Biosynthesis of thiocarboxylic acid-containing natural products

Abstract

Thiocarboxylic acid-containing natural products are rare and their biosynthesis and biological significance remain unknown. Thioplatensimycin (thioPTM) and thioplatencin (thioPTN), thiocarboxylic acid congeners of the antibacterial natural products platensimycin (PTM) and platencin (PTN), were recently discovered. Here we report the biosynthetic origin of the thiocarboxylic acid moiety in thioPTM and thioPTN. We identify a thioacid cassette encoding two proteins, PtmA3 and PtmU4, responsible for carboxylate activation by coenzyme A and sulfur transfer, respectively. ThioPTM and thioPTN bind tightly to β-ketoacyl-ACP synthase II (FabF) and retain strong antibacterial activities. Density functional theory calculations of binding and solvation free energies suggest thioPTM and thioPTN bind to FabF more favorably than PTM and PTN. Additionally, thioacid cassettes are prevalent in the genomes of bacteria, implicating that thiocarboxylic acid-containing natural products are underappreciated. These results suggest that thiocarboxylic acid, as an alternative pharmacophore, and thiocarboxylic acid-containing natural products may be considered for future drug discovery.

Characterization and Crystal Structure of a Nonheme Diiron Monooxygenase Involved in Platensimycin and Platencin Biosynthesis

“…14 The timing of the C-5 hydroxylation was proposed to happen immediately following CoA thioesterification of the ketolide moieties and just prior to A-ring cleavage. 11 If correct, the fermentation profile of the relevant mutant would be expected to be similar to that of the ΔptmA1 mutant as a result of the hydrolysis of CoA-linked intermediates 18 (i.e., fully abolishing PTM (1), PTN (2), thioPTM (3), and thioPTN (4) production 19 and instead accumulating precursors 5 and 9 as well as 13, a precursor of 5 (Figure 2A)). Upon HPLC analysis, the metabolite profile of the ΔptmU3 mutant matched this expectation (Figures 2B and S3), suggesting PtmU3 as the candidate for C-5 hydroxylation.…”

Cryptic Sulfur Incorporation in Thioangucycline Biosynthesis

“…CB00072 and the heterologous host S. albus J1074 (Table S10), so three homologues were selected to mediate the conversion of 9 to TACs using thiosulfate (Figure S34). The three rhodanese enzymes, termed J‐MoeZ (a MoeZ homologue), [2b, 22b] Rhd‐1 (a RhdA homologue), [29] and Rhd‐2 (a GlpE homologue), [30] were produced in E. coli and purified (Figure S35). When 9 was incubated with thiosulfate in the absence of any enzymes, only the thiosulfate adduct 16 was observed, but upon addition of a rhodanese homologue, conversion of 9 to 1 and 2 was observed (≈15 %, Figure 6 B).…”

“…The conversion of thiosulfate to H 2 S has been demonstrated in cell‐free E. coli extract, [27] and the reduction of thiosulfate to H 2 S also has been well established and reviewed [28] . Recent work has also shown rhodanese homologues are involved in the sulfur incorporation in BE‐7585A and thioplatensimycin/thioplatencin [2b, 22b] . Multiple rhodanese gene homologues were identified within the genomes of the native host S .…”

Biosynthesis of Chuangxinmycin Featuring a Deubiquitinase‐like Sulfurtransferase

“…We originally hypothesized that the decapeptide might be cleaved by the predicted JAMM/MPN + protein Cxm3 to expose the functional GG‐tail (Figure 1 A). [5b, 7a,b] However, the co‐incubation of Cxm3 and Cxm4 (Figures S3 and S4) did not give any detectable Cxm4‐GG‐COO − (Figure S5). Whole genome scanning of A. tsinanensis located another putative JAMM/MPN + family SCP peptidase encoding gene cxmJ (named after JAMM/MPN + ) outside the cxm cluster (Figure S6).…”

“…The JAB1/MPN/MOV34 (JAMM/MPN + ) proteins, a superfamily of metallopeptidases ubiquitously distributed in eukaryotes, archaea and bacteria, [6] have been found in bacteria to serve as SCP peptidases to cleave the C ‐terminal peptide, thereby exposing the GG‐tail for the subsequent sulfurization (Figure 1 A). [5b, 7] In eukaryotic and archaeal organisms, the JAMM/MPN + proteins generally act as deubiquitinases (DUBs) by recognizing and cleaving the ubiquitin (UB) motif, which is evolutionarily related to and structurally similar with SCP, of a ubiquitinated protein (Figure 1 B). [6, 8]…”