Biology subjects

Masschelein, J.

Publications and source records attributed to Masschelein, J..

6 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

CAGEcleaner: reducing genomic redundancy in gene cluster mining

SummaryMining homologous biosynthetic gene clusters (BGCs) typically involves searching colocalised genes against large genomic databases. However, the high degree of genomic redundancy in these databases often propagates into the resulting hit sets, complicating downstream analyses and visualisation. To address this challenge, we present CAGEcleaner, a Python-based tool with auxiliary bash scripts designed to reduce redundancy in gene cluster hit sets by dereplicating the genomes that host these hits. CAGEcleaner integrates seamlessly with widely used gene cluster mining tools, such as cblaster and CAGECAT, enabling efficient filtering and streamlining BGC discovery workflows. Availability and implementationSource code and documentation is available at GitHub (https://github.com/LucoDevro/CAGEcleaner) and at Zenodo (https://doi.org/10.5281/zenodo.14726119) under an MIT license. CAGEcleaner comes with its own Conda environment but can also be installed from the Python Package Index (https://pypi.org/project/cagecleaner/). Contactlucas.devrieze@kuleuven.be or joleen.masschelein@kuleuven.be Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2025

Comparative pangenome and mobilome analysis of clostridial species clusters reveals different levels of host adaptation and novel conserved biosynthetic potential

To thrive in diverse ecological niches, bacteria adopt various lifestyles, that range from living freely in the soil to forming close associations with human and animal hosts. However, the impact of these adaptation processes on their genomes and metabolisms remains largely unexplored beyond the genus level. Investigating these evolutionary dynamics at higher taxonomic levels can enhance our understanding of the relationship between host adaptation and their functional capabilities. Here, we examine the evolutionary trajectories and metabolic capabilities of the Clostridia class, which displays a variety of lifestyles and is of high importance for industry, medicine and microbiome research. First, we uncover that the clostridial orders have significantly different adaptation rates. Second, we show that the Oscillospirales order has undergone extensive genomic and functional specialisation toward a host-associated lifestyle, while the Lachnospirales order tends to be at a lower level of host association, retaining a remarkably high number of free-living trait genes and a high degree of metabolic versatility. Third, we reveal substantial differences in genomic architecture and metabolic versatility between the clostridial orders and link these to the progressing stages of host adaptation. Additionally, we identify widely conserved biosynthetic gene clusters, highlighting untapped biosynthetic potential of evolutionary significance. Hence, the beyond-genus level analyses in this study provide valuable new insights into bacterial adaptation with broad implications for evolutionary biology, microbiome research and biotechnology.

bioinformatics↗

bioRxiv2024

Multiplexing bacteriocin synthesis to kill and prevent antimicrobial resistance

Antibiotic resistance represents an emergency for global public health. This calls for using alternative drugs and developing innovative therapies based on a clear understanding of their mechanisms of action and resistance in bacteria. Bacteriocins represent a unique class of natural molecules selectively eliminating bacteria. These secreted proteins exhibit a narrower spectrum of activity compared to conventional broad-spectrum antimicrobials by interacting with specific protein and lipid receptors on bacterial cell envelopes. Despite their diverse molecular structures, the commonality of being genetically encoded makes bacteriocins amenable to synthetic biology design. In using cell-free gene expression (CFE) and continuous-exchange CFE (CECFE), we produced controlled combinations (cocktails) of bacteriocins in single synthesis reactions for the first time. A first set of bacteriocin cocktails comprising both linear and circular proteins allowed the targeting of different bacterial species. Other cocktails were designed to target one bacterial species and considering bacteriocins pathways to cross the cell-envelope. Such combinations demonstrated efficient bacterial eradication and prevention of resistance. We illustrate the effectiveness of these bacteriocin mixtures in eradicating various human pathogenic-multiresistant--isolates. Finally, we highlight their potential as targeted and versatile tools in antimicrobial therapy by testing a combination of bacteriocins for treatment in vivo in the animal model Galleria mellonella.

synthetic biology↗

bioRxiv2023

Escherichia coli Microcin B17 as a chassis for the development of novel antimicrobial peptides.

Withdrawal statementThe authors have withdrawn this manuscript because bioactivity of the reported peptides cannot be confirmed. Scaling up peptide synthesis bioproduction failed to reproduce the original bioactivity profile of the reported microcins (despite appropriate controls). At present, we believe that, in the original bioproduction platform, antibiotics (used in the upstream bacterial growth) co-purified with the microcin - accounting for or enhancing the bioactivity of the isolated peptides. Therefore, the authors do not wish this work to be cited as reference for the project. The DNA assembly platform remains valid and will be reported elsewhere. If you have any questions, please contact the corresponding author.

synthetic biology↗

bioRxiv2019

Pentamycin biosynthesis in Philippine Streptomyces sp. S816: Cytochrome P450-catalysed installation of the C-14 hydroxyl group

Pentamycin is a polyene antibiotic, registered in Switzerland for the treatment of vaginal candidiasis, trichomo-niasis and mixed infections. Chemical instability has hindered its wide-spread application and development as a drug. Here we report the identification of Streptomyces sp. S816, isolated from Philippine mangrove soil, as a pentamycin producer. Genome sequence analysis identified the putative pentamycin biosynthetic gene cluster, which shows a high degree of similarity to the gene cluster responsible for filipin III biosynthesis. The ptnJ gene, which is absent from the filipin III biosynthetic gene cluster, was shown to encode a cytochrome P450 capable of converting filipin III to pentamycin. This confirms that the cluster directs pentamycin biosynthesis, paving the way for biosynthetic engineering approaches to the production of pentamycin analogues. Several other Streptomyces genomes were found to contain ptnJ orthologues clustered with genes encoding polyketide synthases that appear to have similar architectures to those responsible for the assembly of filipin III and pentamycin, suggesting pentamycin production may be common in Streptomyces species.

biochemistry↗