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Journal: Synthetic and Systems Biotechnology
Article Title: Multi-omics analyses of evolved Corynebacterium glutamicum mutants reveal the molecular responses to formaldehyde stress
doi: 10.1016/j.synbio.2026.01.020
Figure Lengend Snippet: Improving the tolerance to formaldehyde via ALE. (A) Growth of FM-1 in minimal medium with 10 g/L glucose and different formaldehyde concentrations. 0 mM (square), 0.5 mM (triangle), 0.8 mM (circle), and 1 mM (inverted triangle). (B) ALE procedure of culture-1 in CGXII minimal medium supplemented with different formaldehyde concentrations and 10 g/L glucose. (C) Growth curve of the evolved mutants in CGXII minimal medium supplemented with 10 g/L glucose and 0.8 mM formaldehyde. (D) Growth curve of evolved mutant in CGXII minimal medium supplemented with 10 g/L glucose and 1.6 mM formaldehyde. (E) Growth curve of evolved mutant in CGXII minimal medium supplemented with 10 g/L glucose. (F) Formaldehyde degradation during cell growth of wild-type C. glutamicum ATCC 13032, FM-1 and FM-3. Values and error bars reflect the mean ± s.d. of three biological replicates (N = 3).
Article Snippet: To assess the toxicity of formaldehyde in C. glutamicum ATCC 13032 lacking the formaldehyde dissimilation pathway, we cultivated a previously developed
Techniques: Mutagenesis
Journal: Synthetic and Systems Biotechnology
Article Title: Multi-omics analyses of evolved Corynebacterium glutamicum mutants reveal the molecular responses to formaldehyde stress
doi: 10.1016/j.synbio.2026.01.020
Figure Lengend Snippet: Effects of single-site mutations on formaldehyde tolerance. (A) Frequency of mutations of four bases in evolved strain FM-3. (B) Growth of strain FM-1 and its derivatives harboring single-site mutations on CGXII minimal agar medium supplemented with 10 g/L glucose and 1 mM formaldehyde. (C) Growth curves of strain FM-1 and its derivatives in CGXII medium supplemented with 10 g/L glucose and 0.8 mM formaldehyde. Values and error bars reflect the mean ± s.d. of three biological replicates (N = 3). Statistical significance at 31 h between FM-1- cgl1199 1015−1032del and FM-1 was determined by unpaired two-tailed Student's t -test: ∗∗∗P < 0.001.
Article Snippet: To assess the toxicity of formaldehyde in C. glutamicum ATCC 13032 lacking the formaldehyde dissimilation pathway, we cultivated a previously developed
Techniques: Two Tailed Test
Journal: Synthetic and Systems Biotechnology
Article Title: Multi-omics analyses of evolved Corynebacterium glutamicum mutants reveal the molecular responses to formaldehyde stress
doi: 10.1016/j.synbio.2026.01.020
Figure Lengend Snippet: Transcriptome analysis of FM-3 and FM-1 cultivated with or without formaldehyde stress. (A) Volcano plots of differential transcription levels in 1F vs. 1N, 3F vs. 3N, 3N vs. 1N, and 3F vs. 1F. (B) Changes in mRNA levels of genes involved in central metabolism and the respiratory chain between FM-3 and FM-1. Only significant changes (log 2 (fold change) ≥1 or ≤ −1, FDR≤0.05) are shown. Upregulated and downregulated genes are indicated with red and blue, respectively. 1F, FM-1 cultivated with formaldehyde stress. 1N, FM-1 cultivated without formaldehyde stress. 3F, FM-3 cultivated with formaldehyde stress. 3N, FM-3 cultivated without formaldehyde stress.
Article Snippet: To assess the toxicity of formaldehyde in C. glutamicum ATCC 13032 lacking the formaldehyde dissimilation pathway, we cultivated a previously developed
Techniques:
Journal: Synthetic and Systems Biotechnology
Article Title: Multi-omics analyses of evolved Corynebacterium glutamicum mutants reveal the molecular responses to formaldehyde stress
doi: 10.1016/j.synbio.2026.01.020
Figure Lengend Snippet: Comparison of proteomes between FM-3 and FM-1 cultivated with formaldehyde or without formaldehyde stress. Functional classification of transcriptome differences based on KEGG_small_class annotation in 3N vs. 1N (A), 3F vs. 1F (B). Proteins with differentially expression in 1F vs. 1N (C) and 3F vs. 3N (D). Only significant changes (log 2 (fold change) ≥1 or ≤ −1, FDR≤0.05) are shown. Proteins exhibiting increased or decreased abundance are highlighted in red and blue, respectively. 1F, FM-1 cultivated with formaldehyde stress. 1N, FM-1 cultivated without formaldehyde stress. 3F, FM-3 cultivated with formaldehyde stress. 3N, FM-3 cultivated without formaldehyde stress.
Article Snippet: To assess the toxicity of formaldehyde in C. glutamicum ATCC 13032 lacking the formaldehyde dissimilation pathway, we cultivated a previously developed
Techniques: Comparison, Functional Assay, Expressing
Journal: Synthetic and Systems Biotechnology
Article Title: Multi-omics analyses of evolved Corynebacterium glutamicum mutants reveal the molecular responses to formaldehyde stress
doi: 10.1016/j.synbio.2026.01.020
Figure Lengend Snippet: Effects of Cgl1590 mutations on formaldehyde tolerance. (A) Amino acid sequence alignment between Cgl1590 and its derivatives. (B) Effects of cgl1590 truncation on formaldehyde tolerance. (C) Effects of cgl1590 knock-out on formaldehyde tolerance. (D) Effects of cgl1590 overexpression on formaldehyde tolerance. Cells were treated with 0.8 mM formaldehyde as stress condition. Values and error bars reflect the mean ± s.d. of three biological replicates (N = 3). Analysis of cell length and morphology of FM-1 without formaldehyde stress (E), FM-1 containing cgl1590 750insG mutation without formaldehyde stress (F), FM-1 with formaldehyde stress (G), and FM-1 strain containing cgl1590 750insG mutation with formaldehyde stress (H). All strains were grown in CGXII minimal medium supplemented with 10 g/L glucose, with or without 0.8 mM formaldehyde, and examined by SEM. Cell length was determined by measuring 70 cells of each strain and analyzed using ImageJ software. Statistical significance at 36 h between FM-1-△ cgl1590 and FM-1 was determined by two-tailed Student's t -test: ∗∗∗P < 0.001.
Article Snippet: To assess the toxicity of formaldehyde in C. glutamicum ATCC 13032 lacking the formaldehyde dissimilation pathway, we cultivated a previously developed
Techniques: Sequencing, Knock-Out, Over Expression, Mutagenesis, Software, Two Tailed Test
Journal: Synthetic and Systems Biotechnology
Article Title: Multi-omics analyses of evolved Corynebacterium glutamicum mutants reveal the molecular responses to formaldehyde stress
doi: 10.1016/j.synbio.2026.01.020
Figure Lengend Snippet: Improving the tolerance to formaldehyde via ALE. (A) Growth of FM-1 in minimal medium with 10 g/L glucose and different formaldehyde concentrations. 0 mM (square), 0.5 mM (triangle), 0.8 mM (circle), and 1 mM (inverted triangle). (B) ALE procedure of culture-1 in CGXII minimal medium supplemented with different formaldehyde concentrations and 10 g/L glucose. (C) Growth curve of the evolved mutants in CGXII minimal medium supplemented with 10 g/L glucose and 0.8 mM formaldehyde. (D) Growth curve of evolved mutant in CGXII minimal medium supplemented with 10 g/L glucose and 1.6 mM formaldehyde. (E) Growth curve of evolved mutant in CGXII minimal medium supplemented with 10 g/L glucose. (F) Formaldehyde degradation during cell growth of wild-type C. glutamicum ATCC 13032, FM-1 and FM-3. Values and error bars reflect the mean ± s.d. of three biological replicates (N = 3).
Article Snippet:
Techniques: Mutagenesis
Journal: Synthetic and Systems Biotechnology
Article Title: Multi-omics analyses of evolved Corynebacterium glutamicum mutants reveal the molecular responses to formaldehyde stress
doi: 10.1016/j.synbio.2026.01.020
Figure Lengend Snippet: Effects of single-site mutations on formaldehyde tolerance. (A) Frequency of mutations of four bases in evolved strain FM-3. (B) Growth of strain FM-1 and its derivatives harboring single-site mutations on CGXII minimal agar medium supplemented with 10 g/L glucose and 1 mM formaldehyde. (C) Growth curves of strain FM-1 and its derivatives in CGXII medium supplemented with 10 g/L glucose and 0.8 mM formaldehyde. Values and error bars reflect the mean ± s.d. of three biological replicates (N = 3). Statistical significance at 31 h between FM-1- cgl1199 1015−1032del and FM-1 was determined by unpaired two-tailed Student's t -test: ∗∗∗P < 0.001.
Article Snippet:
Techniques: Two Tailed Test
Journal: Synthetic and Systems Biotechnology
Article Title: Multi-omics analyses of evolved Corynebacterium glutamicum mutants reveal the molecular responses to formaldehyde stress
doi: 10.1016/j.synbio.2026.01.020
Figure Lengend Snippet: Transcriptome analysis of FM-3 and FM-1 cultivated with or without formaldehyde stress. (A) Volcano plots of differential transcription levels in 1F vs. 1N, 3F vs. 3N, 3N vs. 1N, and 3F vs. 1F. (B) Changes in mRNA levels of genes involved in central metabolism and the respiratory chain between FM-3 and FM-1. Only significant changes (log 2 (fold change) ≥1 or ≤ −1, FDR≤0.05) are shown. Upregulated and downregulated genes are indicated with red and blue, respectively. 1F, FM-1 cultivated with formaldehyde stress. 1N, FM-1 cultivated without formaldehyde stress. 3F, FM-3 cultivated with formaldehyde stress. 3N, FM-3 cultivated without formaldehyde stress.
Article Snippet:
Techniques:
Journal: Synthetic and Systems Biotechnology
Article Title: Multi-omics analyses of evolved Corynebacterium glutamicum mutants reveal the molecular responses to formaldehyde stress
doi: 10.1016/j.synbio.2026.01.020
Figure Lengend Snippet: Comparison of proteomes between FM-3 and FM-1 cultivated with formaldehyde or without formaldehyde stress. Functional classification of transcriptome differences based on KEGG_small_class annotation in 3N vs. 1N (A), 3F vs. 1F (B). Proteins with differentially expression in 1F vs. 1N (C) and 3F vs. 3N (D). Only significant changes (log 2 (fold change) ≥1 or ≤ −1, FDR≤0.05) are shown. Proteins exhibiting increased or decreased abundance are highlighted in red and blue, respectively. 1F, FM-1 cultivated with formaldehyde stress. 1N, FM-1 cultivated without formaldehyde stress. 3F, FM-3 cultivated with formaldehyde stress. 3N, FM-3 cultivated without formaldehyde stress.
Article Snippet:
Techniques: Comparison, Functional Assay, Expressing
Journal: Synthetic and Systems Biotechnology
Article Title: Multi-omics analyses of evolved Corynebacterium glutamicum mutants reveal the molecular responses to formaldehyde stress
doi: 10.1016/j.synbio.2026.01.020
Figure Lengend Snippet: Effects of Cgl1590 mutations on formaldehyde tolerance. (A) Amino acid sequence alignment between Cgl1590 and its derivatives. (B) Effects of cgl1590 truncation on formaldehyde tolerance. (C) Effects of cgl1590 knock-out on formaldehyde tolerance. (D) Effects of cgl1590 overexpression on formaldehyde tolerance. Cells were treated with 0.8 mM formaldehyde as stress condition. Values and error bars reflect the mean ± s.d. of three biological replicates (N = 3). Analysis of cell length and morphology of FM-1 without formaldehyde stress (E), FM-1 containing cgl1590 750insG mutation without formaldehyde stress (F), FM-1 with formaldehyde stress (G), and FM-1 strain containing cgl1590 750insG mutation with formaldehyde stress (H). All strains were grown in CGXII minimal medium supplemented with 10 g/L glucose, with or without 0.8 mM formaldehyde, and examined by SEM. Cell length was determined by measuring 70 cells of each strain and analyzed using ImageJ software. Statistical significance at 36 h between FM-1-△ cgl1590 and FM-1 was determined by two-tailed Student's t -test: ∗∗∗P < 0.001.
Article Snippet:
Techniques: Sequencing, Knock-Out, Over Expression, Mutagenesis, Software, Two Tailed Test
Journal: Bioactive Materials
Article Title: ADGRG1-targeted hypoxia preconditioned extracellular vesicles ameliorate intervertebral disc degeneration by delivering taurine to disrupt the oxidative stress feedback loop-driven ferroptosis in nucleus pulposus cells
doi: 10.1016/j.bioactmat.2026.02.029
Figure Lengend Snippet: ADGRG1 have the capacity to serve as potential target for IVDD treatment. (A) Primary human NPCs were treated with TBHP at concentrations of 50 μM, 100 μM, 200 μM for 12 h, and the cellular ferrous ion levels were assessed by confocal microscopy using FerroOrange probe. FerroOrange fluorescence intensity was quantified, n = 3. Scale bar, 50 μm. (B) GSEA enrichment plots of gene data sets associated with oxidative damage response, ferroptosis, permeabilize mitochondria and mitochondrial respiratory chain complex assembly in TBHP‐treated primary NPCs, compared to the control. (C) Primary NPCs were treated with TBHP for 12 h and cell lysates were subjected to immunoblotting with indicated ADGRG1, IVDD and ferroptosis-related antibodies. (D) Volcano plot of differentially expressed genes in NPCs between the TBHP‐treated group and the control. |log2FC| > 2, FDR < 0.05. (E-F) Primary NPCs were incubated with TBHP for 12 h, followed by immunofluorescent staining with anti-ADGRG1 (green) and anti-4-HNE (red) antibodies and examination by confocal microscopy. The fluorescence intensity was quantified. n = 3. Scale bar, 50 μm. (G) Magnetic resonance imaging (MRI) showed the IVDD Pfirrmann grade of needle puncture IVDD rat models with 25G (MI-IVDD), 21G(MOD-IVDD) and18G (SE-IVDD), and statistical analysis was performed, n = 3. (H) Immunoblotting analysis showed the expression of IVDD markers (COL1A1) and ADGRG1 in IVDD rat models with different degrees of needle-puncture degeneration, n = 3. (I) Feature plots depict the average expression of ADGRG1 (color-scaled) across each cell cluster. (J) Immunoblotting analysis showed the expression of IVDD markers (COL1A1) and ADGRG1 in the NP tissue of clinical MI/SE degenerative IVDs. The relative ADGRG1 grayscale was quantified in (L), n = 10. (K) Representative images for colocalization analysis of ADGRG1 (green), 4-HNE (red) fluorescence in MI and SE NP tissues. n = 5. Scale bar, 50 μm. (L) Relative ADGRG1 grayscale in (J) and fluorescence intensity in (K) were quantified. All data are expressed as the mean ± SD. For panels A) and F–H), data were analyzed using one-way ANOVA with Tukey's multiple comparisons, while panel L) was assessed using a two-tailed unpaired Student's t-test. ∗ P < 0.05. ∗∗ P < 0.01. ∗∗∗ P < 0.001.
Article Snippet: After permeabilization and blocking with 10% goat serum containing 0.2% Triton X-100, the sections were incubated with primary antibodies against ADGRG1 (1:50; sc-390192, Santa Cruz Biotechnology), TOM20(11802-1-AP, Proteintech), 4-HNE(
Techniques: Confocal Microscopy, Fluorescence, Control, Western Blot, Incubation, Staining, Magnetic Resonance Imaging, Expressing, Two Tailed Test
Journal: Bioactive Materials
Article Title: ADGRG1-targeted hypoxia preconditioned extracellular vesicles ameliorate intervertebral disc degeneration by delivering taurine to disrupt the oxidative stress feedback loop-driven ferroptosis in nucleus pulposus cells
doi: 10.1016/j.bioactmat.2026.02.029
Figure Lengend Snippet: In vitro evaluation of the cargo transfer capacity and therapeutic potential of A1TP-HX-EVs. (A) Immunoblotting analysis confirmed the overexpression of GFP-tagged ADGEG1 protein in NPCs by retrovirus. (B) The live-cell workstation demonstrated the uptake of AIE-labeled A1TP-HX-EVs by NPCs in both the control group (GFP) and the ADGRG1 overexpression group (ADGRG1-GFP) within 24 h. (C) Representative images from the live-cell workstation showed the uptake of DPA-labeled HX-EVs at different concentrations by TBHP-treated NPCs within 24 h. Scale bar, 50 μm. (D) Representative images from the live-cell workstation showed the uptake of AIE-labeled A1TP-HX-EVs (DPA 10 μM) by primary NPCs within 24 h after treatment with different concentrations of TBHP for 12h. Scale bar, 50 μm. (E) AIE fluorescence intensity in (C-D) were quantified. n = 3. ∗ P < 0.05. ∗∗ P < 0.01. ns, not significant. (F) Primary NPCs were stained with FerroOrange probe and assessed by confocal microscopy. n = 3. Scale bar, 50 μm. (G) GSEA enrichment analysis of ferroptosis and oxidative damage response-related gene sets in A1TP-HX-EVs‐treated group and TBHP group NPCs. (H) Primary NPCs were induced with 100 μM TBHP for 12 h, and then treated with EVs, HX-EVs or A1TP-HX-EVs for 24 h. Cell lysates were immunoblotted with antibodies against IVDD markers and ferroptosis-related proteins and ADGRG1. (I) GSEA enrichment analysis of the mitochondrial respiratory chain complex assembly and transcriptional activation of mitochondrial biogenesis-related gene sets in A1TP-HX-EVs‐treated group and TBHP group NPCs. (J-K) Representative oxygen consumption traces of primary NPCs induced with TBHP and then treated as indicated for 24 h. Maximal respiration of NPCs were quantified. n = 3. (L) Primary NPCs were induced with TBHP, and then treated as indicated for 24 h, followed by immunofluorescent staining with anti-TOM20 (green) and anti-4-HNE (red) antibodies. n = 3. Scale bar, 50 μm. All data are expressed as the mean ± SD. For B) and E), two‐way ANOVA with Tukey 's multiple comparison tests were used for statistical analysis. For panels F) and K-L), one‐way ANOVA with Tukey's multiple comparison tests were used for statistical analysis. ∗ P < 0.05. ∗∗ P < 0.01. ∗∗∗ P < 0.001. ns, not significant.
Article Snippet: After permeabilization and blocking with 10% goat serum containing 0.2% Triton X-100, the sections were incubated with primary antibodies against ADGRG1 (1:50; sc-390192, Santa Cruz Biotechnology), TOM20(11802-1-AP, Proteintech), 4-HNE(
Techniques: In Vitro, Western Blot, Over Expression, Labeling, Control, Fluorescence, Staining, Confocal Microscopy, Activation Assay, Comparison
Journal: Bioactive Materials
Article Title: ADGRG1-targeted hypoxia preconditioned extracellular vesicles ameliorate intervertebral disc degeneration by delivering taurine to disrupt the oxidative stress feedback loop-driven ferroptosis in nucleus pulposus cells
doi: 10.1016/j.bioactmat.2026.02.029
Figure Lengend Snippet: Taurine is the key small molecule in A1TP-HX-EVs that activated the AMPK/NRF2 pathway to regulate nucleus pulposus cell repair. (A) The LC-MS/MS analysis was used to detect the differential active small molecule components between placental HX-EVs and EVs. (B) The SMPDB enrichment analysis identified pathways related to small molecules that are up-expressed in HX-EVs compared to EVs. The metabolic pathways marked in red are related to ferroptosis inhibition and mitochondrial function. (C) Volcano plot of small molecule in HX-EVs versus EVs. |log2FC| > 0.5, FDR <0.05. (D) The content of taurine in placental MSC (pMSC), hypoxia-induced pMSC(HX-pMSC) and their derived EVs was detected by ELISA. n = 3. (E) Primary NPCs cells were induced with TBHP, and then treated with EVs, HX-EVs, and A1TP-HX-EVs for 24 h. The cell lysates were subjected to ELISA assay to detect taurine content. (F) Two shRNA lentiviruses were designed to knock down TAUT a key enzyme in taurine uptake in pMSC. (G) The content of taurine in TAUT-sh1-pMSC and TAUT-sh2-pMSC derived EVs (KD-HX-EVs) was detected by ELISA. n = 3. (H) Primary NPCs were induced with TBHP, and then treated with A1TP-HX-EVs and A1TP-KD-HX-EVs for 24 h. Cell lysates were immunoblotted with indicated antibodies. (I) Primary NPCs were induced with TBHP, and then treated with A1TP-HX-EVs and A1TP-KD-HX-EVs for 24 h, followed by immunofluorescent staining with anti- TOM20 (green) and anti-4-HNE (red) antibodies. n = 3. Scale bar, 50 μm. (J) A CDO1-overexpressing retrovirus was designed to overexpress CDO1 in pMSCs. (K) The content of taurine in CDO1-OE-pMSC derived EVs (OE-EVs) was detected by ELISA. n = 3. (L) Primary NPCs were induced with TBHP, and then treated with treated A1TP-EVs and A1TP-OE-EVs for 24 h. Cell lysates were immunoblotted with indicated antibodies. (M) Primary NPCs were induced with TBHP, and then treated with A1TP-EVs and A1TP-OE-EVs for 24 h, followed by immunofluorescent staining with anti-TOM20 (green) and anti-4-HNE (red) antibodies. n = 3. Scale bar, 50 μm. (N-O) Representative oxygen consumption traces of primary NPCs induced with TBHP and then treated with A1TP-HX-EVs, A1TP-KD-HX-EVs, or A1TP-OE-EVs for 24 h. Maximal respiration of NPCs were quantified. n = 3. All data are expressed as the mean ± SD. For E), I), M) and O), one‐way ANOVA with Tukey's multiple comparison tests were used for statistical analysis. For D), G) and K), two‐tailed unpaired Student's t‐tests were used for statistical analysis. ∗ P < 0.05. ∗∗ P < 0.01. ∗∗∗ P < 0.001. ns, not significant.
Article Snippet: After permeabilization and blocking with 10% goat serum containing 0.2% Triton X-100, the sections were incubated with primary antibodies against ADGRG1 (1:50; sc-390192, Santa Cruz Biotechnology), TOM20(11802-1-AP, Proteintech), 4-HNE(
Techniques: Liquid Chromatography with Mass Spectroscopy, Inhibition, Derivative Assay, Enzyme-linked Immunosorbent Assay, shRNA, Knockdown, Staining, Comparison, Two Tailed Test