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. 2019 Jul 18;85(15):e00768-19. doi: 10.1128/AEM.00768-19

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.