Proteomics analysis of Pseudomonas plecoglossicida under thermal stress: the Entner-Doudoroff pathway as a temperature-dependent metabolic switch for thermal adaptation
The proteomic basis of thermal adaptation in P. plecoglossicida is revealed and molecular targets for engineering thermotolerant strains to optimize industrial 2-KGA fermentation are provided.
Under severe stress, GO and KEGG enrichment consistently revealed the reinforcement of central carbon and energy metabolism, peroxisome-associated fatty acid turnover, oxidoreductase/redox activities, and translation and nucleotide metabolic pathways.
Dingkang Wang, Li Wang, Yue Xiao et al.· Journal of Proteome Research· 0 citations
This study uncovers that moderate reactive oxygen species (ROS) signaling mediates aeration-dependent thermotolerance in Kluyveromyces marxianus, challenging the long-held paradigm that ROS function solely as toxic metabolic byproducts. Through integrated transcriptomic profiling and RT-qPCR validation, 19 key transcription factors regulating this adaptive response were identified, and functional assays demonstrated that targeted knockout of GSF2 and RIM101 coupled with MED15 overexpression significantly enhances hypoxic thermotolerance. The ERG6-overexpressing strain YZB559 yields 72.45 g/L xylitol at 45 °C under medium-high oxygen (MHO) condition, marking a 20% improvement over the parental strain, while the combinatorially engineered YZB639 (ΔGSF2::MED15) achieves 74.13 g/L xylitol with complete xylose consumption at 46 °C and 30.64 g/L ethanol under micro-oxygen conditions, representing a 23% increase in ethanol production. Notably, at 47 °C, the highest temperature reported for xylitol fermentation, YZB639 accumulates 51.68 g/L xylitol under constant MHO condition, and an optimized two-stage oxygen supply strategy further elevates the titer to 67.78 g/L, with robust performance also observed when using industrial xylose mother liquor as feedstock to produce 57.34 g/L xylitol. This work resolves the fundamental oxygen contradiction between thermotolerance enhancement and product biosynthesis in high-temperature fermentation, providing a transformative strategy for cost-effective and sustainable industrial biomanufacturing.
Zhongmei Hu, Yanjie Li, Na Dong et al.· Bioresource Technology· 0 citations
In the model bacterium Escherichia coli, the Embden-Meyerhof-Parnas (EMP) glycolysis pathway is the primary route for carbohydrate metabolism. However, alternative metabolic routes can be activated depending on genetic configurations and available carbon sources. In this study, E. coli strains lacking key enzymes of the lower EMP pathway-phosphoglycerate kinase or enolase-were subjected to long-term adaptive evolution in continuous culture under a medium swap regime, for growth on D-xylose as the sole carbon and energy source. Through metabolic 13C-labeling experiments on evolved isolates, we found that carbon flux was predominantly rerouted via the Entner-Doudoroff pathway, known to remain silent when wild type cells are fed with D-xylose. To investigate the molecular basis of this growth adaptation, we identified the mutations fixed in the genomes of evolved prototrophic isolates and conducted comprehensive transcriptomic and proteomic analyses. Our study revealed that mutations in key enzymes and transcriptional regulators at various metabolic branching points were essential for effective growth on D-xylose, enabling optimized partitioning of carbon through central metabolism despite the loss of the canonical EMP glycolytic route. The multi-layered regulatory and metabolic adaptations identified in the evolved strains demonstrate the complex nature of evolutionary trajectories and underscore the potential of adaptive evolution to optimize metabolic network function and enzyme utilization in ways that extend rational engineering approaches.
C. Iacometti, Valérie A. Delmas, Mélodie Cadillon et al.· Metabolic Engineering· 0 citations
Temperature constrains stable mycelial growth and production of Oudemansiella raphanipes, but its molecular response to heat stress followed by recovery remains insufficiently resolved. We integrated untargeted LC-MS metabolomics and RNA sequencing to compare control mycelia maintained at 28 °C (HPJZ28) with mycelia exposed to 42 °C for 6 h and then allowed to recover at 28 °C for 2 h (HPJZ42-R). Metabolomic and transcriptomic profiles separated clearly between the two conditions, indicating broad post-heat recovery-associated molecular remodeling. Most differential metabolites were lower in HPJZ42-R, whereas a smaller subset accumulated, suggesting selective metabolic reorganization rather than generalized activation. Transcriptome analysis identified extensive gene-expression remodeling, with 1081 upregulated and 1878 downregulated genes in the HPJZ28 versus HPJZ42-R comparison. Pathway-level analyses implicated central carbon metabolism, lipid metabolism, amino acid metabolism, peroxisome-related processes, and calcium signaling. Because the sampling design included a recovery period and a single post-stress time point, integrated gene–metabolite correlations are interpreted as exploratory associations rather than evidence of direct regulatory coupling. These results provide species-level multi-omics evidence for the post-heat recovery state of O. raphanipes and identify candidate pathways for future functional and physiological validation.
Yangyang Peng, Jianhao Wang, Ling-Jun Xu et al.· Journal of Fungi· 0 citations
Marine heatwaves repeatedly trigger summer mortality of the farmed Pacific oyster (Crassostrea gigas), forcing its haemocytes to reprogramme metabolism under thermal stress. The metabolic nodes governing this adaptation remain poorly defined. Integrating publicly available transcriptomics, single-cell analysis, enzyme inhibition, and molecular dynamics simulation, we identify argininosuccinate synthetase (CgASS) as a key node of this response. Heat stress drove sustained metabolic remodelling of the haemocyte transcriptome, and network analysis placed CgASS at the centre, where it was preferentially expressed in haemocytes and developmentally regulated. Single-cell virtual knockout selectively reshaped minor haemocyte populations, markedly expanding a stress-activated effector population while contracting immunomodulatory and cytoskeletal populations. In vivo inhibition with α-methyl-DL-aspartate raised citrulline, lowered argininosuccinate, and further suppressed respiration and feeding under heat, confirming that CgASS activity sustains aerobic performance. CgASS inactivation constricts arginine supply, thereby depriving both the nNOS–NO pathway that sustains respiration and feeding and the AMD–polyamine pathway that supports cytoprotection. Molecular dynamics revealed that CgASS collapses into an abnormally compact, rigid conformation at 30 °C, constraining the flexibility required for catalysis. Together, these results suggest CgASS as a potential key node of a metabolic compensation–decompensation axis and a molecular target for breeding thermally resilient shellfish.
Haining Wang, Pengcheng Sun, Peng Li et al.· Fishes· 0 citations
This study uncovers a previously unappreciated mechanism of Tps1-mediated heat adaptation in C. deneoformans, by revealing that Tps1 functions as a critical metabolic gatekeeper that safeguards glycolytic flux to sustain growth at elevated temperatures.
V. Yadav, Kahlia A. Carl, J. Heitman et al.· bioRxiv· 0 citations