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Table 2 Key effects of the measured gene expression differences after administration of IQ-143 compared to untreated S. epidermidis RP62A

From: Modeling antibiotic and cytotoxic effects of the dimeric isoquinoline IQ-143 on metabolism and its regulation in Staphylococcus aureus, Staphylococcus epidermidisand human cells

Concentration of IQ-143 (μM) Enzymes affecteda Effect on enzymesb Phenotypic effectsc
0.16 μM SERP0290-zinc-transport_efflux Down-regulated  
  SERP0291-zinc-transporter_import Down-regulated 40% biofilm inhibition
  SERP0292-iron-dicitrate-transporter_import Down-regulated No growth inhibition
  SERP2179-choline/betaine/carnitine-transp_efflux Up-regulated  
1.25 μM SERP0290-zinc-transport_efflux Down-regulated  
  SERP0291-zinc-transporter_import Down-regulated  
  SERP0292-iron-dicitrate-transporter_import Down-regulated  
  SERP0653-FGAM synthetase-rn:R04463 Down regulated  
  SERP0655-amidophosphoribosyltransferase-rn:R01072 Down-regulated  
  SERP0656-AIR synthetase-rn:R04208 Down-regulated  
  SERP0657-GAR formyltransferase-rn:R04325 Down-regulated  
  SERP0658-AICAR transformylase-rn:R04560 Down-regulated ~100% biofilm inhibition
  SERP0659-glycinamide ribonucleotide synthetase-rn:R04144 Down-regulated ~100% growth inhibition
  SERP0686-spermidine/putrescine-transport_import Up-regulated  
  SERP0687-spermidine/putrescine-transport_import Up-regulated  
  SERP0688-spermidine/putrescine-transport_import Up-regulated  
  SERP0765-Uracil-permease-transport_import Up-regulated  
  SERP0831-DNA polymerase-rn:R00375 Up-regulated  
  SERP0831-DNA polymerase-rn:R00376 Up-regulated  
  SERP0831-DNA polymerase-rn:R00378 Up-regulated  
  SERP0831-DNA polymerase-rn:R00379 Up-regulated  
  SERP0841-PNPase-rn:R00437 Up-regulated  
  SERP0841-PNPase-rn:R00439 Up-regulated  
  SERP1403-MultiDrug-transport_efflux Up-regulated  
  SERP1802-cobalt/nickel-transport_efflux Up-regulated  
  SERP1803-cobalt/nickel-transport_efflux Up-regulated  
  SERP1944-MultiDrug-transport_efflux Up-regulated  
  SERP1951-lipoprotein-transport_efflux/import Down-regulated  
  SERP1952-macrolide-transport_efflux Down-regulated  
  SERP1997-formate/nitrite-transport_efflux/import Up-regulated  
  SERP2060-glyerol-transport_import Up-regulated  
  SERP2179-choline/betaine/carnitine-transp_efflux Up-regulated  
  SERP2186-ATP-sulfurylase;-rn:R00529 Down-regulated  
  SERP2283-phosphonate-transport_import Up-regulated  
  SERP2289-MultiDrug-transport_efflux Up-regulated  
  1. aLocus tags are given first (SERP numbers), followed by abbreviated biochemical name and then KEGG reaction numbers (always starting with - m:R...). The effects on S. aureus USA300 were modeled (Table S20 in Additional file 1), are similar overall, and were validated by metabolite measurements. bDown-regulated means that gene expression was halved (or more then halved); up-regulated means that gene expression was doubled (or more than doubled). Specific values are given in Tables S5 and S6 in Additional file 1. All the enzymes with key changes in expression are part of the complete simulated metabolic model. cThe phenotypes are combination effects of the complete networks, not of single modes (see also Figure S2 in Additional file 1).