Table 3. Data for new hrp promoters.

Operon	Function	hrp promoter coordinate	Evidence	qRT-PCR	Published data
					Mucynet al.	Promoters	Genes
371	iaaL indoleacetate-lysine ligase	406210.406238	HBIS	1151.0±177.6	+	FM	FCMo
871	macrolide effluxprotein, putative	939675.939703	HBIS	31.9±3.6	+		Mo
1645	MarR familytranscriptional regulator	1802305.1802333	HBIS	(54.6±14.6)*		M	M
1843	aspartate kinase	2012108.2012136	HBIS	2.2±0.2	+		Mo
2130	LuxR family DNA-binding response regulator	c(2304331.2304359)	HBIS	57.5±11.2	+	M	Mo
2691	TerC familymembrane protein	2984435.2984463	HBIS	49.9±6.0	+		M
2696	mutT/nudixfamily protein	(2990249.2990277)	HBIS	29.2±5.0		M	Mo
3331	protease inhibitor Inh	c(3768950.3768978)	HBIS	17.1±5.2			Mo
3481	Hypothetical protein	3929005.3929032	HBS	(15.6±1.6)*			M1
3721	fabI enoyl-(acyl-carrier-protein) reductase	4199604.4199632	HBIS	(1.4±0.1)*		M	Mo
39483949	Intergenic region	c(4457004.4457031)	HBI	(5.0±1.4)*			M1
4340	insecticidal toxinprotein, putative	c(4895201.4895228)	HBIS	(3.1±0.3)*			Mo
4699	non-ribosomal peptidesynthetase, terminal	c(5328022.5328050)	HBIS	223.4±57.9		M	Mo
4721	Type III chaperone ShcV	c(5346761.5346788)	HBIS	439.7±164.1	+		Mo
4750	Hypothetical protein	5384480.5384507	HBIS	62.8±17.8			Mo
4955	bifunctional thiosulfate	5616671.5616699	HBIS	13.7±3.6		M	Mo
5053	Hypothetical protein	5751475.5751504	HBIS	(209.7±50.5)*		M	Mo
5240	CDP-6-deoxy-delta-3,4-glucoseen reductase	c(5960164.5960192)	HBIS	8.6±1.0			Mo
5618	Type III effectorpseudogene hopAT1	c(922925.922953)	HIS	99.9±7.2		M	M1
5633	conserved protein ofunknown function	15821.15849	HBIS	61.2±9.4			M1
B0003	(identical to PSPTO_5633)

Operon: PSPTO identifier for gene immediately downstream from promoter.

Function: annotated function for operon-identifying gene.

Coordinate: DC3000 genome coordinate for the region bracketing the –35 and –10 regions of the promoter. “c” designates that the promoter is found on the complementary strand.

Evidence: Experimental evidence for hrp promoters from this study.

• H: hrp promoter motif found;

• B: Binding activity for HrpL (ChIP-qPCR) observed;

• I: Induction observed in promoter fusion (threshold = 2.4; 2×negative control);

• S: mRNA 5′-end captured (TSS) within 10 bps from the 3′ end of −10 promoter element. No threshold is applied. Absolute values for read counts appear in Table S5. TSSs from Filiatrault et al. [46] were also taken into consideration.

qRT-PCR: Transcript abundance for regions downstream from hrp promoters in DC3000 compared to that in a ΔhrpL strain. Values in brackets indicate that abundance was measured upstream from coding region. Values are average of one or two biological replicates with three technical replicates and standard deviation.

Published data:

• Mucyn et al.: ‘+’ indicates that the gene was classified as differentially expressed in Table 3 and Table S3 by Mucyn et al. [26].

• Promoters: symbols indicate whether hrp promoters were reported by Chang et al. [22] (C), Fouts et al. [21] (F), or by Ferreira et al. [23] (M).

• Genes: symbols indicate whether genes downstream from hrp promoters were tested and/or reported by Chang et al. [22] (C), Fouts et al. [21] (F), or by Ferreira et al. [23] (M). Genes that showed no differential expression, or which were not tested by Ferreira et al. [23] are designated (M_o) and (M₁), respectively.

No binding evidence for HrpL or upstream hrp promoter motifs were observed in association with 12 of the 14 genes proposed by Mucyn et al. [26] as putative novel HrpL regulon members. These are PSPTO_0829 (clpB protein), PSPTO_0851 (hypothetical protein), PSPTO_1371 (effector locus protein), PSPTO_2129 (sensory box histidine kinase/response regulator), PSPTO_2208 (heat shock protein HtpG), PSPTO_3148 (magnesium chelatase subunit ChII), PSPTO_4210 (ATP-dependent protease La), PSPTO_4332 (hypothetical protein), PSPTO_4376 (chaperonin, 60 kDa), PSPTO_4505 (dnaK protein), PSPTO_4716 (hypothetical protein), and PSPTO_4723 (hypothetical protein).