Biology subjects

de los Santos, E. L. C.

Publications and source records attributed to de los Santos, E. L. C..

4 recordsLinked to original sources

bioRxiv2025

Charting the biosynthetic landscape of hybrid polyketide-nonribosomal peptide-specialized lipids

Polyunsaturated fatty acid (PUFA) synthase-like enzymes are best known for their role in membrane lipid biosynthesis in marine bacteria, but have also been repurposed for the assembly of specialized lipid metabolites with unique biological functions. Here, we illuminate their broader biosynthetic potential by charting the unexplored landscape of hybrid peptide-polyketide-specialized lipid biosynthesis in bacteria. Using a targeted genome mining strategy, we identified more than 60 biosynthetic gene clusters that combine PUFA synthase-like, polyketide synthase (PKS), and nonribosomal peptide synthetase (NRPS) enzymes across diverse bacterial lineages. Comparative analysis revealed extensive diversification of these triple hybrid pathways through gene fusion, domain reshuffling and recruitment of accessory enzymes. We further expand the known repertoire of peptide-polyketide-specialized lipid hybrids by identifying the chitinimines, a new family of amphiphilic metabolites produced by Chitinimonas koreensis featuring a C22 polyunsaturated lipid chain conjugated to a cyclic peptide-polyketide and a pyruvate-derived cyclic acetal moiety. The chitinimines exhibit surfactant properties, as well as moderate antibacterial activity against Gram-positive bacteria and contribute to a growth-promoting interaction between C. koreensis and Salmonella spp. Together, these findings demonstrate that PUFA synthase-like systems are far more versatile than previously appreciated, playing a key role in combinatorial biosynthetic innovation and serving as a rich, untapped source of chemically and functionally diverse specialized lipids.

microbiology↗

bioRxiv2025

An O-acetylated derivative of piericidin A1 produced by Kitasatospora sp. A2-31 has potent activity against the cacao mirid bug, Helopeltis bakeri Poppius

There is an increasing demand for novel biopesticides to protect agricultural products and improve yields. To address this need, extracts from a library of Actinomycetes collected in the Philippines were evaluated against the cacao mirid bug, Helopeltis bakeri Poppius. Analysis of an active ethyl acetate extract from Kitasatospora sp. A2-31 led to the identification of a novel metabolite acetylpiericidin A1 (3) along with the known natural products piericidin A1 (1), piericidin A5 (2), chromomycin A2 (4), chromomycin A3 (5), and olivomycin A (6). Acetylpiericidin A1 demonstrated 100 % mortality against H. bakeri, while other metabolites exhibited either weak or no activity. Whole genome sequencing followed by bioinformatics analysis identified a gene downstream of the piericidin biosynthetic gene cluster that encodes a putative acetyltransferase proposed to catalyze acetylation of the C10 hydroxyl group of piericidin A1. The involvement of this gene in acetylpiericidin A1 biosynthesis was confirmed by (i) introducing an additional copy under the control of the ermE* promoter into Kitasatospora sp. A2-31, resulting in elevated production levels and (ii) through an in vitro enzymatic assay of the corresponding purified recombinant enzyme.

microbiology↗

bioRxiv2025

Molecular basis for depsipeptide HDAC inhibitor combinatorial biosynthesis

Polyketides and nonribosomal peptides are important natural product classes with wide-ranging medical and agricultural applications. The analogous enzymatic logic employed by bacterial modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) enables the assembly of hybrid products. One important group of polyketide-nonribosomal peptide hybrids is exemplified by the HDAC-targeting drug romidepsin. This group is assembled by combinatorial biosynthesis involving fusion of a conserved Zn2+-binding pharmacophore to a variable peptide-based cap. Here, we use gene proximity searching to identify the FR-901375 biosynthetic gene cluster in Pseudomonas chlororaphis subsp. piscium DSM 21509. Comparison of the PKS-NRPS encoded by this gene cluster with those assembling related depsipeptide HDAC inhibitors suggests a novel subunit docking modality enables interaction between the conserved pharmacophore and variable cap biosynthetic machineries. This hypothesis was validated using crosstalk assays, mutagenesis, AlphaFold predictions, and carbene footprinting, providing new insight into the evolution of mechanisms for hybrid polyketide-nonribosomal peptide combinatorial biosynthesis.

biochemistry↗

bioRxiv2024

Early steps of the biosynthesis of the anticancer antibiotic pleurotin

Pleurotin is a meroterpenoid specialised metabolite made by the fungus Hohenbuehelia grisea, and it is a lead anticancer molecule due to its irreversible inhibition of the thioredoxin-thioredoxin reductase system. Total synthesis of pleurotin has previously been achieved, including through a stereoselective route, however its biosynthesis has not been characterised. In this study, we used isotope-labelled precursor feeding to show that the non-terpenoid quinone ring of pleurotin and its congeners is derived from phenylalanine. We sequenced the genome of the pleurotin-producing fungus and used comparative transcriptomics to identify putative genes involved in pleurotin biosynthesis. Additionally, the heterologous expression of a UbiA-like prenyltransferase from H. grisea resulted in the isolation and characterisation of the first predicted pleurotin biosynthetic intermediate, 3-farnesyl-4-hydroxybenzoic acid. This work sets the foundation to fully elucidate the biosynthesis of pleurotin and its congeners, with long-term potential to optimise their production for therapeutic use and engineer the pathway towards the biosynthesis of valuable analogues.

microbiology↗