Search bioRxiv⌕ Search

Biology subjects

Bezdicek, M.

Publications and source records attributed to Bezdicek, M..

3 recordsLinked to original sources

Kineochelins - a novel group of siderophores from an Antarctic bacterium

BackgroundThe global rise of antimicrobial resistance has intensified the search for new microbial metabolites from underexplored environments and taxonomic groups. Extreme and geographically isolated habitats, such as Antarctic terrestrial ecosystems, represent promising reservoirs of novel biosynthetic diversity, particularly among rare and difficult-to-cultivate actinomycetes, where chemical mediators are thought to play key roles in microbial persistence and interaction under resource-limited conditions. ResultsHere, we report the characterization of kineochelins, a previously undescribed group of siderophores produced by an Antarctic isolate, Actinokineospora sp. UV203 representing difficult to cultivate actinomycetes. Structural elucidation revealed a set of closely related congener molecules with a mixed-ligand architecture consistent with metal-chelating activity. Genome mining combined with transcriptomic analysis identified the involvement of a dedicated nonribosomal peptide synthetase-encoding biosynthetic gene cluster responsible for kineochelin production. Comparative genomic analyses showed that, although kineochelin biosynthetic genes share limited homology with those of known mixed-ligand siderophores, their biosynthetic pathways differ substantially in gene content and organization, indicating a distinct evolutionary lineage. Functional characterization of kineochelins demonstrated strong and selective iron chelation, with pronounced affinity for ferric and ferrous iron. Crude culture extracts inhibited the growth of bacterial strains isolated from the same Antarctic environment, suggesting that kineochelin-associated chemistry contributes to iron-mediated competitive interactions within native microbial communities. In addition, kineochelin-enriched fractions exhibited selective inhibitory activity against the opportunistic yeast pathogen Nakaseomyces glabratus and a clinical isolate of Saccharomyces cerevisiae associated with invasive infection. ConclusionsTogether, these findings expand the known chemical and biosynthetic diversity of the genus Actinokineospora and demonstrate that Antarctic rare actinomycetes are a valuable source of novel natural products with potential relevance for microbial ecology and biotechnology. The ecological activities of kineochelins highlight the role of iron acquisition in shaping microbial interactions in extreme environments and underscore the biotechnological potential of metabolites derived from underexplored polar microorganisms.

microbiology↗

Genomic and Phenotypic Comparison of Polyhydroxyalkanoates Producing Strains of genus Caldimonas/Schlegelella

Polyhydroxyalkanoates (PHAs) have emerged as an ecologically friendly alternative to conventional polyesters. In this study, we present a comprehensive analysis of the genomic and phenotypic characteristics of three non-model thermophilic bacteria known for their ability to produce PHAs: Schlegelella aquatica LMG 23380T, Caldimonas thermodepolymerans DSM 15264, and C. thermodepolymerans LMG 21645 accompanied by a comparison with the type strain C. thermodepolymerans DSM 15344T. We have assembled the first complete genomes of these three bacteria and performed the structural and functional annotation. This analysis has provided valuable insights into the biosynthesis of PHAs and has allowed us to propose a comprehensive scheme for the carbohydrate metabolism in the studied bacteria. Through phylogenomic analysis, we have confirmed the synonymity between Caldimonas and Schlegelella genera, and further demonstrated that S. aquatica and S. koreensis, currently classified as orphan species, belong to the Caldimonas genus. SummaryThe genomic and phenotypic analysis of Schlegelella aquatica LMG 23380T and Caldimonas thermodepolymerans DSM 15264 and LMG 21645 sheds light on the production of sustainable polyesters known as polyhydroxyalkanoates (PHAs). The genome assembly and functional annotation highlight key genes related to PHA production and other important traits. Notably, C. thermodepolymerans stands out with its unique xyl operon, making it a highly promising candidate for biotechnological PHA production from xylose-rich lignocellulosic resources. The study emphasizes the importance of a polyphasic approach combining genotypic and phenotypic analyses in prokaryotic taxonomy, emphasizing the need for exploration in the genomic era. By uncovering the key traits of these bacteria, this research opens new horizons towards sustainable production of environmentally friendly polyesters.

microbiology↗

Using Deep Learning for Gene Detection and Classification in Raw Nanopore Signals

Recently, nanopore sequencing has come to the fore as library preparation is rapid and simple, sequencing can be done almost anywhere, and longer reads are obtained than with next-generation sequencing. The main bottleneck still lies in data postprocessing which consists of basecalling, genome assembly, and localizing significant sequences, which is time consuming and computationally demanding, thus prolonging delivery of crucial results for clinical practice. Here, we present a neural network-based method capable of detecting and classifying specific genomic regions already in raw nanopore signals - squiggles. Therefore, the basecalling process can be omitted entirely as the raw signals of significant genes, or intergenic regions can be directly analysed, or if the nucleotide sequences are required, the identified squiggles can be basecalled, preferably to others. The proposed neural network could be included directly in the sequencing run, allowing real-time squiggle processing.

bioinformatics↗