Table 3. PSPTO_1043 promoters examined in this study.
| Gene with putative PSPTO_1043 binding motif | Other genes in locus | Predicted promoter sequence1 | Annotated gene product | CSDeconv score2 | qRT-PCR fold change3 | 1O2 and tBOOH assays4 | %P. syringae genomes with homolog and motif5 |
|---|---|---|---|---|---|---|---|
| PSPTO_0744 | cGATCgacacggctcatccattCGTAtgca | acetyl-CoA acetyltransferase | 22.09 | 11.42 | N/T | 57.85 | |
| PSPTO_1043 | PSPTO_1042 | TGATCCactcttcatcccgctaCGTAacac | RNA polymerase sigma factor RpoERsp, transcriptional activator ChrR | 85.42 | N/A | + | 93.39 |
| PSPTO_1121 ( phrB) | PSPTO_1120-PSPTO_1114 | aGATCCataacgccgagctgctCGTAcagg | see Table 2 | 67.29 | 14.29 | + | 90.91 |
| PSPTO_1372 (hopAA1-1) | aGcaCtgcgctgttcaaacttcCGTAgaac | type III effector HopAA1-1 | 2.99 | N/S | N/T | 9.09 | |
| PSPTO_1900 | PSPTO_1901 ( bphO ), PSPTO_1902 ( bphP) | TGATCCgcatctttacgaaacaCGTAcatc | hypothetical protein, bacteriophytochrome heme oxygenase (BphO), bacteriophytochrome histidine kinase (BphP) | 9.05 | 12.85* | 0 | N/D |
| PSPTO_2591 | TGATCCagtgtgcgcctgcctgCGTAtgtt | diguanylate cyclase | 86.94 | 21.42 | N/T | 82.64 | |
| PSPTO_2593 | PSPTO_2592 ( saxG) | TGAgCCaatattgactcaaagcCGTAcaaa | multidrug resistance protein, AcrA/AcrE family; aliphatic isothiocyanate resistance protein SaxG, AcrB/AcrD/ AcrF family | 28.19 | 1.38 | N/T | 61.98 |
| PSPTO_2615 | TGATCCctgcctatacaacataCGTAtgtc | GAF domain-containing protein | 5.00 | 2.12 | N/T | 61.16 | |
| PSPTO_2853 | caaaCCataagcattctcaactCGTActaa | TonB-dependent receptor | 12.45 | N/S | N/T | 1.65 | |
| PSPTO_3893 | TGATCCaaagcatggctgctatCGTAagca | glyoxalase | 23.14 | 107.42 | N/T | 90.08 | |
| PSPTO_3907 | gaAcCaggcgtgcgtccaataaCGTAtaag | hypothetical protein | 19.28 | 3.44 | N/T | 73.55 | |
| PSPTO_4231 ( tctD) | PSPTO_4230 | gcATCCgggcgcctgttttacaCGTAcccg | DNA-binding response regulator TctD; sensor histidine kinase TctE | 4.56 | 7.15 | N/T | 86.78 |
| PSPTO_4335 | TGATCtaggctgtgtttaccaaCGTActaa | hypothetical protein | 95.33 | 102.39 | N/T | 53.72 | |
| PSPTO_4530 ( katG) | TaATCtgatgatcgctgtgcgaCGTAtctg | catalase/peroxidase HPI | 60.35 | 41.23 | + | 75.21 | |
| PSPTO_4675 | caAaCtaggtgatctcgatcttCGTAgaaa | Sir2 family transcriptional regulator | 7.98 | 4.23 | N/T | 9.09 | |
| PSPTO_4702 | aacTCtacccctaccgacttttCGTAcaaa | ISPssy, transposase | 3.41 | 3.35 | N/T | 2.48 | |
| PSPTO_4723 | gaAaCgacattgagtcttttttCGTAcaaa | hypothetical protein | 4.26 | 4.19 | N/T | 3.31 | |
| PSPTO_4843 | TGATCCacctgcccgcaagcaaCGTAgcgg | esterase/lipase/ thioesterase family protein | 20.92 | 10.13 | N/T | 84.30 |
Boldface indicates loci induced by PSPTO_1043 overexpression.
1 Each locus’s predicted promoter sequence. Underlined uppercase letters are used to indicate which bases match the consensus sequence, TGATCCnnnnnnnnnnnnnnnnCGTAnnnn.
2 Score reported by CSDeconv for the peak upstream of the gene.
3 qRT-PCR fold change (if statistically significant) after overexpression of PSPTO_1043 as shown in Fig 2. N/A = not applicable. PSPTO_1043 was overexpressed in the RT-PCR experiments. N/S = not significant.
4 Induction observed in the 1O2 and tBOOH lux assays shown in Figs 4 and 5. “+” = induced, “0” = not induced, “N/T” = not tested.
5 Percentage of P. syringae genomes that contain a homolog for the gene with an upstream PSPTO_1043 motif. N/D = no data, explanation in S1 Text
* PSPTO_1901 (bphO) tested.