BMC Genomics 2009, 10(Suppl 2):S4 http://www.biomedcentral.com/1471-2164/10/S2/S4 Table 1: Differential expression of P. multocida genes involved in SOS response Product Name AMX* CTC* GeneID 1244239 1244433 1244528 1244611 1244637 1244659 1244737 1244795 1244828 1244993 1245061 1245083 1245184 1245314 1243539 1243679 1243758 1243814 1244020 1244323 1244324 1244459 1244499 1244507 1244526 1244563 1244666 1244774 1244823 1245063 1245164 1245177 1245268 1245298 1243785 1244083 1244087 1245051 1245095 1245163 ImpA DNA-binding protein Fis LexA repressor Hypothetical protein PM1264 Transcriptional repressor protein MetJ Hypothetical protein PM1312 DNA-directed RNA polymerase subunit alpha Hypothetical protein PM1448 Hypothetical protein PM1481 Hypothetical protein PM1646 Hypothetical protein PM1714 DNA-directed RNA polymerase subunit beta' ATP-dependent helicase HepA DNA-binding transcriptional activator GutM Hypothetical protein PM0192 Hypothetical protein PM0332 DNA-dependent helicase II DNA polymerase IV Hypothetical protein PM0673 Holliday junction DNA helicase B Holliday junction DNA helicase motor protein DeaD DNA repair protein RadC DNA polymerase III subunit beta Primosomal replication protein N DNA polymerase III subunit delta MutY RecQ DNA gyrase subunit B NAD-dependent DNA ligase LigA Recombinase A DNA mismatch repair protein ATP-dependent RNA helicase RhlB Excinuclease ABC subunit A Hypothetical protein PM0438 Hypothetical protein PM0736 Hypothetical protein PM0740 ClpB ATP-dependent protease ATP-binding subunit Recombination regulator RecX Locus impA fis lexA - metJ - rpoA - - - - rpoC hepA gutM recJ recN uvrD dinP - ruvB ruvA deaD radC dnaN priB holA mutY recQ gyrB ligA recA mutS rhlB uvrA ftsH DnaK dnaJ clpB hslU recX -0.52 ns ns -0.78 -0.53 -0.56 ns -0.81 -0.53 -0.62 -0.74 ns -0.77 -0.55 -0.77 ns ns -0.76 -0.63 ns ns -0.78 -0.52 ns ns ns -0.68 -0.86 ns -0.84 ns -0.87 -0.73 -0.78 -0.94 ns -0.74 -0.66 -0.70 -0.54 -0.53 ns 1.60 -0.57 -0.74 -0.68 -0.77 -0.70 -0.51 ns -0.91 -0.76 -0.77 -0.69 -0.79 ns ns -0.83 -0.81 -0.78 ns -0.72 -0.60 ns ns -0.88 -0.86 -0.84 1.36 1.08 ns -0.78 -0.83 ns -0.80 -0.74 -0.79 ns ns -0.78 ENR* 4.55 1.41 9.87 ns -0.80 -0.31 1.27 1.29 -0.51 -0.70 ns -0.87 1.69 -0.62 1.24 11.54 4.26 1.83 -0.47 2.37 3.39 -0.67 -0.65 1.41 1.67 1.38 1.17 1.11 1.45 1.56 9.96 1.50 1.07 2.57 1.13 1.50 1.29 2.14 2.58 6.44 * Ratio of treatment/control normalized intensities. ns: no significant change in gene expression with sub-MIC of antibiotic. ion transport and metabolism) and Q (secondary metab- olites biosynthesis, transport and catabolism). Effects of antibiotics on known target genes We observed altered expression of some of the known tar- gets (direct or inferred based on mechanism of action) with each antibiotic. CTC reduced the expression of genes encoding ribosomal proteins S4 and S7, which interact with tetracyclines [16]. One quarter-MIC of ENR resulted in a 1.5 fold increase in the expression of gyrB, which encodes a known ENR target, DNA gyrase B (Table 2). We had previously reported that the expression of RecA pro- tein increased in response to sub-MIC of ENR [10], and in the current study we detected increased expression of recA. With AMX, except for the expression of ponC, there were no detectable differences in the expression of genes encoding penicillin binding proteins (pbp). There was a 50% decrease in ponC (pbp) gene expression. However, this was a not an AMX specific effect, as all three antibiot- ics caused a decrease in ponC gene expression. While regulation of expression of known targets is an expected response to antibiotics, it is not a consistent find- ing; expression of the target is usually not affected. For example, microarray analysis showed that enrofloxacin, trimethoprim, brodimoprim, and cefquinome had no effects on expression of their targets in P. multocida [12]. However, even though expression of the known antibiotic Page 3 of 10 (page number not for citation purposes)