An advanced bioinformatics approach for analyzing RNA-seq data reveals sigma H-dependent regulation of competence genes in Listeria monocytogenes

Table 2 σ^H promoter sequences for the σ^H-dependent operons identified in this study

Promoters	L. monocytogenes			L. innocua	L. welshimeri	L. ivanovii	L. seeligeri
	Lineage I	Lineage II	Lineage III
comGA
-35 signal	AAAGGATTT	AAAGGATTT	AAAGGATTT	AAAGGATTT	NF^c	AAAGGATTT	GAAGGATTT
-10 signal	GAGGAAT	GAAGAAT	GAAGAAT	GTAGAAT	NF	GCAGAAT	GCAGAAT
LMRG_00908
-35 signal	GAAGGACTT	GAAGGACTT	GAAGGACTT	GAAGGACTT	GAAGGACTT	GAAGGACTT	GAAGGACTT
-10 signal	GGCGAAT	GGCGAAT	GGCGAAT	GGCGAAT	GTCGAAT	GTCGAAT	GTCGAAT
comEA
-35 signal	AAAGGAATT	AAAGGATTT	AAAGG(G/A)TTT ^a	AAAGGAATT	NF	NF	AGAGGATTA
-10 signal	GGCGAAT	GGCGAAT	GGCGAAT	GGCGAAT	NF	NF	GGCGAAT
LMRG_01010
-35 signal	AGAGGATTA	AGAGGATTA	AGAGGATTA	AGAGGATTA	AGAGGATTA	AGAGGATTA	AGAGGATTA
-10 signal	GGCGAAT	GGCGAAT	GGCGAAT	GGCGAAT	GGCGAAT	CGCGAAT	GGCGAAT
coiA
-35 signal	AAAGGAATT	AAAGGAATT	AAAGGAATT	NF	NF	NF	NF
-10 signal	GGCGAAT	GGCGAAT	GGCGAAT	NF	NF	NF	NF
lytG
-35 signal	GAAGGAAAT	GAAGGAAAT	GAAGGAAAT	NF	NF	NF	NF
-10 signal	G(G/A)AGAAT ^b	GGAGAAT	GAAGAAT	NF	NF	NF	NF

^aAll L. monocytogenes lineage III serotype 4a strains show the sequence AAAGGGTTT, while one lineage III serotype 4c strain shows the sequence AAAGGATTT
^bTwo L. monocytogenes lineage I strain (i.e., SLCC2540 and L312) show the sequence GGAGAAT, while all other lineage I strains show the sequence GAAGAAT
^c NF: Not found

ISSN: 1471-2164