TABLE 2.
Genes with increased expression in the ΔrseA strain compared with the ΔrpoE strain
| ID | Gene | Ratioa | Description of gene product | Putative TUb | Characteristics |
|---|---|---|---|---|---|
| Regulatory function | |||||
| XCC1267 | rpoE2 | 4.28 | RNA polymerase σ factor σE | XCC1267, -68, -69 | Transcription initiation |
| XCC3771 | rpoH | 1.52 | Heat shock RNA polymerase factor σH | Response to heat; transcription initiation | |
| XCC3348 | 1.48 | Putative sensor-response regulator hybrid | XCC3347, -48 | Two-component signal transduction system (phosphorelay) | |
| Metabolism | |||||
| XCC2432 | fadE2 | 3.42 | Putative acyl-coenzyme A dehydrogenase | XCC2430, -31, -32 | Oxidation reduction |
| XCC3937 | baf | 3.14 | Putative type III pantothenate kinase | XCC3938, -37, -36 | Positive regulation of transcription |
| XCC3047 | bioI | 1.45 | Putative cytochrome P450 hydroxylase | Heme b metabolic process | |
| (NC_003902: 3492579-3492659, plus strandc) | pqqA | 1.41 | Putative coenzyme PQQ biosynthesis protein A | XCC2937, -38, -39, -40, -41 | Pyrroloquinoline quinone biosynthetic process |
| XCC1588 | 1.32 | Putative sulfite oxidase subunit YedY | Electron carrier activity | ||
| XCC3906 | 1.31 | Putative cytochrome B561 | XCC3905, -06 | Respiratory electron transport chain | |
| Protein synthesis and fate | |||||
| XCC1269 | mucD | 2.91 | Putative periplasmic protease | XCC1267, -68, -69 | Proteolysis |
| XCC1047 | hspA | 2.02 | Low-molecular-wt heat shock protein | Response to stress | |
| XCC3493-like degradation complex | hslU | 1.83 | Chaperone subunit of a proteasome | XCC3493, -94 | Response to stress |
| XCC3227 | moxR | 1.67 | MoxR-like AAA+ ATPase chaperone | XCC3227, -26, -25, -, 24, -23, -22 | ATPase activity |
| XCC2393 | htpG | 1.53 | Molecular chaperone Hsp90 family | Protein folding | |
| XCC1535 | -d | 1.41 | FKPB-type peptidyl-prolyl cis-trans isomerase | Protein folding | |
| XCC1475 | dnaJ | 1.36 | Molecular chaperone Hsp40 family | XCC1474, -75 | Response to heat; protein folding |
| XCC3450 | prc | 1.34 | Putative carboxyl-terminal processing protease | Proteolysis | |
| XCC1474 | dnaK | 1.31 | Molecular chaperone Hsp70 family | XCC1474, -75 | Response to heat; protein folding |
| T3S, translocation, and regulation machinery | |||||
| XCC1240 | hpa1 | 2.15 | Harpin-like elicitor protein (T3SS-dependent secreted protein) | ||
| XCC1217 | hrpF | 2.04 | Type III translocon protein | Interaction with host via protein secreted by T3SS | |
| XCC1246 | 1.99 | Type III effector protein (XopAL class) | Pathogenesis | ||
| XCC1241 | hpa2d | 1.78 | Lytic transglycosylase-like | ||
| XCC1222 | hrpD6 | 1.64 | Type III secretion system component | XCC1222, -21, -20, -19 | Protein secretion by the T3SS |
| XCC1220 | hpaB | 1.54 | Global T3S chaperone | XCC1222, -21, -20, -19 | T3SS |
| XCC2565 | 1.50 | Leucin-rich-repeat-containing protein/type III effector protein (XopAC class) | Pathogenesis | ||
| XCC4186 | 1.49 | Leucin-rich-repeat-containing protein/type III effector (XopL class) | Pathogenesis | ||
| XCC1221 | hrpE | 1.47 | Type III secretion system pilus protein | XCC1222, -21, -20, -19 | T3SS complex |
| XCC2896 | psvA | 1.42 | Peptidase C48 family/type III effector protein (XopD class) | Proteolysis | |
| XCC1224 | hpaA | 1.34 | Type III secreted virulence factor | XCC1222, -21, -20, -19 | Interaction with host via protein secreted by T3SS |
| XCC1219 | hrpW | 1.33 | Harpin pectate lyase | XCC1222, -21, -20, -19 | Interaction with host via protein secreted by T3SS |
| Cell envelope | |||||
| XCC0539 | ompW3 | 1.39 | Putative outer membrane protein | Cell outer membrane | |
| XCC2266 | pglAd | 1.31 | Putative polygalacturonase | Carbohydrate metabolic process | |
| XCC3925 | ecnAd,e | 1.31 | Putative entericine A | Response to toxin | |
| Unknown function | |||||
| XCC1308 | -d | 2.22 | Hypothetical protein | XCC1306, -07, -08 | |
| XCC0401 | 2.06 | Hypothetical protein/ribosomal protein S30Ae/σ54 modulation protein | Primary metabolic process | ||
| (NC_003902: 3290964-3290833, minus strandc) | 2.05 | Small putative membrane protein | |||
| XCC3224 | 2.03 | Hypothetical membrane protein | XCC3227, -26, -25, -24, -23, -22 | ||
| XCC1244 | 1.95 | Hypothetical protein | |||
| XCC0944 | -d | 1.83 | Conserved hypothetical protein | ||
| XCC3226 | 1.54 | Hypothetical protein | XCC3227, -26, -25, -24, -23, -22 | ||
| XCC3798 | -d | 1.47 | Calcium-binding EF hand motif | Calcium ion binding | |
| XCC3887 | 1.35 | Hypothetical protein | |||
| XCC2566 | 1.35 | Putative carboxymethylenebutenolidase | Hydrolase activity | ||
| XCC0863 | -d,e | 1.33 | Putative membrane protein | ||
| XCC1736 | -d | 1.33 | Putative secreted protein | XCC1737, -36, -35, -34 | Catalytic activity |
a
Ratio, averaged expression ratio of σE induced (ΔrseA)/no σE (ΔrpoE).
b
TUs are listed in chromosomal order.
c
Nonannotated gene in the genome of X. campestrispv.campestris ATCC 33913. Genomic location contains X. campestrispv.campestris ATCC 33913 chromosome accession number followed by the start coordinate, end coordinate, and strand.
d
A predicted cleavable signal sequence.
e
Predicted transmembrane helices.