TABLE 2.

Genes preceded by promoters recognized by σX

GeneaPromoter region (σX dependent)b5′UTRcROMAdOverlapping recognition by other ECF σ factor(s)eReporter fusionfReference(s)
−35         −10 . .
sigXtgtaaTGTAACTTTTcaagctattcataCGACaaaaaag17++20
csbBaaaatTGTAACaaaaaacag-gtttaaaCGACtttaaaa80+++*+22
lytRaacaaTGAAACTTTTtttta-taaaaaaCGACtatttta84++22
rapDtaaaaTGTAACcaactgtcaatgagagcCGTCaaaagtt45+22
divlCatgttTGAAACTTcTtcctgtgaaaatgCGTCtaacttt113+σW (RO), σM (RF)+22, 35
abhaagcggGAAACTTTTtcaaagtttcattCGTCtacgata62σW (RO)+22
bcrCttattTGAAACTTTTcatgagtaagattaGTCtactaaa24++σM (RF, PE)+7
ywnJttttcTGTtACTTTTtgctttgttttacCGTCtatgtag38+++σW (RO)This work
pbpXtttttgacAACTTTTttagggctttattCGTCtaacaaa40σW (RF)+This work
dltAaaaaaTGAAACTTTTtgagc-atctgatCGTCaaataat204++This work
pssAtttccTGTAACgcTattcga-tcactatCGTCaaataat34++*+This work
  • a The first gene in each known or putative σX-dependent operon and its (σX-dependent) promoter region are listed.

  • b Note that the promoter consensus defined here includes an extended −35 region that includes the downstream T-rich segment and two additional bases in the −10 region that appear to be important for promoter discrimination by σX (double underline) or σW (single underline) (see the text).

  • c The known or estimated distance from the transcription start site to the start codon of the gene is indicated in nucleotides.

  • d The strength of the signal detected in the ROMA (EσX) experiment (Fig. 1) is indicated. An asterisk indicates that the downstream genes were also identified by ROMA.

  • e This promoter is recognized by other ECF σ factors, as confirmed by runoff transcription (RO), reporter fusion (RF), or primer extension (PE).

  • f +, the indicated promoter region gives σX-dependent β-galactosidase activity with a reporter fusion. −, no activity was detected for the reporter fusion.