Proteomic Insights into Salt-Stress Tolerance in Zygosaccharomyces rouxii Revealed by Data-Independent Acquisition Mass Spectrometry.

Combined Proteomic and Metabolomic Analyses of Palmitoleic Acid-Associated Responses to Salt Stress in Zygosaccharomyces rouxii.

Zygosaccharomyces rouxii is an important halotolerant yeast in high-salt fermentations, although the systems underlying its salt adaptation and nutritional regulation remain unknown. We characterized Z. rouxii CGMCC 3791 growing in YPD under control conditions or 120 g/L NaCl and assessed palmitoleic acid supplementation during salt stress. DIA-based LC-MS/MS proteomics and UPLC-Orbitrap metabolomics were combined with KEGG enrichment and pathway mapping. PCA effectively differentiated the three groups across both omics layers, demonstrating that palmitoleic acid induces a unique reprogramming beyond the salt-only response. The enrichment analysis revealed the coordinated regulation of amino acid metabolism, glutathione-associated redox activities, ABC transporters, oxidative phosphorylation, and cofactor pathways, including pantothenate and CoA biosynthesis. Integrated mapping demonstrated increased purine-related intermediates (FAICAR, IMP, ADP, and inosine) and lipid-related remodeling. Overall, these results suggest that palmitoleic acid may contribute to salt-stress adaptation in Z. rouxii by modulating energy and nucleotide turnover, while helping maintain redox balance and metabolic flexibility.

Proteomics analysis of Pseudomonas plecoglossicida under thermal stress: the Entner-Doudoroff pathway as a temperature-dependent metabolic switch for thermal adaptation

Physiological and multi-omic insights into the adaptation mechanisms of Planococcus halotolerans SCU63T to high-salinity and low-temperature co-stress.

High-salinity and low-temperature co-stress often impairs microbial function and disrupts their ecological balance, and thus understanding the adaptive mechanisms of psychrotolerant and halotolerant microorganisms is essential for their application in environmental remediation. The strain Planococcus halotolerans SCU63T can survive under extreme conditions of 15% NaCl and 0 °C. Physiological analyses revealed that, under co-stress, cells developed a thicker capsule, accumulated more intracellular sodium (increased from 2.25 to 3.41 g/kg), and exhibited significantly elevated membrane permeability. Genome annotation identified numerous co-stress-responsive genes, including but not limited to cspA, desA, betA/B, opuA/D, proX, nhaC, mnhA-G, trkA, and trkH. Transcriptomic data further demonstrated that these genes regulate ABC transporters, branched-chain amino acid and osmoprotectant metabolism, membrane transport, and cellular homeostasis. Metabolomic profiling confirmed that, under co‑stress, the strain not only accumulated proline derivatives and upregulated glycosylated products and certain alkaloids, but also underwent significant changes in molecules associated with membrane lipid remodeling and fatty acid derivatives. Collectively, these findings advance our understanding of microbial tolerance to concurrent stressors and provide a promising microbial resource for the remediation of saline soils in winter and high-salt as well as low-temperature industrial wastewater.

Integrated proteomic and acetylomic analyses reveal the metabolic reprogramming associated with increased tylosin-equivalent concentration in Streptomyces xinghaiensis sf106-B1.

Deciphering the metabolic basis of high-yield antibiotic production in Streptomyces is crucial for strain optimization. Atmospheric and room-temperature plasma (ARTP) mutagenesis of Streptomyces xinghaiensis sf106 generated a mutant with a 30% increase in tylosin-equivalent concentration (μg/mL). 4D-FastDIA quantitative proteomics identified 279 differentially abundant proteins enriched in the Type I polyketide synthase (PKS) pathway, with increased abundance of key macrolide-biosynthesis-related proteins. Lysine-acetylome profiling identified 1152 differentially abundant acetylation sites and revealed altered acetylation of enzymes involved in fatty acid metabolism and the tricarboxylic acid (TCA) cycle, suggesting adjustments in central metabolism associated with acyl-CoA precursor availability and energy generation. Integration of proteomic and acetylomic data suggests coordinated changes in protein abundance and lysine acetylation associated with the increased tylosin-equivalent concentration. These results highlight candidate nodes for rational metabolic engineering of S. xinghaiensis.

Comparative Metabolomic Profiling Reveals Salinity Tolerance Mechanisms in a Rice Introgression Line

Rice (Oryza sativa) is highly sensitive to salinity, yet the metabolic mechanisms underlying salt tolerance remains incompletely understood. In this study, we performed leaf tissue-specific untargeted metabolomic profiling of the salt-tolerant introgression line JN100 (JN), its donor parent Nona Bokra (NB), and its recurrent parent Jupiter (JU) to characterize metabolic responses to salt stress. Comparative analysis identified differentially accumulated metabolites (DAMs) spanning diverse chemical classes, including amino acids, sugars and carbohydrates, lipids, organic acids, cofactors, electron carriers, and nucleotides. Under salt stress (SS), 201 DAMs (89 upregulated and 112 downregulated) were detected in JN relative to JU. Notably, metabolites such as allantoin, glycitin, nicotinamide ribotide, D-arabinono-1,4-lactone, violanthin, L-methionine S-oxide, ribitol, lysine, rutin, glutamine, pantothenic acid, and quinic acid, showed significant differential accumulation. Pathway enrichment analysis revealed significant enrichment of arginine biosynthesis, purine metabolism, and alanine, aspartate, and glutamate metabolism, indicating extensive reprogramming of nitrogen and energy-associated metabolic pathways under salinity stress. Integration of transcriptomic and metabolomic datasets from the SS experiments further identified ten differentially expressed genes (DEGs) associated with the metabolite network in the JN vs. JU comparison. Among these, OsDHQDT/SDH, OsFd-GOGAT, phenylalanyl-tRNA synthetase, OsP5CS1, OsP5CS2, and a pyridoxal phosphate-dependent transferase were linked to metabolites involved in shikimate, amino acid, and proline metabolism. Collectively, these results demonstrate that salinity tolerance in rice is associated with coordinated transcriptional and metabolic reprogramming that supports oxidative stress mitigation and adaptive stress responses.

Metabolic Reprogramming During Heat Stress and Short-Term Recovery in Oudemansiella raphanipes Revealed by Integrated Metabolomics and Transcriptomics

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.