Table 1.
Primary cellular role of genes that affect curli production.
| Function | COG Group | Number (% Total) | Genes (Dark Mutants Are Bold) |
|---|---|---|---|
| Information Storage | |||
| Translation, ribosome structure, and biogenesis | J | 13 (4.2) | efp, miaA, pcnB, poxA, rbfA, rimK, rimM, rplA, rpsF, rpsT, rsgA, srmB, truB |
| Transcription | K | 43 (13.8) | aaeR, arcA, asnC, cpxR, crp, cra, csgD, cusR, cysB, cytR, dksA, fliT, fhlA, flgM, gcvA, greA, hdfR, hfq, ihfA, ihfB, mlrA, mtlR, nagK, nanK, nusB, ompR, perR, purR, puuR, rcsB, rffC, rpoN, rpoS, rpoZ, rstA, sdiA, srlR, treR, waaH, xapR, ydcI, yieP, ynaK |
| DNA replication, recombination, and repair | L | 11 (3.5) | atl, dam, dnaG, dnaT, ihfA, ihfB, nudC, nudL, priA, rnhA, rppH |
| Cellular processes | |||
| Cell envelope biogenesis, outer membrane | M | 29 (9.3) | csgA, csgB, csgE, csgF, csgG, cusB, galU, lpp, mdoH, mltA, mltB , nlpD, ompC, ompF, rcsF, pal, rfe, rffA, rffT, slp, tolc, waaC, waaD, waaE, waaF, waaG, waaP, wzxE, ycgV |
| Cell motility and secretion | N | 5 (1.6) | cpxP, flgM, fliI, tolA, ycbR |
| Posttranslational modification, protein turnover, chaperones | O | 11 (3.5) | ccmA, clpA, clpP, clpX, dnaK, lon, sspA, surA, yfgC, yjjW, yncG |
| Inorganic ion transport and metabolism | P | 14 (4.5) | cpxP, cysC, cysI, ddpD, dps, fepB, fepC, fepD, fepG, fes, mdfA, mdoG, nhaA, yoeE |
| Signal transduction mechanisms | T | 23 (7.4) | arcA, clpX, cpxA, cpxP, cpxR, crp, cusR, dksA, envZ, fhlA, gmr, kdpD, narQ, ompR, qseC, rseA, rstA, rstB, uspE, ydaM, yedV, yeiL, zraR |
| Defense Mechanism | V | 2 (0.6) | cusB, yfeW |
| Metabolism | |||
| Energy production and conversion | C | 37 (11.9) | aceE, aegA, appC, aspA, atpA, atpB, atpC, atpE, atpF, atpG, atpH, dlgD, fadH, hybD, lpd, nuoA, nuoB, nuoC, nuoE, nuoF, nuoG, nuoJ, nuoK, nuoM, nuoN, putA, racC, sdhA, sdhB, sdhC, sdhD, sucA, sucC, ubiF, ubiH, ydiT, yjjW |
| Amino acid transport and metabolism | E | 28 (9.0) | argC, aroA, aroB, aroC, aroD, aroE, aroH, aroK, aroP, aspA, aspC, carA, carB, cysE, ddpD, eamA, glnA, gmhB, mdfA, metC, pepT, proW, speB, trpA, trpB, trpC, trpD, trpE |
| Nucleotide transport and metabolism | F | 22 (7.1) | carA, carB, cmk, cyaA, guaB, ndk, purA, purC, purD, purE, purF, purH, purK, purL, purM, purU, pyrB, pyrC, pyrD, pyrE, pyrF, thyA |
| Carbohydrate transport and metabolism | G | 21 (6.7) | eamA, fbp, glmM, glvG, glxK, gmhA, gnd, lapB, lsrF, mdfA, nagA, nagC, nagK, nanE, nanK, pgm, ptsH, ptsI, rafD, tktA, tpiA |
| Coenzyme metabolism | H | 8 (3.8) | cysG, fepC, lipA, lipB, pdxH, rimK, trpA, trpB, ubiE, ubiF, ubiG, ubiH |
| Lipid metabolism | I | 3 (1.0) | fabF, fabH, fadJ |
| Secondary metabolites | Q | 2 (0.6) | fabF, paaI |
| Poorly characterized | |||
| General function prediction | R | 14 (4.5) | essQ, ilvG, iptB, nudL, php, rapZ, rppH, uidC, ybcI, ybgC, ydeJ, yeiR, ygfZ, yheV, ynjD, yqaB |
| Unknown/Other | S,U | 22 (7.1) | mdoC, rodZ, tolB, tolQ, tolR, tomb, torI, tpr, ybaM, ybaP, yciC, ydaF, ydaT, ydbH, yecH, yedQ, yeeN, yfcL, ygiU, yicC, ykgH, ymgE |
COG: clusters of orthologous groups.