Table 1. Top RhpR-binding genes.

Fold enrichment	Gene	Function	Position	Category	IR sequence	EMSA	Distance to ATG	Fold-change in rhpS−
3.86565	rpoD	RNA polymerase, sigma 70	overlap end	nucleic acid	GTATCN6GACAC	Y		NS
3.77545	PSPPH3076	hypothetical	upstream	hypothetical	GTAACN6GACAC	Y	−100	−3.6 ± 1.1
3.74968	PSPPH3654	TetR family transcription factor	upstream	regulatory	GTATAN6GTTAC	Y	−40	NS
3.66732	PSPPH5053	aminotransferase	downstream	metabolism	GTACCN6GATAC	Y		−2.7 ± 0.4
3.60794	PSPPH2185	histidine kinase	upstream	regulatory	ATTACN6GGCAC	N	−421	NS
3.46699	PSPPH4247	GAF/GGDEF/EAL protein	upstream	regulatory	GTAACN6CATAC	Y	−145	−2.5 ± 0.5
3.43841	tonB4	siderophore transporter	upstream	transporter	GTTCCN6CTTAC	Y	−211	−2.7 ± 0.4
3.4234	PSPPH4712	anti-CoA dehydrogenase	overlap end	metabolism	GTAACN6GATGC	Y		−4.6 ± 0.7
3.36312	PSPPH4241	LuxR family transcription factor	upstream	regulatory	GTTTCN6GATAC	Y	−50	−6.0 ± 3.0
3.36139	PSPPH3845	arsC family protein	upstream	metabolism	GTGACN6GGTAC	N	−87	NS
3.32106	hrpR	T3SS	upstream	virulence	ATTTCN6GATAC	Y	−958	Abolished (5)
3.31158	PSPPH4977	GNAT family acetyltransferase	inside	metabolism	ATATCN6GATAC	Y	239	+3 ± 1.0
3.23885	PSPPH1035	lipoprotein	upstream	metabolism	GAAGCN6GATAC	Y	−121	NS
3.20849	PSPPH0775	chaperone protein	inside	transporter	AGATCN5GTTAC	N	340	NS
3.20031	PSPPH0813	hypothetical	upstream	hypothetical	GTTTCN6GATAC	Y	−120	−3.3 ± 1.0
3.19561	PSPPH1086	lipoprotein	upstream	hypothetical	GCAAAN6GATAC	Y	−90	NS
3.18272	PSPPH0100	recombinase	inside	nucleic acid	GGATTN6GATAC	Y	732	NS
3.12415	rlmL	23S rRNA methyltransferase	overlap end	metabolism	TGTACN6GTTAC	Y		NS
3.11668	PSPPH2002	Ca binding protein	upstream	regulatory	GTATCN6CGTAC	N	−72	NS
3.11231	folE	GTP cyclohydrolase	upstream	metabolism	GTAAGN6GATAC	Y	−41	−2.1 ± 0.1
2.88548	hopR1	T3SS effector	inside	virulence	GTATGN6GATAC	Y	242	−2.2 ± 0.6
2.63489	flhA	flagellar biosynthesis protein	upstream	cell envelop	GCAACN6GATAC	Y	−59	−2.6 ± 0.9
2.35805	hopG1	T3SS effector	overlap end	virulence	CCTACN6GTTAC	Y		−17.1 ± 1.6
2.33503	fliL	flagellar basal body protein	upstream	cell envelop	GATTCN6GACAC	Y	−76	NS
2.28869	pilS	two-component system	inside	regulatory	ATGTCN6GGTAC	Y	437	−3.6 ± 1.4
2.20673	rhpR	TCS	upstream	virulence	GTATCN6GATAC	Y	−69	+>10 (23)
2.17765	avrE1	T3SS effector	inside	virulence	GACATN6GTTAC	Y	3127	−7.6 ± 3.0

Mismatches are underlined in IR sequences. Y: positive in EMSA; N: negative in EMSA; NS: no significance in qRT-PCR.