Biology subjects

Peeters, E.

Publications and source records attributed to Peeters, E..

18 recordsLinked to original sources

bioRxiv2026

PERTURBATION OF THE AMINO ACID STRESS RESPONSE PATHWAY EXPOSES A METABOLIC VULNERABILITY IN MULTIPLE AGGRESSIVE CANCER SUBTYPES

Cancer cells frequently experience nutrient limitation and depend on adaptive stress-response pathways to maintain metabolic homeostasis. Here, we show that pharmacological perturbation of amino acid stress signaling exerts broad anti-tumor activity across multiple aggressive malignancies, including acute lymphoblastic leukemia, acute myeloid leukemia, triple-negative breast cancer, ovarian cancer, and neuroblastoma. Sensitivity to pathway modulation is associated with a chronic stress-adapted metabolic state marked by constitutive amino acid response signaling, elevated NFE2L2 expression, and reduced mitochondrial abundance despite evidence of efficient oxidative metabolism. Mechanistically, we demonstrate that the ATP-competitive compound GCN2-IN-6 does not phenocopy genetic GCN2 suppression and exhibits context-dependent effects on the amino acid stress response. Nevertheless, tumors experiencing chronic metabolic stress remain exquisitely sensitive to disruption of this adaptive network, regardless of whether signaling is perturbed through canonical inhibition or paradoxical activation. Collectively, our findings identify chronic metabolic stress adaptation as an actionable vulnerability and establish off-balancing amino acid stress signaling as a therapeutic strategy across multiple cancer types

cancer biology↗

bioRxiv2026

Liquid-state surface fermentation as a platform for pure mycelium materials production

Liquid-state surface fermentation (LSSF) is emerging as an alternative to submerged and solid-state fermentation for producing pure mycelium materials (PMM), yet a systematic framework linking culture geometry, substrate consumption, inoculum preparation and material properties is lacking. Here, we characterised LSSF with Trametes versicolor across culture volumes and inoculation strategies. The biomass accumulation model described a trade-off between colonisation speed and biomass accumulation. Smaller volumes, with a higher specific interfacial area, colonised the surface earlier and converted glucose more efficiently (up to 0.64 g g-1), but depleted it prematurely and produced less biomass. After pellicle formation, glucose was consumed at a common volumetric rate (~1.0 g L-1 d-1), having glucose availability as a limiting factor for pellicle densification. In deeper cultures, much of the glucose consumed early was not recovered in the pellicle, indicating competition from submerged growth. Backlit transmittance imaging provided a non-destructive estimate of pellicle biomass and of its spatial heterogeneity. Inoculum source and processing determined material performance: liquid-derived inocula and a shaken incubation step increased biomass, an additional blending step produced more homogeneous and stronger pellicles. These results provide process-level design rules for LSSF and a basis for its application to PMM production.

bioengineering↗

bioRxiv2026

Inoculum-to-interface distance tunes productivity in static liquid cultures of wood-decay fungi

Static liquid cultures of wood-decay fungi underpin applications in materials, food, and medicine, yet the mechanisms governing pellicle formation remain poorly understood, limiting rational optimisation at scale. We developed a time-lapse scanning and image analysis platform to visualise the process of pellicle formation across five white-rot fungal species, of which Trametes versicolor formed the thickest, heaviest pellicles and completed formation fastest. Kymographs revealed a reproducible four-stage sequence after inoculation and sedimentation of the biomass: recovery of viability, upward growth, pellicle initiation, and thickening. We formalised this as a model in which the time to pellicle establishment is determined by the distance between the settled biomass and the liquid-air interface. Increasing liquid depth relative to a fixed inoculum loading raised biomass and mat thickness, but prolonged formation. The results identify surface proximity as the dominant predictor of initiation timing. By fixing the inoculum at the liquid-air interface with a membrane, we validated that minimising the distance between the sedimented mycelium and the liquid surface accelerated and stabilised formation without compromising on pellicle biomass. By exposing the most relevant control variables, this work provides a quantitative basis for designing reliable liquid-state surface fermentations for emerging applications involving mycelium.

bioengineering↗

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↗

bioRxiv2026

High-resolution transcriptome analysis reveals a multilayered and dynamic transcriptional architecture in the archaeal virus SSV1

Fuselloviridae infecting thermoacidophilic Sulfolobales are among the best-studied archaeal viruses, with the Saccharolobus Spindle Shaped Virus 1 (SSV1)-Saccharolobus solfataricus interaction serving as a model system. After infection, SSV1 establishes a chronic infection with new virions continuously budding from the infected cell. UV irradiation triggers virus replication, increased virion production and a tightly orchestrated temporal transcription cycle. However, gene regulatory mechanisms post-UV-induction remain elusive. In this study, we investigated the SSV1 transcriptomic landscape post-UV-induction using high-resolution, long-read ONT-cappable-RNA-sequencing. Through end-to-end sequencing of primary transcripts, we generated a comprehensive transcript map of SSV1, identifying 21 transcription start sites (TSSs), including 12 newly described sites, and 19 termination sites (TTSs), of which 9 are novel. This enabled refinement of transcription units and operon structures across the genome. Five new antisense RNAs were discovered, including one encoded antisense to the open reading frame of a putative viral toxin gene a291, which we hypothesize to be a cis-encoded regulatory RNA. In addition, spontaneous recombination between two direct repeats in the SSV1 structural genes vp1 and vp3 was confirmed. To our knowledge, this is the first implementation of cappable-seq for an archaeal virus, and the first base-resolution analysis of the SSV1 transcriptome. It reveals a previously unappreciated level of transcriptional complexity, illustrating how high-resolution transcriptomics can deepen understanding of viral transcriptome architecture and regulatory networks. ImportanceArchaeal viruses remain among the least understood viruses in the virosphere, despite their ecological and evolutionary significance. Saccharolobus Spindle Shaped Virus 1 (SSV1) is a key model for the study of virus-host interactions in archaea. Yet, its gene regulatory mechanisms have remained poorly resolved. Here, we provide the first base-pair resolution transcriptome of an archaeal virus, revealing a complex and multi-layered transcriptional architecture. We uncover alternative transcription start and termination sites, as well as antisense transcription, pointing to regulatory mechanisms beyond a simple temporal gene expression program. These findings suggest that archaeal viruses use sophisticated transcriptional and post-transcriptional mechanisms similar to those in bacterial and eukaryotic viruses. By establishing a high-resolution map of the SSV1 transcriptome, this work advances our understanding of archaeal virus biology.

microbiology↗

bioRxiv2025

Development and characterisation of a promoter library for Sulfolobus acidocaldarius

The hyperthermoacidophilic archaeon Sulfolobus acidocaldarius is a promising production host for industrial biotechnology applications due to its ability to thrive in extreme conditions. However, the lack of well-characterised genetic parts and tools, particularly promoters, limits its potential for metabolic engineering. In this study, we developed the first promoter library for S. acidocaldarius by randomising specific regions of the core promoter sequence of PSaci 2137, a promoter known to function in both S. acidocaldarius and Escherichia coli. The library was initially screened in E. coli using mKate2, a red fluorescent reporter protein, and seven promoters were selected for characterisation in S. acidocaldarius using the thermostable {beta}-galactosidase reporter LacS. The resulting promoter collection exhibited a 5-fold range of expression levels in S. acidocaldarius, spanning from low to high constitutive expression when compared to S. acidocaldarius promoters Psac7d and PmalE. This study demonstrates a successful workflow for generating and characterising S. acidocaldarius promoters, providing a valuable toolkit for fine-tuning gene expression and optimising metabolic pathways in this extremophilic archaeon. The design principles established here can be extended to other archaeal systems with similar promoter architectures.

synthetic biology↗

bioRxiv2025

Development and characterisation of pNarsenic: a naringenin-inducible biosensor for arsenic in Escherichia coli

Whole-cell biosensors detecting the heavy metal arsenic have been widely studied for their potential in environmental monitoring. And while inducible biosensors have been shown to be an effective tool to tune the operational range, a thoroughly characterised inducible biosensor is currently lacking. Here, we present an Escherichia coli biosensor for arsenic in which the transcription factor gene arsR is inducible by naringenin, a plant-derived secondary metabolite. Increasing naringenin concentrations reduced the basal output while increasing both the dynamic range and sensing threshold of the biosensor dose-response curves, but the operational ranges appeared constrained by a fixed upper limit. Comparison with a previously published phenomenological model revealed good overall agreement between experimental data and model predictions, except for the behaviour of the maximum output and threshold. This work expands the biosensor toolbox with a profoundly characterised arsenic biosensor and raises a potential practical limit to dose-response curve engineering by tuning transcription factor expression alone. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/678503v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@c15051org.highwire.dtl.DTLVardef@180214forg.highwire.dtl.DTLVardef@10afa84org.highwire.dtl.DTLVardef@1c51bba_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2025

Transcriptional regulation of the type II fatty acid synthase complex in Rhodococcus opacus

Rhodococcus opacus is an oleaginous actinobacterium with considerable potential for lipid-based bioproduction, as well as for utilising a variety of carbon sources as substrates, including renewable, cost-effective resources. Although its capacity for triacylglycerol accumulation is well established, the regulatory logic that governs its fatty acid and mycolic acid biosynthesis is still poorly understood. Here, we investigated the transcriptional control of the type II fatty acid synthase (FASII) pathway in R. opacus PD630, revealing a regulatory architecture that is more complex than previously assumed. Differential gene expression analysis showed that environmental cues, including temperature, pH, carbon-to-nitrogen ratio and the presence of free fatty acids influence the FASII gene cluster expression in a non-uniform manner. This phenomenon suggests the presence of internal transcription start sites and modular regulation within the cluster. We identified three lipid-responsive transcription factors, MabRRO, FadR1RO and FadR2RO, that are all capable of binding the fasII promoter in vitro. DNA binding of FadR1RO and FadR2RO was disrupted by long-chain acyl-CoA molecules, indicating ligand-dependent control. Together, these findings reveal previously unrecognised layers of transcriptional regulation in the R. opacus FASII pathway and highlight both conserved and divergent regulatory features within the Mycobacteriales lineage. Featured Image O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/678588v2_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@456a6dorg.highwire.dtl.DTLVardef@14e3d1forg.highwire.dtl.DTLVardef@18ed368org.highwire.dtl.DTLVardef@1d979a6_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Beyond the canonical PHA synthase: insights into transcriptional expression and functions of phaC paralogs in Haloferax mediterranei

The halophilic archaeon Haloferax mediterranei is a promising candidate for polyhydroxyalkanoate production, offering several advantages due to its extremophilic physiology. While its primary polyhydroxyalkanoate synthase, a class III enzyme composed of PhaCHme and PhaEHme subunits, has been well characterized, the genome encodes three additional phaC paralogs (phaC1, phaC2 and phaC3), which were previously labeled as cryptic and remain poorly understood. In this study, we systematically investigated these paralogs by employing a targeted bioinformatics pipeline, revealing notable diversity in polyhydroxyalkanoate synthases among Halobacteriales and underscoring the distinctiveness of H. mediterranei. We further analyzed the native transcriptional expression profiles of all phaC paralogs under three physiologically relevant conditions: growth-limiting and growth-permissive conditions, as well as valeric acid supplementation to alter polyhydroxyalkanoate monomer composition. RT-qPCR analysis demonstrated that all three paralogs are transcriptionally active and differentially expressed, refuting earlier assumptions of their cryptic nature. Expression patterns were found not to correlate to polymer composition but to be dependent on growth phase, suggesting a potential physiological role for each paralog in native polyhydroxyalkanoate metabolism. These findings offer new insights into the functional complexity of polyhydroxyalkanoate biosynthesis in H. mediterranei and lay the groundwork for future metabolic engineering aimed at optimizing biopolymer production.

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↗

bioRxiv2025

Effects of genomic location on ectopic integration and gene expression of a reporter gene cassette in Sulfolobus acidocaldarius

In eukaryotes and bacteria, it is well-established that the genomic location of ectopic gene integration influences the expression level due to replication-associated gene dosage effects as well as effects mediated by chromatin organization. In contrast, in archaea, the impact of genomic location on gene expression remained unexplored. Here, we investigated this impact in the model archaeon Sulfolobus acidocaldarius, a crenarchaeal species that has a chromatin architecture with mixed eukaryotic-like and bacterial-like features. We aimed to integrate a standardized {beta}-galactosidase (lacS) reporter cassette into diverse loci in the genome of S. acidocaldarius SK-1 for a comparative analysis. Nine integration mutant strains were successfully obtained, for which qRT-PCR analysis and lacS reporter gene assays revealed significant variation in transcriptional and translational expression of the reporter, respectively, demonstrating that genomic location strongly influences gene expression in S. acidocaldarius. However, variability in transcription levels and its regulation was shown to be primarily driven by transcriptional activity of neighboring genes, due to the high coding density in the S. acidocaldarius genome as well as a lack of insulator elements. Interestingly, translational activity exhibited a more apparent correlation with the distance to the closest origin of replication (R2 = 0.432) as compared to transcriptional activity (R2 = 0.026). In conclusion, this study not only provides insights into genome context effects, but also provides inspiration for the future design of genomic knock-in constructions in S. acidocaldarius.

microbiology↗

bioRxiv2024

In-silico identification of archaeal DNA-binding proteins

The rapid advancement of next-generation sequencing technologies has generated an immense volume of genetic data. However, this data is unevenly distributed, with well-studied organisms being disproportionately represented, while other organisms, such as from archaea, remain significantly underexplored. The study of archaea is particularly challenging due to the extreme environments they inhabit and the difficulties associated with culturing them in the laboratory. Despite these challenges, archaea likely represent a crucial evolutionary link between eukaryotic and prokaryotic organisms, and their investigation could shed light on the early stages of life on Earth. Yet, a significant portion of archaeal proteins are annotated with limited or inaccurate information. Among the various classes of archaeal proteins, DNA-binding proteins are of particular importance. While they represent a large portion of every known proteome, their identification in archaea is complicated by the substantial evolutionary divergence between archaeal and the other better studied organisms. To address the challenges of identifying DNA-binding proteins in archaea, we developed Xenusia, a neural network-based tool capable of screening entire archaeal proteomes to identify DNA-binding proteins. Xenusia has proven effective across diverse datasets, including metagenomics data, successfully identifying novel DNA-binding proteins, with experimental validation of its predictions. Xenusia is available as a PyPI package, with source code accessible at https://github.com/grogdrinker/xenusia, and as a Google Colab web server application at https://colab.research.google.com/drive/1c4eb4sEz8OsBqHL62XDFrqmwa7CxImww?usp=sharing.

bioinformatics↗

bioRxiv2024

De novo synthesis of fatty acids in Archaea via an archaeal fatty acid synthase complex

Archaea synthesize membranes using isoprenoid-based ether lipids, whereas Bacteria and Eukarya use fatty acid-based ester lipids. While the factors responsible for this "lipid divide" remain unclear, this has important implications for understanding the evolutionary history of eukaryotes, which likely originated from within the Archaea and therefore changed membrane composition from isoprenoid-based to fatty acid-based lipids. Here, using 13C labelling studies, we demonstrate that the archaeal model organisms Sulfolobus acidocaldarius and Haloferax volcanii are capable of de novo fatty acid synthesis. Biochemical characterization and in vitro pathway reconstitution identify the key enzymes of a newly proposed fatty acid synthesis pathway in S. acidocaldarius and show that ketothiolase, ketoacyl-CoA reductase, and hydroxyacyl-CoA dehydratase form a stable assembly mediated by a DUF35 domain protein, which represents the first characterization of an archaeal fatty acid synthase complex. The final step is catalysed by an NADPH-dependent enoyl-CoA reductase. Deletion of the enoyl-CoA reductase demonstrate that this pathway operates in vivo in S. acidocaldarius. The presented results including phylogenetic analysis reveal that the potential to synthesize fatty acids is widespread across archaeal lineages. Collectively, our findings demonstrate that archaea are capable of synthesizing fatty acids, elucidate the molecular mechanisms involved in this process and provide additional insights into the evolutionary histories of fatty acid synthesis in archaea.

microbiology↗

bioRxiv2024

Protein kinase Sut1 from the Crenarchaeon Sulfolobus acidocaldarius displays tyrosine phosphorylation activity

Protein phosphorylation is a key cellular signaling mechanism that exists in all life forms. Unlike Bacteria and Eukarya, in which protein phosphorylation has thoroughly been studied, post-translational modification by means of phosphorylation have only been limitedly explored in Archaea. A previous study of the phosphoproteome of the model Crenarchaeon Sulfolobus acidocaldarius revealed a widespread occurrence of protein phosphorylation, especially on tyrosine residues. Moreover, several (putative) transcription factors, including AbfR1 and FadR, were previously shown to be phosphorylated on tyrosine residues, a phenomenon that is directly linked to a phosphorylation-mediated regulation of these transcription factors. Despite this potentially important role for tyrosine phosphorylation in S. acidocaldarius, to our knowledge, a kinase capable of directly phosphorylating tyrosine residues has not yet been identified in this organism, neither in Archaea as a whole. Here, we identify and characterize a protein kinase in S. acidocaldarius, Sut1, which displays tyrosine phosphorylation activity in vitro and represents a novel protein kinase family that is widespread in different archaeal organisms.

microbiology↗

bioRxiv2023

Application of polystyrene sulfonate (PSS) for inhibiting toxicity of ALS/FTD-linked dipeptide repeats

The GGGGCC (G4C2) expansion in the noncoding region of C9orf72 is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The repeat region is translated into five different dipeptide repeat proteins (DPRs), of which the arginine-rich DPRs (R-DPRs) poly- GR (GRn) and poly-PR (PRn) are highly neurotoxic. In this study, we characterized the protective effect against R- DPR toxicity of polystyrene sulfonate (PSS), an FDA-approved drug applied in hyperkalemia, in biochemical, cellular and iPSC-derived motor neuron (MN) models. We found that PSS, in a length-dependent manner, interacts very tightly with R-DPRs, and releases their bound RNA in R-DPR - RNA mixtures. PSS significantly influences the liquid- liquid phase separation (LLPS) of R-DPRs elicited by RNA and reduces their ensuing cell toxicity in Neuro-2a cells. PSS is cell penetrable, and it can effectively rescue the inhibitory effect R-DPRs on axonal mitochondrial transport in iPSC-derived MNs. Shorter (n < 340) variants of PSS are not toxic either to cells or to mice upon intracerebroventricular injection up to 1 mM concentration. Our results suggest that its polymeric nature endows PSS with an advantageous effect in C9-ALS providing a potential therapeutic tool against this debilitating neurodegenerative disease.

molecular biology↗

bioRxiv2022

Transcriptional and translational dynamics underlying heat shock response in the thermophilic Crenarchaeon Sulfolobus acidocaldarius

High-temperature stress is critical for all organisms and induces a profound cellular response. For Crenarchaeota, little information is available on how heat shock affects cellular processes and on how this response is regulated. In this work, we set out to study heat shock response in the thermoacidophilic model crenarchaeon Sulfolobus acidocaldarius, which thrives in volcanic hot springs and has an optimal growth temperature of 75{degrees}C. Pulse-labeling experiments demonstrated that a temperature shift to 86{degrees}C induces a drastic reduction of the transcriptional and translational activity, but that RNA and protein neosynthesis still occurs. By combining RNA sequencing and TMT-labeled mass spectrometry, an integrated mapping of the transcriptome and proteome was performed. This revealed that heat shock causes an immediate change in the gene expression profile, with RNA levels of half of the genes being affected, followed by the more subtle reprogramming of the protein landscape. A limited correlation was observed in differential expression on the RNA and protein level, suggesting that there is a prevalence of post-transcriptional and post-translational regulation upon heat shock. Furthermore, based on the finding that promoter regions of heat shock regulon genes lack a conserved DNA-binding motif, we propose that heat-shock responsive transcription regulation is likely not to be accomplished by a classical transcription factor. Instead, in contrast to histone-harboring Euryarchaeota that have heat-shock transcription factors, it is hypothesized that Sulfolobales and other histone-lacking thermophilic archaea employ an evolutionary ancient mechanism relying on temperature-responsive changes in DNA organization and compaction, induced by the action of nucleoid-associated proteins.

microbiology↗

bioRxiv2020

Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes in Pantoea agglomerans KM1, a potential opportunistic pathogen

Pantoea agglomerans is a Gram-negative aerobic bacillus causing a wide range of opportunistic infections in humans including septicemia, pneumonia, septic arthritis, wound infections and meningitis. To date, the determinants of virulence, antibiotic resistance, metabolic features conferring survival and host-associated pathogenic potential of this bacterium remain largely underexplored. In this study, we sequenced and assembled the whole-genome of P. agglomerans KM1 isolated from kimchi in South Korea. The genome contained one circular chromosome of 4,039,945 bp, 3 mega plasmids, and 2 prophages. The phage-derived genes encoded integrase, lysozyme and terminase. Six CRISPR loci were identified within the bacterial chromosome. Further in-depth analysis showed that the genome contained 13 antibiotic resistance genes conferring resistance to clinically important antibiotics such as penicillin G, bacitracin, rifampicin, vancomycin, and fosfomycin. Genes involved in adaptations to environmental stress were also identified which included factors providing resistance to osmotic lysis, oxidative stress, as well as heat and cold shock. The genomic analysis of virulence factors led to identification of a type VI secretion system, hemolysin, filamentous hemagglutinin, and genes involved in iron uptake and sequestration. Finally, the data provided here show that, the KM1 isolate exerted strong immunostimulatory properties on RAW 264.7 macrophages in vitro. Stimulated cells produced Nitric Oxide (NO) and pro-inflammatory cytokines TNF-, IL-6 and the anti-inflammatory cytokine IL-10. The upstream signaling for production of TNF-, IL-6, IL-10, and NO depended on TLR4 and TLR1/2. While production of TNF-, IL-6 and NO involved solely activation of the NF-{kappa}B, IL-10 secretion was largely dependent on NF-{kappa}B and to a lesser extent on MAPK Kinases. Taken together, the analysis of the whole-genome and immunostimulatory properties provided in-depth characterization of the P. agglomerans KM1 isolate shedding a new light on determinants of virulence that drive its interactions with the environment, other microorganisms and eukaryotic hosts.

genomics↗

bioRxiv2019

Mechanical, physical and chemical characterisation of mycelium-based composites with different types of lignocellulosic substrates

The current physical goods economy produces materials by extracting finite valuable resources without taking their end of the life and environmental impact into account. Modernity leaves us with devasted landscapes of depleted resources, waste landfill, queries, oil platforms. At the time of the Anthropocene, the various effects the human role has on the constitution of the soils create an acceleration of material entropy. It is the terrestrial entanglement of fungal materials that we investigate in this paper by offering an alternative fabrication paradigm based on the growth of resources rather than on extraction. Unlike the latter, biologically augmented building materials can be grown by combining micro-organisms such as fungal mycelium with agricultural plant-based waste. In this study, we investigate the production process, the mechanical, hygrothermal and chemical properties of mycelium-based composites with different types of lignocellulosic reinforcement fibres combined with a white rot fungus, Trametes versicolor. Together, they form an interwoven three-dimensional filamentous network binding the feedstock into a lightweight material. The mycelium-based material is heat-killed after the growing process. This is the first study reporting the dry density, the Youngs modulus, the compressive stiffness, the stress-strain curves, the thermal conductivity, the water absorption rate and a complete FTIR analyse of mycelium-based composites by making use of a disclosed protocol with T. versicolor and five different type of fibres (hemp, flax, flax waste, softwood, straw) and fibre conditions (loose, chopped, dust, pre-compressed and tow). These experimental results show that mycelium-composites can fulfil the requirements of thermal insulation. The thermal conductivity and water absorption coefficient of the mycelium composites with flax, hemp, and straw have an overall good insulation behaviour in all the aspects compared to conventional unsustainable materials. The conducted tests reveal that the mechanical performances of the mycelium-based composites depend more on the fibre condition, size, and processing than on the chemical composition of the fibres.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC=\"FIGDIR/small/569749_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (40K):\norg.highwire.dtl.DTLVardef@1306289org.highwire.dtl.DTLVardef@195161corg.highwire.dtl.DTLVardef@de9355org.highwire.dtl.DTLVardef@9aea50_HPS_FORMAT_FIGEXP M_FIG Graphical abstract\n\nC_FIG HighlightsO_LIThe type of fibre influences the colonisation of mycelium: samples containing flax, hemp, straw and flax-waste resulted in a well-developed composite\nC_LIO_LIThe type of fibre has a smaller influence on the compressive stiffness than the fibre processing and size.\nC_LIO_LIPre-compression and chopped fibres (particle size <5mm) improve the compressive mechanical properties of mycelium composites.\nC_LIO_LIThe thermal conductivity and water absorption coefficient of the mycelium composites with flax, hemp, and straw have an overall good insulation behaviour in all the aspects compared to conventional unsustainable materials.\nC_LI

microbiology↗