For complete gene names and the fold changes in gene expression
see Additional file 1: Analyzed microarray data. Table 4 Nutrient-acquisition, replication and virulence genes expressed differentially* by the BALF-exposed malT mutant Type of the product encoded by the differentially expressed gene Up-regulated genes Down-regulated CBL-0137 mouse genes Biofilm-formation proteins pgaA, pgaC, tadF, apfB Toxin apxIVA Factors imparting resistance to antimicrobials ostA, ccp Peptidoglycan and LPS biosynthetic enzymes cpxD, mrdA dacA, murA, mltA, dacB, mreD, fbB1, kdsB, gmhA Membrane proteins ompP1 ompW, oapB Amino acid transporters brnQ, sdaC Carbohydrate transporter mtlA ptsB, rbsD Iron transport proteins cbiO exbD2, afuB_2, frpB, yfeC, exbB2 Protein/peptide transport proteins dppF Other cation transporters ptsN Cell division fic Lipid transporters glpF Factors involved in adaptation to unusual environment relA DNA transformation
comEA, comF DNA degradation proteins xseA Selleck P5091 DNA replication, recombination proteins recG, rdgC, recJ xerC, recR, priB, polA, ligA, recA, Protein-fate proteins htpX, prlC ecfE Nucleotide metabolism enzymes purC, purD, purT Phopholipid and fatty acid biosynthesis and degradation enzymes namA accA, fabD * Differential expression of a gene in the malT mutant is relative to the level of expression of the gene in the wild-type organism (Kinesin inhibitor reference sample). For complete gene names and the fold changes Tobramycin in gene expression see Additional file 1: Analyzed microarray data. Expression of selected genes representing biological functional categories of interest was also measured by real-time PCR analysis (Table 5). A good
corroboration in the context of the up- and down-regulation of the genes was found between the microarray and real-time PCR data. Table 5 Verification of microarray data by real-time PCR Gene Putative function ΔΔCT ± SD Fold change by real-time PCR Fold change by microarray1 dmsA (T) Anaerobic dimethyl sulfoxide reductase chain A precursor 3.45 ± 1.41 0.091 (0.03-0.24) 0.15 dmsA (R) 0 ± 0.51 1 (0.69-1.42) dmsB (T) Anaerobic dimethyl sulfoxide reductase chain B 2.54 ± 1.61 0.17 (0.05-0.52) 0.34 dmsB (R) 0 ± 0.46 1 (0.72-1.38) napB (T) Nitrate reductase cytochrome c-type subunit 2.24 ± 0.41 0.21 (0.15-0.28) 0.17 napB (R) 0 ± 0.49 1 (0.71-1.40) napF (T) Ferredoxin-type protein NapF 2.24 ± 0.46 0.21 (0.07-0.61) 0.09 napF (R) 0 ± 0.47 1 (0.71-1.39) napD (T) Putative napD protein 2.39 ± 0.34 0.18 (0.14-0.24) 0.18 napD (R) 0 ± 0.54 1 (0.68-1.46) ilvH (T) Acetolactate synthase small subunit -2.60 ± 0.36 6.08 (4.68-7.90) 6.14 ilvH (R) 0 ± 0.45 1 (0.70-1.41) pgaA (T) Biofilm PGA synthesis protein PgaA precursor -2.04 ± 1.08 4.11 (1.94-8.70) 8.18 pgaA (R) 0 ± 0.74 1 (0.59-1.