Living GenoChemetics by hyphenating synthetic biology and synthetic chemistry in vivo

Marrying synthetic biology with synthetic chemistry provides a powerful approach toward natural product diversification, combining the best of both worlds: expediency and synthetic capability of biogenic pathways and chemical diversity enabled by organic synthesis. Biosynthetic pathway engineering can be employed to insert a chemically orthogonal tag into a complex natural scaffold affording the possibility of site-selective modification without employing protecting group strategies. Here we show that, by installing a sufficiently reactive handle (e.g., a C–Br bond) and developing compatible mild aqueous chemistries, synchronous biosynthesis of the tagged metabolite and its subsequent chemical modification in living culture can be achieved. This approach can potentially enable many new applications: for example, assay of directed evolution of enzymes catalyzing halo-metabolite biosynthesis in living cells or generating and following the fate of tagged metabolites and biomolecules in living systems. We report synthetic biological access to new-to-nature bromo-metabolites and the concomitant biorthogonal cross-coupling of halo-metabolites in living culture

Assay for the Enantiomeric Analysis of [²H₁]-Fluoroacetic Acid: Insight into the Stereochemical Course of Fluorination during Fluorometabolite Biosynthesis in <em>Streptomyces cattleya</em>

A sensitive method for the configurational analysis of (R)- and (S)-[H-2(1)]-fluoroacetate has been developed using H-2{H-1}-NMR in a chiral liquid crystalline solvent. This has enabled biosynthetic experiments to be conducted which reveal stereochemical details on biological fluorination occurring during the biosynthesis of fluoroacetate and 4-fluorothreonine in the bacterium Streptomyces cattleya. In particular, feeding experiments to S. cattleya with isotopically labeled (1R, 2R)- and (1S, 2R)-[1-H-2(1)]-glycerol 3d and 3e and [2,3-H-2(4)]-Succinate 4a gave rise to samples of enantiomerically enriched [2-H-2(1)]-fluoroacetates 1a. The predominant enantiomer resulting from each experiment suggests that the stereochemical course of biological fluorination takes place with an overall retention of configuration between a glycolytic intermediate and fluoroacetate 1. Consequently, this outcome suggests that the stereochemical course of the recently identified fluorinase enzyme which mediates a reaction between fluoride ion and S-adenosyl-L-methionine (SAM), occurs with an inversion of configuration.</p

Assay for the Enantiomeric Analysis of [²H₁]-Fluoroacetic Acid: Insight into the Stereochemical Course of Fluorination during Fluorometabolite Biosynthesis in <em>Streptomyces cattleya</em>

A sensitive method for the configurational analysis of (R)- and (S)-[H-2(1)]-fluoroacetate has been developed using H-2{H-1}-NMR in a chiral liquid crystalline solvent. This has enabled biosynthetic experiments to be conducted which reveal stereochemical details on biological fluorination occurring during the biosynthesis of fluoroacetate and 4-fluorothreonine in the bacterium Streptomyces cattleya. In particular, feeding experiments to S. cattleya with isotopically labeled (1R, 2R)- and (1S, 2R)-[1-H-2(1)]-glycerol 3d and 3e and [2,3-H-2(4)]-Succinate 4a gave rise to samples of enantiomerically enriched [2-H-2(1)]-fluoroacetates 1a. The predominant enantiomer resulting from each experiment suggests that the stereochemical course of biological fluorination takes place with an overall retention of configuration between a glycolytic intermediate and fluoroacetate 1. Consequently, this outcome suggests that the stereochemical course of the recently identified fluorinase enzyme which mediates a reaction between fluoride ion and S-adenosyl-L-methionine (SAM), occurs with an inversion of configuration.</p

Biogenesis of the Unique 4′,5′-Dehydronucleoside of the Uridyl Peptide Antibiotic Pacidamycin

The pacidamycins belong to a class of antimicrobial nucleoside antibiotics that act by inhibiting the clinically unexploited target translocase I, a key enzyme in peptidoglycan assembly. As with other nucleoside antibiotics, the pacidamycin 4',5'-dehydronucleoside portion is an essential pharmacophore. Here we show that the biosynthesis of the pacidamycin nucleoside in Streptomyces coeruleorubidus proceeds through three steps from uridine. The transformations involve oxidation of the 5'-alcohol by Pac11, transamination of the resulting aldehyde by Pac5, and dehydration by the Cupin-domain protein Pac13.</p

Halogenases: powerful tools for biocatalysis (mechanisms applications and scope)

The market sizes for halogenated compounds are huge; in contrast to synthetic chemical alternatives, halogenating enzymes afford the highly regiospecific incorporation of a halogen into an organic molecule, there is therefore great opportunity for the development of industrially relevant halogenases. Here we overview the main classes of halogenases, the mechanisms through which they operate and their structures. We also look at recent applications of halogenases in areas such as metabolite engineering and late stage CH activation. Opportunities and bottlenecks are discussed

Halogenases: structures and functions

Over 5000 halogenated natural products have been reported so far, many of these arising from the marine environment. The introduction of a halogen into a molecule can significantly impact its bioavailability and bioactivity. More recently enzymatic halogenation has been used to enable late stage functionalisation through site-selective halogenation and cross-coupling. Halogenases are becoming increasingly valued tools. This review outlines the various classes of halogenases that have been discovered, and examines these from both a structural and a mechanistic perspective, reflecting upon the many recent advances in halogenase discovery