Biology subjects

Sedlar, K.

Publications and source records attributed to Sedlar, K..

3 recordsLinked to original sources

bioRxiv2026

Salt-induced osmotic stress remodels osmoadaptive gene expression and physiology in the polyhydroxyalkanoate-accumulating thermophilic bacterium Caldimonas thermodepolymerans

Caldimonas thermodepolymerans is a thermophilic polyhydroxyalkanoate (PHA)-producing bacterium with strong potential for sustainable bioplastic production. Besides serving as intracellular carbon and energy storage compounds, PHAs are increasingly associated with bacterial stress resistance and cellular robustness. This study aimed to investigate the physiological and transcriptomic response of C. thermodepolymerans to osmotic stress induced by elevated NaCl concentrations. Growth analysis demonstrated tolerance up to a supplementation of 2% NaCl, while moderate salt concentrations enhanced PHA accumulation, reaching 65% cell dry weight at 1.5% NaCl supplementation. To better understand the bacterial response to osmotic stress, RNA sequencing was performed under sublethal salt stress conditions. Differential expression analysis revealed major changes in genes related to osmoprotection, trehalose metabolism and type VI secretion systems, whereas motility and chemotaxis genes were strongly repressed. Phenotypic assays confirmed increased biofilm formation and reduced swarming motility under salt-induced osmotic stress. Although canonical PHA biosynthesis genes were not significantly differentially expressed, increased polymer accumulation suggests other underlying mechanisms linked to osmoadaptation. Together, these findings demonstrate that osmotic stress induces metabolic, physiological and regulatory responses in C. thermodepolymerans, highlighting the importance of PHA in stress adaptation besides its industrial applicability.

microbiology↗

bioRxiv2025

Tracking polyhydroxyalkanoate biosynthesis in thermophilic microorganisms

Polyhydroxyalkanoates are biopolyesters synthesized and stored in intracellular granules by diverse prokaryotes. Despite intense research efforts and prior evidence of a rather widespread phylogenetic occurrence of the related genetic machinery, reports on extreme thermophilic and hyperthermophilic polyhydroxyalkanoates producers remain scarce. However, thermophilic cell factories for bioplastic production would serve as an excellent example of Next-Generation Industrial Biotechnology. In this study, we aim to address this research gap by establishing a bioinformatics pipeline to mine genomes of extremely and moderately thermophilic microorganisms for signatures of potential polyhydroxyalkanoate production. Based on a collection of verified protein sequences of polyhydroxyalkanoate polymerase PhaC, the key biosynthetic enzyme, carefully curated sets of thermophilic bacterial and archaeal genomes were screened. This revealed that although PhaC-encoding genes are prevalent in diverse moderately thermophilic bacteria, they are absent in the considered extreme thermophilic bacteria. In contrast, a few limited examples of extreme thermophilic archaea were found to encode putative phaC genes embedded within a typical polyhydroxyalkanoate synthesis operon in their genomes, namely within the genera Ferroglobus, Geoglobus and Archaeoglobus, while no hits were found in extreme thermophilic bacteria. The latter included Thermus thermophilus, which was previously reported as a polyhydroxyalkanoates producer. This was refuted in our bioinformatics analysis and moreover, the predicted absence of polyhydroxyalkanoates synthesis in T. thermophilus was experimentally confirmed by employing various extraction and analytical methods. Based on the findings in this study, we conclude that polyhydroxyalkanoate production is very scarce in extreme thermophiles and hyperthermophiles, for reasons that remain to be elucidated. HighlightsO_LIA bioinformatics pipeline was constructed to screen thermophilic genomes for PhaC. C_LIO_LIPHA production is widespread in moderate thermophiles but rare in extreme thermophiles. C_LIO_LIExtreme thermophilic archaea belonging to specific genera exceptionally harbor PHA synthesis genes. C_LIO_LINo PHA synthesis genes were found in extreme thermophilic bacteria like Thermus spp. C_LIO_LIExperimental work confirmed the absence of PHAs in Thermus thermophilus. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/652502v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@11fafe3org.highwire.dtl.DTLVardef@1548075org.highwire.dtl.DTLVardef@bd9ebaorg.highwire.dtl.DTLVardef@fff3e0_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

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↗