Figure 1.
Fermentation profiles of encapsulated and free S. cerevisiae.
Glucose and ethanol concentration profiles of encapsulated (◊, □) and free (▵, ○) cells during anaerobic batch cultivations.
Table 1.
Key yields during anaerobic batch cultivations of free and encapsulated S. cerevisiae.
Figure 2.
S. cerevisiae encapsulated in alginate chitosan capsules.
Capsules full of cells at the time of sampling for proteome analysis. Major unit of the ruler is in centimetres.
Figure 3.
Proteome based pair-wise comparison of encapsulated and free S. cerevisiae.
Volcano plot illustrating the distribution of all proteins identified with the nLC-MS/MS approach. Significantly up- and down-regulated proteins (|fold change| ≥1.3, x-axis; FDR adjusted p value≤0.05, y-axis) are highlighted in green and red respectively. Statistically up- and down-regulated proteins with non-significant biological changes (|fold change| <1.3) are shown in light green and orange, respectively, and proteins with non-significant differences between the free and encapsulated yeast are shown in grey.
Figure 4.
Functional classification and cellular localization of proteins identified by the nLC-MS/MS approach.
Distribution of functional categories (A) and cellular localizations (B) of identified proteins in encapsulated and free S. cerevisiae, showing the number of proteins in the respective fold change class (non-regulated – black, up-regulated – grey, down-regulated – white) per functional category and cellular localization, respectively. Numbers next to bars indicate the total number of proteins in the category when extending past the y-axis range.
Table 2.
Functional categories enriched among down-regulated proteins.
Table 3.
Functional categories enriched among up-regulated proteins.
Figure 5.
The proteomic response on the central carbon metabolism upon encapsulation of yeast.
The central carbon metabolism is presented with up-regulated proteins with fold changes (encapsulated cells compared to free cells) in green, down-regulated proteins with fold changes in red and unaffected proteins with the measured fold changes in grey. The first number represents the fold change obtained by n-LC-MS/MS. Where applicable, this is followed by the average fold change obtained from 2-D DIGE spots with unique significant protein hits, and the average fold change obtained from spots with significant hits for co-migrating proteins in 2-D DIGE.
Figure 6.
Correlation between the proteomic methods 2-D DIGE and nLC-MS/MS with TMT®.
Correlation between the average ratios of 31 proteins (with single significant hits in spots on the gel) (A and B) and 33 co-migrating proteins (with two or more significant hits per spot on the gel, giving uncertainties in the quantification of each individual protein in the spot) (C and D) proteins obtained by 2-D DIGE (RDIGE) and nLC-MS/MS (RMS/MS). A and C, the ratios obtained by nLC-MS/MS divided by the mean ratios obtained by 2-D DIGE, for single significant hit spots and spots with co-migrating proteins respectively. Triangles indicate extremely up-regulated proteins (fold change >2.5) as measured by the nLC-MS/MS approach and squares indicate proteins showing different sign of the fold change in the two approaches. The proteins were sorted by increasing fold change values obtained by the 2-D DIGE approach and divided into three groups, depending on the expression according to 2-D DIGE. Proteins marked with * had invariant expression in the nLC-MS/MS approach, and those marked with “were up-regulated. Proteins in parentheses (Sam2p) had extremely large RSD among the replicates in nLC-MS/MS and missing values indicate that the protein was not detected in the nLC-MS/MS approach (Ssa2p, Rpl9bp, Rps0bp). B and D, correlation plots of the ratios obtained by DIGE (x-axis) against the ratios obtained by nLC-MS/MS (y-axis), for unique (B) and co-migrating (D) protein spots, respectively. Extremely up- or down-regulated proteins (triangles) as well as the three and eight proteins showing different expression with the two methods (squares) were excluded from the calculation of the correlation.