Fig. 2
Quantification of the intracellular proteins and carbohydrate-active enzyme (CAZy) family proteins of T. guizhouense in different treatments based on SWATH analysis. a Location and total abundances for each grouped protein identified by SWATH analysis. RI: ribosome, ER: endoplasmic reticulum, CY: cytoplasm/cytosol, NU: nucleus, GA: Golgi apparatus, Mit: mitochondria, CW: cell wall, CS: cytoskeleton, PM: plasma membrane, VA: vacuole, PE: peroxisome, VE: vesicle. b Volcano plot of all the identified proteins with different abundances between T37 and T28. The P-value was plotted against the expression fold change of all detected proteins within the different groups. Data points in the lower center area of the plots (cyan circles) display unchanged or proteins with no significant fold change. Data points in the upper quadrants indicate proteins (filled circles) with significant negative (blue circles) and positive (red circles) changes in protein abundance. c Protein–protein interaction (PPI) analysis in T37 compared with T28. The nodes are proteins (circles) or KEGG/CAZy categories (yellow diamonds); the edges are protein interactions defined by KEGG or CAZy databases. Protein node sizes indicate the log10 of protein expression values. Node colors represent the fold change (red, upregulated; blue, downregulated) of protein expression values between different treatments. Numbers 1 to 15 indicate different pathways. 1: Glycoside hydrolase, 2: starch and sucrose metabolism, 3: oxidative phosphorylation, 4: fatty acid biosynthesis, 5: citrate cycle (TCA cycle), 6: auxiliary activities, 7: proteasome, 8: purine metabolism, 9. Ribosome, 10: Glycolysis/Gluconeogenesis, 11: Carbohydrate esterases, 12: Spliceosome, 13: Transport, 14: Protein processing in the ER, 15: Other glycan degradation. d Abundance ratio of the proteins involved in the critical pathway based on SWATH (T37/T28). Nodes represent the fold change (red, upregulated significantly; blue, downregulated significantly; yellow and green, no significant difference) of protein content values between different treatments. RI: ribosome, GG: glycolysis/gluconeogenesis, MM: microbial metabolism in diverse environments, PM: pyruvate metabolism, PP: protein processing in the ER, FA: fatty acid metabolism, TCA: TCA cycle. e, Hierarchical cluster analysis of the CAZy family proteins between T28 and T37. Red and blue indicate relatively high and low protein abundance, respectively, and white indicates equal median abundance