Fig. 3: Proteome remodeling during A. castellanii encystment.

a Proteogenomic pipeline and proteome coverage. The number of genes identified in the genome of reference of A. castellanii strain Neff as well as in the de novo transcriptome are plotted next to the number of protein sequences in the proteome of reference in Uniprot. These were utilized to generate a custom proteomics database for protein identification by MS/MS. In this data set, we identified 8677 protein groups matched to sequences from the proteome of reference (“Uniprot”), the transcriptome (“trans.”) or present in both (gray). The protein groups quantified at both transcript and protein (“prot.”) level are presented on the right, next to the number of protein groups significantly regulated in the transcriptome (green), le proteome (purple) or both (black). b Normalized distribution of the log2-transformed fold changes relative to T0 control in the proteome (purple) and the corresponding transcripts (green) in the control condition (left) and during encystment (right). Time points are indicated next to the corresponding density. c Clusters of significantly regulated protein groups. The dot plot is color-coded with the mean of log2-transformed fold change relative to the control condition (0 h) for each cluster during encystment and in the control condition (1, 4, 8 h). The size of each dot is proportional to the number of protein groups per cluster (indicated on the right). Significantly enriched GO terms in the different protein clusters are indicated on the right side of the plot (cellular component, biological process and molecular function are represented with a circle, a triangle and a square, respectively). The detailed outputs of the enrichment can be found in Supplementary Data 2 file. d Comparison of transcript- and protein-level regulation. The log2-transformed fold changes relative to T0 of protein groups from each cluster presented in (c) were plotted next to the corresponding transcripts at the three time points (x-axis) in the control (gray) and encystment condition (transcripts and protein groups are in green and purple, respectively). Median values are presented by a horizontal bar.