092 0.022 ENERGY METABOLISM_AMINO ACIDS AND AMINES 0.135 0.008 ENERGY METABOLISM_ATP-PROTON MOTIVE FORCE INTERCONVERSION,
BIOSYNTHESIS AND DEGRADATION OF POLYSACCHARIDES, PYRUVATE DEHYDROGENASE 0.005 ENERGY METABOLISM_GLYCOLYSIS_GLUCONEOGENESIS 0.088 0.238 ENERGY METABOLISM_SUGARS AND TCA CYCLE 0.077 0.089 SIGNAL TRANSDUCTION_PTS 0.033 0.008 CELL ENVELOPE_BIOSYNTHESIS AND DEGRADATION OF MUREIN SACCULUS AND PEPTIDOGLYCAN 0.068 0.015 CELL ENVELOPE_BIOSYNTHESIS AND DEGRADATION OF SURFACE POLYSACCHARIDES GW-572016 purchase AND LIPOPOLYSACCHARIDES 0.000 0.009 0.228 CELL ENVELOPE_OTHER 0.087 CELLULAR PROCESSES_CELL DIVISION 0.238 0.051 CELLULAR PROCESSES_PATHOGENESIS 0.237 CELLULAR PROCESSES_TOXIN PRODUCTION AND RESISTANCE 0.068 CENTRAL INTERMEDIARY METABOLISM_NITROGEN METABOLISM AND AMINO SUGARS 0.046 CENTRAL INTERMEDIARY METABOLISM_OTHER
0.140 PURINES, PYRIMIDINES, NUCLEOSIDES, AND NUCLEOTIDES 0.000 0.036 REGULATORY FUNCTIONS_OTHER 0.169 AR-13324 cost PROTEIN SYNTHESIS_TRNA AMINOACYLATION 0.083 PROTEIN FATE_DEGRADATION OF PROTEINS, PEPTIDES, AND GLYCOPEPTIDES 0.238 0.220 PROTEIN FATE_PROTEIN eFT-508 concentration AND PEPTIDE SECRETION AND TRAFFICKING 0.071 0.020 PROTEIN FATE_PROTEIN MODIFICATION AND REPAIR_PROTEIN FOLDING AND STABILIZATION 0.132 0.000 PROTEIN SYNTHESIS_RIBOSOMAL PROTEINS: SYNTHESIS AND MODIFICATION_TRANSLATION FACTORS 0.001 0.005 PROTEIN SYNTHESIS_TRNA AND RRNA BASE MODIFICATION 0.241 TRANSCRIPTION 0.030 DNA METABOLISM 0.249 Downregulation corresponds to negative correlation and upregulation corresponds to positive correlation with the fosfomycin concentration. Numbers show false discovery rates (FDR). Only gene sets Adenylyl cyclase with FDR < 0.25 in at least one time point are shown; bold is used when FDR < 0.05. To strengthen the reliability of the microarray data, qPCR analysis was performed for five differentially expressed genes - two peptidoglycan biosynthesis genes, murZ and sgtB, autolysin gene atl, cofactor biosynthesis gene ribB and oligopeptide transporter gene oppB (Figure 4). Figure 4 Verification
of microarray results by qPCR. Differential expression of atl, murZ, oppB, ribB, and sgtB genes was measured after 40 min of treatment with 1 μg/ml (t40c1) and 4 μg/ml (t40c4) of fosfomycin. The histograms show log2 fold changes (log2FC). The filled bars show qPCR data and the patterned bars microarray data. Cell envelope synthesis is strongly affected by fosfomycin treatment The GSEA results showed that specific subgroups of genes in the cell envelope group were regulated differently (Table 1). Genes involved in murein and peptidoglycan biosynthesis, including teichoic acid biosynthesis genes, were upregulated, while surface polysaccharide metabolism genes were downregulated. To interpret the changes in gene expression we visualized the data in Pathway Studio software.