Most striking were the changes in protein synthesis (0.6% vs. 18.1% in vitro and in vivo, respectively) and purine, pyrimidine and nucleotide
biosynthesis Ferrostatin-1 order (1.2% vs. 5.8%). In contrast, activity decreases in vivo were denoted for regulatory processes (4.9% vs. 1.8%), cell envelope functions (5.6% vs. 2.3%) and transport (10.5% vs. 7%). Overall, the graphic in Figure 5 clearly illustrates that the SD1 cells adapt to the host intestinal environment by alternating a multitude of their cellular pathways and processes. Figure 3 SD1 differential protein expression analysis using the two-tailed Z-test. Approximately 300 proteins were found to be differentially expressed at 99% confidence, including 151 in vivo and 142 in vitro SD1 proteins selleck using
the two-tailed Z-test utility in the APEX tool application. Figure 4 Hierarchial clustering (HCL) analysis of differentially expressed SD1 proteins based on APEX abundance values using MeV. Protein abundance values from the in vitro sample are represented on the left, with in vivo protein abundances on the right. Abundance magnitude is depicted as a color gradient, with red indicating an increase in protein abundance, green indicating a corresponding decrease in abundance, and black for the median level of abundance. Based on biological interests, example clusters are enlarged to depict differentially expressed proteins. Figure 5 Representation of functional role categories of SD1 proteins. Proteins identified from 2D-LC-MS/MS experiments of S. dysenteriae cells were analyzed based on protein functional Histone demethylase assignments in the CMR database for the genome of SD1 strain Sd197. Distribution of role categories of SD1 proteins cultured from stationary phase cells (in vitro) are shown in the panel
on the left (5A) and cells isolated from gut environment of infected piglets (in vivo) are depicted on the right (5B). Differential expression analysis of the APEX datasets revealed several biochemical processes that appeared to be important for the pathogen to infect the piglets and to survive in their intestinal environment. Strongly altered abundances in the in vivo environment pertained to proteins involved in mechanisms of acid resistance (GadB, AdiA, HdeB, WrbA), the switch from aerobic to anaerobic respiration and mixed acid fermentation (PflA, PflB, PykF, Pta), oxidative stress (YfiD, YfiF, SodB) and other general cellular stress responses involving cold and heat shock proteins (CspA, CspE, ClpB). The in vivo responses suggested enhanced bacterial stress under oxygen- and nutrient-limited conditions in the host gut environment. In contrast, the in vitro proteome was defined by high abundances of enzymes involved in fatty acid oxidation (FadA, FadB, FadD, etc.) and aerobic respiration (GltA, IcdA, SdhA, SucA, etc.).