TABLE 1.
Functional classification of genes with statistically significant decreases and increases in mRNA level in E. coli strain BW25113a
| Category and expression status | GO concerned | P value | Gene examples |
|---|---|---|---|
| Overexpressed | |||
| Cell wall and adhesion | GO:0009103; lipopolysaccharide biosynthetic process | 2.66E−14 | waaO, wbbJ, arnC, wcaB, waaB, waaJ, waaY, waaU, rfbA, rfbC |
| GO:0022610; biological adhesion | 8.85E−12 | dgcZ, elfA, yadK, yehA, pgaC, yeeJ, csgB, csgF, csgE, csgG | |
| GO:0043711; pilus organization | 4.79E−10 | htrE, yehB, ybgQ, elfC, sfmD, ydeT, yqiG, fimD, sfmC, elfD | |
| Response to host | GO:0006952; defense response | 4.50E−07 | casE, casD, casC, casB, casA, abpA, abpB, rzpD, rrrQ, rzpR |
| GO:0009243; O antigen biosynthetic process | 4.86E−05 | rfbC, rfbD, rfbB, rfbA, wbbI, rfbX | |
| Response to acidic pH | GO:0010447; response to acidic pH | 6.07E−05 | cadB, yjaA, hdeA, iraM, oxc, frc, glsA, yagU, evgS, hdeB |
| Copper ion homeostasis | GO:0006878; cellular copper ion homeostasis | 7.59E−04 | cusA, cusB, cusC, cusF |
| Involved in glucarate catabolic process | GO:0019394; glucarate catabolic process | 1.67E−04 | garKLR, gudD |
| Underexpressed | |||
| Locomotion | GO:0040011; locomotion | 1.28E−24 | fliL, flgB, flgC, flgG, flgD, flgE, flgF, motA, fdrA, fliG |
| Cellular respiration | GO:0045333; cellular respiration | 6.09E−15 | frdB, hyaA, hyaB, pflD, fdoG, fdoH, frdA, frdC, frdD, hybB |
| Primary metabolism | GO:0019321; pentose metabolic process | 2.11E−10 | rbsD, rbsK, xylA, araD, araA, araB, xylF, xylG, xylH, rhaD |
| GO:0016052; carbohydrate catabolic process | 3.19E−9 | treC, lacZ, melA, malS, gldA, hybA, gatY, uidA, gntK, gntP, gntT | |
| GO:0008643; carbohydrate transport | 4.84E−09 | kdgT, gntP, gntT, ptsG, yiaO, melB, rbsA, srlB, frwC, treB | |
| GO:0071941; nitrogen cycle metabolic process | 2.45E−08 | argG, argI, argF, carA, ygeW, napC, nirB, narG, nirD, nirC | |
| GO:0006099; tricarboxylic acid cycle | 5.99E−07 | sdhD, sdhC, sdhB, acnA, sucA, fumB, mdh, sdhA, sucD, sucC |
a
mRNA levels were examined in E. coli strain BW25113 in modified M9-DHA medium and compared to values for M9 glucose medium (60). The Clusters of Orthologous Groups (COG) were used for grouping.