroxyl group. Accordingly, chloramphenicol oxidation either depends on standalone glucose-methanol-choline (GMC)-type flavoenzymes, or on additional aldehyde dehydrogenases that boost overall turnover. These enzymes also enable the inactivation of the chloramphenicol analogues thiamphenicol and azidamfenicol, but not of the C3-fluorinated florfenicol. Notably, distinct isofunctional enzymes can be found in Gram-positive (e. g., Streptomyces sp.) and Gram-negative (e. g., Sphingobium sp.) bacteria, which presumably evolved their selectivity for chloramphenicol independently based on phylogenetic analyses. Mechanistic and structural studies provide further insights into the catalytic mechanisms of these biotechnologically interesting enzymes, which, in sum, are both a curse and a blessing by contributing to the spread of antibiotic resistance as well as to the bioremediation of chloramphenicol.
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Affiliation(s)
- Lei Zhang
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Marina Toplak
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Raspudin Saleem-Batcha
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Lars Höing
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Roman Jakob
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research UFZ GmbH, Leipzig, Germany.,German Centre for Integrative Biodiversity Research, (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany.,University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstraße 34, 04103, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research UFZ GmbH, Leipzig, Germany.,German Centre for Integrative Biodiversity Research, (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany.,University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstraße 34, 04103, Leipzig, Germany
| | - Timm Maier
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Robin Teufel
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
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8
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Zhang L, Esquembre LA, Xia SN, Oesterhelt F, Hughes CC, Brötz-Oesterhelt H, Teufel R. Antibacterial Synnepyrroles from Human-Associated Nocardiopsis sp. Show Protonophore Activity and Disrupt the Bacterial Cytoplasmic Membrane. ACS Chem Biol 2022; 17:2836-2848. [PMID: 36179367 DOI: 10.1021/acschembio.2c00460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Actinobacteria have traditionally been an important source of bioactive natural products, although many genera remain poorly explored. Here, we report a group of distinctive pyrrole-containing natural products, named synnepyrroles, from Nocardiopsis synnemataformans. Detailed structural characterization by mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy combined with isotope-labeling experiments revealed their molecular structures and biosynthetic precursors acetate, propionate, aspartate, and (for branched analogues) valine. The biosynthetic data points toward an unusual pathway for pyrrole formation via condensation of aspartate with diverse fatty acids that give rise to a unique pyrrole-3,4-dicarboxylate core and variable linear or terminally branched alkyl side chains. In addition, the bioactivity and mode of action of synnepyrrole A were characterized in Bacillus subtilis. Orienting assessment of the phenotype of synnepyrrole A-treated bacteria by high-resolution microscopy suggested the cytoplasmic membrane as the target structure. Further characterization of the membrane effects demonstrated dissipation of the membrane potential and intracellular acidification indicative of protonophore activity. At slightly higher concentrations, synnepyrrole A compromised the barrier function of the cytoplasmic membrane, allowing the passage of otherwise membrane-impermeable dye molecules.
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Affiliation(s)
- Lei Zhang
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Lidia Alejo Esquembre
- Department of Microbial Bioactive Compounds, Interfaculty Institute for Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
| | - Shu-Ning Xia
- Department of Microbial Bioactive Compounds, Interfaculty Institute for Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
| | - Filipp Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute for Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany
| | - Chambers C Hughes
- Department of Microbial Bioactive Compounds, Interfaculty Institute for Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany.,Cluster of Excellence EXC 2124: Controlling Microbes to Fight Infection, University of Tübingen, 72076 Tübingen, Germany.,German Center for Infection Research, Partner Site Tübingen, 72076 Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute for Microbiology and Infection Medicine, University of Tübingen, 72076 Tübingen, Germany.,Cluster of Excellence EXC 2124: Controlling Microbes to Fight Infection, University of Tübingen, 72076 Tübingen, Germany.,German Center for Infection Research, Partner Site Tübingen, 72076 Tübingen, Germany
| | - Robin Teufel
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, Klingelbergstrasse 50, University of Basel, 4056 Basel, Switzerland
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9
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Toplak M, Nagel A, Frensch B, Lechtenberg T, Teufel R. An acetyltransferase controls the metabolic flux in rubromycin polyketide biosynthesis by direct modulation of redox tailoring enzymes. Chem Sci 2022; 13:7157-7164. [PMID: 35799824 PMCID: PMC9215129 DOI: 10.1039/d2sc01952c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/16/2022] [Indexed: 01/14/2023] Open
Abstract
The often complex control of bacterial natural product biosynthesis typically involves global and pathway-specific transcriptional regulators of gene expression, which often limits the yield of bioactive compounds under laboratory conditions. However, little is known about regulation mechanisms on the enzymatic level. Here, we report a novel regulatory principle for natural products involving a dedicated acetyltransferase, which modifies a redox-tailoring enzyme and thereby enables pathway furcation and alternating pharmacophore assembly in rubromycin polyketide biosynthesis. The rubromycins such as griseorhodin (grh) A are complex bioactive aromatic polyketides from Actinobacteria with a hallmark bisbenzannulated [5,6]-spiroketal pharmacophore that is mainly installed by two flavoprotein monooxygenases. First, GrhO5 converts the advanced precursor collinone into the [6,6]-spiroketal containing dihydrolenticulone, before GrhO6 effectuates a ring contraction to afford the [5,6]-spiroketal. Our results show that pharmacophore assembly in addition involves the acetyl-CoA-dependent acetyltransferase GrhJ that activates GrhO6 to allow the rapid generation and release of its labile product, which is subsequently sequestered by ketoreductase GrhO10 and converted into a stable intermediate. Consequently, the biosynthesis is directed to the generation of canonical rubromycins, while the alternative spontaneous [5,6]-spiroketal hydrolysis to a ring-opened pathway product is thwarted. Presumably, this allows the bacteria to rapidly adjust the biosynthesis of functionally distinct secondary metabolites depending on nutrient and precursor (i.e. acetyl-CoA) availability. Our study thus illustrates how natural product biosynthesis can be enzymatically regulated and provides new perspectives for the improvement of in vitro enzyme activities and natural product titers via biotechnological approaches. Characterization of the acetyltransferase GrhJ reveals the surprising acetylation of flavoenzyme GrhO6 in rubromycin polyketide biosynthesis, showcasing a novel principle for the enzymatic regulation of secondary metabolic pathways.![]()
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Affiliation(s)
- Marina Toplak
- Faculty of Biology, University of Freiburg Schänzlestrasse 1 79104 Freiburg Germany
| | - Adelheid Nagel
- Faculty of Biology, University of Freiburg Schänzlestrasse 1 79104 Freiburg Germany
| | - Britta Frensch
- Faculty of Biology, University of Freiburg Schänzlestrasse 1 79104 Freiburg Germany
| | - Thorsten Lechtenberg
- Faculty of Biology, University of Freiburg Schänzlestrasse 1 79104 Freiburg Germany
| | - Robin Teufel
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
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10
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Mouli MSSV, Mishra AK. Synthesis, characterization and photophysical studies of the flavopeptide conjugates as model for the covalently linked flavoenzymes. J CHEM SCI 2022. [DOI: 10.1007/s12039-022-02050-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Purdy TN, Moore BS, Lukowski AL. Harnessing ortho-Quinone Methides in Natural Product Biosynthesis and Biocatalysis. JOURNAL OF NATURAL PRODUCTS 2022; 85:688-701. [PMID: 35108487 PMCID: PMC9006567 DOI: 10.1021/acs.jnatprod.1c01026] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The implementation of ortho-quinone methide (o-QM) intermediates in complex molecule assembly represents a remarkably efficient strategy designed by Nature and utilized by synthetic chemists. o-QMs have been taken advantage of in biomimetic syntheses for decades, yet relatively few examples of o-QM-generating enzymes in natural product biosynthetic pathways have been reported. The biosynthetic enzymes that have been discovered thus far exhibit tremendous potential for biocatalytic applications, enabling the selective production of desirable compounds that are otherwise intractable or inherently difficult to achieve by traditional synthetic methods. Characterization of this biosynthetic machinery has the potential to shine a light on new enzymes capable of similar chemistry on diverse substrates, thus expanding our knowledge of Nature's catalytic repertoire. The presently known o-QM-generating enzymes include flavin-dependent oxidases, hetero-Diels-Alderases, S-adenosyl-l-methionine-dependent pericyclases, and α-ketoglutarate-dependent nonheme iron enzymes. In this review, we discuss their diverse enzymatic mechanisms and potential as biocatalysts in constructing natural product molecules such as cannabinoids.
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Affiliation(s)
- Trevor N Purdy
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92093, United States
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093, United States
| | - April L Lukowski
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92093, United States
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12
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Iyer A, Reis RAG, Agniswamy J, Weber IT, Gadda G. Discovery of a new flavin N5-adduct in a tyrosine to phenylalanine variant of d-Arginine dehydrogenase. Arch Biochem Biophys 2022; 715:109100. [PMID: 34864048 DOI: 10.1016/j.abb.2021.109100] [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: 10/29/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/02/2022]
Abstract
d-Arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) catalyzes the flavin-dependent oxidation of d-arginine and other d-amino acids. Here, we report the crystal structure at 1.29 Å resolution for PaDADH-Y249F expressed and co-crystallized with d-arginine. The overall structure of PaDADH-Y249F resembled PaDADH-WT, but the electron density for the flavin cofactor was ambiguous, suggesting the presence of modified flavins. Electron density maps and mass spectrometric analysis confirmed the presence of both N5-(4-guanidino-oxobutyl)-FAD and 6-OH-FAD in a single crystal of PaDADH-Y249F and helped with the further refinement of the X-ray crystal structure. The versatility of the reduced flavin is apparent in the PaDADH-Y249F structure and is evidenced by the multiple functions it can perform in the same active site.
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Affiliation(s)
- Archana Iyer
- Department of Chemistry, Georgia State University, Atlanta, GA, 30302, USA
| | - Renata A G Reis
- Department of Chemistry, Georgia State University, Atlanta, GA, 30302, USA
| | - Johnson Agniswamy
- Department of Biology, Georgia State University, Atlanta, GA, 30302, USA
| | - Irene T Weber
- Department of Chemistry, Georgia State University, Atlanta, GA, 30302, USA; Department of Biology, Georgia State University, Atlanta, GA, 30302, USA
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, GA, 30302, USA; Department of Biology, Georgia State University, Atlanta, GA, 30302, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302, USA.
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13
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Toplak M, Teufel R. Three Rings to Rule Them All: How Versatile Flavoenzymes Orchestrate the Structural Diversification of Natural Products. Biochemistry 2021; 61:47-56. [PMID: 34962769 PMCID: PMC8772269 DOI: 10.1021/acs.biochem.1c00763] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
The structural diversification
of natural products is instrumental
to their versatile bioactivities. In this context, redox tailoring
enzymes are commonly involved in the modification and functionalization
of advanced pathway intermediates en route to the mature natural products.
In recent years, flavoprotein monooxygenases have been shown to mediate
numerous redox tailoring reactions that include not only (aromatic)
hydroxylation, Baeyer–Villiger oxidation, or epoxidation reactions
but also oxygenations that are coupled to extensive remodeling of
the carbon backbone, which are often central to the installment of
the respective pharmacophores. In this Perspective, we will highlight
recent developments and discoveries in the field of flavoenzyme catalysis
in bacterial natural product biosynthesis and illustrate how the flavin
cofactor can be fine-tuned to enable chemo-, regio-, and stereospecific
oxygenations via distinct flavin-C4a-peroxide and flavin-N5-(per)oxide
species. Open questions remain, e.g., regarding the breadth of chemical
reactions enabled particularly by the newly discovered flavin-N5-oxygen
adducts and the role of the protein environment in steering such cascade-like
reactions. Outstanding cases involving different flavin oxygenating
species will be exemplified by the tailoring of bacterial aromatic
polyketides, including enterocin, rubromycins, rishirilides, mithramycin,
anthracyclins, chartreusin, jadomycin, and xantholipin. In addition,
the biosynthesis of tropone natural products, including tropolone
and tropodithietic acid, will be presented, which features a recently
described prototypical flavoprotein dioxygenase that may combine flavin-N5-peroxide
and flavin-N5-oxide chemistry. Finally, structural and mechanistic
features of selected enzymes will be discussed as well as hurdles
for their application in the formation of natural product derivatives
via bioengineering.
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Affiliation(s)
- Marina Toplak
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Robin Teufel
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
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14
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Taeufer T, Argüello Cordero MA, Petrosyan A, Surkus A, Lochbrunner S, Pospech J. Photophysical and Electrochemical Properties of Pyrimidopteridine‐Based Organic Photoredox Catalysts. CHEMPHOTOCHEM 2021. [DOI: 10.1002/cptc.202100159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tobias Taeufer
- Leibniz Institute for Catalysis Albert-Einstein-Str. 29a 18059 Rostock Germany
| | | | - Andranik Petrosyan
- Leibniz Institute for Catalysis Albert-Einstein-Str. 29a 18059 Rostock Germany
| | - Annette‐E. Surkus
- Leibniz Institute for Catalysis Albert-Einstein-Str. 29a 18059 Rostock Germany
| | - Stefan Lochbrunner
- Institute for Physics and Department of Life Light and Matter Universität Rostock 18051 Rostock Germany
| | - Jola Pospech
- Leibniz Institute for Catalysis Albert-Einstein-Str. 29a 18059 Rostock Germany
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15
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Matthews A, Schönfelder J, Lagies S, Schleicher E, Kammerer B, Ellis HR, Stull F, Teufel R. Bacterial flavoprotein monooxygenase YxeK salvages toxic S-(2-succino)-adducts via oxygenolytic C-S bond cleavage. FEBS J 2021; 289:787-807. [PMID: 34510734 DOI: 10.1111/febs.16193] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/18/2021] [Accepted: 09/09/2021] [Indexed: 01/23/2023]
Abstract
Thiol-containing nucleophiles such as cysteine react spontaneously with the citric acid cycle intermediate fumarate to form S-(2-succino)-adducts. In Bacillus subtilis, a salvaging pathway encoded by the yxe operon has recently been identified for the detoxification and exploitation of these compounds as sulfur sources. This route involves acetylation of S-(2-succino)cysteine to N-acetyl-2-succinocysteine, which is presumably converted to oxaloacetate and N-acetylcysteine, before a final deacetylation step affords cysteine. The critical oxidative cleavage of the C-S bond of N-acetyl-S-(2-succino)cysteine was proposed to depend on the predicted flavoprotein monooxygenase YxeK. Here, we characterize YxeK and verify its role in S-(2-succino)-adduct detoxification and sulfur metabolism. Detailed biochemical and mechanistic investigation of YxeK including 18 O-isotope-labeling experiments, homology modeling, substrate specificity tests, site-directed mutagenesis, and (pre-)steady-state kinetics provides insight into the enzyme's mechanism of action, which may involve a noncanonical flavin-N5-peroxide species for C-S bond oxygenolysis.
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Affiliation(s)
| | | | - Simon Lagies
- Institute of Organic Chemistry, University of Freiburg, Germany
| | - Erik Schleicher
- Institute of Physical Chemistry, University of Freiburg, Germany
| | - Bernd Kammerer
- Institute of Organic Chemistry, University of Freiburg, Germany.,BIOSS Center for Biological Signaling Studies, University of Freiburg, Germany
| | - Holly R Ellis
- Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Frederick Stull
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | - Robin Teufel
- Faculty of Biology, University of Freiburg, Germany
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16
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Purdy TN, Kim MC, Cullum R, Fenical W, Moore BS. Discovery and Biosynthesis of Tetrachlorizine Reveals Enzymatic Benzylic Dehydrogenation via an ortho-Quinone Methide. J Am Chem Soc 2021; 143:3682-3686. [PMID: 33656337 DOI: 10.1021/jacs.0c12415] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ortho-quinone methides (o-QMs) are reactive intermediates in biosynthesis that give rise to a variety of intra- and intermolecular cyclization/addition products in bacteria, fungi, and plants. Herein, we report a new metabolic deviation of an o-QM intermediate in a benzylic dehydrogenation reaction that links the newly described marine bacterial natural products dihydrotetrachlorizine and tetrachlorizine. We discovered these novel dichloropyrrole-containing compounds from actinomycete strain AJS-327 that unexpectedly harbors in its genome a biosynthetic gene cluster (BGC) of striking similarity to that of chlorizidine, another marine alkaloid bearing a different carbon skeleton. Heterologous expression of the homologous flavin-dependent oxidoreductase enzymes Tcz9 and Clz9 revealed their native functions in tetrachlorizine and chlorizidine biosynthesis, respectively, supporting divergent oxidative dehydrogenation and pyrrolizine-forming reactions. Swapping these berberine bridge enzyme-like oxidoreductases, we produced cyclized and dehydrogenated analogs of tetrachlorizine and chlorizidine, including a dearomatized chlorizidine analog that stabilizes an o-QM via conjugation with a 3H-pyrrolizine ring.
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17
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Paul CE, Eggerichs D, Westphal AH, Tischler D, van Berkel WJH. Flavoprotein monooxygenases: Versatile biocatalysts. Biotechnol Adv 2021; 51:107712. [PMID: 33588053 DOI: 10.1016/j.biotechadv.2021.107712] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/27/2021] [Accepted: 02/06/2021] [Indexed: 12/13/2022]
Abstract
Flavoprotein monooxygenases (FPMOs) are single- or two-component enzymes that catalyze a diverse set of chemo-, regio- and enantioselective oxyfunctionalization reactions. In this review, we describe how FPMOs have evolved from model enzymes in mechanistic flavoprotein research to biotechnologically relevant catalysts that can be applied for the sustainable production of valuable chemicals. After a historical account of the development of the FPMO field, we explain the FPMO classification system, which is primarily based on protein structural properties and electron donor specificities. We then summarize the most appealing reactions catalyzed by each group with a focus on the different types of oxygenation chemistries. Wherever relevant, we report engineering strategies that have been used to improve the robustness and applicability of FPMOs.
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Affiliation(s)
- Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Daniel Eggerichs
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Tischler
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands.
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18
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Liu J, Liu A, Hu Y. Enzymatic dimerization in the biosynthetic pathway of microbial natural products. Nat Prod Rep 2021; 38:1469-1505. [PMID: 33404031 DOI: 10.1039/d0np00063a] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Covering: up to August 2020The dramatic increase in the identification of dimeric natural products generated by microorganisms and plants has played a significant role in drug discovery. The biosynthetic pathways of these products feature inherent dimerization reactions, which are valuable for biosynthetic applications and chemical transformations. The extraordinary mechanisms of the dimerization of secondary metabolites should advance our understanding of the uncommon chemical rules for natural product biosynthesis, which will, in turn, accelerate the discovery of dimeric reactions and molecules in nature and provide promising strategies for the total synthesis of natural products through dimerization. This review focuses on the enzymes involved in the dimerization in the biosynthetic pathway of microbial natural products, with an emphasis on cytochrome P450s, laccases, and intermolecular [4 + 2] cyclases, along with other atypical enzymes. The identification, characterization, and catalytic landscapes of these enzymes are also introduced.
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Affiliation(s)
- Jiawang Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.
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19
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Toplak M, Matthews A, Teufel R. The devil is in the details: The chemical basis and mechanistic versatility of flavoprotein monooxygenases. Arch Biochem Biophys 2020; 698:108732. [PMID: 33358998 DOI: 10.1016/j.abb.2020.108732] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/15/2020] [Accepted: 12/19/2020] [Indexed: 02/07/2023]
Abstract
The ubiquitous flavoenzymes commonly catalyze redox chemistry such as the monooxygenation of organic substrates and are both widely utilized in nature (e.g., in primary and secondary metabolism) and of significant industrial interest. In this work, we highlight the structural and mechanistic characteristics of the distinct types of flavoprotein monooxygenases (FPMOs). We thereby illustrate the chemical basis of FPMO catalysis, which enables reactions such as (aromatic) hydroxylation, epoxidation, (de)halogenation, heteroatom oxygenation, Baeyer-Villiger oxidation, α-hydroxylation of ketones, or non-oxidative carbon-hetero bond cleavage. This seemingly unmatched versatility in oxygenation chemistry results from extensive fine-tuning and regiospecific functionalization of the flavin cofactor that is tightly controlled by the surrounding protein matrix. Accordingly, FPMOs steer the formation of covalent flavin-oxygen adducts for oxygen transfer in the form of the classical flavin-C4a-(hydro)peroxide or the recently discovered N5-functionalized flavins (i.e. the flavin-N5-oxide and the flavin-N5-peroxide), while in rare cases covalent oxygen adduct formation may be foregone entirely. Finally, we speculate about hitherto undiscovered flavin-mediated oxygenation reactions and compare FPMOs to cytochrome P450 monooxygenases, before addressing open questions and challenges for the future investigation of FPMOs.
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Affiliation(s)
- Marina Toplak
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Arne Matthews
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Robin Teufel
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany.
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20
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Duan Y, Petzold M, Saleem‐Batcha R, Teufel R. Bacterial Tropone Natural Products and Derivatives: Overview of their Biosynthesis, Bioactivities, Ecological Role and Biotechnological Potential. Chembiochem 2020; 21:2384-2407. [PMID: 32239689 PMCID: PMC7497051 DOI: 10.1002/cbic.201900786] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/02/2020] [Indexed: 12/05/2022]
Abstract
Tropone natural products are non-benzene aromatic compounds of significant ecological and pharmaceutical interest. Herein, we highlight current knowledge on bacterial tropones and their derivatives such as tropolones, tropodithietic acid, and roseobacticides. Their unusual biosynthesis depends on a universal CoA-bound precursor featuring a seven-membered carbon ring as backbone, which is generated by a side reaction of the phenylacetic acid catabolic pathway. Enzymes encoded by separate gene clusters then further modify this key intermediate by oxidation, CoA-release, or incorporation of sulfur among other reactions. Tropones play important roles in the terrestrial and marine environment where they act as antibiotics, algaecides, or quorum sensing signals, while their bacterial producers are often involved in symbiotic interactions with plants and marine invertebrates (e. g., algae, corals, sponges, or mollusks). Because of their potent bioactivities and of slowly developing bacterial resistance, tropones and their derivatives hold great promise for biomedical or biotechnological applications, for instance as antibiotics in (shell)fish aquaculture.
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Affiliation(s)
- Ying Duan
- Faculty of BiologyUniversity of Freiburg79104FreiburgGermany
| | - Melanie Petzold
- Faculty of BiologyUniversity of Freiburg79104FreiburgGermany
| | | | - Robin Teufel
- Faculty of BiologyUniversity of Freiburg79104FreiburgGermany
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21
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Abstract
Flavin-dependent enzymes catalyze a wide variety of biological reactions that are important for all types of living organisms. Knowledge gained from studying the chemistry and biological functions of flavins and flavin-dependent enzymes has continuously made significant contributions to the development of the fields of enzymology and metabolism from the 1970s until now. The enzymes have been applied in various applications such as use as biocatalysts in synthetic processes for the chemical and pharmaceutical industries or in the biodetoxification and bioremediation of toxic or unwanted compounds, and as biosensors or biodetection tools for quantifying various agents of interest. Many flavin-dependent enzymes are also prime targets for drug development. Based on their reaction mechanisms, they can be classified into five categories: oxidase, dehydrogenase, monooxygenase, reductase, and redox neutral flavin-dependent enzymes. In this chapter, the general properties of flavin-dependent enzymes and the nature of their chemical reactions are discussed, along with their practical applications.
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22
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Petsi M, Zografos AL. 2,5-Diketopiperazine Catalysts as Activators of Dioxygen in Oxidative Processes. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01847] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Marina Petsi
- Department of Chemistry, Main University Campus, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Alexandros L. Zografos
- Department of Chemistry, Main University Campus, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
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23
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Tsypik O, Makitrynskyy R, Frensch B, Zechel DL, Paululat T, Teufel R, Bechthold A. Oxidative Carbon Backbone Rearrangement in Rishirilide Biosynthesis. J Am Chem Soc 2020; 142:5913-5917. [PMID: 32182053 DOI: 10.1021/jacs.9b12736] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The structural diversity of type II polyketides is largely generated by tailoring enzymes. In rishirilide biosynthesis by Streptomyces bottropensis, 13C-labeling studies previously implied extraordinary carbon backbone and side-chain rearrangements. In this work, we employ gene deletion experiments and in vitro enzyme studies to identify key biosynthetic intermediates and expose intricate redox tailoring steps for the formation of rishirilides A, B, and D and lupinacidin A. First, the flavin-dependent RslO5 reductively ring-opens the epoxide moiety of an advanced polycyclic intermediate to form an alcohol. Flavin monooxygenase RslO9 then oxidatively rearranges the carbon backbone, presumably via lactone-forming Baeyer-Villiger oxidation and subsequent intramolecular aldol condensation. While RslO9 can further convert the rearranged intermediate to rishirilide D and lupinacidin A, an additional ketoreductase RslO8 is required for formation of the main products rishirilide A and rishirilide B. This work provides insight into the structural diversification of aromatic polyketide natural products via unusual redox tailoring reactions that appear to defy biosynthetic logic.
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Affiliation(s)
- Olga Tsypik
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Straße 19, 79104 Freiburg, Germany
| | - Roman Makitrynskyy
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Straße 19, 79104 Freiburg, Germany
| | - Britta Frensch
- Faculty of Biology, Schänzlestraße 1, 79104 Freiburg, Germany
| | - David L Zechel
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston K7L 3N6, Ontario, Canada
| | - Thomas Paululat
- Organic Chemistry, University of Siegen, Adolf-Reichwein-Straße 2, 57068 Siegen, Germany
| | - Robin Teufel
- Faculty of Biology, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Andreas Bechthold
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Straße 19, 79104 Freiburg, Germany
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24
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Manenda MS, Picard MÈ, Zhang L, Cyr N, Zhu X, Barma J, Pascal JM, Couture M, Zhang C, Shi R. Structural analyses of the Group A flavin-dependent monooxygenase PieE reveal a sliding FAD cofactor conformation bridging OUT and IN conformations. J Biol Chem 2020; 295:4709-4722. [PMID: 32111738 DOI: 10.1074/jbc.ra119.011212] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/26/2020] [Indexed: 02/02/2023] Open
Abstract
Group A flavin-dependent monooxygenases catalyze the cleavage of the oxygen-oxygen bond of dioxygen, followed by the incorporation of one oxygen atom into the substrate molecule with the aid of NADPH and FAD. These flavoenzymes play an important role in many biological processes, and their most distinct structural feature is the choreographed motions of flavin, which typically adopts two distinct conformations (OUT and IN) to fulfill its function. Notably, these enzymes seem to have evolved a delicate control system to avoid the futile cycle of NADPH oxidation and FAD reduction in the absence of substrate, but the molecular basis of this system remains elusive. Using protein crystallography, size-exclusion chromatography coupled to multi-angle light scattering (SEC-MALS), and small-angle X-ray scattering (SEC-SAXS) and activity assay, we report here a structural and biochemical characterization of PieE, a member of the Group A flavin-dependent monooxygenases involved in the biosynthesis of the antibiotic piericidin A1. This analysis revealed that PieE forms a unique hexamer. Moreover, we found, to the best of our knowledge for the first time, that in addition to the classical OUT and IN conformations, FAD possesses a "sliding" conformation that exists in between the OUT and IN conformations. This observation sheds light on the underlying mechanism of how the signal of substrate binding is transmitted to the FAD-binding site to efficiently initiate NADPH binding and FAD reduction. Our findings bridge a gap currently missing in the orchestrated order of chemical events catalyzed by this important class of enzymes.
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Affiliation(s)
- Mahder S Manenda
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Marie-Ève Picard
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Liping Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Normand Cyr
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Xiaojun Zhu
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Julie Barma
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - John M Pascal
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Manon Couture
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Changsheng Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Rong Shi
- Département de Biochimie, de Microbiologie, et de Bio-informatique, PROTEO, Université Laval, Québec G1V 0A6, Canada .,Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
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25
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Aminoperoxide adducts expand the catalytic repertoire of flavin monooxygenases. Nat Chem Biol 2020; 16:556-563. [DOI: 10.1038/s41589-020-0476-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/08/2020] [Indexed: 11/08/2022]
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26
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Khusnutdinova AN, Xiao J, Wang PH, Batyrova KA, Flick R, Edwards EA, Yakunin AF. Prenylated FMN: Biosynthesis, purification, and Fdc1 activation. Methods Enzymol 2019; 620:469-488. [PMID: 31072498 DOI: 10.1016/bs.mie.2019.03.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Prenylated flavin mononucleotide (prFMN) is a recently discovered flavin cofactor produced by the UbiX family of FMN prenyltransferases, and is required for the activity of UbiD-like reversible decarboxylases. The latter enzymes are known to be involved in ubiquinone biosynthesis and biotransformation of lignin, aromatic compounds, and unsaturated aliphatic acids. However, exploration of uncharacterized UbiD proteins for biotechnological applications is hindered by our limited knowledge about the biochemistry of prFMN and prFMN-dependent enzymes. Here, we describe experimental protocols and considerations for the biosynthesis of prFMN in vivo and in vitro, in addition to cofactor extraction and application for activation of UbiD proteins.
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Affiliation(s)
- Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Johnny Xiao
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Po-Hsiang Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Khorcheska A Batyrova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada; Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, United Kingdom.
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27
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Hauptmann R, Petrosyan A, Fennel F, Argüello Cordero MA, Surkus A, Pospech J. Pyrimidopteridine
N
‐Oxide Organic Photoredox Catalysts: Characterization, Application and Non‐Covalent Interaction in Solid State. Chemistry 2019; 25:4325-4329. [DOI: 10.1002/chem.201900118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/05/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Richy Hauptmann
- Leibniz Institute for Catalysis at theUniversity of Rostock Albert-Einstein-Strasse 29a 18059 Rostock Germany
| | - Andranik Petrosyan
- Leibniz Institute for Catalysis at theUniversity of Rostock Albert-Einstein-Strasse 29a 18059 Rostock Germany
| | - Franziska Fennel
- Institut für Physik, Dynamik molekularer SystemeUniversität Rostock Albert-Einstein-Str. 23–24 18059 Rostock Germany
| | - Miguel A. Argüello Cordero
- Leibniz Institute for Catalysis at theUniversity of Rostock Albert-Einstein-Strasse 29a 18059 Rostock Germany
- Institut für Physik, Dynamik molekularer SystemeUniversität Rostock Albert-Einstein-Str. 23–24 18059 Rostock Germany
| | - Annette‐E. Surkus
- Leibniz Institute for Catalysis at theUniversity of Rostock Albert-Einstein-Strasse 29a 18059 Rostock Germany
| | - Jola Pospech
- Leibniz Institute for Catalysis at theUniversity of Rostock Albert-Einstein-Strasse 29a 18059 Rostock Germany
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28
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Adak S, Begley TP. Hexachlorobenzene Catabolism Involves a Nucleophilic Aromatic Substitution and Flavin-N5-Oxide Formation. Biochemistry 2019; 58:1181-1183. [DOI: 10.1021/acs.biochem.9b00012] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sanjoy Adak
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
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29
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Adak S, Begley TP. Flavin-N5-oxide intermediates in dibenzothiophene, uracil, and hexachlorobenzene catabolism. Methods Enzymol 2019; 620:455-468. [DOI: 10.1016/bs.mie.2019.03.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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30
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Saleem-Batcha R, Teufel R. Structural methods for probing the interaction of flavoenzymes with dioxygen and its surrogates. Methods Enzymol 2019; 620:349-363. [DOI: 10.1016/bs.mie.2019.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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31
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Insights into the enzymatic formation, chemical features, and biological role of the flavin-N5-oxide. Curr Opin Chem Biol 2018; 47:47-53. [DOI: 10.1016/j.cbpa.2018.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/31/2018] [Accepted: 08/07/2018] [Indexed: 11/22/2022]
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Tian W, Sun C, Zheng M, Harmer JR, Yu M, Zhang Y, Peng H, Zhu D, Deng Z, Chen SL, Mobli M, Jia X, Qu X. Efficient biosynthesis of heterodimeric C 3-aryl pyrroloindoline alkaloids. Nat Commun 2018; 9:4428. [PMID: 30356123 PMCID: PMC6200733 DOI: 10.1038/s41467-018-06528-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/11/2018] [Indexed: 12/04/2022] Open
Abstract
Many natural products contain the hexahydropyrrolo[2, 3-b]indole (HPI) framework. HPI containing chemicals exhibit various biological activities and distinguishable structural arrangement. This structural complexity renders chemical synthesis very challenging. Here, through investigating the biosynthesis of a naturally occurring C3-aryl HPI, naseseazine C (NAS-C), we identify a P450 enzyme (NascB) and reveal that NascB catalyzes a radical cascade reaction to form intramolecular and intermolecular carbon–carbon bonds with both regio- and stereo-specificity. Surprisingly, the limited freedom is allowed in specificity to generate four types of C3-aryl HPI scaffolds, and two of them were not previously observed. By incorporating NascB into an engineered strain of E. coli, we develop a whole-cell biocatalysis system for efficient production of NAS-C and 30 NAS analogs. Interestingly, we find that some of these analogs exhibit potent neuroprotective properties. Thus, our biocatalytic methodology offers an efficient and simple route to generate difficult HPI framework containing chemicals. The hexahydropyrrolo[2, 3-b]indole (HPI) framework is found in many natural products. Here, the authors discover a P450 enzyme and develop a whole-cell biocatalysis system that produces the HPI naseseazine C (NAS-C) and 30 NAS-C analogs, several of which show neuroprotective properties.
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Affiliation(s)
- Wenya Tian
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
| | - Chenghai Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
| | - Mei Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
| | - Jeffrey R Harmer
- Centre for Advanced Imaging, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Mingjia Yu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, 100081, Beijing, China
| | - Yanan Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
| | - Haidong Peng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
| | - Dongqing Zhu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
| | - Shi-Lu Chen
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, 100081, Beijing, China
| | - Mehdi Mobli
- Centre for Advanced Imaging, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Xinying Jia
- Centre for Advanced Imaging, The University of Queensland, St. Lucia, QLD 4072, Australia.
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China.
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Heine T, van Berkel WJH, Gassner G, van Pée KH, Tischler D. Two-Component FAD-Dependent Monooxygenases: Current Knowledge and Biotechnological Opportunities. BIOLOGY 2018; 7:biology7030042. [PMID: 30072664 PMCID: PMC6165268 DOI: 10.3390/biology7030042] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 12/11/2022]
Abstract
Flavoprotein monooxygenases create valuable compounds that are of high interest for the chemical, pharmaceutical, and agrochemical industries, among others. Monooxygenases that use flavin as cofactor are either single- or two-component systems. Here we summarize the current knowledge about two-component flavin adenine dinucleotide (FAD)-dependent monooxygenases and describe their biotechnological relevance. Two-component FAD-dependent monooxygenases catalyze hydroxylation, epoxidation, and halogenation reactions and are physiologically involved in amino acid metabolism, mineralization of aromatic compounds, and biosynthesis of secondary metabolites. The monooxygenase component of these enzymes is strictly dependent on reduced FAD, which is supplied by the reductase component. More and more representatives of two-component FAD-dependent monooxygenases have been discovered and characterized in recent years, which has resulted in the identification of novel physiological roles, functional properties, and a variety of biocatalytic opportunities.
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Affiliation(s)
- Thomas Heine
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
| | - Willem J H van Berkel
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - George Gassner
- Department of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA.
| | - Karl-Heinz van Pée
- Allgemeine Biochemie, Technische Universität Dresden, 01062 Dresden, Germany.
| | - Dirk Tischler
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
- Microbial Biotechnology, Ruhr University Bochum, Universitätsstr. 150, 44780 Bochum, Germany.
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Zheng Q, Gong Y, Guo Y, Zhao Z, Wu Z, Zhou Z, Chen D, Pan L, Liu W. Structural Insights into a Flavin-Dependent [4 + 2] Cyclase that Catalyzes trans-Decalin Formation in Pyrroindomycin Biosynthesis. Cell Chem Biol 2018; 25:718-727.e3. [DOI: 10.1016/j.chembiol.2018.03.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/28/2018] [Accepted: 03/12/2018] [Indexed: 12/13/2022]
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Enzymatic control of dioxygen binding and functionalization of the flavin cofactor. Proc Natl Acad Sci U S A 2018; 115:4909-4914. [PMID: 29686059 DOI: 10.1073/pnas.1801189115] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The reactions of enzymes and cofactors with gaseous molecules such as dioxygen (O2) are challenging to study and remain among the most contentious subjects in biochemistry. To date, it is largely enigmatic how enzymes control and fine-tune their reactions with O2, as exemplified by the ubiquitous flavin-dependent enzymes that commonly facilitate redox chemistry such as the oxygenation of organic substrates. Here we employ O2-pressurized X-ray crystallography and quantum mechanical calculations to reveal how the precise positioning of O2 within a flavoenzyme's active site enables the regiospecific formation of a covalent flavin-oxygen adduct and oxygenating species (i.e., the flavin-N5-oxide) by mimicking a critical transition state. This study unambiguously demonstrates how enzymes may control the O2 functionalization of an organic cofactor as prerequisite for oxidative catalysis. Our work thus illustrates how O2 reactivity can be harnessed in an enzymatic environment and provides crucial knowledge for future rational design of O2-reactive enzymes.
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Wang PH, Khusnutdinova AN, Luo F, Xiao J, Nemr K, Flick R, Brown G, Mahadevan R, Edwards EA, Yakunin AF. Biosynthesis and Activity of Prenylated FMN Cofactors. Cell Chem Biol 2018; 25:560-570.e6. [PMID: 29551348 DOI: 10.1016/j.chembiol.2018.02.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 12/06/2017] [Accepted: 02/07/2018] [Indexed: 10/17/2022]
Abstract
Prenylated flavin mononucleotide (prFMN) is a recently discovered cofactor required by the UbiD family of reversible decarboxylases involved in ubiquinone biosynthesis, biological decomposition of lignin, and biotransformation of aromatic compounds. This cofactor is synthesized by UbiX-like prenyltransferases catalyzing the transfer of the dimethylallyl moiety of dimethylallyl-monophosphate (DMAP) to FMN. The origin of DMAP for prFMN biosynthesis and the biochemical properties of free prFMN are unknown. We show that in Escherichia coli cells, DMAP can be produced by phosphorylating prenol using ThiM or dephosphorylating DMAPP using Nudix hydrolases. We produced 14 active prenyltransferases whose properties enabled the purification and characterization of protein-free forms of prFMN. In vitro assays revealed that the UbiD-like ferulate decarboxylase (Fdc1) can be activated by free prFMNiminium or C2'-hydroxylated prFMNiminium under both oxidized and reduced conditions. These insights into the biosynthesis and properties of prFMN will facilitate further elucidation of the biochemical diversity of reversible UbiD (de)carboxylases.
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Affiliation(s)
- Po-Hsiang Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
| | - Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
| | - Fei Luo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
| | - Johnny Xiao
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
| | - Kayla Nemr
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada; Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3E5, Canada.
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada.
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Reed KB, Alper HS. Expanding beyond canonical metabolism: Interfacing alternative elements, synthetic biology, and metabolic engineering. Synth Syst Biotechnol 2018; 3:20-33. [PMID: 29911196 PMCID: PMC5884228 DOI: 10.1016/j.synbio.2017.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/08/2017] [Accepted: 12/09/2017] [Indexed: 12/15/2022] Open
Abstract
Metabolic engineering offers an exquisite capacity to produce new molecules in a renewable manner. However, most industrial applications have focused on only a small subset of elements from the periodic table, centered around carbon biochemistry. This review aims to illustrate the expanse of chemical elements that can currently (and potentially) be integrated into useful products using cellular systems. Specifically, we describe recent advances in expanding the cellular scope to include the halogens, selenium and the metalloids, and a variety of metal incorporations. These examples range from small molecules, heteroatom-linked uncommon elements, and natural products to biomining and nanotechnology applications. Collectively, this review covers the promise of an expanded range of elemental incorporations and the future impacts it may have on biotechnology.
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Affiliation(s)
- Kevin B. Reed
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
| | - Hal S. Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, USA
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38
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Romero E, Gómez Castellanos JR, Gadda G, Fraaije MW, Mattevi A. Same Substrate, Many Reactions: Oxygen Activation in Flavoenzymes. Chem Rev 2018; 118:1742-1769. [DOI: 10.1021/acs.chemrev.7b00650] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Elvira Romero
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - J. Rubén Gómez Castellanos
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Giovanni Gadda
- Departments of Chemistry and Biology, Center for Diagnostics and Therapeutics, and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
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Preparation and Characterization of the Favorskiiase Flavoprotein EncM and Its Distinctive Flavin-N5-Oxide Cofactor. Methods Enzymol 2018; 604:523-540. [DOI: 10.1016/bs.mie.2018.01.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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40
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Flavin-catalyzed redox tailoring reactions in natural product biosynthesis. Arch Biochem Biophys 2017; 632:20-27. [DOI: 10.1016/j.abb.2017.06.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 06/09/2017] [Accepted: 06/10/2017] [Indexed: 11/21/2022]
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41
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Flavin-N5-oxide: A new, catalytic motif in flavoenzymology. Arch Biochem Biophys 2017; 632:4-10. [PMID: 28784589 DOI: 10.1016/j.abb.2017.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 11/22/2022]
Abstract
Flavin-N5-oxide is a recently discovered intermediate used by EncM (1,3-diketone oxidation), DszA (sulfone monooxygenase) and RutA (amide monooxygenase). This review describes the mechanism of these enzymes and proposes criteria for the identification of additional Flavin-N5-oxide dependent enzymes.
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42
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Adak S, Begley TP. RutA-Catalyzed Oxidative Cleavage of the Uracil Amide Involves Formation of a Flavin-N5-oxide. Biochemistry 2017; 56:3708-3709. [PMID: 28661684 PMCID: PMC6040642 DOI: 10.1021/acs.biochem.7b00493] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
RutA is a novel flavoenzyme on the uracil catabolic pathway that catalyzes uracil ring opening by a unique amide oxidation reaction. Here we provide evidence that this reaction also involves the formation of a flavin-N5-oxide.
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Affiliation(s)
- Sanjoy Adak
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
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43
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Piano V, Palfey BA, Mattevi A. Flavins as Covalent Catalysts: New Mechanisms Emerge. Trends Biochem Sci 2017; 42:457-469. [DOI: 10.1016/j.tibs.2017.02.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/06/2017] [Accepted: 02/14/2017] [Indexed: 10/20/2022]
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44
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Agarwal V, Miles ZD, Winter JM, Eustáquio AS, El Gamal AA, Moore BS. Enzymatic Halogenation and Dehalogenation Reactions: Pervasive and Mechanistically Diverse. Chem Rev 2017; 117:5619-5674. [PMID: 28106994 PMCID: PMC5575885 DOI: 10.1021/acs.chemrev.6b00571] [Citation(s) in RCA: 248] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Naturally produced halogenated compounds are ubiquitous across all domains of life where they perform a multitude of biological functions and adopt a diversity of chemical structures. Accordingly, a diverse collection of enzyme catalysts to install and remove halogens from organic scaffolds has evolved in nature. Accounting for the different chemical properties of the four halogen atoms (fluorine, chlorine, bromine, and iodine) and the diversity and chemical reactivity of their organic substrates, enzymes performing biosynthetic and degradative halogenation chemistry utilize numerous mechanistic strategies involving oxidation, reduction, and substitution. Biosynthetic halogenation reactions range from simple aromatic substitutions to stereoselective C-H functionalizations on remote carbon centers and can initiate the formation of simple to complex ring structures. Dehalogenating enzymes, on the other hand, are best known for removing halogen atoms from man-made organohalogens, yet also function naturally, albeit rarely, in metabolic pathways. This review details the scope and mechanism of nature's halogenation and dehalogenation enzymatic strategies, highlights gaps in our understanding, and posits where new advances in the field might arise in the near future.
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Affiliation(s)
- Vinayak Agarwal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Zachary D. Miles
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
| | | | - Alessandra S. Eustáquio
- College of Pharmacy, Department of Medicinal Chemistry & Pharmacognosy and Center for Biomolecular Sciences, University of Illinois at Chicago
| | - Abrahim A. El Gamal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Bradley S. Moore
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego
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45
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Tabib CR, Brodl E, Macheroux P. Evidence for the generation of myristylated FMN by bacterial luciferase. Mol Microbiol 2017; 104:1027-1036. [PMID: 28345146 DOI: 10.1111/mmi.13676] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2017] [Indexed: 11/28/2022]
Abstract
The genes responsible for the light production in bioluminescent bacteria are present as an operon, luxCDABEG. Many strains of Photobacteria carry an additional gene, termed luxF. X-ray crystallographic analysis of LuxF revealed the presence of four molecules of a flavin derivative, i.e. 6-(3'-(R)-myristyl) flavin adenine mononucleotide (myrFMN) non-covalently bound to the homodimer. In the present study, we exploited the binding of myrFMN to recombinant apo-LuxF to explore the occurrence of myrFMN in various bioluminescent bacteria. MyrFMN was detected in all bacterial strains tested including Vibrio and Aliivibrio indicating that it is more widely occurring in bioluminescent bacteria than previously assumed. We also show that apo-LuxF captures myrFMN and thereby relieves the inhibitory effect on luciferase activity. Thus our results provide support for the hypothesis that LuxF acts as a scavenger of myrFMN in bioluminescent bacteria. However, the source of myrFMN remained obscure. To address this issue, we established a cofactor regeneration enzyme-catalyzed cascade reaction that supports luciferase activity in vitro for up to 3 days. This approach enabled us to unambiguously demonstrate that myrFMN is generated in the bacterial bioluminescent reaction. Based on this finding we postulate a reaction mechanism for myrFMN generation that is based on the luciferase reaction.
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Affiliation(s)
- Chaitanya R Tabib
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, A-8010, Graz, Austria
| | - Eveline Brodl
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, A-8010, Graz, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, A-8010, Graz, Austria
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46
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Konjik V, Brünle S, Demmer U, Vanselow A, Sandhoff R, Ermler U, Mack M. Die Kristallstruktur von RosB: Einblicke in den Reaktionsmechanismus des ersten Mitglieds einer flavodoxinähnlichen Enzymfamilie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Valentino Konjik
- Hochschule Mannheim; Paul-Wittsack-Straße 10 68163 Mannheim Deutschland
| | - Steffen Brünle
- Max-Planck-Institut für Biophysik; Max-von-Laue-Straße 3 60438 Frankfurt am Main Deutschland
| | - Ulrike Demmer
- Max-Planck-Institut für Biophysik; Max-von-Laue-Straße 3 60438 Frankfurt am Main Deutschland
| | - Amanda Vanselow
- Hochschule Mannheim; Paul-Wittsack-Straße 10 68163 Mannheim Deutschland
| | - Roger Sandhoff
- Deutsches Krebsforschungszentrum (DKFZ); Im Neuenheimer Feld 280 69120 Heidelberg Deutschland
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik; Max-von-Laue-Straße 3 60438 Frankfurt am Main Deutschland
| | - Matthias Mack
- Hochschule Mannheim; Paul-Wittsack-Straße 10 68163 Mannheim Deutschland
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47
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Konjik V, Brünle S, Demmer U, Vanselow A, Sandhoff R, Ermler U, Mack M. The Crystal Structure of RosB: Insights into the Reaction Mechanism of the First Member of a Family of Flavodoxin-like Enzymes. Angew Chem Int Ed Engl 2016; 56:1146-1151. [DOI: 10.1002/anie.201610292] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Valentino Konjik
- Mannheim University of Applied Sciences; Paul-Wittsack-Strasse 10 68163 Mannheim Germany
| | - Steffen Brünle
- Max-Planck-Institute for Biophysics; Max-von-Laue-Strasse 3 60438 Frankfurt am Main Germany
| | - Ulrike Demmer
- Max-Planck-Institute for Biophysics; Max-von-Laue-Strasse 3 60438 Frankfurt am Main Germany
| | - Amanda Vanselow
- Mannheim University of Applied Sciences; Paul-Wittsack-Strasse 10 68163 Mannheim Germany
| | - Roger Sandhoff
- German Cancer Research Center (DKFZ); Im Neuenheimer Feld 280 69120 Heidelberg Germany
| | - Ulrich Ermler
- Max-Planck-Institute for Biophysics; Max-von-Laue-Strasse 3 60438 Frankfurt am Main Germany
| | - Matthias Mack
- Mannheim University of Applied Sciences; Paul-Wittsack-Strasse 10 68163 Mannheim Germany
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48
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Abstract
The dibenzothiophene catabolic pathway converts dibenzothiophene to 2-hydroxybiphenyl and sulfite. The third step of the pathway, involving the conversion of dibenzothiophene sulfone to 2-(2-hydroxyphenyl)-benzenesulfinic acid, is catalyzed by a unique flavoenzyme DszA. Mechanistic studies on this reaction suggest that the C2 hydroperoxide of dibenzothiophene sulfone reacts with flavin to form a flavin-N5-oxide. The intermediacy of the flavin-N5-oxide was confirmed by LC-MS analysis, a co-elution experiment with chemically synthesized FMN-N5-oxide and (18)O2 labeling studies.
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Affiliation(s)
- Sanjoy Adak
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
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49
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Biosynthesis of coral settlement cue tetrabromopyrrole in marine bacteria by a uniquely adapted brominase-thioesterase enzyme pair. Proc Natl Acad Sci U S A 2016; 113:3797-802. [PMID: 27001835 DOI: 10.1073/pnas.1519695113] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Halogenated pyrroles (halopyrroles) are common chemical moieties found in bioactive bacterial natural products. The halopyrrole moieties of mono- and dihalopyrrole-containing compounds arise from a conserved mechanism in which a proline-derived pyrrolyl group bound to a carrier protein is first halogenated and then elaborated by peptidic or polyketide extensions. This paradigm is broken during the marine pseudoalteromonad bacterial biosynthesis of the coral larval settlement cue tetrabromopyrrole (1), which arises from the substitution of the proline-derived carboxylate by a bromine atom. To understand the molecular basis for decarboxylative bromination in the biosynthesis of 1, we sequenced two Pseudoalteromonas genomes and identified a conserved four-gene locus encoding the enzymes involved in its complete biosynthesis. Through total in vitro reconstitution of the biosynthesis of 1 using purified enzymes and biochemical interrogation of individual biochemical steps, we show that all four bromine atoms in 1 are installed by the action of a single flavin-dependent halogenase: Bmp2. Tetrabromination of the pyrrole induces a thioesterase-mediated offloading reaction from the carrier protein and activates the biosynthetic intermediate for decarboxylation. Insights into the tetrabrominating activity of Bmp2 were obtained from the high-resolution crystal structure of the halogenase contrasted against structurally homologous halogenase Mpy16 that forms only a dihalogenated pyrrole in marinopyrrole biosynthesis. Structure-guided mutagenesis of the proposed substrate-binding pocket of Bmp2 led to a reduction in the degree of halogenation catalyzed. Our study provides a biogenetic basis for the biosynthesis of 1 and sets a firm foundation for querying the biosynthetic potential for the production of 1 in marine (meta)genomes.
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