TABLE 3.

Candidate PIP box-regulated promoters of T3SS-associated genes and/or hrpG-induced genes (hgi) from X. campestris pv. vesicatoria strain 85-10

Gene/operon and category	CDSa	Evidenceb	PIP box sequencec	Distance 1 (bp)d	−10 Sequence	Distance 2 (bp)e	Reference
T3SS core components
hrpB1	0427	gus	TTCGCCAGCGAATTCCGATATTCGC	31	TAGCGT	44	45
hrcU	0426	hgi-3 hgi-206	TTCGCCAGGCCATCCACACATTCGC	31	CACAAT	32	31, 45
hrcQ	0423	gus	TTCGCCGGACCAGCTATCGCTTCGC	31	TACTTT	211	45
hrcD	0418	gus	TTCGCCCATGACCATGCAGCTTCGC	31	TAGATT	218	45
hrpF	0411	hgi-34	TTCGCCAAAATAGTTCGT	28	CAACAT	94	31, 45
T3SS-associated components
hpaF	0409	hgi-203	TTCGCCAGGCGATGCAGCCTCTTCGC	30	TAGCCT	46	31, 32
hpaH	0441	hgi-81	TTCGCTTGCCTATTAAGTGTTTCGT	31	TATGTT	176	31, 32
hpaJ	2440	RT-PCR					30
xopA	0440	hgi-27	TTCGCTTGCACAAGCGTAATTTCGC	31	TACTGT	93	31, 32
Type III effector genes
avrBs1	d0104	Const. gus					12, 35
avrBs2	0052	ND	TTCGCATCCGGGCGGTACTTTTCGC	30	TTTACT	28	37
avrRxvf	0471	Const. gus	TTCGCATTATTGCCTAGATCTTCGC	31	TCTAAT	6	6, 46
ecff	3785	Const. by RT-PCR	TTCGTCGTCCCAGCCAGGACTTCGG	31	TACAGT	483	27
xopB	0581	hgi-25 hgi-66 hgi-80	TTCGCCGTCCCAACCATGACTTCGG	30	CAAACT	346	31
xopC	2435	hgi-37 hgi-41	TTCGCTCTCAGACGGGTTTTTTCTC	30	TAAAAT	193	30, 31
xopD	0437	gus	ATCGCTTCAGAGGAAGCTTGTTCGT	32	TAAATT	684	32
xopF1	0414	ND	TTCGTGTATGGCGCAGGTGGTTCGC	32	GACAAT	57	34
xopF2	2942	ND	TTCGTGCGTTGCGCCGGTGATTCGC	31	GACACT	53	34
xopJ	2156	hgi-11	TTCGTCGTCACAGCTATGACTTCGG	30	CAAACT	29	30, 31
xopN	2944	ND	TTCGCGCAGTGCATTCACCACTTCGC	32	CAGGAA	114	34
xopO	1055	ND	TTCGGAATGGTGGAAAATTTTTCCT	31	CATCAT	31	34
xopP	1236	ND	TTCGTCTCAGTCACCACGCATTCGC	32	TACTAA	340	34
xopQ	4438	hgi-63	TTCGTCGCCGCACACAGGAATTCAC	31	TAACGT	145	31, 34
xopX	0572	ND	TTCTTCCTGCAACGCAGTAGTTCGC	30	CAAATG	57	25
Uncharacterized genes	d0093	hgi-1	TTCTCTAACGCGGCGATTACTTCCG	30	TACTGT	29	31
	0041/0042	hgi-100	TTCGCTTGCCAATCTAGCGTTTCCG	31	CAGACT	28	31
	0324	hgi-69	TTCGCATACGCAAGCGGGATTTCCA	31	TATGCT	10	31
	0536	hgi-49, RT-PCR	TTCGCGGCGCGCGCGCCAGCTTCGT	31	CATACT	248	This study
	0845	hgi-128 hgi-130	ATCGTTTTACGCACACAGAGTTCGC	31	GAGAAT	38	31
	0869	hgi-9					31
	1512	hgi-213	TTCGTGCGCTGAGGTGTCGCATCGC	32	CAACGT	15	31
	2568	hgi-6, RT-PCR	TTCGCACACGCACCCTTGCATTCGC	32	TATGAT	191	This study
	2729	hgi-127, RT-PCR	TTCGCTTTGCATCGCTGCACTTCGT	30	TATGGT	120	31; this study
	2993/2994	hgi-94/hgi-52, RT-PCR					31; this study
	3013	hgi-208	TTCCGTTTGATCGGCAGCACTTCGC	30	AACGAT	184	31
	3406	hgi-16					31
	3407	hgi-98, RT-PCR	TTCGGCCAAGCTTACGTCAACTCGC	31	CATGCT	293	31; this study
	3765	hgi-133, RT-PCR	TTCGTTTTTGGAGCGCCGCGTGCGG	30	CACACT	79	This study
	4423	hgi-40					31
	4424	hgi-221, RT-PCR	TTCGTTTGCTGCGGCGGCGCTTCGT	31	TACGAT	81	This study

^aNumber of CDS according to the genome annotation (40).

^bExperimental evidence for HrpX-dependent expression. All hgi genes (hrpG-induced genes) originated from a cDNA-AFLP screen (31); gus indicates experimental evidence from a beta-glucuronidase reporter gene fusion. Const., constitutive expression; ND, not determined.

^cPIP box half-sites and conserved nucleotides of the −10 region are shown in bold. Nucleotides deviating from the consensus are underlined.

^dDistance in base pairs between the end of the PIP box and the −10 promoter motif.

^eDistance in base pairs between the end of the −10 promoter motif and the predicted translational start codon.

^favrRxv and ecf were not upregulated in minimal medium when present on a plasmid (6, 27).