Convergent and divergent biosynthetic strategies towards phosphonic acid natural products

Abstract

The phosphonate class of natural products have received significant interests in the post-genomic era due to the relative ease with which their biosynthetic genes may be identified and the resultant final products be characterized. Recent large-scale studies of the elucidation and distributions of phosphonate pathways have provided a robust landscape for deciphering the underlying biosynthetic logic. A recurrent theme in phosphonate biosynthetic pathways is the interweaving of enzymatic reactions across different routes, which enables diversification to elaborate chemically novel scaffolds. Here, we provide a few vignettes of how Nature has utilized both convergent and divergent biosynthetic strategies to compile pathways for production of novel phosphonates. These examples illustrate how common intermediates may either be generated or intercepted to diversify chemical scaffolds and provides a starting point for both biotechnological and synthetic biological applications towards new phosphonates by similar combinatorial approaches.

Figure 1.

(A) Chemical structures of bioactive phosphonate (Pn) natural products. (B) Common intermediates in the biosynthesis of the compounds in panel A and other Pns. Note the chemical similarity between the various intermediates, which may help in their deployment across different biosynthetic pathways.

Figure 2.

Core biosynthetic pathways for Pn NPs. Early branchpoints immediately diverge from PnPy and are in blue. Intermediary steps from PnAA are in orange and 2HEPn in purple. Enzymes catalyzing transformations are accordingly colored. Pn NPs produced from each pathway are boxed. TA (transaminase); Rd (reductase); Fe/2OG-DO (non-heme iron and 2-oxoglutarate- dependent dioxygenase); MPnS (methylphosphonate synthase); HEPD (2-hydroxyethylphosphonate dioxygenase).

Figure 3.

The biosynthetic pathway for valinophos extends from PnLac. A series of valinyl-dipeptides are esterified to DHPPA, via ATP-Grasp ligase enzymes. Both PnLac (blue) and DHPPA (green) as branchpoints for Pn NPs for cryptic BGCs encoded among diverse bacteria.

Figure 4.

The biosynthetic pathway for argolaphos extends from HMP (purple) to AMP (pink). AglA, a member of the YqcI/YqcG superfamily, was identified as a heme monooxygenase that catalyzed Nε-hydroxyarginine formation. Bioinformatic analyses suggest HMP and AMP as branchpoints for Pn NPs among cryptic BGCs.

Figure 5.

(A) Biosynthetic pathways for fosfomycin production in pseudomonads (top pathway) and in streptomycetes (bottom pathway). Both pathways diverge at the common intermediate phosphonopyruvate (PnPy) and then reconverge through the production of (S)-2-HPP. In both pathways, the mononuclear nonheme-iron dependent peroxidase HppE to produce fosfomycin. (B) Proposed mechanism for epoxidation catalyzed by HppE using hydrogen peroxide as a cofactor to produce fosfomycin. Heterolysis of the O-O bond directs formation of the Fe(IV)=O (ferryl) intermediate obviating the need for an external reductase. Following hydrogen atom abstraction at C1, electron transfer from the substrate to the ferryl followed by ring closure. (C) Proposed mechanism for oxidative decarboxylation as carried out by the di-iron enzyme PsfC. Hydrogen atom abstraction at C3 by the ferryl generates a C radical which can undergo decarboxylation by either (top pathway) direct homolytic decarboxylation, or (bottom pathway) electron transfer from the substrate radical to the ferryl, followed by heterolytic decarboxylation.

Figure 6.

(A) Divergent routes direct the formation of the structurally related fosmidomycins FR900098 (from Streptomyces rubellomurinus) and dehydrofosmidomycin (from Streptomyces lavendulae). The pathways diverge at PnPy through different intermediates, similar to those in the two divergent fosfomycin pathways. The dehydrofosmidomycin pathways involves an unusual rearrangement catalyzed by the nonheme-iron 2OG-dependent enzyme DfmD (B) Proposed two step mechanism for the DfmD-catalyzed homologation towards the production of methyldehydrofosmidomycin from trimethyl-AEP. In the first step, one equivalence of 2OG is consumed to generate a ferryl that triggers hydrogen atom abstraction to generate the vinyl intermediate. The stereochemistry of the C=C bond is drawn as cis for simplicity, but this has yet to be determined. The second step, hydrogen atom abstraction by a new ferryl species enables ring formation en route to the chain elongated product.