Table 1.

σ³²-regulon members

(A) Genes induced upon overexpression of rpoH (as determined by transcription profiling) with validated upstream σ³² promoter. (B) Genes induced upon overexpression of rpoH (as determined by transcription profiling) but with no validated σ³² promoters. (C) Genes not induced after overexpression of σ³² (as determined by transcription profiling) but with identified confirmed σ³² promoters derived from the literature. (Transcription unit) TUs are listed in chromosomal order; genes within a unit are listed in order of transcription; genes in parenthesis are induced but are not predicted to be translated since the σ³² promoter is internal; in a few instances, a single TU has multiple σ³² promoters (both the dnaK dnaJ yi81_1 yi82_1 and htpG operons have two; mutL mia hfq hflX hflK hflC operon has three); they are counted as one TU, thus total TUs activated by σ³² are 66 in number (listed in A and B). (Ratio) averaged expression ratio of (rpoH-induced)/rpoH^wt (time points, 10 min) of first gene in TU; induction kinetics from SOM (Fig. 1) are also included. (F) Fast; (S) slow; (St) strong; (W) weak. (σ³² Promoter) Identified or predicted σ³² promoter sequences. (Distance) Number of nucleotides of 5′ end of −35 motif upstream of translation start point of the first gene in the TU. (Sequence) σ³² promoter sequence with the conserved −35 elements, −10 elements, and the start of transcription underlined. (Evidence) Evidence for σ³² promoter; (K) previously known; (P) predicted by both MEME and BioProspector; (R) confirmed by 5′RACE PCR; (T) confirmed by in vitro transcriptions; (Tf) tested by in vitro transcriptions, but no σ³²-dependent transcripts were detected. Note that the expression ratio of mutL is not available because of the low signal intensity in microarrays; expression ratio of repE and rrnB are not available because of the missing spots on the microarrays; exact +1 sites of yafD and yggV are not available because of the inaccurate sequencing results in 5′RACE; +1 site of holC is 8 nt downstream of the proposed translation start site, suggesting a possible alternative translation start site.