TABLE 3.
Genes differentially expressed by overexpression of RpoE in H. ducreyi
| Function and gene | Description of product | 5 min |
10 min |
||
|---|---|---|---|---|---|
| Fold changea | P value | Fold changea | P value | ||
| Upregulated genes | |||||
| Envelope | |||||
| Lipopolysaccharide biogenesis and exportb | |||||
| neuAc | CMP N-acetylneuraminic acid synthetase | 2.0 | 5.5E−21 | ||
| lst | Lipooligosaccharide sialyltransferase | 2.3 | 3.3E−22 | ||
| lsgAc | Putative lipopolysaccharide biosynthesis protein | 3.0 | 9.3E−40 | 4.3 | 2.4E−86 |
| lsgD | Possible lipooligosaccharide n-acetylglucosamine glycosyltransferase | 2.8 | 5.3E−44 | 4.7 | 1.4E−107 |
| lsgE | Putative lipooligosaccharide galactosyltransferase | 2.0 | 1.2E−21 | 3.8 | 9.0E−81 |
| lsgF | Putative lipooligosaccharide galactosyltransferase | 2.0 | 5.4E−19 | 3.9 | 6.4E−76 |
| lgtB | Lipooligosaccharide galactosyltransferase II | 3.8 | 2.9E−24 | 4.9 | 3.7E−50 |
| waaF | ADP-heptose-lipooligosaccharide heptosyltransferase II | 3.9 | 5.0E−61 | 6.7 | 3.6E−142 |
| lpxL | Lipid A acyltransferase | 2.3 | 1.9E−32 | ||
| lpxH | UDP-2,3-diacylglucosamine hydrolase | 2.2 | 3.5E−23 | ||
| lpxD | UDP-3-O-(3-hydroxymyristoyl) glucosamine N-acyltransferase | 2.6 | 4.6E−36 | ||
| lpxA | UDP-N-acetylglucosamine O-acyltransferase | 2.1 | 5.6E−24 | ||
| gcp | Putative sialylglycoprotease | 2.5 | 4.8E−28 | 3.3 | 1.8E−56 |
| fabZ | (3R)-Hydroxymyristoyl-acyl carrier protein dehydratase | 2.5 | 2.6E−33 | ||
| galE | UDP-glucose-4-epimerase | 2.2 | 5.0E−21 | 3.3 | 1.1E−56 |
| rmlBc | dTDP-d-glucose 4,6-dehydratase | 2.1 | 2.9E−23 | ||
| glmMc | Phosphoglucosamine mutase | 3.2 | 1.0E−50 | 5.2 | 4.4E−115 |
| ftsH | Cell division protein FtsH | 2.5 | 5.5E−31 | 3.8 | 2.7E−75 |
| HD0552 | Lipopolysaccharide export system permease protein | 3.1 | 2.1E−43 | 4.8 | 5.2E−99 |
| HD0553 | Lipopolysaccharide export system permease protein | 2.6 | 1.9E−34 | 3.7 | 3.5E−77 |
| HD0586 | Lipopolysaccharide export system ATP-binding protein | 2.7 | 3.1E−30 | 3.8 | 1.5E−69 |
| Outer membrane protein assembly and insertion | |||||
| D15/bamA | Outer membrane protein D-15 | 2.5 | 1.4E−28 | 4.3 | 1.2E−82 |
| smpA/bamE | Small protein A | 8.4 | 1.0E−130 | 15.0 | 8.0E−252 |
| lppc | 15-kDa outer membrane lipoprotein | 7.0 | 1.9E−117 | 10.8 | 2.4E−212 |
| lolA | Outer membrane lipoprotein carrier protein | 6.3 | 6.2E−132 | 11.6 | 1.0E−257 |
| Peptidoglycan metabolism | |||||
| murA | UDP-N-acetylglucosamine-1-carboxyvinyltransferase | 3.5 | 2.1E−52 | 5.7 | 8.7E−120 |
| ampG | Permease and possible signal transducer AmpG | 2.4 | 4.1E−24 | 3.8 | 2.2E−67 |
| ampD | Anhydro-N-acetylmuramyl-tripeptide amidase | 7.7 | 4.1E−130 | 13.9 | 1.6E−252 |
| uppSc | Undecaprenyl pyrophosphate synthetase | 8.1 | 2.1E−133 | 11.8 | 8.4E−227 |
| nlpD | Lipoprotein | 2.5 | 3.5E−28 | 4.8 | 4.6E−96 |
| prc | Tail-specific protease | 3.8 | 1.0E−66 | 5.5 | 4.1E−130 |
| mepA | Penicillin-insensitive murein endopeptidase A | 2.5 | 2.9E−29 | ||
| dacA | d-Alanyl-d-alanine carboxypeptidase fraction A | 2.0 | 7.6E−26 | 2.8 | 3.4E−60 |
| lysA | Diaminopimelate decarboxylase | 3.0 | 2.6E−61 | ||
| HD0112 | N-Acetylmuramoyl-l-alanine amidase | 2.4 | 1.1E−04 | 2.7 | 1.2E−06 |
| HD0501 | N-Acetylmuramoyl-acetylmuramoyl-l-alanine amidase | 2.6 | 2.9E−32 | ||
| HD0922 | Hypothetical protein | 2.6 | 9.3E−35 | 5.4 | 1.7E−108 |
| HD1339 | Hypothetical protein | 3.5 | 6.6E−63 | 5.1 | 3.0E−124 |
| Periplasmic chaperones and folding catalysts | |||||
| degP | Periplasmic serine protease do | 7.8 | 1.2E−135 | 13.0 | 5.2E−249 |
| ecfE | Protease EcfE | 3.7 | 3.9E−55 | 5.3 | 1.1E−108 |
| dsbA | Probable thiol:disulfide interchange protein | 3.9 | 8.1E−56 | 6.3 | 1.7E−126 |
| surAc | Peptidyl-prolyl cis-trans isomerase | 3.5 | 5.7E−50 | 4.3 | 1.7E−87 |
| dsbC | Thiol:disulfide interchange protein | 3.4 | 7.1E−55 | 5.3 | 1.4E−119 |
| Pilus | |||||
| fimAc | Possible fimbrial major pilin protein | 2.4 | 1.7E−26 | ||
| fimB | Possible fimbrial structural subunit | 2.2 | 2.4E−17 | ||
| fimC | Probable fimbrial outer membrane usher protein | 2.1 | 1.1E−19 | ||
| fimD | Probable periplasmic fimbrial chaperone | 2.1 | 4.2E−20 | ||
| Other envelope components | |||||
| hlp | Lipoprotein Hlp | 3.0 | 7.2E−39 | 3.8 | 5.3E−72 |
| lspA | Lipoprotein signal peptidase | 2.7 | 1.0E−33 | 3.9 | 2.2E−77 |
| yfeB | Iron (chelated) transporter, ATP-binding protein | 3.4 | 8.1E−49 | 4.4 | 1.3E−87 |
| cdsA | CDP-diglyceride pyrophosphorylase | 6.3 | 2.7E−108 | 8.7 | 8.3E−184 |
| comAc | Possible competence protein A-like protein | 2.1 | 1.8E−10 | 2.8 | 1.0E−23 |
| HD1126 | Leader peptidase HopD | 2.1 | 3.3E−10 | ||
| HD1820 | ABC transporter ATP binding protein | 2.5 | 2.8E−23 | 3.8 | 3.6E−62 |
| HD1821 | ABC transporter | 2.4 | 2.0E−19 | 3.6 | 1.8E−52 |
| oapA | Opacity associated protein A | 6.0 | 4.6E−102 | 9.9 | 6.7E−200 |
| oapB | Opacity associated protein B | 4.5 | 4.2E−72 | 7.4 | 5.6E−153 |
| Cytoplasm | |||||
| DNA mismatch repair | |||||
| topB1 | DNA topoisomerase III | 2.5 | 1.1E−34 | ||
| ssb2 | Single-stranded DNA-binding protein | 2.8 | 9.3E−27 | ||
| topB2 | DNA topoisomerase III | 2.3 | 7.6E−28 | ||
| sbcBc | Exodeoxyribonuclease I | 2.9 | 1.7E−36 | 3.9 | 2.2E−74 |
| trpH | TrpH-like protein | 2.3 | 8.4E−31 | ||
| dnaX | DNA polymerase III subunits gamma and tau | 2.8 | 3.2E−31 | 4.1 | 2.8E−71 |
| holB | DNA polymerase III delta′ subunit | 3.1 | 5.3E−35 | 4.8 | 6.5E−88 |
| mutYc | A/G-specific adenine glycosylase | 2.5 | 2.3E−44 | ||
| recJ | Single-stranded-DNA-specific exonuclease RecJ | 3.0 | 2.0E−47 | 5.2 | 7.2E−120 |
| gam | Putative mu phage host nuclease inhibitor protein | 2.1 | 2.9E−06 | ||
| recQ | ATP-dependent DNA helicase | 2.0 | 4.3E−21 | ||
| uvrD | DNA helicase II | 2.2 | 2.4E−19 | 3.8 | 2.5E−66 |
| uvrB | Excinuclease ABC subunit B | 2.3 | 5.4E−29 | ||
| mutT | 7,8-Dihydro-8-oxoguanine-triphosphatase | 4.6 | 1.2E−79 | 6.9 | 6.0E−153 |
| aptc | Adenine phosphoribosyltransferase | 3.7 | 1.2E−44 | 5.0 | 6.3E−89 |
| tmk | Thymidylate kinase | 3.4 | 4.3E−43 | 5.3 | 3.6E−102 |
| upp | Uracil phosphoribosyltransferase | 3.2 | 1.2E−59 | ||
| RNA modification | |||||
| trmAc | tRNA (uracil-5-)-methyltransferase | 2.2 | 2.1E−31 | ||
| miaA | tRNA delta-2-isopentylpyrophosphate transferase | 4.1 | 4.2E−62 | 5.8 | 6.0E−120 |
| rsuA | Ribosomal small subunit pseudouridine synthase A | 3.3 | 8.7E−57 | 4.3 | 3.7E−102 |
| ksgA | Dimethyladenosine transferase | 3.0 | 2.7E−36 | 3.7 | 1.8E−67 |
| tgt | tRNA-guanine transglycosylase | 2.3 | 2.0E−27 | ||
| rluA | Pseudouridylate synthase | 4.5 | 8.9E−71 | 6.8 | 1.1E−139 |
| rumB | 23S rRNA (uracil-5-)-methyltransferase | 3.7 | 2.0E−42 | 4.6 | 8.5E−73 |
| rimK | Ribosomal protein S6 modification protein | 6.4 | 4.7E−116 | 11.5 | 2.2E−232 |
| HD1138 | tRNA pseudouridine synthase C | 2.4 | 3.6E−28 | 3.7 | 3.4E−74 |
| HD1770 | Nitrogen regulatory protein | 2.0 | 1.2E−20 | 2.5 | 4.9E−41 |
| Regulation of gene expression | |||||
| rpoH | RNA polymerase sigma 32 factor | 4.5 | 8.9E−73 | 6.4 | 4.4E−135 |
| rseA | Possible sigma E factor negative regulatory protein | 4.9 | 1.5E−79 | 6.6 | 5.2E−139 |
| rseC | Possible sigma E factor regulatory protein | 2.8 | 9.0E−40 | 3.5 | 3.1E−71 |
| cpxR | Transcriptional regulatory protein CpxR | 3.0 | 1.9E−42 | 4.3 | 1.6E−90 |
| cpxA | Sensor kinase CpxA | 2.4 | 1.1E−27 | 3.2 | 5.0E−58 |
| ptsN | Phosphotransferase system, nitrogen regulatory IIA-like protein | 2.5 | 4.2E−28 | 3.8 | 2.2E−69 |
| hfq | Putative host factor I protein | 3.0 | 1.2E−35 | 4.1 | 3.9E−73 |
| glnB | Putative nitrogen regulatory protein P-II | 2.6 | 5.3E−35 | 3.9 | 8.0E−83 |
| argRc | Arginine repressor | 2.3 | 4.5E−29 | ||
| asnC | Transcription regulatory protein, AsnC | 2.0 | 4.0E−19 | 2.6 | 8.3E−42 |
| cysB | Cys regulon transcriptional activator | 4.3 | 5.7E−75 | 7.0 | 3.2E−156 |
| fabR | DNA-binding transcriptional repressor FabR | 4.2 | 2.0E−74 | 6.6 | 8.3E−151 |
| Cofactor biosynthesis | |||||
| mogAc | Molybdopterin biosynthesis protein | 2.7 | 3.2E−38 | 4.1 | 2.9E−90 |
| ispH | Hydroxymethylbutenyl pyrophosphate reductase | 2.2 | 5.5E−22 | 3.4 | 3.0E−62 |
| visC | Probable monooxygenase | 2.7 | 3.0E−40 | ||
| hemY | HemY protein | 2.3 | 4.8E−40 | ||
| hemX | Putative uroporphyrinogen III C-methyltransferase | 2.2 | 2.3E−39 | ||
| modA | Molybdate-binding periplasmic protein | 3.1 | 4.7E−48 | ||
| modB | Molybdenum ABC transporter, permease protein | 2.8 | 6.2E−41 | ||
| modC | Molybdenum ABC transporter, ATP-binding protein | 2.7 | 4.7E−39 | ||
| lipA | Lipoic acid synthetase | 3.0 | 2.3E−58 | ||
| lipB | Lipoate biosynthesis protein B | 2.1 | 2.3E−27 | 3.3 | 8.3E−74 |
| rpiA | Ribose 5-phosphate isomerase A | 2.7 | 1.6E−39 | 4.9 | 1.2E−111 |
| mdh | Malate dehydrogenase | 3.2 | 1.0E−41 | 4.4 | 2.7E−84 |
| HD0261 | Hypothetical protein | 3.7 | 4.6E−53 | 5.6 | 4.5E−115 |
| HD1410 | Hypothetical protein | 2.9 | 1.1E−35 | 4.0 | 1.1E−74 |
| Amino acid biosynthesis | |||||
| argH | Arginosuccinate lyase | 2.9 | 4.8E−41 | ||
| aroC | Chorismate synthase | 2.4 | 2.8E−31 | ||
| cysZ | Cysteine synthetase | 2.8 | 1.3E−35 | 4.6 | 1.1E−89 |
| Monosaccharide metabolism | |||||
| pflB | Formate acetyltransferase | 2.4 | 3.7E−34 | 3.8 | 4.5E−89 |
| citC | Citrate lyase synthetase | 3.6 | 5.0E−72 | ||
| citDc | Citrate lyase gamma chain | 3.1 | 3.5E−51 | ||
| citE | Citryl coenzyme A lyase subunit | 2.9 | 6.4E−54 | ||
| citF | Citrate coenzyme A transferase subunit | 2.1 | 8.2E−26 | ||
| Stress adaptation | |||||
| surEc | Acid phosphatase stationary-phase survival protein | 5.0 | 5.0E−90 | 8.9 | 2.2E−191 |
| proQ | Possible ProP effector | 4.5 | 3.1E−79 | 6.1 | 3.8E−141 |
| mazGc | MazG protein | 3.1 | 5.9E−46 | 4.2 | 5.6E−88 |
| Miscellaneous | |||||
| vacB | RNase R, virulence associated VacB-like protein | 2.9 | 1.2E−33 | 5.1 | 4.1E−98 |
| hflX | GTP-binding protein HflX | 2.4 | 4.5E−25 | ||
| Downregulated genes | |||||
| Envelope | |||||
| ccmD | Cytochrome c maturation protein D | −2.1 | 2.2E−04 | ||
| ompA2c | Major outer membrane protein-like protein OmpA2 | −2.6 | 2.3E−45 | ||
| ompP2A | Outer membrane protein P2-like protein | −2.3 | 1.7E−30 | ||
| ompP2B | Outer membrane protein P2-like protein | −2.2 | 8.1E−19 | −2.7 | 5.3E−36 |
| Cytoplasm | |||||
| purM | Phosphoribosylformylglycinamidine cyclo-ligase | −2.7 | 7.0E−10 | ||
| pyrE | Orotate phosphoribosyltransferase | −2.1 | 7.9E−28 | ||
a
Mean fold change in expression of genes in 35000HP(pDG9) compared to 35000HP(pDG10) at 5 or 10 min after induction of RpoE; the fold change was normalized by dividing the fold change at 5 or 10 min with that of 0 min.
b
Differentially expressed genes were categorized into different functional categories using DAVID bioinformatics resources.
c
First gene of a known or putative operon predicted by the DOOR database.