Research Topics

For at least 3.5 billion years microorganisms have been evolving chemical strategies to capture chemical energy, to build complex structure from simple precursors, and to recycle almost any complex organic material. The corresponding enzymes, cascades and pathways are now being discovered by rapid genome sequencing and provide an immense repository of functional molecular systems that may be used to develop bio-based and sustainable technologies. In this context the Seebeck laboratory examines catalysed and uncatalyzed reactions that form or cleave carbon-sulfur bonds under physiologically relevant conditions. Our objectives are i) to decipher the mechanisms of these reactions, ii) to understand how the involved enzymes may have emerged, and iii) how enzymes can be changed, improved or integrated into artificial systems to create new biotechnology. Finally, we also strive to discover and develop new organic chemistry by emulating biochemical processes. This research program led to the following key achievements.

Oxygen-Dependent Ergothioneine Biosynthesis 

Ergothioneine is an emergent factor in the redox homeostasis of human cells, and is believed to serve as a vitamin-like antioxidant in bacteria, fungi plants and animals. We have discovered the enzymes that mediate O₂-dependent ergothioneine biosynthesis in bacteria and fungi.^1,2 Our findings have stimulated several companies to develop fermentative processes to produce ergothioneine for the food and health market. 

Discovery of the Oxygen-Independent Biosynthesis of Ergothioneine.

Broad scientific consensus has formed around the idea that ergothioneine primarily protects cells against reactive oxygen species. Our discovery that anaerobic bacteria also make ergothioneine, and that ergothioneine biosynthesis most likely emerged before the Great Oxygenation Event, suggest that this compound may also play important cellular roles under anoxic conditions. We have characterized the structure and catalytic mechanism of the enzyme that catalyzes O₂-independent C-S bond formation in this pathway. Bioinformatic analysis showed that this enzyme represents a diverse enzyme family that catalyze sulfurization of heterocycles, hinting at the existence of a heretofore undisclosed class of sulfur natural products.³ 

Novel Type of Non-heme Iron Enzyme

The central C-S bond forming reaction in O₂-dependent ergothioneine biosynthesis is catalysed by anovel type of non-heme iron enzyme – the sulfoxide synthases This enzyme class emerged from the fusion of two protein types that are not involved in iron-catalyzed O₂-activating enzymes. Our group has characterized the structure and catalytic mechanism of this enzyme class.⁴

1. Seebeck, F. P. In Vitro Reconstitution of Mycobacterial Ergothioneine Biosynthesis. J. Am. Chem. Soc., 2010, 132, 19, 6632–6633. 

2. Stampfli, A. R.; Blankenfeldt, W.; Seebeck, F. P. Structural Basis of Ergothioneine Biosynthesis. Curr. Opin. Struct. Biol., 2020, 65, 1-8. 

3. Stampfli, A. R.; Seebeck, F. P. The Catalytic Mechanism of Sulfoxide Synthase. Curr. Opin. Chem. Biol., 2020, 59, 111-118.

4.  Leisinger, F.; Burn, R.; Meury, M.; Lukat, P.; Seebeck, F. P. Structural and Mechanistic Basis for Anaerobic Ergothioneine Biosynthesis. J. Am. Chem. Soc., 2019, 141, 17, 6906–6914. 

The selenium-derivative of ergothioneine has been isolated from blue-fin tuna and from humans with a seafood-rich diet. Despite structural similarity to ergothioneine, selenoneine shows very different chemical behavior that may be exploited for therapeutic purpose. Our work provides synthetic access to this precocious compound paving the way for systematic pharmacological studies.⁵

5. Lim, D.; Gründemann, D.; Seebeck, F. P. Total Synthesis and Functional Characterization of Selenoneine. Angew. Chem. Int. Ed., 2019, 58,15026–15030.

Formylglycine-generating enzyme (FGE) is a novel type of mononuclear copper-dependent enzyme. It utilizes a copper-binding site that is unprecedented for O₂-activating enzymes.⁶ High-resolution crystal structures demonstrated that FGE binds O₂ in the active site juxtaposed but not coordinated to the catalytic Cu center.^7,8 We anticipate that this unusual structure will provide new inspiration for the design of molecular oxidation catalysts. In addition, our work establishes a molecular explanation for the inactivating effect of certain point mutations in FGE identified in patients with multiple sulfatase deficiency.

6. Knop, M.; Engi, P.; Lemnaru, R.; Seebeck, F. P. In Vitro Reconstitution of Formylglycine-Generating Enzymes Requires Copper(I). ChemBioChem, 2015, 16, 2147-2150.

7. Miarzlou, D. A.; Leisinger, F.; Joss, D.; Häussinger, D.; Seebeck, F. P. Structure of formylglycine-generating enzyme in complex with copper and a substrate reveals an acidic pocket for binding and activation of molecular oxygen. Chem. Sci., 2019, 10, 7049–7058. 

8. Leisinger, F.; Miarzlou, D. A.; Seebeck, F. P. Non-Coordinative Binding of O₂ at the Active Centerof a Copper-Dependent Enzyme. Angew.Chem.Int.Ed., 2021, 60, 6154–6159.

Methyltransferases catalyse regio-, chemo- and stereoselective addition of methyl groups to C-, N-, O-, P-, and S-nucleophiles in complex biomolecules. To harness such activities for preparative biocatalysis, we developed a protocol that allows the use of methyl iodide, instead of S-adenosylmethionine as the stoichiometric methyl donor. Since the first publication of this method in 2019, five different applications of this method have been published by four different groups in Angew. Chem. Int. Ed., demonstrating the versatility and flexibility of this approach.^9-13

9. Liao, C.; Seebeck, F. P. S-adenosylhomocysteine as a methyl transfer catalyst in biocatalytic methylation reactions. Nat. Cat., 2019, 2, 696-701. 

10. Liao, C.; Seebeck, F. P. Aysmmetric β-Methylation of L- and D-α-Amino Acids by a Self-Contained Enzyme Cascade.Angew. Chem. Int. Ed., 2020, 59, 7184-7187.

11. Beliaeva, M. A.; Burn, R.; Lim, D.; Seebeck, F. P. In Vitro Production of Ergothioneine Isotopologues. Angew. Chem. Int. Ed., 2021, 60, 5209-5212. 

12. Tang, Q.; Grathwol, C. W.; Aslan-Üzel, A. S.; Wu, S.; Link, A.; Pavlidis, I. V.; Badenhorst, C. P. S.; Bornscheuer, U. T. Directed Evolution of a Halide Methyltransferase Enables Biocatalytic Synthesis of Diverse SAM Analogs.Angew. Chem. Int. Ed., 2021, 60, 1524-1527. 

13. Schneider, P.; Henßen, B.; Paschold, B.; Chapple, B. P.; Schatton, M.; Seebeck, F. P.; Classen, T.; Pietruszka, J. Biocatalytic C3-Indole Methylation - A Useful Tool for the Natural-Product-Inspired Stereoselective Synthesis of Pyrroloindoles. Angew. Chem. Int. Ed., 2021, 60, 23412-23418.