There is an error in the legend for Table 2. Footnote 5 is incorrect. It should read “Gene(s) adjacent to binding site. Parentheses indicate an intragenic binding site, while those that are underlined are in the antisense orientation and those not underlined are in the sense orientation.”
Table 2. FliA promoters and expression of associated genes.
| Normalized gene expression1 | ||||||
| Peak Center2 , 3 | FAT4 Score | Motif Center2 , 3 | Motif | Gene/Operon5 | Motile MG1655 | ΔfliA 6 |
| 265447 | 24 | 265472 | GATGAATGCGCTGTGTATTGCCGATAAC | (yafY)ykfB | (93)118 | (30*)42* |
| 426893 | 5 | 426874 | AAGGGAATTGCCGTGTTAAACCGTTATC | (secD) | 183 | 170 |
| 669828 | 10 | 669799 | TAAAGATTTCATATCAACCGTCGATAAA | (holA) | 190 | 170 |
| 788978 | 2 | 789005 | TAAAGTTCGCGTGATGGCAGCCGATTAT | (galK) | 232 | 224 |
| 794226 | 32 | 794199 | TCAACTTCCTGCTTTTCCTGCCGATATT | modABC | 182 | 61* |
| 815234 | 4 | 815204 | TCAACTCACGCCCCAGATTGCCGATATA | (ybhK) | 46 | 46 |
| 816109 | 2 | 816141 | TAGAGTGTTTAGTGGTTATGCCGATACT | ybhK | 46 | 46 |
| 946162 | 2 | 946134 | TATGCTAATGCAGAATTTCTCCGATAAT | (ycaD)ycaM | (7)7 | (4)7 |
| 1030917 | 1 | 1030887 | TCTGGAACCCTTTCGGGTCGCCGGTTTT | (serT)hyaA | (274)0 | (154)0 |
| 1049918 | 2 | 1049983 | TAAGGAAATTGTTACGAAAGCTATTAAT | insB-4/cspH converg. | - | - |
| 1129384 | 48 | 1129409 | TAAAGATTACCCGTCCCTTGCCGATAAA | flgMN | 451 | 318 |
| 1137565 | 47 | 1137556 | TCAAGTCCGGCGGGTCGCTGCCGATAAT | flgKL | 318 | 138 |
| 1241331 | 2 | 1241357 | TAAGTAAAACGCTGTCTCTGCCGCTAAT | cvrA | 43 | 28 |
| 1243779 | 67 | 1243800 | TTAAGTTTTGTTAACTGTGACCGATAAA | ycgR | 104 | 0* |
| 1490461 | 23 | 1490443 | TAAGTAATTACCGTCAAGTGCCGATGAC | trg | 108 | 4* |
| 1512636 | 3 | 1512671 | GCTGGGAATAAACCATATTGCCGATAAA | (ydcU) | 7 | 10 |
| 1644411 | 16 | 1644394 | TAAAGATTTTTTTGTGCATGCCGATAGT | flxA | 280 | 2* |
| 1676085 | 1 | 1676104 | TAATATTTTGCGAGTTCACGCCGAAATA | pntA | 140 | 169 |
| 1823008 | 44 | 1823029 | AACGTAAATCACCCGAGTTGCCGATAAC | ves | 18 | 0 |
| 1840188 | 1 | 1840186 | TAACGTTATTGTCTCTGCTACTGATAAC | ynjH | 29 | 2* |
| 1970737 | 57 | 1970761 | TAAAGTTTCCCCCCTCCTTGCCGATAAC | tar-tap-cheRBYZ | 251 | 0* |
| 1975314 | 101 | 1975347 | TAAACTTTCCCAGAATCCTGCCGATATT | (flhC)motAB-cheAW | (320)302 | (107*)1* |
| 1979379 | 2 | 1979356 | TGAAATTGCACCAGATCGAGCCGATAAT | (otsA) | 26 | 27 |
| 1999845 | 91 | 1999853 | TGCAGAAACGGATAATCATGCCGATAAC | fliAYZ | 1257 | 15* |
| 2001692 | 110 | 2001721 | TAAAGGTTGTTTTACGACAGACGATAAC | fliC | 2319 | 11* |
| 2001856 | 43 | 2001841 | TAAACTTTGCGCAATTCAGACCGATAAC | fliDST | 633 | 356 |
| 2017629 | 18 | 2017601 | TCAAGACGCAGGATAATTAGCCGATAAG | fliLMNOPQR | 989 | 980 |
| 2232326 | 3 | 2232358 | TAACAAAACGCTGTAAGCGGCCGATATC | (preT) | 49 | 47 |
| 2484776 | 2 | 2484747 | TCAACTTCAACCACAATGGGTCGATATC | (evgS) | 23 | 33 |
| 2683494 | 2 | 2683512 | AAAGCGTGAAATGAACATTGCCGATTAT | (glyA) | 375 | 415 |
| 2850743 | 51 | 2850785 | TAAAATTATAGGCGTCGGTGCCGATAAC | (hypD) | 6 | 7 |
| 2860228 | 2 | 2860201 | TAAGGATCTTGGTCTGGTTGCCGATACA | (ygbJ)ygbK | (12)13 | (10)10 |
| 3082647 | 11 | 3082628 | TAAAGATGCCGGAAGAGTAGCCGATATG | (speA) | 133 | 193 |
| 3101896 | 3 | 3101871 | GGCGCAACGGCAGATTGCTGCCGATAAC | (mutY)yggX | (128)369 | (104)370 |
| 3217148 | 21 | 3217162 | TAAAGATAACCGCAGCGGGGCCGACATA | aer | 225 | 12* |
| 3246148 | 2 | 3246175 | AAAGCGACCAATTAACAGCGCCGATAAA | (yqjA) | 140 | 130 |
| 3339939 | 2 | 3339902 | TAAACTTCTGCTGCGCGTAAACGATATT | (kdsD)kdsC | (158)228 | (155)241 |
| 3524439 | 9 | 3524407 | CAAGTTAAACTCCACGCTTGCCGATAGC | yrfF | 62 | 53 |
| 3677244 | 67 | 3677273 | TAAAGTTCTGCCCTTACGCGCCGATAAT | yhjH | 511 | 2* |
| 3706702 | 1 | 3706643 | TCCTCTATCACCGACCAAATTCGAAAAG | (proK) | 62 | 44 |
| 3844022 | 11 | 3844039 | TAAAAAAGCGATTGGCGCTGCCGATGGT | (uhpT) | 25 | 1 |
| 3846459 | 1 | 3846440 | AAAACAGGGTCGCTAACAGGCCGATATC | (uhpC) | 9 | 8 |
| 4016533 | 1 | 4016575 | GAGAGTTTTTTCATTGCCTGCCGATAAT | (rmuC) | 60 | 78 |
| 4119023 | 1 | 4118999 | TACAGATTTTGTCGATTTCGTCGATAAA | (hslU) | 1085 | 1337 |
| 4131349 | 3 | 4131304 | TAAACAGGCGAAGAAATTTGCCGATATG | (metF) | 6 | 3 |
| 4162805 | 3 | 4162795 | TGAAGGCGCAGCACGCAGTGACGATAAC | (btuB) | 72 | 92 |
| 4228823 | 6 | 4228793 | GAAAGAGTATCTGGTGACGGTCGATAAA | (rluF) | 73 | 73 |
| 4327161 | 19 | 4327146 | TAAAGTTCTGGCAGAGCAGGTCGATGAA | (yjdA)yjcZ | (111)52 | (11*)1* |
| 4564123 | 1 | 4564096 | GAATAAACTGCAGATCTTTGCCGATATT | (yjiN) | 17 | 17 |
| 4589660 | 94 | 4589638 | TAAAGTTTTTCCTTTCCAGGCCGAAAAT | tsr | 630 | 9* |
| 4591362 | 3 | 4591380 | AAAGATTAATCTCCTTATGCCCGATAAC | tsr/yjiZ convergent | - | - |
| 4621181 | 1 | 4621145 | TACAGCCCCCGCCATCCATGCCGATAAC | (lplA) | 30 | 31 |
Normalized gene expression values generated by Rockhopper. Expression values are for first gene in operon. Values in parentheses correspond with gene name in parentheses.
Peak centers and motif centers refer to genome coordinates relative to NC_000913.2.
Peak centers and motif centers in italics are likely false positives, based on the location of the motif relative to the peak center.
Fold Above Threshold (FAT).
Gene(s) adjacent to binding site. Parentheses indicate an intragenic binding site, while those that are underlined are in the antisense orientation and those not underlined are in the sense orientation.
Asterisks indicate significant differential expression (as defined in Methods) between motile MG1655 and ΔfliA.
Reference
- 1. Fitzgerald DM, Bonocora RP, Wade JT (2014) Comprehensive Mapping of the Escherichia coli Flagellar Regulatory Network. PLoS Genet 10(10): e1004649 doi:10.1371/journal.pgen.1004649 [DOI] [PMC free article] [PubMed] [Google Scholar]