Table 3. Functional analysis of the genetic response of E. coli cells to ionic silver.
Selected functional categories enriched (p-value < 0.05) in groups of genes with generally strongly down-regulated expression (clusters 3 and 4), weakly down-regulated expression (cluster 5) and up-regulated expression (cluster 6) are included. For each category, associated genes are also listed.
| Functional category | Gene |
|---|---|
| Strong down-regulation (clusters 3 and 4) | |
| Metabolic process | |
| Glycolysis | sucA, lpd, eno, fbaAB, gpmAM, pykF, pgi |
| Glyoxylate cycle | aceA,B,K, iclR |
| Galactitol | gatA,B,C,D |
| Amino acids | folD, ilvH,I,D,B, hisA,B,C,D,F,G,H,I, trpC,D,E, aroA,C,G,K, pheA |
| Bases | adk, fold, guaA, gmk, purB,C,D,F,K,H,L,M,N,T,U, carA,B, pyrCDGH, relA, spoT, thyA |
| Glycogen energy reserve | glgB,C,P,X |
| Transport | |
| Maltose | malE,F,K |
| Proteins and peptides | dppA,B,C,D,F, oppA,B,C,D,F, secA,B, lolB,C,E, tatA,B |
| Iron | fecIR, fep, fes, fhuC,E, feoAB, tolC, tonB, entACDE, fiu, efeO, fre |
| Lipopolysaccharides | lptA,B,C,D |
| Electrons | frdA, napA, narG, nirB, nuoA,B,C,E,F,G,H,I,J,K,L,M,N, cyoA,B,C, sucB,C,D, sdhA,C,D, aceA,B,K, lpd, dld, ppc |
| Protons | atpB,D,F,H,I |
| Membrane biogenesis | |
| Lipopolysaccharides | rfbAC,D,X, waaF,G,Q, wbbI,J,K, rffEG, rfaD, rmlB, rfc, rfe, glf, cld, lpxD,H,P, kdsD, glmU, gmhB, yijP |
| Cell outer membrane | bamA,D, lptD, hlpA, surA |
| Cell shape regulation | murB,C,E, mreB,C,D, rodZ, dacA, ftsW, mpl, mraY, yafK, glmU, ispU |
| Translation | |
| Ribosome generation | rsuA, rluB,D,E |
| tRNA synthetase | aspS, gltX, glyS,Q, hisS, lysS, metG, pheS, trpS |
| Translation termination | frr, prfA,B,C |
| Cell motility, chemotaxis and flagellum organization | cheA,B,R,W,Y,Z, dppA, flgA,B,C,D,E,F,G,H,I,J,K,L,M,N, flhA,C, fliC,D,F,G,H,I,J,K,L,M,N,O,S,T, frdA, motA,B, rbsB, tap, tar, tsr, yhjH |
| Small down-regulation (cluster 5) | |
| Transport | |
| Copper ion transmembrane | zupT, cusA,B,C,F |
| Organic anion | abgT, glcA, phnC,J,L,O,P, gltS, ychM |
| Protein secretion (type II system) | hofC, yghF, gspC,E,F,G,J |
| Gluconate | ygbN, dsdX, gntP, idnT, yjhF |
| Metabolic process | |
| Aromatic compound | paaF,G,H,J, hcaC,D,F, mhpC,D,E,F, tyrR, feaB, hcaB, tnaA |
| Organic acids | dgoA,D,K, yjjM, cynT,S,X |
| Arabinose | araA,C, sgbE, fucI,K |
| Purines | yagR,S, allA,C, xdhA,B,C,D |
| Arginine | speA, astB,C,D,E |
| Up-regulation (cluster 6) | |
| Response to stimulus | |
| Stress | clpB, dnaJ,K, htpG,X, lon, pspA,B,C,D,G, raiA, psiE, dps, ibpA,B, ydeI, rmf, bhsA, ariR, yodD, zinT, ygaW, ygiW, yhbO, ytfE, tisB, mntH |
| Heat | dnaJ,K, htpG, lon, pspA, ibpA,B, yhbO |
| Hydrogen peroxide | ydeI, ariR, yodD, ygiW |
| Copper ion | cueO, copA |
| Cadmium ion | zintT, ygiW |
| Acidity | asr, yodD |
| Transport | |
| Divalent metal ion | chaA, mgtA, mntH |
| Inorganic anion | yfeO, narU, sbp |
| Biofilm formation | ydeH,I, bhsA, ariR, yodD, msqR, ygiW |
| Homeostasis | |
| Cellular sodium ion | chaA, nhaA |
| Biosynthetic process | |
| Methionine | metA,B,F,R, mmuM |
| Arginine | argA,B,C |