The genome-wide binding profile of the Sulfolobus solfataricustranscription factor Ss-LrpB shows binding events beyond direct transcription regulation

Table 1 Overview of the Ss-LrpB-specific ChIP-enriched regions that are also enriched in LysM-specific ChIP-chip analysis

Target name	Genomic coordinate peak start	Genomic coordinate peak stop	Relative position to LysM-specific peak	Presence of Ss-LrpB binding motif	Presence of LysM binding motif	Class
Sso0154	129616	130620	Inside	-	-	III
Sso5317	131930	133008	Including	-	+	II
Ssot18	290428	291131	Inside	+	-	I
Ssot28	589572	590362	overlap (89%)	-	+	II
Sso6904	835210	835839	Inside	-	+	II
Sso1027	885479	886771	Inside	+	-	I
Sso1114	960343	961574	Including	-	-*	III
Sso1118	964702	966378	Including	-	-*	III
Sso1135	974250	975551	overlap (99%)	+	-*	I
Sso1272	1095398	1097098	Inside	+	-*	I
Sso1371	1206614	1207226	overlap (97%)	+	-*	I
Sso1389	1232759	1233642	overlap (99%)	+	-*	I
CRISPR4	1260282	1261337	Including	+	-*	I
Sso1433	1286420	1286928	Inside	+	-*	I
Sso1463	1321798	1323084	overlap (98%)	-	-*	III
Sso1890	1705187	1705830	Inside	-	-*	III
Sso2043	1859092	1860291	overlap (75%)	-	+	II
Sso2159	1985046	1985784	Inside	-	-*	III
Sso2233	2050931	2052374	Including	+	-*	I
Sso2289	2099312	2099902	Inside	-	-*	III
Sso2309	2111358	2112389	Inside	-	-*	III
Sso2310	2113136	2114378	overlap (93% )	-	-*	III
Sso2334	2132622	2134455	Including	-	+	II
Sso2404	2187776	2188318	Inside	-	-*	III
Sso2678	2437317	2437768	overlap (96%)	-	-*	III
Sso2801	2561656	2562152	overlap (57%)	-	-*	III
Sso2833	2594520	2595831	overlap (96%)	-	-*	III
Sso3002	2742947	2743947	Including	-	-*	III
Sso3072	2827204	2828448	overlap (94%)	+	-*	I

The presence of an Ss-LrpB binding motif (measured by EMSA) or a LysM binding motif (either measured by EMSA or predicted in silico (indicated by an asterisk) [16]) is indicated. Classes are defined as follows: class I: binding region that contains an Ss-LrpB binding motif and exhibits binding to Ss-LrpB but not LysM in vitro; class II: binding region that contains a LysM binding motif and exhibits binding to LysM but not Ss-LrpB in vitro; class III: binding region that does not contain an Ss-LrpB or LysM binding motif and does not interact with any of the two proteins in vitro. Ranking is according to genomic location.