Table 2. Distribution of the binding sites of each RNAP holoenzyme.
| Sigma | Total no. holoenzyme binding sites | Within Spacers | Inside Genes | Constitutive promoters | ||||
|---|---|---|---|---|---|---|---|---|
| Type-A | Type-B | Type-C | Type-A spacer | Type-B spacer | Total | |||
| RpoD | 1320 | 177 | 317 | 49 | 777 (60%) | 177~354 | 317 | 494~671 |
| 543 (40%) | ||||||||
| RpoS | 218 | 50 | 79 | 16 | 73 (33%) | 50~100 | 79 | 129~179 |
| 125 (67%) | ||||||||
| RpoH | 133 | 41 | 60 | 6 | 26 (20%) | 41~82 | 60 | 101~142 |
| 107 (80%) | ||||||||
| RpoF | 105 | 7 | 27 | 3 | 68 (65%) | 7~14 | 27 | 34~41 |
| 37 (35%) | ||||||||
| RpoE | 126 | 29 | 48 | 7 | 42 (33%) | 29~58 | 48 | 77~106 |
| 84 (67%) | ||||||||
RNAP holoenzyme was reconstituted from the sigma-free core enzyme and 4-fold molar excess of each sigma subunit. The binding site of each holoenzyme on the genome of E. coli K-12 W3110 was determined in vitro using the improved Genomic SELEX screening system. Details of the experimental procedures are described previously [26]. The number of constitutive promoters were estimated based on the location of holoenzyme-binding sites. The number of constitutive promoters recognized by RpoD holooenzyme were described in the previous report [27].