Physiological and Metabolic Responses of Zymomonas mobilis to Lignocellulosic Hydrolysate
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ABSTRACT: This study provides a systems-level evaluation of how Zymomonas mobilis responds to hydrolysate stress, revealing distinct physiological and lipid membrane remodeling responses.
INSTRUMENT(S): Liquid Chromatography MS - negative - reverse phase
PROVIDER: MTBLS12808 | MetaboLights | 2025-08-01
REPOSITORIES: MetaboLights
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Project description:This study provides a systems-level evaluation of how Zymomonas mobilis responds to hydrolysate stress, revealing distinct physiological and lipid membrane remodeling responses.
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Project description:<p><em>Candida albicans</em>, a World Health Organization critical-priority fungal pathogen, represents the predominant cause of candidemia. Therapeutic failure is sometimes driven by antifungal tolerance, a phenotype distinct from resistance, whose underlying mechanisms remain incompletely defined. Here, we identify the peroxisomal protein Pex8 as a key regulator of tolerance to both azoles and amphotericin B. Although neither deletion nor overexpression of <em>PEX8</em> altered minimum inhibitory concentrations, both modifications significantly reduced drug tolerance, as demonstrated by reduced fractional growth (FoG20) and impaired survival under drug pressure. Mechanistically, RNA-seq analysis revealed that <em>PEX8</em> overexpression suppresses ergosterol biosynthesis genes and reprograms stress-response pathways, providing a molecular basis for the observed azole tolerance attenuation. Complementary lipidomic profiling demonstrated that <em>PEX8</em> genetic manipulations induce extensive membrane lipid remodeling, characterized by specific alterations in ceramide and lysophospholipid subclasses, thereby revealing an ergosterol-independent mechanism underlying amphotericin B tolerance attenuation. Phenotypically, <em>PEX8</em> overexpression attenuated serum-induced hyphal morphogenesis and reduced virulence in a Galleria mellonella infection model, consistent with downregulation of hyphal-associated and virulence-related genes. Our findings establish Pex8 as a central coordinator of oxidative stress adaptation, membrane homeostasis, filamentation, and pathogenicity, revealing a promising target for combating antifungal tolerance.</p>
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Project description:Regulation of gene expression is an important aspect of insulin’s physiological action, however, most studies rely on in vitro systems or pharmacological doses of insulin. Here, we demonstrate that under euglycemic-clamp conditions, physiological levels of insulin regulate over 1500 transcripts in muscle and 1000 transcripts in liver. These include expected pathways related to glucose and lipid utilization, mitochondrial function and autophagy in muscle, and glucose production and steroidogenesis in liver, as well as unexpected pathways, such as mRNA splicing, chromatin remodeling, and regulation of hepatocyte nuclear factors. Insulin also regulates over 100 non-coding RNAs in muscle and liver. These changes in coding and non-coding RNAs, refined by alternative splicing, provide an integrated transcriptional network underlying the complexity of insulin action in vivo.
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Project description:Previous evaluation by different molecular and physiological assays of Staphylococcus aureus (S. aureus) responses to heat shock exposure yielded a still fragmentary view of the mechanisms determining bacterial survival or death at supra-physiological temperatures. This study analyzed diverse facets of S. aureus heat-shock adjustment by recording global transcriptomic and metabolic responses of bacterial cultures shifted for 10 min from 37oC to a sub-lethal (43oC) or eventually lethal (48oC) temperature. A relevant metabolic model of the combined action of specific stress response mechanisms with more general, energy-regulating metabolic pathways in heat-shocked S. aureus was designed. While S. aureus cultures shifted to 43oC or left at 37oC showed marginal differences in growth and survival rates, bacterial cultures exposed to 48oC showed a rapid growth arrest followed by a subsequent decline in viable counts. The most substantial heat shock-induced changes at both 43oC and 48oC occurred in transcript levels of HrcA- and CtsR-regulated genes, encoding classical chaperones DnaK and GroESL, and some Hsp100/Clp ATPases components, respectively. Other metabolic pathways up-regulated by S. aureus exposure at 48oC included genes encoding several enzymes coping with oxidative stress, and DNA damage, or/and impaired osmotic balance. Some major components of the pentose phosphate cycle and gluconeogenesis were also up-regulated, which reflected depletion of free glucose by bacterial cultures grown in Mueller-Hinton broth prior to heat shock. In contrast, most purine- and pyrimidine-synthesis pathway components and amino acyl-tRNA synthetases were down-regulated at 48oC, as well as arginine deiminase and major fermentative pathway components, such as alcohol, lactate and formate dehydrogenases. Despite the heat-induced, increased requirements for ATP-dependent macromolecular repair mechanisms combined with declining energy sources, intracellular ATP levels remained remarkably constant during heat shock. In conclusion, the sequential loss of replication and viability at 48oC cannot be explained by significant reductions in intracellular ATP levels, but may reflect ATP rerouting for macromolecular repair mechanisms and cell survival. Our metabolic model also suggests that heat-stressed S. aureus should down-regulate the production of potential, DNA-damaging reactive oxygen species that might result from electron transport-generated ATP, involving excessive levels of free heavy metals, in particular iron. Keywords: Staphylococcus aureus; heat shock; stress responses; transcriptomic profiling; physiological adjustment Comparative transcriptomic profiling of late log phase cultures of S. aureus ISP794, exposed to 43°C vs. 37°C, or 48°C vs. 37°C. We performed triplicate measurements from independently grown cultures for each heat stress condition.
2010-06-19 | E-GEOD-12920 | biostudies-arrayexpress
Project description:Vascular flow delivers nutrients and imposes hemodynamic forces that govern vessel behavior in health and disease, yet fully human systems that recapitulate and tune physiological intraluminal flow in three-dimensional (3D) tissues are lacking. We developed VIVOS (Vascularized In Vitro Organ Systems), a platform that couples perfused human vascular beds to tunable pumps, generating continuous intraluminal flow through millimetre-scale vessels and 3D tissues at physiological shear stresses and pressures. VIVOS supports integration and perfusion of diverse human organoids and tissues, including lung organoids, cerebral organoids, vascular organoids, breast spheroids, and human retinal explants, as well as enables direct measurement and control of pressure, shear stress, and perfusion-dominant compound transport over extended culture periods. By tuning intraluminal flow and applying single-cell transcriptomics, we uncover a remodeling program in which laminar shear stress acts through a YAP/TAZ-TEAD “switch” to rewire an Apelin ligand-receptor axis and bias tip-stalk endothelial states, reshaping human vascular networks and linking hemodynamic cues to cell state transitions. We further model fast-flow arteriovenous malformations (AVMs) from Hereditary Hemorrhagic Telangiectasia and show that BMP9 constrains vessel caliber and perfusion while antagonizing a VEGF-driven angiogenic program, generating flow-quantified AVM-like lesions in a fully human 3D context. Together, these findings establish VIVOS as a generalizable platform that links physiological intraluminal flow to endothelial state transitions and vessel remodeling, enabling preclinical testing and mechanistic dissection of flow-regulated vascular pathologies in perfused 3D human tissues under defined hemodynamic conditions.
2026-03-23 | GSE318596 | GEO
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