Single-step Replacement of an Unreactive C-H Bond by a C-S Bond Using Polysulfide as the Direct Sulfur Source in Anaerobic Ergothioneine Biosynthesis

Heterologous and High Production of Ergothioneine in Bacillus licheniformis by Using Genes from Anaerobic Bacteria

PURPOSE

This study aimed to utilize genetically engineered Bacillus licheniformis for the production of ergothioneine (EGT). Given the value of EGT and the application of Bacillus licheniformis in enzyme preparation production, we cloned the key enzymes (EanA and EanB) from Chlorbium limicola. Through gene alignment, new ergothioneine synthase genes (EanAN and EanBN) were identified and then expressed in Bacillus licheniformis to construct strains. Additionally, we investigated the factors influencing the yield of EGT and made a comparison with Escherichia coli.

METHODS

The relevant genes were cloned and transferred into Bacillus licheniformis. Fermentation experiments were conducted under different conditions for yield analysis, and the stability of this bacterium was also evaluated simultaneously.

RESULTS

The constructed strains were capable of producing EGT. Specifically, the yield of the EanANBN strain reached (643.8 ± 135) mg/L, and its stability was suitable for continuous production.

CONCLUSIONS

Genetically engineered Bacillus licheniformis demonstrates potential in the industrial-scale production of EGT. Compared with Escherichia coli, it has advantages, thus opening up new possibilities for the application and market supply of EGT.

The Catalytic Mechanism of Key Enzymes Involved in the Synthesis of Ergothioneine in Lentinula edodes

C-S lyase is a crucial enzyme responsible for the formation of sulfur-containing flavor compounds in Lentinula edodes. We investigated the involvement of C-S lyase in the synthesis of ergothioneine (EGT) in L. edodes, a high-producing edible mushroom. Through experimental and computational approaches, we identified Lecsl2, a C-S lyase, as a key enzyme involved in EGT synthesis in L. edodes. We characterized the enzymatic catalytic mechanism of Egt1 and Egt2, the two enzymes primarily catalyzing EGT synthesis in fungi. The results showed that Egt1 interacted with His, SAM, and Cys to form the intermediate product Her-sul, while Egt2, a PLP-dependent enzyme, cleaved the C-S bond on Her-sul to produce EGT. However, our findings suggested that Egt2 in L. edodes might not form a covalent bond with PLP, unlike the previously reported catalytic mechanism of Egt2 involving covalent catalysis. The study provided new insights into the synthesis pathway of EGT in L. edodes and highlighted the need for further investigation into the catalytic mechanism of Egt2 in this species.

The structural and functional analysis of mycobacteria cysteine desulfurase-loaded encapsulin

Encapsulin nanocompartments loaded with dedicated cargo proteins via unique targeting peptides, play a key role in stress resistance, iron storage and natural product biosynthesis. Mmp1 and cysteine desulfurase (Enc-CD) have been identified as the most abundant representatives of family 2 encapsulin systems. However, the molecular assembly, catalytic mechanism, and physiological functions of the Mmp1 encapsulin system have not been studied in detail. Here we isolate and characterize an Enc-CD-loaded Mmp1 encapsulin system from Mycobacterium smegmatis mc2155. The cryo-EM structure of the Mmp1 encapsulin and the crystal structure of the naked cargo Enc-CD have been determined. The structure shows that the Mmp1 protomer assembles two conformation models, the icosahedron (T = 1) and homodecamer, with the resolution of 2.60 Å and 2.69 Å. The Enc-CD at 2.10 Å resolution is dimeric and loaded into the Mmp1 (T = 1) encapsulin through the N-terminal long disordered region. Mmp1 encapsulin protects Enc-CD against oxidation as well as to maintain structural stability. These studies provide new insights into the mechanism by which Enc-CD-loaded encapsulin stores sulfur and provides a framework for discovery of new anti-mycobacterial therapeutics.

Ergothioneine and its congeners: anti-ageing mechanisms and pharmacophore biosynthesis

Ergothioneine, Ovothiol, and Selenoneine are sulfur/selenium-containing histidine-derived natural products widely distributed across different organisms. They exhibit significant antioxidant properties, making them as potential lead compounds for promoting health. Increasing evidence suggests that Ergothioneine is positively correlated with healthy ageing and longevity. The mechanisms underlying Ergothioneine's regulation of the ageing process at cellular and molecular levels are beginning to be understood. In this review, we provide an in-depth and extensive coverage of the anti-ageing studies on Ergothioneine and discuss its possible intracellular targeting pathways. In addition, we highlight the recent efforts in elucidating the biosynthetic details for Ergothioneine, Ovothiol, and Selenoneine, with a particular focus on the study of their pharmacophore-forming enzymology.

Biochemical and Structural Characterization of OvoATh2: A Mononuclear Nonheme Iron Enzyme from Hydrogenimonas thermophila for Ovothiol Biosynthesis

Ovothiol A and ergothioneine are thiol-histidine derivatives with sulfur substitutions at the δ-carbon or ε-carbon of the l-histidine imidazole ring, respectively. Both ovothiol A and ergothioneine have protective effects on many aging-related diseases, and the sulfur substitution plays a key role in determining their chemical and biological properties, while factors governing sulfur incorporation regioselectivities in ovothiol and ergothioneine biosynthesis in the corresponding enzymes (OvoA, Egt1, or EgtB) are not yet known. In this study, we have successfully obtained the first OvoA crystal structure, which provides critical information to explain their C-S bond formation regioselectivity. Furthermore, OvoATh2 exhibits several additional activities: (1) ergothioneine sulfoxide synthase activity akin to Egt1 in ergothioneine biosynthesis; (2) cysteine dioxygenase activity using l-cysteine and l-histidine analogues as substrates; (3) cysteine dioxygenase activity upon mutation of an active site tyrosine residue (Y406). The structural insights and diverse chemistries demonstrated by OvoATh2 pave the way for future comprehensive structure-function correlation studies.

An S=1 Iron(IV) Intermediate Revealed in a Non-Heme Iron Enzyme-Catalyzed Oxidative C-S Bond Formation

Ergothioneine (ESH) and ovothiol A (OSHA) are two natural thiol-histidine derivatives. ESH has been implicated as a longevity vitamin and OSHA inhibits the proliferation of hepatocarcinoma. The key biosynthetic step of ESH and OSHA in the aerobic pathways is the O2 -dependent C-S bond formation catalyzed by non-heme iron enzymes (e.g., OvoA in ovothiol biosynthesis), but due to the lack of identification of key reactive intermediate the mechanism of this novel reaction is unresolved. In this study, we report the identification and characterization of a kinetically competent S=1 iron(IV) intermediate supported by a four-histidine ligand environment (three from the protein residues and one from the substrate) in enabling C-S bond formation in OvoA from Methyloversatilis thermotoleran, which represents the first experimentally observed intermediate spin iron(IV) species in non-heme iron enzymes. Results reported in this study thus set the stage to further dissect the mechanism of enzymatic oxidative C-S bond formation in the OSHA biosynthesis pathway. They also afford new opportunities to study the structure-function relationship of high-valent iron intermediates supported by a histidine rich ligand environment.

The many facets of sulfur incorporation in natural product biosynthesis

Sulfur-containing natural products (S-containing NPs) exhibit diverse chemical structures and biosynthetic machineries. Unraveling the intricate chemistry of S-incorporation requires innovative and multidisciplinary approaches. In this review, we surveyed the landscape of S-containing NP biosynthetic machineries, classified the S-incorporation chemistry into four distinct classes, and highlighted each of the four classes with representative examples from recent studies. All highlighted chemistry has been correlated to the genes encoding the biosynthetic machineries of the S-containing NPs, which open new opportunities to discover S-containing NPs through genome mining. These examples should inspire the community to explore uncharted territories in NP research, promoting further advancements in both novel S-containing NP discovery and S-incorporation chemistry.

How nature incorporates sulfur and selenium into bioactive natural products

Living organisms have evolved various strategies to incorporate sulfur and selenium into bioactive natural products. These chalcogen-containing compounds serve important and diverse biological functions for their producers and many of them are essential medicines against infectious diseases and cancer. We review recent advances in the biosynthesis of some sulfur/selenium-containing natural products with a focus on the formation or cleavage of C-S/C-Se bonds. We highlight unusual enzymes that catalyze these transformations, describe their proposed mechanisms, and discuss how understanding these enzymes may facilitate the discovery and synthesis of novel natural products containing sulfur or selenium.

How to Stabilize Carbenes in Enzyme Active Sites without Metal Ions

Carbenes are highly reactive compounds with unique value to synthetic chemistry. However, a small number of natural enzymes have been shown to utilize carbene chemistry, and artificial enzymes engineered with directed evolution required transition metal ions to stabilize the carbene intermediates. To facilitate the design of broader classes of enzymes that can take advantage of the rich carbene chemistry, it is thus important to better understand how to stabilize carbene species in enzyme active sites without metal ions. Motivated by our recent studies of the anaerobic ergothioneine biosynthesis enzyme EanB, we examine carbene-protein interaction with both cluster models and QM/MM simulations. The cluster calculations find that an N-heterocyclic carbene interacts strongly with polar and positively charged protein motifs. In particular, the interaction between a guanidinium group and carbene is as strong as ∼30 kcal/mol, making arginine a great choice for the preferential stabilization of carbenes. We also compare the WT EanB and its mutant in which the key tyrosine was replaced by a non-natural analogue (F2Tyr) using DFTB3/MM simulations. The calculations suggest that the carbene intermediate in the F2Tyr mutant is more stable than that in the WT enzyme by ∼3.5 kcal/mol, due to active site rearrangements that enable a nearby arginine to better stabilize the carbene in the mutant. Overall, the current work lays the foundation for the pursuit of enzyme designs that can take advantage of the unique chemistry offered by carbenes without the requirement of metal ions.

Sulfur incorporation into biomolecules: recent advances

Sulfur is an essential element for a variety of cellular constituents in all living organisms and adds considerable functionality to a wide range of biomolecules. The pathways for incorporating sulfur into central metabolites of the cell such as cysteine, methionine, cystathionine, and homocysteine have long been established. Furthermore, the importance of persulfide intermediates during the biosynthesis of thionucleotide-containing tRNAs, iron-sulfur clusters, thiamin diphosphate, and the molybdenum cofactor are well known. This review briefly surveys these topics while emphasizing more recent aspects of sulfur metabolism that involve unconventional biosynthetic pathways. Sacrificial sulfur transfers from protein cysteinyl side chains to precursors of thiamin and the nickel-pincer nucleotide (NPN) cofactor are described. Newer aspects of synthesis for lipoic acid, biotin, and other compounds are summarized, focusing on the requisite iron-sulfur cluster destruction. Sulfur transfers by using a noncore sulfide ligand bound to a [4Fe-4S] cluster are highlighted for generating certain thioamides and for alternative biosynthetic pathways of thionucleotides and the NPN cofactor. Thioamide formation by activating an amide oxygen atom via phosphorylation also is illustrated. The discussion of these topics stresses the chemical reaction mechanisms of the transformations and generally avoids comments on the gene/protein nomenclature or the sources of the enzymes. This work sets the stage for future efforts to decipher the diverse mechanisms of sulfur incorporation into biological molecules.

Discovery and Characterization of the Metallopterin-Dependent Ergothioneine Synthase from Caldithrix abyssi

Ergothioneine is a histidine derivative with a 2-mercaptoimidazole side chain and a trimethylated α-amino group. Although the physiological function of this natural product is not yet understood, the facts that many bacteria, some archaea, and most fungi produce ergothioneine and that plants and animals have specific mechanisms to absorb and distribute ergothioneine in specific tissues suggest a fundamental role in cellular life. The observation that ergothioneine biosynthesis has emerged multiple times in molecular evolution points to the same conclusion. Aerobic bacteria and fungi attach sulfur to the imidazole ring of trimethylhistidine via an O₂-dependent reaction that is catalyzed by a mononuclear non-heme iron enzyme. Green sulfur bacteria and archaea use a rhodanese-like sulfur transferase to attach sulfur via oxidative polar substitution. In this report, we describe a third unrelated class of enzymes that catalyze sulfur transfer in ergothioneine production. The metallopterin-dependent ergothioneine synthase from Caldithrix abyssi contains an N-terminal module that is related to the tungsten-dependent acetylene hydratase and a C-terminal domain that is a functional cysteine desulfurase. The two modules cooperate to transfer sulfur from cysteine onto trimethylhistidine. Inactivation of the C-terminal desulfurase blocks ergothioneine production but maintains the ability of the metallopterin to exchange sulfur between ergothioneine and trimethylhistidine. Homologous bifunctional enzymes are encoded exclusively in anaerobic bacterial and archaeal species.

Ergothioneine, Ovothiol A, and Selenoneine-Histidine-Derived, Biologically Significant, Trace Global Alkaloids

The history, chemistry, biology, and biosynthesis of the globally occurring histidine-derived alkaloids ergothioneine (10), ovothiol A (11), and selenoneine (12) are reviewed comparatively and their significance to human well-being is discussed.

OvoAMtht from Methyloversatilis thermotolerans ovothiol biosynthesis is a bifunction enzyme: thiol oxygenase and sulfoxide synthase activities

Mononuclear non-heme iron enzymes are a large class of enzymes catalyzing a wide-range of reactions. In this work, we report that a non-heme iron enzyme in Methyloversatilis thermotolerans, OvoA_Mtht, has two different activities, as a thiol oxygenase and a sulfoxide synthase. When cysteine is presented as the only substrate, OvoA_Mtht is a thiol oxygenase. In the presence of both histidine and cysteine as substrates, OvoA_Mtht catalyzes the oxidative coupling between histidine and cysteine (a sulfoxide synthase). Additionally, we demonstrate that both substrates and the active site iron's secondary coordination shell residues exert exquisite control over the dual activities of OvoA_Mtht (sulfoxide synthase vs. thiol oxygenase activities). OvoA_Mtht is an excellent system for future detailed mechanistic investigation on how metal ligands and secondary coordination shell residues fine-tune the iron-center electronic properties to achieve different reactivities.

Modulation of OvoA_Mtht's dual activities: sulfoxide synthase and thiol oxygenase.

Metabolic adaptations to marine environments: molecular diversity and evolution of ovothiol biosynthesis in Bacteria

Ovothiols are sulfur-containing amino acids synthesized by marine invertebrates, protozoans, and bacteria. They act as pleiotropic molecules in signaling and protection against oxidative stress. The discovery of ovothiol biosynthetic enzymes, sulfoxide synthase OvoA and β-lyase OvoB, paves the way for a systematic investigation of ovothiol distribution and molecular diversification in nature. In this work, we conducted genomic and metagenomics data mining to investigate the distribution and diversification of ovothiol biosynthetic enzymes in Bacteria. We identified the bacteria endowed with this secondary metabolic pathway, described their taxonomy, habitat and biotic interactions in order to provide insight into their adaptation to specific environments. We report that OvoA and OvoB are mostly encountered in marine aerobic Proteobacteria, some of them establishing symbiotic or parasitic relationships with other organisms. We identified a horizontal gene transfer event of OvoB from Bacteroidetes living in symbiosis with Hydrozoa. Our search within the Ocean Gene Atlas revealed the occurrence of ovothiol biosynthetic genes in Proteobacteria living in a wide range of pelagic and highly oxygenated environments. Finally, we tracked the evolutionary history of ovothiol biosynthesis from marine bacteria to unicellular eukaryotes and metazoans. Our analysis provides new conceptual elements to unravel the evolutionary and ecological significance of ovothiol biosynthesis.

Implications for an imidazol-2-yl carbene intermediate in the rhodanase-catalyzed C-S bond formation reaction of anaerobic ergothioneine biosynthesis

In the anaerobic ergothioneine biosynthetic pathway, a rhodanese domain containing enzyme (EanB) activates tne hercynine's sp² ε-C-H Dona ana replaces it with a C-S bond to produce ergothioneine. The key intermediate for this trans-sulfuration reaction is the Cys412 persulfide. Substitution of the EanB-Cys412 persulfide with a Cys412 perselenide does not yield the selenium analog of ergothioneine, selenoneine. However, in deuterated buffer, the perselenide-modified EanB catalyzes the deuterium exchange between hercynine's sp² ε-C-H bond and D₂O. Results from QM/MM calculations suggest that the reaction involves a carbene intermediate and that Tyr353 plays a key role. We hypothesize that modulating the pK_a of Tyr353 will affect the deuterium-exchange rate. Indeed, the 3,5-difluoro tyrosine containing EanB catalyzes the deuterium exchange reaction with k _ex of ~10-fold greater than the wild-type EanB (EanB_WT). With regards to potential mechanisms, these results support the involvement of a carbene intermediate in EanB-catalysis, rendering EanB as one of the few carbene-intermediate involving enzymatic systems.

In Vitro Production of Ergothioneine Isotopologues

Ergothioneine is an emerging component of the redox homeostasis system in human cells and in microbial pathogens, such as Mycobacterium tuberculosis and Burkholderia pseudomallei. The synthesis of stable isotope-labeled ergothioneine derivatives may provide important tools for deciphering the distribution, function, and metabolism of this compound in vivo. We describe a general protocol for the production of ergothioneine isotopologues with programmable ² H, ¹⁵ N, ¹³ C, ³⁴ S, and ³³ S isotope labeling patterns. This enzyme-based approach makes efficient use of commercial isotope reagents and is also directly applicable to the synthesis of radio-isotopologues.