. 2011 Jul;193(13):3186–3196. doi: 10.1128/JB.00272-11

Table 2.

Genes or operon positively controlled by SigH and with a SigH consensus sequence in their promoter region

Gene^a	Promoter recognized by SigH^b	Expression ratio in sigH mutant/strain 630E	Function
spo0A*	taGGAGGAATAtaattttggagtGTCGAATat	0.2	Stage 0 sporulation protein A
CD2492	aaGAAGGAATTataatgtcgagtATCGTATaa	0.35	Histidine kinase associated to Spo0A
soj	atACAGGAATTgatgctaagtatAATGAAAta	0.56	Sporulation initiation inhibitor
spoIIAA*	ttGAAGGAATAaaaat-ataattATAGAATtg	0.03	Anti-sigma F factor antagonist
spoVS*	atAAAGGTTTTcttaaaacgattATAGAAGta	0.03	Stage V sporulation protein S
spoVG*	aaAGAGGATATccctagttgttcATAGAATta	0.01	Regulator required for spore cortex synthesis
CD3673	atAAAGGAATTattaaagtagatGCAGAAAta	0.21	Putative stage 0 sporulation protein, Spo0J-like
CD3569	aaGAAGGGTTTagtgaagatgatATAGAAAag	0.33	Sporulation-specific protease
ftsZ*	aaAAAGGAAAAtttac-gtttttGTGGAATat	0.34	Cell division protein FtsZ
minC*	taAAAGGGTTTaaagc-gtatttGAAGAATat	0.09	Cell division regulator
CD2624	taAAAGGGTTTaaagc-gtatttGAAGAATat	0.33	Conserved hypothetical protein
sigA2	aaGGAGGATATtgctg-ttagaaGTAGAATaa	0.05	Transcription
CD0142*	aaAGAGGATTAtgaga-gttcgtGTAGAATat	0.14	Putative RNA-binding protein
CD0838	taCAAGGATTTtaaag-ataaatATAGAAAtt	0.26	DNA-binding protein
gapN	ttATAGGtAAAcgtttatgaaaaAAAGAAAtg	0.48	Glyceraldehyde-3-P dehydrogenase
glgC*	agGAAGGATATggaaa-ttaaagGTCGAATta	0.19	Glucose-1-P adenylyltransferase
fdhF	taAGAGGAATTgtgag-aaaattGTTGAATtt	0.31	Formate dehydrogenase
cobT	atAAAGGAAATgaaca-taaaatGTAGAATaa	0.35	Nicotinate-nucleotide-dimethylbenzimidazole
CD3456	agGGAGGAATTatttt-atgaaaAAAGAATtt	0.49	5-Formyltetrahydrofolate cycloligase
CD2738	agGGAGGGATAatattgcaagagAGAGAAGaa	0.49	Putative cytosine permease
CD0760	gtTTAGGATAAataaattttattATGGAAAaa	0.4	Putative Ca²⁺/Na⁺ antiporter
CD2789	caAGAGGAgAAgttattaagtgcAATGAATgc	0.39	Putative adhesin Cwp66
CD0440	atAAAGGAAAAtattc-ttttatGTAGAATta	0.25	Putative cell wall-binding protein
CD2518	aaGGAGGAAAAgaaaa-tttaatGTAGAATta	0.14	Cell surface protein
lplA	ttAAAGGAgTTtttat-attattGTCGAATta	0.34	Lipoate protein-ligase
CD3458	ttAAAGGAAATtgtaggtagtttATCGAATtg	0.07	Membrane protein
CD2800	ctATAGGAAcTgttaaatctaaaAAAGAAGaa	0.06	Membrane protein
CD2295	taGGAGGGATTttatg-gattttGGGGAATtt	0.28	Membrane protein
CD1590	aaAAAGGAAAAcgtctaaagtatTGGAATTac	0.44	Membrane protein
CD0865	taACAGGATTTatgtaggtgtttATAGAAAta	0.08	Putative ADP-ribose binding protein
CD2447	taGAAGGAATTttgctataacatGTAGAAAtt	0.06	Putative histidine triad (HIT) protein
CD3654	aaAGAGGAAGAacgtatagttaaGGAGAATat	0.24	Putative DNA replication protein
CD0022	aaAGAGGACAAttacctccagatGTAGAAAta	0.04	Elongation factor G (EF-G)
CD2137 (frr)	atAAAGGTATTtgagcttacaacAGAGAATat	0.4	Ribosome-recycling factor
CD1941	aaGTAGGTATAtataacaaggaaACAGAACcc	0.05	Unknown function
CD1543A	atAAAGGAAAAacctcttttaatGTAGAAAct	0.07	Unknown function
CD1264	aaAGAGGAAAAatcatt-ttaatGTAGAATaa	0.08	Unknown function
CD1061	ccAGAGGATATgaaagagttaatATCGAAAtt	0.25	Unknown function
CD1317	taAAAGGAAAGacaggat-aaatATAGAAAtt	0.42	Unknown function
CD1622	atAAAGGGTTTagagggcataatATAGAATaa	0.46	Unknown function

The transcriptional start site was identified for underlined genes. We used the search pattern program of the GenoList Web server (http://genodb.pasteur.fr/cgi-bin/WebObjects/GenoList) to detect the presence of the consensus sequence of B. subtilis SigH-dependent promoters (A/G)NAGGA(A/T)₃-N_11-12-(A/G)NNGAAT in the 200-bp region upstream of C. difficile genes, allowing two mismatches. An asterisk indicates genes or operons with a SigH promoter in B. subtilis (9).

The −10 and −35 boxes are indicated by uppercase letters.