High-resolution profiles of the Streptococcus mitis CSP signaling pathway reveal core and strain-specific regulated genes

Table 2 Alignment of putative ComE box sequences upstream of clusters of S. mitis type strain and SK321 orthologues of early genes

Function in competence	Annotation	Gene locus^a	Consensus^b
			aCAnTTcaG	12	aCAgTTgaG		−10 site
Regulation	comA	SP0042	GCAGTTGGG	12	TCATTTGGG	32	TAAGAT
		SM12261_0048	GCATTTGGG	12	GCATTTGGG	32	TAAGAT
		SMSK321_1310	GCAGTTGGG	12	GCATTTGGG	32	TAAGAT
	comC	SP2237	ACACTTTGG	12	ACAGTTGAG	31	TATAAT
		SM12261_0788	ACACTTGGG	12	ACAGTTGAG	31	TATAAT
		SMSK321_5’1634	ACACTTGGG	12	ACAGTTGAG	31	TATAAT
	comW	SP0018	CCATTTTTG	10	GCACTTAAa	38	TATACT
		SM12261_0016	CtttTTGAG	12	ACAATTCAG	31	TAGAAT
		SMSK321_0337	CttTTTGAa	12	GCAATTCAG	31	TAGAAT
	sigX1	SP0014	GCAGTTTAG	12	ACAGaaTGG	32	TAGACT
		SM12261_0014	GCAGTTGAG	12	ACAGaaTAG	32	TAGACT
		SMSK321_1651	GCAGTTTAG	12	ACAGaaTGG	32	TAAACT
	sigX2	SP2006	GCAGTTTAG	12	ACAGaaTGG	32	TAGACT
		SM12261_0613	GCAGTTTAG	12	ACAGaaTGG	31	TAAACT
		SMSK321_1251	GCAGTTTAG	12	ACAGaaTGG	32	TAGACT
Fratricide immunity	comM	SP1945	ACATTTGAG	10	ACAGTTCTC	13	TATAAT
		SM12261_0911	GCATTTTAG	12	ACAGTTGAG	32	TATAAT
		SMSK321_1653	GCATTTTAG	12	ACAGTTGAG	32	TATAAT
Unknown functions	ribF	SP1110	ACACTTCAt	12	ACATTTCAG	27	TATGAT
		SM12261_0833	ACACTTCAG	12	ACATTTCAG	27	TATGAT
		SMSK321_1087	TCAGTTCAG	12	ACATTTGGG	27	TATGAT
	Peptide deformylase	SP1549	ACAGTTGAG	11	GCAGTTATc	20	TATAAT
		SM12261_1162	ACAGTTTAG	11	GCAGTTATc	20	TATAAT
		SMSK321_0137	ACAGTTGAG	11	GCAGTTGCc	20	TATAAT
	ABC transporter	SP1717	ACAATTCAG	12	ACAGTTGAG	31	TATAAT
		SM12261_0940	ACAATTCAG	12	ACAGTTGAG	31	TATAAT
		SMSK321_1696	ACAATTCAG	12	ACAGTTGAG	31	TATAAT
	SPFH domain	SP2156	ACAATTCAc	12	ACATTTCAG	42	TATAAT
	SPFH domain	SMSK321_1581	ACAATTCAc	12	ACATTTCAG	42	TATAAT
	Hypoth. protein	SP0429	–	–	CCAGTTGAG	32	TATACT
	Hypoth. protein	SMSK321_0027	ACACTTCAG	12	ACAGTTGAG	31	TATACT

Bases matching the direct repeat consensus for S. pneumoniae are highlighted in bold [8]. Bases divergent from the consensus are represented by lower case letters. A TIGR4 orthologue and its ComE-box sequence is described for each S. mitis gene
^aGene number from HOMD
^bConsensus sequence in pneumococcus according to [8]

ISSN: 1471-2164