A Nonconventional Archaeal Fluorinase Identified by In Silico Mining for Enhanced Fluorine Biocatalysis

. 2022 Jun 03 ; 12 (11) : 6570-6577. [epub] 20220519

Status PubMed-not-MEDLINE Jazyk angličtina Země Spojené státy americké Médium print-electronic

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid35692250

Fluorinases, the only enzymes known to catalyze the transfer of fluorine to an organic molecule, are essential catalysts for the biological synthesis of valuable organofluorines. However, the few fluorinases identified so far have low turnover rates that hamper biotechnological applications. Here, we isolated and characterized putative fluorinases retrieved from systematic in silico mining and identified a nonconventional archaeal enzyme from Methanosaeta sp. that mediates the fastest SN2 fluorination rate reported to date. Furthermore, we demonstrate enhanced production of fluoronucleotides in vivo in a bacterial host engineered with this archaeal fluorinase, paving the way toward synthetic metabolism for efficient biohalogenation.

Zobrazit více v PubMed

Cros A.; Alfaro-Espinoza G.; de Maria A.; Wirth N. T.; Nikel P. I. Synthetic Metabolism for Biohalogenation. Curr. Opin. Biotechnol. 2022, 74, 180–193. 10.1016/j.copbio.2021.11.009. PubMed DOI

Walker M. C.; Chang M. C. Y. Natural and Engineered Biosynthesis of Fluorinated Natural Products. Chem. Soc. Rev. 2014, 43 (18), 6527–6536. 10.1039/C4CS00027G. PubMed DOI

Harsanyi A.; Sandford G. Organofluorine Chemistry: Applications, Sources and Sustainability. Green Chem. 2015, 17 (4), 2081–2086. 10.1039/C4GC02166E. DOI

Inoue M.; Sumii Y.; Shibata N. Contribution of Organofluorine Compounds to Pharmaceuticals. ACS Omega 2020, 5 (19), 10633–10640. 10.1021/acsomega.0c00830. PubMed DOI PMC

Ogawa Y.; Tokunaga E.; Kobayashi O.; Hirai K.; Shibata N. Current Contributions of Organofluorine Compounds to the Agrochemical Industry. iScience 2020, 23 (9), 101467.10.1016/j.isci.2020.101467. PubMed DOI PMC

O’Hagan D. Understanding Organofluorine Chemistry. An Introduction to the C–F Bond. Chem. Soc. Rev. 2008, 37, 308–319. 10.1039/B711844A. PubMed DOI

Carvalho M. F.; Oliveira R. S. Natural Production of Fluorinated Compounds and Biotechnological Prospects of the Fluorinase Enzyme. Crit. Rev. Biotechnol. 2017, 37 (7), 880–897. 10.1080/07388551.2016.1267109. PubMed DOI

Deng H.; O’Hagan D.; Schaffrath C. Fluorometabolite Biosynthesis and the Fluorinase from Streptomyces cattleya. Nat. Prod. Rep. 2004, 21 (6), 773–784. 10.1039/b415087m. PubMed DOI

O’Hagan D.; Schaffrath C.; Cobb S. L.; Hamilton J. T.; Murphy C. D. Biochemistry: Biosynthesis of an Organofluorine Molecule. Nature 2002, 416 (6878), 279.10.1038/416279a. PubMed DOI

Schaffrath C.; Deng H.; O’Hagan D. Isolation and Characterisation of 5′-Fluorodeoxyadenosine Synthase, a Fluorination Enzyme from Streptomyces cattleya. FEBS Lett. 2003, 547 (1–3), 111–114. 10.1016/S0014-5793(03)00688-4. PubMed DOI

Zhu X.; Robinson D. A.; McEwan A. R.; O’Hagan D.; Naismith J. H. Mechanism of Enzymatic Fluorination in Streptomyces cattleya. J. Am. Chem. Soc. 2007, 129 (47), 14597–14604. 10.1021/ja0731569. PubMed DOI PMC

Deng H.; Ma L.; Bandaranayaka N.; Qin Z.; Mann G.; Kyeremeh K.; Yu Y.; Shepherd T.; Naismith J. H.; O’Hagan D. Identification of Fluorinases from Streptomyces sp Ma37, Nocardia brasiliensis, and Actinoplanes sp N902–109 by Genome Mining. ChemBioChem. 2014, 15 (3), 364–368. 10.1002/cbic.201300732. PubMed DOI

Ma L.; Li Y.; Meng L.; Deng H.; Li Y.; Zhang Q.; Diao A. Biological Fluorination from the Sea: Discovery of a SAM-Dependent Nucleophilic Fluorinating Enzyme from the Marine-Derived Bacterium Streptomyces xinghaiensis NRRL B24674. RSC Adv. 2016, 6, 27047–27051. 10.1039/C6RA00100A. DOI

Sooklal S. A.; de Koning C.; Brady D.; Rumbold K. Identification and Characterisation of a Fluorinase from Actinopolyspora mzabensis. Protein Expr. Purif. 2020, 166, 105508.10.1016/j.pep.2019.105508. PubMed DOI

Eustáquio A. S.; Pojer F.; Noel J. P.; Moore B. S. Discovery and Characterization of a Marine Bacterial SAM-Dependent Chlorinase. Nat. Chem. Biol. 2008, 4 (1), 69–74. 10.1038/nchembio.2007.56. PubMed DOI PMC

Deng H.; Cobb S. L.; McEwan A. R.; McGlinchey R. P.; Naismith J. H.; O’Hagan D.; Robinson D. A.; Spencer J. B. The Fluorinase from Streptomyces cattleya is Also a Chlorinase. Angew. Chem., Int. Ed. Engl. 2006, 45 (5), 759–762. 10.1002/anie.200503582. PubMed DOI PMC

Deng H.; O’Hagan D. The Fluorinase, the Chlorinase and the Duf-62 Enzymes. Curr. Opin. Chem. Biol. 2008, 12 (5), 582–592. 10.1016/j.cbpa.2008.06.036. PubMed DOI

Pereira P. R. M.; Araújo J. O.; Silva J. R. A.; Alves C. N.; Lameira J.; Lima A. H. Exploring Chloride Selectivity and Halogenase Regioselectivity of the Sall Enzyme through Quantum Mechanical/Molecular Mechanical Modeling. J. Chem. Inf. Model. 2020, 60 (2), 738–746. 10.1021/acs.jcim.9b01079. PubMed DOI

Hauer B. Embracing Nature’s Catalysts: A Viewpoint on the Future of Biocatalysis. ACS Catal. 2020, 10 (15), 8418–8427. 10.1021/acscatal.0c01708. DOI

Martinelli L.; Nikel P. I. Breaking the State-of-the-Art in the Chemical Industry with New-to-Nature Products via Synthetic Microbiology. Microb. Biotechnol. 2019, 12 (2), 187–190. 10.1111/1751-7915.13372. PubMed DOI PMC

Nieto-Domínguez M.; Nikel P. I. Intersecting Xenobiology and Neo-Metabolism to Bring Novel Chemistries to Life. ChemBioChem. 2020, 21 (18), 2551–2571. 10.1002/cbic.202000091. PubMed DOI

Walker M. C.; Thuronyi B. W.; Charkoudian L. K.; Lowry B.; Khosla C.; Chang M. C. Expanding the Fluorine Chemistry of Living Systems Using Engineered Polyketide Synthase Pathways. Science 2013, 341 (6150), 1089–1094. 10.1126/science.1242345. PubMed DOI PMC

O’Hagan D.; Deng H. Enzymatic Fluorination and Biotechnological Developments of the Fluorinase. Chem. Rev. 2015, 115 (2), 634–649. 10.1021/cr500209t. PubMed DOI

Sun H.; Yeo W. L.; Lim Y. H.; Chew X.; Smith D. J.; Xue B.; Chan K. P.; Robinson R. C.; Robins E. G.; Zhao H.; Ang E. L. Directed Evolution of a Fluorinase for Improved Fluorination Efficiency with a Non-Native Substrate. Angew. Chem., Int. Ed. 2016, 55 (46), 14277–14280. 10.1002/anie.201606722. PubMed DOI

Sun H.; Zhao H.; Ang E. L. A Coupled Chlorinase–Fluorinase System with a High Efficiency of trans-Halogenation and a Shared Substrate Tolerance. Chem. Commun. 2018, 54 (68), 9458–9461. 10.1039/C8CC04436H. PubMed DOI PMC

Thomsen M.; Vogensen S. B.; Buchardt J.; Burkart M. D.; Clausen R. P. Chemoenzymatic Synthesis and in situ Application of S-Adenosyl-L-Methionine Analogs. Org. Biomol. Chem. 2013, 11 (43), 7606–7610. 10.1039/c3ob41702f. PubMed DOI PMC

Calero P.; Volke D. C.; Lowe P. T.; Gotfredsen C. H.; O’Hagan D.; Nikel P. I. A Fluoride-Responsive Genetic Circuit Enables in vivo Biofluorination in Engineered Pseudomonas putida. Nat. Commun. 2020, 11 (1), 5045.10.1038/s41467-020-18813-x. PubMed DOI PMC

Scherlach K.; Hertweck C. Mining and Unearthing Hidden Biosynthetic Potential. Nat. Commun. 2021, 12 (1), 3864.10.1038/s41467-021-24133-5. PubMed DOI PMC

Hon J.; Borko S.; Stourac J.; Prokop Z.; Zendulka J.; Bednar D.; Martinek T.; Damborský J. EnzymeMiner: Automated Mining of Soluble Enzymes with Diverse Structures, Catalytic Properties and Stabilities. Nucleic Acids Res. 2020, 48 (W1), W104–W109. 10.1093/nar/gkaa372. PubMed DOI PMC

Vanacek P.; Sebestova E.; Babkova P.; Bidmanova S.; Daniel L.; Dvořák P.; Stepankova V.; Chaloupkova R.; Brezovsky J.; Prokop Z.; Damborský J. Exploration of Enzyme Diversity by Integrating Bioinformatics with Expression Analysis and Biochemical Characterization. ACS Catal. 2018, 8 (3), 2402–2412. 10.1021/acscatal.7b03523. DOI

Kumar S.; Stecher G.; Li M.; Knyaz C.; Tamura K. Mega X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol. Biol. Evol. 2018, 35 (6), 1547–1549. 10.1093/molbev/msy096. PubMed DOI PMC

Huang F.; Haydock S. F.; Spiteller D.; Mironenko T.; Li T. L.; O’Hagan D.; Leadlay P. F.; Spencer J. B. The Gene Cluster for Fluorometabolite Biosynthesis in Streptomyces cattleya: A Thioesterase Confers Resistance to Fluoroacetyl-Coenzyme A. Chem. Biol. 2006, 13 (5), 475–484. 10.1016/j.chembiol.2006.02.014. PubMed DOI

McMurry J. L.; Chang M. C. Y. Fluorothreonyl-tRNA Deacylase Prevents Mistranslation in the Organofluorine Producer Streptomyces cattleya. Proc. Natl. Acad. Sci. U.S.A. 2017, 114 (45), 11920–11925. 10.1073/pnas.1711482114. PubMed DOI PMC

Ma L.; Bartholomé A.; Tong M. H.; Qin Z.; Yu Y.; Shepherd T.; Kyeremeh K.; Deng H.; O’Hagan D. Identification of a Fluorometabolite from Streptomyces sp. MA37: (2R3S4S)-5-Fluoro-2,3,4-Trihydroxypentanoic Acid. Chem. Sci. 2015, 6, 1414.10.1039/C4SC03540B. PubMed DOI PMC

Eustáquio A. S.; McGlinchey R. P.; Liu Y.; Hazzard C.; Beer L. L.; Florova G.; Alhamadsheh M. M.; Lechner A.; Kale A. J.; Kobayashi Y.; Reynolds K. A.; Moore B. S. Biosynthesis of the Salinosporamide A Polyketide Synthase Substrate Chloroethylmalonyl-Coenzyme A from S-Adenosyl-L-Methionine. Proc. Natl. Acad. Sci. U.S.A. 2009, 106 (30), 12295–12300. 10.1073/pnas.0901237106. PubMed DOI PMC

Zhao C.; Li P.; Deng Z.; Ou H. Y.; McGlinchey R. P.; O’Hagan D. Insights into Fluorometabolite Biosynthesis in Streptomyces cattleya DSM46488 through Genome Sequence and Knockout Mutants. Bioorg. Chem. 2012, 44, 1–7. 10.1016/j.bioorg.2012.06.002. PubMed DOI

Boël G.; Letso R.; Neely H.; Price W. N.; Wong K. H.; Su M.; Luff J.; Valecha M.; Everett J. K.; Acton T. B.; Xiao R.; Montelione G. T.; Aalberts D. P.; Hunt J. F. Codon Influence on Protein Expression in E. coli Correlates with mRNA Levels. Nature 2016, 529 (7586), 358–363. 10.1038/nature16509. PubMed DOI PMC

Kittilä T.; Calero P.; Fredslund F.; Lowe P. T.; Tezé D.; Nieto-Domínguez M.; O’Hagan D.; Nikel P. I.; Welner D. H. Oligomerization Engineering of the Fluorinase Enzyme Leads to an Active Trimer That Supports Synthesis of Fluorometabolites in vitro. Microb. Biotechnol. 2022, 15 (5), 1622–1632. 10.1111/1751-7915.14009. PubMed DOI PMC

Wirth N. T.; Nikel P. I. Combinatorial Pathway Balancing Provides Biosynthetic Access to 2-Fluoro-cis,cis-Muconate in Engineered Pseudomonas putida. Chem. Catal. 2021, 1 (6), 1234–1259. 10.1016/j.checat.2021.09.002. PubMed DOI PMC

Nikel P. I.; de Lorenzo V. Pseudomonas putida as a Functional chassis for Industrial Biocatalysis: From Native Biochemistry to Trans-Metabolism. Metab. Eng. 2018, 50, 142–155. 10.1016/j.ymben.2018.05.005. PubMed DOI

Volke D. C.; Calero P.; Nikel P. I. Pseudomonas putida. Trends Microbiol. 2020, 28 (6), 512–513. 10.1016/j.tim.2020.02.015. PubMed DOI

Sánchez-Pascuala A.; Fernández-Cabezón L.; de Lorenzo V.; Nikel P. I. Functional Implementation of a Linear Glycolysis for Sugar Catabolism in Pseudomonas putida. Metab. Eng. 2019, 54, 200–211. 10.1016/j.ymben.2019.04.005. PubMed DOI

Bitzenhofer N. L.; Kruse L.; Thies S.; Wynands B.; Lechtenberg T.; Rönitz J.; Kozaeva E.; Wirth N. T.; Eberlein C.; Jaeger K. E.; Nikel P. I.; Heipieper H. J.; Wierckx N.; Loeschcke A. Towards Robust Pseudomonas Cell Factories to Harbour Novel Biosynthetic Pathways. Essays Biochem. 2021, 65 (2), 319–336. 10.1042/EBC20200173. PubMed DOI PMC

Nejnovějších 20 citací...

Zobrazit více v
Medvik | PubMed

Engineering Dehalogenase Enzymes Using Variational Autoencoder-Generated Latent Spaces and Microfluidics

. 2025 Feb 24 ; 5 (2) : 838-850. [epub] 20250213

Machine Learning-Guided Protein Engineering

. 2023 Nov 03 ; 13 (21) : 13863-13895. [epub] 20231013

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...