TABLE 3.
Numbers of significantly up- and downregulated E. coli MG1655 genes in each functional group for the E. coli strains during biofilm growth in urine compared to the level of expression during planktonic growth in urine
| Functional group | No. (%) of genesa |
||||||
|---|---|---|---|---|---|---|---|
| Upregulated genes in biofilm |
Downregulated genes in biofilm |
Total | |||||
| M366 | MS2034 | 83972 | M366 | MS2034 | 83972 | ||
| Amino acid transport and metabolism | 28 (9) | 39 (13) | 36 (12) | 93 (31) | 102 (34) | 85 (29) | 296 |
| Carbohydrate transport and metabolism | 39 (13) | 40 (13) | 37 (12) | 81 (27) | 94 (32) | 90 (30) | 298 |
| Cell cycle control, mitosis, and meiosis | 6 (19) | 9 (29) | 7 (23) | 8 (26) | 9 (29) | 6 (19) | 31 |
| Cell motility | 4 (4) | 7 (8) | 14 (15) | 4 (4) | 4 (4) | 3 (3) | 91 |
| Cell wall/membrane biogenesis | 25 (13) | 28 (14) | 28 (14) | 45 (23) | 54 (27) | 37 (19) | 200 |
| Coenzyme transport and metabolism | 22 (20) | 24 (22) | 23 (21) | 16 (15) | 24 (22) | 16 (15) | 108 |
| Defense mechanisms | 2 (6) | 3 (9) | 9 (26) | 6 (17) | 9 (26) | 1 (3) | 35 |
| Energy production and conversion | 25 (10) | 21 (9) | 32 (13) | 71 (30) | 84 (35) | 74 (31) | 240 |
| Function unknown | 45 (18 | 52 (21) | 65 (26) | 50 (20) | 61 (25) | 43 (17) | 247 |
| General function prediction only | 48 (18) | 45 (17) | 68 (25) | 48 (18) | 61 (23) | 42 (16) | 269 |
| Inorganic ion transport and metabolism | 24 (15) | 32 (20) | 40 (25) | 22 (14) | 34 (21) | 18 (11) | 160 |
| Intracellular trafficking and secretion | 9 (25) | 13 (36) | 8 (22) | 5 (14) | 4 (11) | 7 (19) | 36 |
| Lipid transport and metabolism | 12 (17) | 12 (17) | 11 (15) | 12 (17) | 18 (25) | 17 (24) | 71 |
| Nucleotide transport and metabolism | 19 (24) | 19 (24) | 14 (18) | 10 (13) | 20 (26) | 13 (17) | 78 |
| Posttranslational modification, protein turnover, and chaperones | 19 (16) | 25 (21) | 31 (26) | 22 (18) | 31 (26) | 19 (16) | 119 |
| Replication, recombination, and repair | 26 (16) | 30 (18) | 33 (20) | 20 (12) | 23 (14) | 18 (11) | 165 |
| Secondary metabolites biosynthesis, transport, and catabolism | 4 (7) | 5 (9) | 5 (9) | 16 (30) | 20 (37) | 16 (30) | 54 |
| Signal transduction mechanisms | 19 (16) | 19 (16) | 37 (32) | 19 (16) | 28 (24) | 11 (9) | 116 |
| Transcription | 65 (28) | 73 (31) | 74 (31) | 24 (10) | 35 (15) | 26 (11) | 235 |
| Translation | 40 (26) | 48 (31) | 26 (17) | 20 (13) | 22 (14) | 55 (35) | 156 |
| Not in COGsb | 175 (16) | 190 (18) | 217 (20) | 100 (9) | 164 (15) | 126 (12) | 1,065 |
| MG1655 (total of above genes) | 656 (16) | 734 (18) | 815 (20) | 692 (17) | 901 (22) | 723 (18) | 4,070 |
a
Values in boldface indicate the functional groups with the highest percentage of differentially regulated genes for each E. coli strain.
b
COGs, clusters of orthologous groups.